master-refs.bib

% This file was created with JabRef 2.9.2.
% Encoding: MacRoman

@STRING{AHG = {Annals of Human Genetics}}

@STRING{AJHG = {American Journal of Human Genetics}}

@STRING{ARB = {Annual Review of Biochemistry}}

@STRING{ARCB = {Annual Review of Cell Biology}}

@STRING{BI = {Bioinformatics}}

@STRING{BIOGEN = {Biochemical Genetics}}

@STRING{BJLS = {Biological Journal of the Linnean Society}}

@STRING{BMB = {Bulletin of Mathematical Biology}}

@STRING{BMCBI = {BMC Bioinformatics}}

@STRING{CABIOS = {Computer Applications in the Biosciences}}

@STRING{CACM = {Communications of the ACM}}

@STRING{CELL = {Cell}}

@STRING{COCB = {Current Opinion in Cell Biology}}

@STRING{COGD = {Current Opinion in Genetics and Development}}

@STRING{ComputChem = {Computers and Chemistry}}

@STRING{COSB = {Current Opinion in Structural Biology}}

@STRING{CSHSQB = {Cold Spring Harbor Symposia Quantitative Biology}}

@STRING{EMBO = {EMBO Journal}}

@STRING{EVO = {Evolution}}

@STRING{GB = {Genome Biology}}

@STRING{GEN = {Genetics}}

@STRING{GR = {Genome Research}}

@STRING{JBSD = {Journal of Biomolecular Structure and Dynamics}}

@STRING{JCB = {Journal of Computational Biology}}

@STRING{JMB = {Journal of Molecular Biology}}

@STRING{JME = {Journal of Molecular Evolution}}

@STRING{JRSS = {Journal of the Royal Statistical Society, B}}

@STRING{JTB = {Journal of Theoretical Biology}}

@STRING{MBE = {Molecular Biology and Evolution}}

@STRING{MBIO = {Mathematical Biosciences}}

@STRING{MCB = {Molecular Cell Biology}}

@STRING{ME = {Methods in Enzymology}}

@STRING{MPE = {Molecular Phylogenetics and Evolution}}

@STRING{NAR = {Nucleic Acids Research}}

@STRING{Nature = {Nature}}

@STRING{NB = {Nature Biotechnology}}

@STRING{NC = {Neural Computation}}

@STRING{NG = {Nature Genetics}}

@STRING{NNB = {Nature New Biology}}

@STRING{PE = {Protein Engineering}}

@STRING{PHTRANSRB = {Philosophical Transactions of the Royal Society B}}

@STRING{PLOSCOMPBIO = {PLoS Computational Biology}}

@STRING{PNAS = {Proceedings of the National Academy of Sciences, USA}}

@STRING{PROCROYB = {Proceedings of the Royal Society B}}

@STRING{PROT = {Proteins}}

@STRING{PROTSCI = {Protein Science}}

@STRING{Science = {Science}}

@STRING{S = Science}

@STRING{SIAM = {SIAM Journal of Applied Mathematics}}

@STRING{SYSB = {Systematic Biology}}

@STRING{SZ = {Systematic Zoology}}

@STRING{TIBTECH = {Trends in Biotechnology}}

@STRING{TIGS = {Trends in Genetics}}

@ARTICLE{birney07,
  author = {{ENCODE} project consortium},
  title = {{I}dentification and analysis of functional elements in 1\% of the
	human genome by the {E}{N}{C}{O}{D}{E} pilot project},
  journal = Nature,
  year = {2007},
  volume = {7146},
  pages = {799--816}
}

@article{baridosottani2019,
author = {Joëlle Barido-Sottani  and Gabriel Aguirre-Fernández  and Melanie J. Hopkins  and Tanja Stadler  and Rachel Warnock },
title = {Ignoring stratigraphic age uncertainty leads to erroneous estimates of species divergence times under the fossilized birth\&\#x2013;death process},
journal = {Proceedings of the Royal Society B: Biological Sciences},
volume = {286},
number = {1902},
pages = {20190685},
year = {2019},
doi = {10.1098/rspb.2019.0685}
}

@ARTICLE{abella12,
  author = {Juan Abella and David M. Alba and Josep M. Robles and Alberto Valenciano
	and Cheyenn Rotgers and Ra\"ul Carmona and Plinio Montoya and Jorge
	Morales},
  title = {\textit{{K}retzoiarctos} gen. nov., the Oldest Member of the Giant
	Panda Clade},
  journal = {PLoS One},
  year = {2012},
  volume = {17},
  pages = {e48985}
}

@ARTICLE{abella2011,
  author = {Abella, J and Montoya, P and Morales, J},
  title = {Una nueva especie de \textit{{A}griarctos} ({A}iluropodinae, {U}rsidae,
	{C}arnivora) en la localidad de {N}ombrevilla 2 ({Z}aragoza, {E}spa{\~n}a)},
  journal = {Estudios Geol{\'o}gicos},
  year = {2011},
  volume = {67},
  pages = {187--191},
  number = {2}
}

@ARTICLE{ackerly00,
  author = {D. D. Ackerly},
  title = {Taxon sampling, correlated evolution, and independent contrasts},
  journal = {Evolution},
  year = {2000},
  volume = {54},
  pages = {1480--1492}
}

@ARTICLE{adachi96,
  author = {J. Adachi and M. Hasegawa},
  title = {{MOLPHY Version 2.3}: {P}rograms for molecular phylogenetics based
	on maximum likelihood},
  journal = {Computer Science Monographs},
  year = {1996},
  volume = {28},
  pages = {1--150}
}

@ARTICLE{adachi95,
  author = {J. Adachi and M. Hasegawa},
  title = {Phylogeny of whales: {D}ependence of the inference on species sampling},
  journal = MBE,
  year = {1995},
  volume = {12},
  pages = {177--179}
}

@ARTICLE{adachi92,
  author = {J. Adachi and M. Hasegawa},
  title = {Amino acid substitution of proteins coded for in mitochondrial {DNA}
	during mammalian evolution},
  journal = {Jpn. J. Genet.},
  year = {1992},
  volume = {67},
  pages = {187--197}
}

@ARTICLE{adachi00,
  author = {J. Adachi and P. Waddell and W. Martin and M. Hasegawa},
  title = {Plastid genome phylogeny and a model of amino acid substitution for
	proteins encoded by chloroplast {DNA}},
  journal = JME,
  year = {2000},
  volume = {50},
  pages = {348--358}
}

@ARTICLE{adey94,
  author = {N. B. Adey and T. O. Tollefsbol and A. B. Sparks and M. H. Edgell
	and C. A. Hutchison},
  title = {Molecular resurrection of an extinct ancestral promoter for mouse
	{L1}},
  journal = PNAS,
  year = {1994},
  volume = {91},
  pages = {1569--1573}
}

@ARTICLE{adkins91,
  author = {R. M. Adkins and R. L. Honeycutt},
  title = {Molecular phylogeny of the superorder {A}rchonta},
  journal = PNAS,
  year = {1991},
  volume = {88},
  pages = {10317--10321}
}

@ARTICLE{Agresti2001,
  author = {Agresti, Alan and Min, Yongyi},
  title = {On Small-Sample Confidence Intervals for Parameters in Discrete Distributions},
  journal = {Biometrics},
  year = {2001},
  volume = {57},
  pages = {963--971},
  number = {3},
  publisher = {International Biometric Society},
  url = {http://www.jstor.org/stable/3068439}
}

@ARTICLE{Aho1981,
  author = {Aho, AV and Sagiv, Y. and Szymanski, TG and Ullman, JD},
  title = {Inferring a Tree from Lowest Common Ancestors with an Application
	to the Optimization of Relational Expressions},
  journal = {SIAM Journal on Computing},
  year = {1981},
  volume = {10},
  pages = {405}
}

@ARTICLE{aitkin91,
  author = {Aitkin, M. N.},
  title = {Posterior {B}ayes factor},
  journal = {Journal of the Royal Statistical Society, series B},
  year = {1991},
  volume = {53},
  pages = {111--12}
}

@ARTICLE{aldous01,
  author = {Aldous, D.},
  title = {Stochastic Models and Descriptive Statistics for Phylogenetic Trees,
	from {Y}ule to Today},
  journal = {Statistical Science},
  year = {2001},
  volume = {16},
  pages = {23--34}
}

@INPROCEEDINGS{aldous85,
  author = {D. Aldous},
  title = {Exchangeability and related topics},
  booktitle = {\'Ecole d'\'Et\'e de Probabilit\'es de Saint-Flour XIII-1983},
  year = {1985},
  pages = {1--198},
  publisher = {Springer, Berlin}
}

@ARTICLE{Aldous2005,
  author = {Aldous, D. and Popovic, L.},
  title = {A critical branching process model for biodiversity},
  journal = {Advances in Applied Probability},
  year = {2005},
  volume = {37},
  pages = {1094--1115},
  number = {4},
  publisher = {Applied Probability Trust}
}

@ARTICLE{alfaro06,
  author = {M. E. Alfaro and J. P. Huelsenbeck},
  title = {Comparative performance of {B}ayesian and {AIC}-based measures of
	phylogenetic model uncertainty},
  journal = SYSB,
  year = {2006},
  volume = {55},
  pages = {89--96}
}

@ARTICLE{Alfaro2003,
  author = {Alfaro, Michael E. and Zoller, Stefan and Lutzoni, F.},
  title = {Bayes or Bootstrap? A Simulation Study Comparing the Performance
	of {B}ayesian {M}arkov Chain {M}onte {C}arlo Sampling and Bootstrapping
	in Assessing Phylogenetic Confidence},
  journal = MBE,
  year = {2003},
  volume = {20},
  pages = {255-266},
  number = {2},
  doi = {10.1093/molbev/msg028},
  eprint = {http://mbe.oxfordjournals.org/content/20/2/255.full.pdf+html},
  url = {http://mbe.oxfordjournals.org/content/20/2/255.abstract}
}

@ARTICLE{Allen2001,
  author = {Allen, B.L. and Steel, Mike},
  title = {Subtree Transfer Operations and Their Induced Metrics on Evolutionary
	Trees},
  journal = {Annals of Combinatorics},
  year = {2001},
  volume = {5},
  pages = {1--15},
  number = {1},
  publisher = {Springer}
}

@ARTICLE{allman08a,
  author = {E. S. Allman and C. An\'e and J. A. Rhodes},
  title = {Identifiability of a {M}arkovian model of molecular evolution with
	gamma-distributed rates},
  journal = {Advances in Applied Probability},
  year = {2008},
  volume = {40},
  pages = {228--249}
}

@ARTICLE{allman09,
  author = {E. S. Allman and J. A. Rhodes},
  title = {The identifiability of covarion models in phylogenetics},
  journal = {IEEE/ACM Transactions in Computational Biology and Bioinformatics},
  year = {2009},
  volume = {6},
  pages = {76--88}
}

@ARTICLE{allman08b,
  author = {E. S. Allman and J. A. Rhodes},
  title = {Identifying evolutionary trees and substitution parameters for the
	general {M}arkov model with invariable sites},
  journal = {Mathematical Biosciences},
  year = {2008},
  volume = {211},
  pages = {18--33}
}

@ARTICLE{alroy1999,
  author = {Alroy, John},
  title = {The fossil record of {N}orth {A}merican mammals: evidence for a {P}aleocene
	evolutionary radiation},
  journal = SYSB,
  year = {1999},
  volume = {48},
  pages = {107--118},
  number = {1}
}

@ARTICLE{altekar04,
  author = {G. Altekar and S. Dwarkadas and J. P. Huelsenbeck and F. Ronquist},
  title = {Parallel {M}etropolis coupled {M}arkov chain {M}onte {C}arlo for
	{B}ayesian phylogenetic inference},
  journal = BI,
  year = {2004},
  volume = {20},
  pages = {407--415}
}

@ARTICLE{ammerman92,
  author = {L. K. Ammerman and D. M. Hillis},
  title = {A molecular test of bat relationships: {M}onophyly or diphyly?},
  journal = SYSB,
  year = {1992},
  volume = {41},
  pages = {222--232}
}

@ARTICLE{ane07,
  author = {C. An\'e and B. Larget and D. A. Baum and S. D. Smith and A. Rokas},
  title = {Bayesian estimation of concordance among gene trees},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {412--426}
}

@ARTICLE{ane05,
  author = {C. An\'e and M. J. Sanderson},
  title = {Missing the forest for the trees: {P}hylogenetic compression and
	its implications for inferring complex evolutionary histories},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {146--157}
}

@ARTICLE{andolfatto05,
  author = {P. Andolfatto},
  title = {Adaptive evolution of non-coding {DNA} in {D}rosophila},
  journal = {Nature},
  year = {2005},
  volume = {437},
  pages = {1149--1153}
}

@ARTICLE{andrews1977,
  author = {Andrews, P and Tobien, H},
  title = {New {M}iocene locality in Turkey with evidence on the origin of \textit{{R}amapithecus}
	and \textit{{S}ivapithecus}},
  journal = {Nature},
  year = {1977},
  volume = {268},
  pages = {699},
  number = {5622}
}

@ARTICLE{antonelli2011,
  author = {Antonelli, Alexandre and Sanmart{\'i}n, Isabel},
  title = {Mass extinction, gradual cooling, or rapid radiation? {R}econstructing
	the spatiotemporal evolution of the ancient angiosperm genus \textit{{H}edyosmum}
	({C}hloranthaceae) using empirical and simulated approaches},
  journal = SYSB,
  year = {2011},
  volume = {60},
  pages = {596--615},
  number = {5}
}

@ARTICLE{antoniak74,
  author = {C. E. Antoniak},
  title = {Mixtures of {D}irichlet processes with applications to non-parametric
	problems},
  journal = {Annals of Statistics},
  year = {1974},
  volume = {2},
  pages = {1152--1174}
}

@INPROCEEDINGS{arima13,
  author = {S. Arima and L. Tardella},
  title = {IDR},
  booktitle = {{B}ayesian Phylogenetics: Methods, Algorithms, and Applications},
  year = {2013},
  editor = {M.-H. Chen and L. Kuo and P. Lewis},
  pages = {145},
  publisher = {Sinauer Associates}
}

@ARTICLE{arisbrosou07,
  author = {Stephane Aris-Brosou},
  title = {Dating Phylogenies with Hybrid Local Molecular Clocks},
  journal = {PLoS One},
  year = {2007},
  volume = {2},
  pages = {e879}
}

@ARTICLE{arisbrosou03,
  author = {Stephane Aris-Brosou and Ziheng Yang},
  title = {Bayesian models of episodic evolution support a late precambrian
	explosive diversification of the {M}etazoa},
  journal = MBE,
  year = {2003},
  volume = {20},
  pages = {1947--54},
  number = {12},
  month = {Nov}
}

@ARTICLE{arisbrosou02,
  author = {Stephane Aris-Brosou and Ziheng Yang},
  title = {Effects of models of rate evolution on estimation of divergence dates
	with special reference to the {M}etazoan {18S} ribosomal {RNA} phylogeny},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {703--714}
}

@ARTICLE{arora96,
  author = {R. Arora and C. Priano and A. Jacobson and D. R. Mills},
  title = {Cis-acting elements within an {RNA} coliphage genome: {F}old as you
	please, but fold you must!!},
  journal = JMB,
  year = {1996},
  volume = {258},
  pages = {433--446}
}

@ARTICLE{asmussen92,
  author = {S. Asmussen and P. W. Glynn and H. Thorisson},
  title = {Stationary detection in the initial transient problem},
  journal = {ACM Transactions on Modeling and Computer Simulation},
  year = {1992},
  volume = {2},
  pages = {130--157}
}

@ARTICLE{ayers12,
  author = {D. L. Ayers and A. Darling and D. J. Zwickl and P. Beerli and M.
	T. Holder and P. O. Lewis and J. P. Huelsenbeck and F. Ronquist and
	D. L. Swofford and M. P. Cummings and A. Rambaut and M. A. Suchard},
  title = {{BEAGLE}: An Application Programming Interface and High-Performance
	Computing Library for Statistical Phylogenetics},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {170--173}
}

@ARTICLE{aze2011,
  author = {Aze, Tracy and Ezard, Thomas HG and Purvis, Andy and Coxall, Helen
	K and Stewart, Duncan RM and Wade, Bridget S and Pearson, Paul N},
  title = {A phylogeny of {C}enozoic macroperforate planktonic foraminifera
	from fossil data},
  journal = {Biological Reviews},
  year = {2011},
  volume = {86},
  pages = {900--927},
  number = {4}
}

@ARTICLE{Bader2006,
  author = {Bader, D.A. and Roshan, U. and Stamatakis, A.},
  title = {Computational Grand Challenges in Assembling the Tree of Life: Problems
	and Solutions},
  journal = {Advances in Computers},
  year = {2006},
  volume = {68},
  pages = {128},
  publisher = {ACADEMIC PRESS, INC}
}

@ARTICLE{baele12,
  author = {Baele, Guy and Lemey, Philippe and Bedford, Trevor and Rambaut, Andrew
	and Suchard, Marc A. and Alekseyenko, Alexander V.},
  title = {Improving the Accuracy of Demographic and Molecular Clock Model Comparison
	While Accommodating Phylogenetic Uncertainty},
  journal = MBE,
  year = {2012},
  volume = {30},
  pages = {2157--2167}
}

@ARTICLE{baele13,
  author = {Baele, Guy and Li, Wai Lok Sibon and Drummond, Alexei J. and Suchard,
	Marc A. and Lemey, Philippe},
  title = {Accurate Model Selection of Relaxed Molecular Clocks in {B}ayesian
	Phylogenetics},
  journal = MBE,
  year = {2013},
  volume = {30},
  pages = {239--243}
}

@ARTICLE{Bahl2011,
  author = {Bahl, Justin and Nelson, Martha I. and Chan, Kwok H. and Chen, Rubing
	and Vijaykrishna, Dhanasekaran and Halpin, Rebecca A. and Stockwell,
	Timothy B. and Lin, Xudong and Wentworth, David E. and Ghedin, Elodie
	and Guan, Yi and Malik Peiris, J. S. and Riley, Steven and Rambaut,
	Andrew and Holmes, Edward C. and Smith, Gavin J. D.},
  title = {Temporally structured metapopulation dynamics and persistence of
	influenza A H3N2 virus in humans},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2011}
}

@ARTICLE{bailey92,
  author = {W. J. Bailey and J. L. Slightom and M. Goodman},
  title = {Rejection of the ``Flying Primate'' hypothesis by phylogenetic evidence
	from $\epsilon$-globin gene},
  journal = {Science},
  year = {1992},
  volume = {256},
  pages = {86--89}
}

@ARTICLE{bailly03,
  author = {X. Bailly and R. Leroy and S. Carney and O. Collin and F. Zal and
	A. Toulmond and D. Jollivet},
  title = {The loss of the hemoglobin {H2S}-binding function in annelids from
	sulfide-free habitats reveals molecular adaptation driven by {D}arwinian
	positive selection.},
  journal = PNAS,
  year = {2003},
  volume = {100},
  pages = {5885--5890}
}

@ARTICLE{baker2006,
  author = {Baker, Allan J and Pereira, Sergio Luiz and Haddrath, Oliver P and
	Edge, Kerri-Anne},
  title = {Multiple gene evidence for expansion of extant penguins out of {A}ntarctica
	due to global cooling},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2006},
  volume = {273},
  pages = {11--17},
  number = {1582},
  publisher = {The Royal Society}
}

@ARTICLE{baker91,
  author = {R. J. Baker and R. L. Honeycutt and R. A. Van Den Bussche},
  title = {Examination of the monophyly of bats: {R}estriction map of the ribosomal
	{DNA} cistron},
  journal = {Bulletin of the American Museum of Natural History},
  year = {1991},
  volume = {206},
  pages = {42--53}
}

@ARTICLE{bapst2012,
  author = {Bapst, David W},
  title = {paleotree: an {R} package for paleontological and phylogenetic analyses
	of evolution},
  journal = {Methods in Ecology and Evolution},
  year = {2012},
  volume = {3},
  pages = {803--807},
  number = {5},
  publisher = {Wiley Online Library}
}

@ARTICLE{barley10,
  author = {A. J. Barley and P. Q. Spinks and R. C. Thomson and H. B. Shaffer},
  title = {Fourteen nuclear genes provide phylogenetic resolution for difficult
	nodes in the turtle tree of life},
  journal = MPE,
  year = {2010},
  volume = {55},
  pages = {1189--1194}
}

@ARTICLE{barry87,
  author = {D. Barry and J. A. Hartigan},
  title = {Statistical analysis of hominoid molecular evolution},
  journal = {Statistical Science},
  year = {1987},
  volume = {2},
  pages = {191--210}
}

@ARTICLE{baryshnikov2002,
  author = {Baryshnikov, Gennady F},
  title = {Late {M}iocene \textit{{I}ndarctos punjabiensis atticus} ({C}arnivora,
	{U}rsidae) in {U}kraine with survey of \textit{{I}ndarctos} records
	from the former {USSR}},
  journal = {Russian J. Theriol},
  year = {2002},
  volume = {1},
  pages = {83--89},
  number = {2}
}

@INPROCEEDINGS{baserga93,
  author = {S. J. Baserga and J. A. Steitz},
  title = {The diverse world of small ribonucleoproteins},
  booktitle = {The {RNA} {W}orld},
  year = {1993},
  editor = {R. F. Gesteland and J. F. Atkins},
  pages = {359--381},
  publisher = {Cold Spring Harbor Press}
}

@ARTICLE{Bastert2002,
  author = {Oliver Bastert and Dan Rockmore and Peter F. Stadler and Gottfried
	Tinhofer},
  title = {Landscapes on Spaces of Trees},
  journal = {Applied Mathematics and Computation},
  year = {2002},
  volume = {131},
  pages = {439--459},
  optmonth = {September},
  optnumber = {2},
  optpages = {439-459},
  optvolume = {131},
  url = {citeseer.ist.psu.edu/bastert01landscapes.html}
}

@ARTICLE{bastolla01,
  author = {U. Bastolla and J. Farwer and E. W. Knapp and M. Vendruscolo},
  title = {How to guarantee optimal stability for most representative structures
	in the protein data bank},
  journal = {Proteins},
  year = {2001},
  volume = {44},
  pages = {79--96}
}

@ARTICLE{battistuzzi2010,
  author = {Battistuzzi, Fabia U. and Filipski, Alan and Hedges, S. Blair and
	Kumar, Sudhir},
  title = {Performance of relaxed-clock methods in estimating evolutionary divergence
	times and their credibility intervals},
  journal = MBE,
  year = {2010},
  volume = {27},
  pages = {1289--1300}
}

@BOOK{Baum2004,
  title = {The {MRP} method},
  publisher = {Kluwer Academic Pub},
  year = {2004},
  author = {Baum, B.R. and Ragan, M.A.},
  pages = {17--34},
  journal = {Phylogenetic Supertrees: Combining Information to Reveal the Tree
	of Life}
}

@ARTICLE{Baum1992,
  author = {Baum, Bernard R.},
  title = {Combining Trees as a Way of Combining Data Sets for Phylogenetic
	Inference, and the Desirability of Combining Gene Trees},
  journal = {Taxon},
  year = {1992},
  volume = {41},
  pages = {3--10},
  number = {1}
}

@ARTICLE{bayes63,
  author = {T. Bayes},
  title = {An essay towards solving a problem in the doctrine of chances},
  journal = {Philosophical Transactions of the Royal Society of London},
  year = {1763},
  volume = {53},
  pages = {370--418}
}

@BOOK{bayes36,
  title = {An {I}ntroduction to the {D}octrine of {F}luxions, and a {D}efence
	of the {M}athematicians against the objections of the {A}uthor of
	the {A}nalyst},
  publisher = {unknown publisher},
  year = {1736},
  author = {T. Bayes},
  address = {unknown address}
}

@ARTICLE{beatty79,
  author = {J. Beatty and W. L. Fink},
  title = {Review of `{S}implicity' by {E}. {S}ober},
  journal = SZ,
  year = {1979},
  volume = {28},
  pages = {643--651}
}

@MANUAL{Beerli2008,
  title = {Migrate version 3.0 - a maximum likelihood and {B}ayesian estimator
	of gene flow using the coalescent.},
  author = {Peter Beerli},
  month = {July},
  year = {2008},
  url = {http://popgen.scs.edu/migrate.html}
}

@ARTICLE{Beerli2001,
  author = {Beerli, Peter and Felsenstein, Joseph},
  title = {Maximum likelihood estimation of a migration matrix and effective
	population sizes in n subpopulations by using a coalescent approach},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2001},
  volume = {98},
  pages = {4563-4568},
  number = {8},
  doi = {10.1073/pnas.081068098},
  eprint = {http://www.pnas.org/content/98/8/4563.full.pdf+html},
  url = {http://www.pnas.org/content/98/8/4563.abstract}
}

@ARTICLE{beerli99,
  author = {P. Beerli and J. Felsenstein},
  title = {Maximum likelihood estimation of migration rates and effective population
	umbers in two populations using a coalescent approach},
  journal = {Genetics},
  year = {1999},
  volume = {152},
  pages = {763--773}
}

@ARTICLE{Beiko2006,
  author = {Beiko, R. and Keith, J. and Harlow, T. and Ragan, M.},
  title = {Searching for Convergence in Phylogenetic {M}arkov Chain {M}onte
	{C}arlo},
  journal = SYSB,
  year = {2006},
  volume = {55},
  pages = {553--565},
  number = {4}
}

@ARTICLE{beiko05,
  author = {R. G. Beiko and T. J. Harlow and M. A. Ragan},
  title = {Highways of gene sharing in prokaryotes},
  journal = PNAS,
  year = {2005},
  volume = {102},
  pages = {14332--14337}
}

@ARTICLE{bell34,
  author = {E. T. Bell},
  title = {Exponential numbers},
  journal = {American Mathematics Monthly},
  year = {1934},
  volume = {41},
  pages = {411--419}
}

@ARTICLE{bell2014strap,
  author = {Bell, Mark A and Lloyd, Graeme T},
  title = {strap: an {R} package for plotting phylogenies against stratigraphy
	and assessing their stratigraphic congruence},
  journal = {Palaeontology},
  year = {2014},
  publisher = {Wiley Online Library}
}

@ARTICLE{benton03,
  author = {M. J. Benton and F. J. Ayala},
  title = {Dating the tree of life},
  journal = {Science},
  year = {2003},
  volume = {300},
  pages = {1698--1700}
}

@ARTICLE{benton07,
  author = {M. J. Benton and P. C. J. Donoghue},
  title = {Paleontological evidence to date the tree of life},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {26--53}
}

@ARTICLE{benton00,
  author = {M. J. Benton and M. A. Wills and R. Hitchin},
  title = {Quality of the fossil record through time},
  journal = {Nature},
  year = {2000},
  volume = {403},
  pages = {534--537}
}

@ARTICLE{berger94,
  author = {J. Berger},
  title = {An Overview of Robust {B}ayesian Analysis},
  journal = {Test},
  year = {1994},
  volume = {3},
  pages = {5--124}
}

@ARTICLE{berger99,
  author = {J. O. Berger and B. Liseo and R. L. Wolpert},
  title = {Integrated likelihood methods for eliminating nuisance parameters},
  journal = {Statistical Science},
  year = {1999},
  volume = {14},
  pages = {1--28}
}

@ARTICLE{Besag1993,
  author = {Besag, Julian and Green, Peter J.},
  title = {Spatial Statistics and {B}ayesian Computation},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  year = {1993},
  volume = {55},
  pages = {25--37},
  publisher = {Blackwell Publishing for the Royal Statistical Society},
  url = {http://www.jstor.org/stable/2346064}
}

@ARTICLE{billera01,
  author = {L. Billera and S. Holmes and K. Vogtmann},
  title = {Geometry of the space of phylogenetic trees},
  journal = {Advances in Applied Mathematics},
  year = {2001},
  volume = {27},
  pages = {733--767}
}

@ARTICLE{Bininda-Emonds2004,
  author = {Bininda-Emonds, O.R.P.},
  title = {The evolution of supertrees},
  journal = {Trends in Ecology \& Evolution},
  year = {2004},
  volume = {19},
  pages = {315--322},
  number = {6}
}

@BOOK{Bininda-Emonds2004a,
  title = {Phylogenetic Supertrees: Combining Information to Reveal the Tree
	of Life},
  publisher = {Kluwer Academic Pub},
  year = {2004},
  author = {Bininda-Emonds, ORP}
}

@INPROCEEDINGS{bishop87,
  author = {M. J. Bishop and A. E. Friday},
  title = {Tetrapod relationships: {T}he molecular evidence},
  booktitle = {Molecules and {M}orphology in {E}volution: {C}onflict or {C}ompromise?},
  year = {1987},
  editor = {C. Patterson},
  pages = {123--140},
  publisher = {Cambridge University Press}
}

@ARTICLE{bishop85,
  author = {M. J. Bishop and A. E. Friday},
  title = {Evolutionary trees form nucleic acid and protein sequences},
  journal = PROCROYB,
  year = {1985},
  volume = {226},
  pages = {271--302}
}

@ARTICLE{bjork1970,
  author = {Bjork, Philip Reese},
  title = {The {C}arnivora of the {H}agerman local fauna (late {P}liocene) of
	{S}outhwestern Idaho},
  journal = {Transactions of the American Philosophical Society},
  year = {1970},
  volume = {60},
  pages = {3--54},
  number = {7}
}

@ARTICLE{blake92,
  author = {R. D. Blake and S. T. Hess and J. Nicholson-Tuell},
  title = {The influence of nearest neighbors on the rate and pattern of spontaneous
	point mutations},
  journal = JME,
  year = {1992},
  volume = {34},
  pages = {189--200}
}

@ARTICLE{blanquart08,
  author = {S. Blanquart and N. Lartillot},
  title = {A site- and time-heterogeneous model of amino acid replacement},
  journal = MBE,
  year = {2008},
  volume = {25},
  pages = {842--858}
}

@ARTICLE{Blanquart2006,
  author = {Blanquart, Samuel and Lartillot, Nicolas},
  title = {A {B}ayesian Compound Stochastic Process for Modeling Nonstationary
	and Nonhomogeneous Sequence Evolution},
  journal = MBE,
  year = {2006},
  volume = {23},
  pages = {2058-2071}
}

@ARTICLE{Bokma2009,
  author = {Bokma, F.},
  title = {Problems detecting density-dependent diversification on phylogenies},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2009},
  volume = {276},
  pages = {993},
  number = {1659},
  publisher = {The Royal Society}
}

@OTHER{bollback04,
  author = {J. Bollback},
  booktitle = {Statistical Methods in Molecular Evolution},
  editor = {R. Nielsen},
  publisher = {Springer-Verlag},
  title = {Predictive distributions and posterior mappings},
  year = {2004}
}

@ARTICLE{bollback01,
  author = {J. Bollback and J. P. Huelsenbeck},
  title = {Phylogenetic relationships, genome evolution, and host specificity
	of single-stranded {RNA} bacteriophage ({F}amily {L}eviviridae)},
  journal = JME,
  year = {2001},
  volume = {52},
  pages = {117--128}
}

@ARTICLE{Bouckaert2014,
  author = {Bouckaert, Remco and Heled, Joseph and K{\"u}hnert, Denise and Vaughan,
	Tim and Wu, Chieh-Hsi and Xie, Dong and Suchard, Marc A and Rambaut,
	Andrew and Drummond, Alexei J},
  title = {BEAST 2: A Software Platform for {B}ayesian Evolutionary Analysis},
  journal = {PLoS computational biology},
  year = {2014},
  volume = {10},
  pages = {e1003537},
  number = {4}
}

@PHDTHESIS{Bourque1978a,
  author = {Bourque, M.},
  title = {{Arbres de Steiner et r\'{e}seaux dont varie l'emplagement de certains
	sommets}},
  school = {Ph. D. diss., Universite de Montreal, Quebec, Canada},
  year = {1978}
}

@PHDTHESIS{bourque78,
  author = {M. Bourque},
  title = {Arbres de Steiner et reseaux dont varie l'emplagement de certains
	sommets},
  school = {University of Montreal},
  year = {1978}
}

@ARTICLE{bradley07,
  author = {R. K. Bradley and I. Holmes},
  title = {Transducers: an emerging probabilistic framework for modeling indels
	on trees},
  journal = BI,
  year = {2007},
  volume = {23},
  pages = {3258--3262}
}

@ARTICLE{brandley08,
  author = {M. C. Brandley and J. P. Huelsenbeck and J. J. Wiens},
  title = {Rates and patterns in the evolution of snake-like body form in squamate
	reptiles: {E}vidence for repeated re-evolution of lost digits and
	long-term persistence of intermediate body forms},
  journal = {Evolution},
  year = {2008},
  volume = {62},
  pages = {2042--2064}
}

@ARTICLE{brandley05,
  author = {M. C. Brandley and A. Schmitz and T. W. Reeder},
  title = {Partitioned {B}ayesian analyses, partition choice, and the phylogenetic
	relationships of scincid lizards},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {373--390}
}

@ARTICLE{bray04,
  author = {N. Bray and L. Pachter},
  title = {{MAVID}: Constrained ancestral alignment of multiple sequences},
  journal = GR,
  year = {2004},
  volume = {14},
  pages = {693--699}
}

@ARTICLE{Britton2007,
  author = {Britton, T. and Svennblad, B. and Erixon, P. and Oxelman, B.},
  title = {Bayesian support is larger than bootstrap support in phylogenetic
	inference: a mathematical argument},
  journal = {Mathematical Medicine and Biology},
  year = {2007},
  volume = {24},
  pages = {401},
  number = {4},
  publisher = {IMA}
}

@ARTICLE{Brocchieri2001,
  author = {Brocchieri, L.},
  title = {Phylogenetic Inferences from Molecular Sequences: Review and Critique},
  journal = {Theoretical Population Biology},
  year = {2001},
  volume = {59},
  pages = {27--40},
  number = {1}
}

@ARTICLE{brochier02,
  author = {C. Brochier and H. Philippe},
  title = {Phylogeny: {A} non-hyperthermophilic ancestor for {B}acteria},
  journal = {Nature},
  year = {2002},
  volume = {417},
  pages = {244}
}

@ARTICLE{brochu97,
  author = {C. A. Brochu},
  title = {Morphology, fossils, divergence timing, and the phylogenetic relationships
	of \textit{{G}avialis}},
  journal = SYSB,
  year = {1997},
  volume = {46},
  pages = {479--522}
}

@ARTICLE{brochu2012,
  author = {Brochu, Christopher A and Parris, David C and Grandstaff, Barbara
	Smith and Denton Jr, Robert K and Gallagher, William B},
  title = {A new species of \textit{{B}orealosuchus} {(Crocodyliformes, Eusuchia)}
	from the {Late Cretaceous--Early Paleogene of New Jersey}},
  journal = {Journal of Vertebrate Paleontology},
  year = {2012},
  volume = {32},
  pages = {105--116},
  number = {1},
  publisher = {Taylor \& Francis}
}

@ARTICLE{Brooks1981,
  author = {Brooks, Daniel R.},
  title = {Hennig's Parasitological Method: A Proposed Solution},
  journal = SZ,
  year = {1981},
  volume = {30},
  pages = {229--249},
  number = {3},
  url = {http://www.jstor.org/stable/2413247}
}

@ARTICLE{Brooks1998c,
  author = {Brooks,Stephen},
  title = {Markov chain {M}onte {C}arlo method and its application},
  journal = {Journal of the Royal Statistical Society: Series D (The Statistician)},
  year = {1998},
  volume = {47},
  pages = {69-100},
  number = {1},
  doi = {10.1111/1467-9884.00117},
  eprint = {http://www.blackwell-synergy.com/doi/pdf/10.1111/1467-9884.00117},
  url = {http://www.blackwell-synergy.com/doi/abs/10.1111/1467-9884.00117}
}

@ARTICLE{Brooks1998b,
  author = {Brooks, S.P. and Gelman, A.},
  title = {General methods for monitoring convergence of iterative simulations},
  journal = {Journal of Computational and Graphical Statistics},
  year = {1998},
  volume = {7},
  pages = {434--455},
  number = {4},
  publisher = {JSTOR}
}

@ARTICLE{Brooks1998,
  author = {Brooks, S.P. and Roberts, G.O.},
  title = {Assessing convergence of {M}arkov chain {M}onte {C}arlo algorithms},
  journal = {Statistics and Computing},
  year = {1998},
  volume = {8},
  pages = {319--335},
  number = {4},
  publisher = {Citeseer}
}

@ARTICLE{Brooks1998a,
  author = {Brooks, S.P. and Roberts, G.O.},
  title = {Convergence assessment techniques for {M}arkov chain {M}onte {C}arlo},
  journal = {Statistics and Computing},
  year = {1998},
  volume = {8},
  pages = {319--335},
  number = {4},
  publisher = {Springer}
}

@ARTICLE{brooks2003,
  author = {Brooks, Stephen P and Giudici, PAULO and Roberts, Gareth O},
  title = {Efficient construction of reversible jump {M}arkov chain {M}onte
	{C}arlo proposal distributions},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2003},
  volume = {65},
  pages = {3--39},
  number = {1},
  publisher = {Wiley Online Library}
}

@ARTICLE{brower00,
  author = {A. V. Z. Brower},
  title = {Phylogenetic relationships among the {N}ymphalidae ({L}epidoptera)
	inferred from partial sequences of the wingless gene},
  journal = PROCROYB,
  year = {2000},
  volume = {267},
  pages = {1201--1211}
}

@ARTICLE{brown07,
  author = {J. M. Brown and A. R. Lemmon},
  title = {The importance of data partitioning and the utility of {B}ayes factors
	in {B}ayesian phylogenetics},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {643--655}
}

@ARTICLE{brown93,
  author = {M. Brown and R. Hughey and A. Krogh and I. S. Mian and K. Sj{\"o}lander
	and D. Haussler},
  title = {Using {D}irichlet Mixture Priors to Derive Hidden {M}arkov Models
	for Protein Families},
  journal = {Proc. of First Int. Conf. on Intelligent Systems for Molecular Biology},
  year = {1993},
  pages = {47--55}
}

@ARTICLE{brown11,
  author = {Brown, Richard and Yang, Ziheng},
  title = {Rate variation and estimation of divergence times using strict and
	relaxed clocks},
  journal = {BMC Evolutionary Biology},
  year = {2011},
  volume = {11},
  pages = {271}
}

@ARTICLE{brown82,
  author = {W. M. Brown and E. M. Prager and A. Wang and A. C. Wilson},
  title = {Mitochondrial {DNA} sequences of primates, tempo and mode of evolution},
  journal = JME,
  year = {1982},
  volume = {18},
  pages = {225--239}
}

@ARTICLE{bruno99,
  author = {W. J. Bruno and A. L. Halpern},
  title = {Topological bias and inconsistency of maximum likelihood using wrong
	models},
  journal = MBE,
  year = {1999},
  volume = {16},
  pages = {564--566}
}

@ARTICLE{Bryant2004,
  author = {Bryant, D.},
  title = {The Splits in the Neighborhood of a Tree},
  journal = {Annals of Combinatorics},
  year = {2004},
  volume = {8},
  pages = {1--11},
  number = {1},
  publisher = {Springer}
}

@PHDTHESIS{Bryant1997,
  author = {Bryant, D.},
  title = {{Building Trees, Hunting for Trees, and Comparing Trees: Theory and
	Methods in Phylogenetic Analysis}},
  school = {University of Canterbury},
  year = {1997}
}

@ARTICLE{Bryant1996,
  author = {David Bryant},
  title = {Hunting for trees in binary character sets},
  journal = {Journal of Computational Biology},
  year = {1996},
  volume = {3},
  pages = {275-288}
}

@ARTICLE{bryant00,
  author = {D. Bryant and J. Tsang and P. Kearney and M. Li},
  title = {Computing the quartet distance between evolutionary trees},
  journal = {Proceedings of the ACM-SIAM Symposium on Discrete Algorithms},
  year = {2000}
}

@ARTICLE{buckley2000,
  author = {Buckley, Gregory A and Brochu, Christopher A and Krause, David W
	and Pol, Diego},
  title = {A pug-nosed crocodyliform from the {L}ate {C}retaceous of {M}adagascar},
  journal = {Nature},
  year = {2000},
  volume = {405},
  pages = {941--944},
  number = {6789},
  publisher = {Nature Publishing Group}
}

@ARTICLE{bull93,
  author = {J. J. Bull and J. P. Huelsenbeck and C. W. Cunningham and D. L. Swofford
	and P. J. Waddell},
  title = {Partitioning and combining data in phylogenetic analysis},
  journal = SYSB,
  year = {1993},
  volume = {42},
  pages = {384--397}
}

@ARTICLE{bulmer86,
  author = {M. Bulmer},
  title = {Neighboring base effects on substitution rates in pseudo genes},
  journal = MBE,
  year = {1986},
  volume = {3},
  pages = {322--329}
}

@ARTICLE{vandenbussche98,
  author = {R. A. van den Bussche and R. J. Baker and J. P. Huelsenbeck and D.
	M. Hillis},
  title = {Base compositional bias and phylogenetic analyses: {A} test of the
	{``Flying DNA''} hypothesis},
  journal = MPE,
  year = {1998},
  volume = {13},
  pages = {408--416}
}

@ARTICLE{cameron07,
  author = {S. Cameron and H. M. Hines and P. H. Williams},
  title = {A comprehensive phylogeny of bumble bees ({B}ombus)},
  journal = {Biological journal of the Linnean Society},
  year = {2007},
  volume = {91},
  pages = {161--188}
}

@ARTICLE{camin65,
  author = {J. H. Camin and R. R. Sokal},
  title = {A method for deducing branching sequences in a phylogeny},
  journal = {Evolution},
  year = {1965},
  volume = {19},
  pages = {311--326}
}

@ARTICLE{cann87,
  author = {R. L. Cann and M. Stoneking and A. C. Wilson},
  title = {Mitochondrial {DNA} and human evolution},
  journal = {Nature},
  year = {1987},
  volume = {325},
  pages = {31--36}
}

@ARTICLE{cannarozzi07,
  author = {G. Cannarozzi and A. Schneider and G. Gonnet},
  title = {A phylogenomic study of human, dog, and mouse},
  journal = PLOSCOMPBIO,
  year = {2007},
  volume = {3},
  pages = {9--14}
}

@ARTICLE{cao98,
  author = {Y. Cao and A. Janke and P. J. Waddell and M. Westerman and O. Takenaka
	and S. Murata and N. Okada and S. P\"a\"abo and M. Hasegawa},
  title = {Conflict amongst individual mitochondrial proteins in resolving the
	phylogeny of eutherian orders},
  journal = JME,
  year = {1998},
  volume = {47},
  pages = {307--322}
}

@ARTICLE{cardinal2013,
  author = {Cardinal, Sophie and Danforth, Bryan N},
  title = {Bees diversified in the age of eudicots},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2013},
  volume = {280},
  pages = {20122686},
  number = {1755}
}

@BOOK{carlin00,
  title = {Bayes and Empirical {B}ayes Methods for Data Analysis},
  publisher = {Chapman and Hall/CRC},
  year = {2000},
  author = {B. P. Carlin and T. A. Louis},
  address = {Boca Raton},
  edition = {second}
}

@ARTICLE{Cavalli-Sforza1967,
  author = {Cavalli-Sforza, L. L. and Edwards, A. W. F.},
  title = {Phylogenetic Analysis: Models and Estimation Procedures},
  journal = {Evolution},
  year = {1967},
  volume = {21},
  pages = {550--570},
  number = {3},
  publisher = {Society for the Study of Evolution},
  url = {http://www.jstor.org/stable/2406616}
}

@ARTICLE{cavalli-sforza67,
  author = {L. L. Cavalli-Sforza and A. W. F. Edwards},
  title = {Phylogenetic analysis. {M}odels and estimation procedures},
  journal = {American Journal of Human Genetics},
  year = {1967},
  volume = {19},
  pages = {233--257}
}

@BOOK{cavalli-sforza94,
  title = {History and {G}eography of {H}uman {G}enes},
  publisher = {Princeton University Press},
  year = {1994},
  author = {L. L. Cavalli-Sforza and P. Menozzi and A. Piazza},
  address = {Princeton, New Jersey}
}

@ARTICLE{cavelaars00,
  author = {A. E. J. M. Cavelaars and A. E. Kunst and J. J. M. Geurts and R.
	Crialesi and L. Gr\"otvedt and U. Helmert and E. Lahelma and O. Lundberg
	and A. Mielck and N. Kr. Rasmussen and E. Regidor and T. Spuhler
	and J. P. Mackenbach},
  title = {Persistent variations in average height between countries and between
	socio-economic groups: {A}n overview of 10 European countries},
  journal = {Annals of Human Biology},
  year = {2000},
  volume = {27},
  pages = {407--421}
}

@ARTICLE{cavender78,
  author = {J. A. Cavender},
  title = {Taxonomy with confidence},
  journal = {Mathematical Biosciences},
  year = {1978},
  volume = {40},
  pages = {301--316}
}

@ARTICLE{cavender87,
  author = {J. A. Cavender and J. Felsenstein},
  title = {Invariants of phylogenies in a simple case with discrete states},
  journal = {Journal of Classification},
  year = {1987},
  volume = {4},
  pages = {57--71}
}

@ARTICLE{cech86,
  author = {T. R. Cech and B. L. Bass},
  title = {Biological catalysis by {RNA}},
  journal = {Annual Review of Biochemistry},
  year = {1986},
  volume = {55},
  pages = {599--629}
}

@ARTICLE{chan05,
  author = {Chan, Kai M. A. and Moore, Brian R.},
  title = {SymmeTREE: whole-tree analysis of differential diversification rates},
  journal = BI,
  year = {2005},
  volume = {21},
  pages = {1709--1710}
}

@ARTICLE{chandrasekharan96,
  author = {U. M. Chandrasekharan and S. Sanker and M. J. Glynias and S. S. Karnik
	and A. Husain},
  title = {Angiotensin II-forming activity in a reconstructed ancestral chymase},
  journal = {Science},
  year = {1996},
  volume = {271},
  pages = {1483--1489}
}

@ARTICLE{chang00,
  author = {B. S. W. Chang and M. J. Donoghue},
  title = {Recreating ancestral proteins},
  journal = {Trends in Ecology and Evolution},
  year = {2000},
  volume = {15},
  pages = {109--114}
}

@ARTICLE{chang02,
  author = {B. S. W. Chang and K. J\"onsson and M. A. Kazmi and M. J. Donoghue
	and T. P. Sakmar},
  title = {Recreating a functional ancestral {A}rchosaur visual pigment},
  journal = MBE,
  year = {2002},
  volume = {19},
  pages = {502--505}
}

@ARTICLE{charleston95,
  author = {M. A. Charleston},
  title = {Toward a characterization of landscapes of combinatorial optimization
	problems, with special attention to the phylogeny problem},
  journal = JCB,
  year = {1995},
  volume = {2},
  pages = {439--450}
}

@PHDTHESIS{charleston94,
  author = {M. A. Charleston},
  title = {Factors affecting the performance of phylogenetic methods},
  school = {Massey University},
  year = {1994}
}

@ARTICLE{chase93,
  author = {M. W. Chase and D. E. Soltis and R. G. Olmstead and D. Morgan and
	D. H. Les and B. D. Mishler and M. R. Duvall and R. A. Price and
	H. G. Hills and Y. Qiu and K. A. Kron and J. H. Rettig and E. Conti
	and J. D. Palmer and J. R. Manhart and K. J. Sytsma and H. J. Michaels
	and W. J. Kress and K. G. Karol and W. D. Clark and M. Hedren and
	B. S. Gaut and R. K. Jansen and K. Kim and C. F. Wimpee and J. F.
	Smith and G. R. Furnier and S. H. Strauss and Q. Xiang and G. M.
	Plunkett and P. S. Soltis and S. M. Swensen and S. E. Williams and
	P. A. Gadek and C. J. Quinn and L. E. Eguiarte and E. Golenberg and
	G. H. Learn and S. W. Graham and S. C. H. Barrett and S. Dayanandan
	and V. A. Albert},
  title = {Phylogenetics of seed plants: {A}n analysis of nucleotide sequences
	from the plastid gene rbcL},
  journal = {Annals Missouri Botanical Garden},
  year = {1993},
  volume = {80},
  pages = {528--580}
}

@BOOK{Chen2001,
  title = {Monte {C}arlo methods in {B}ayesian computation},
  publisher = {Springer},
  year = {2001},
  author = {Chen, M.H. and Shao, Q.M. and Ibrahim, J.G.},
  isbn = {0387989358}
}

@ARTICLE{chothia86,
  author = {C. Chothia and A. M. Lesk},
  title = {The relation between the divergence of sequence and structure in
	proteins},
  journal = {EMBO J},
  year = {1986},
  volume = {5},
  pages = {823--826}
}

@ARTICLE{churcher1993,
  author = {Churcher, CS and Morgan, AV and Carter, LD},
  title = {\textit{{A}rctodus simus} from the {A}laskan {A}rctic slope},
  journal = {Canadian Journal of Earth Sciences},
  year = {1993},
  volume = {30},
  pages = {1007--1013},
  number = {5}
}

@ARTICLE{clark03,
  author = {A. G. Clark and S. Glanowski and R. Nielsen and P. D. Thomas and
	A. Kejariwal and M. A. Todd and D. M. Tanenbaum and D. Civello and
	F. Lu and B. Murphy and S. Ferriera and G. Wang, X. Zheng and T.
	J. White and J. J. Sninsky and M. D. Adams and M. Cargill},
  title = {Inferring nonneutral evolution from human-chimp-mouse orthologous
	gene trios},
  journal = {Science},
  year = {2003},
  volume = {302},
  pages = {1960--1963}
}

@ARTICLE{Clark1999,
  author = {Clark, E. and Quinn, A.},
  title = {A data-driven {B}ayesian sampling scheme for unsupervised image segmentation},
  journal = {Acoustics, Speech, and Signal Processing, 1999. ICASSP '99. Proceedings.,
	1999 IEEE International Conference on},
  year = {1999},
  volume = {6},
  pages = {3497-3500 vol.6},
  doi = {10.1109/ICASSP.1999.757596}
}

@BOOK{clark1972,
  title = {Arctoid Genetic Characters as Related to the Genus \emph{{P}arictis}},
  publisher = {Field Museum of Natural History},
  year = {1972},
  author = {Clark, John and Guensburg, Thomas Edgar},
  volume = {1150},
  address = {Chicago, Ill.}
}

@ARTICLE{clarke2007,
  author = {Clarke, Julia A and Ksepka, Daniel T and Stucchi, Marcelo and Urbina,
	Mario and Giannini, Norberto and Bertelli, Sara and Narv{\'a}ez,
	Yanina and Boyd, Clint A},
  title = {Paleogene equatorial penguins challenge the proposed relationship
	between biogeography, diversity, and Cenozoic climate change},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2007},
  volume = {104},
  pages = {11545--11550},
  number = {28},
  publisher = {National Acad Sciences}
}

@ARTICLE{cliften01,
  author = {P. Cliften and L. W. Hillier and L. Fulton and T. Graves and T. Miner
	W. R. Gish and R. H. Waterston and M. Johnston},
  title = {Surveying {\it {S}accharomyces} genomes to identify functional elements
	by comparative {DNA} sequence analysis},
  journal = {Genome Research},
  year = {2001},
  volume = {11},
  pages = {1175--1186}
}

@ARTICLE{cliften03,
  author = {P. Cliften and P. Sudarsanam and A. Desikan and L. Fulton and B.
	Fulton and J. Majors and R. Waterson and B. A. Cohen and M. Johnston},
  title = {Finding functional features in {\it {S}accharomyces} genomes by phylogenetic
	footprinting},
  journal = {Science},
  year = {2003},
  volume = {301},
  pages = {71--76}
}

@ARTICLE{Clopper1934,
  author = {Clopper, C. J. and Pearson, E. S.},
  title = {The use of confidence or fiducial limits illustrated in the case
	of the binomial},
  journal = {Biometrika},
  year = {1934},
  volume = {26},
  pages = {404-413},
  number = {4},
  doi = {10.1093/biomet/26.4.404},
  eprint = {http://biomet.oxfordjournals.org/cgi/reprint/26/4/404.pdf},
  url = {http://biomet.oxfordjournals.org}
}

@ARTICLE{colless82,
  author = {D. H. Colless},
  title = {Review of Phylogenetics: The theory and practice of phylogenetic
	systematics II},
  journal = SZ,
  year = {1982},
  volume = {31},
  pages = {100--104}
}

@ARTICLE{Constantinescu1995,
  author = {Constantinescu, M. and Sankoff, D.},
  title = {An efficient algorithm for supertrees},
  journal = {Journal of Classification},
  year = {1995},
  volume = {12},
  pages = {101--112},
  number = {1},
  publisher = {Springer}
}

@ARTICLE{cornish85,
  author = {A. Cornish-Bowden},
  title = {Nomenclature for incompletely specified bases in nucleic acid sequences:
	{R}ecommendations 1984},
  journal = {Nucleic Acids Research},
  year = {1985},
  volume = {13},
  pages = {3021--3030}
}

@ARTICLE{Cowles1999,
  author = {Cowles, M.K. and Roberts, G.O. and Rosenthal, J.S.},
  title = {Possible biases induced by MCMC convergence diagnostics},
  journal = {Journal of Statistical Computation and Simulation},
  year = {1999},
  volume = {64},
  pages = {87},
  number = {1},
  publisher = {Citeseer}
}

@ARTICLE{Cowles1998,
  author = {Cowles, M.K. and Rosenthal, J.S.},
  title = {A simulation approach to convergence rates for {M}arkov chain {M}onte
	Carlo algorithms},
  journal = {Statistics and Computing},
  year = {1998},
  volume = {8},
  pages = {115--124},
  number = {2},
  publisher = {Springer}
}

@ARTICLE{Cowles1996,
  author = {Cowles, Mary Kathryn and Carlin, Bradley P.},
  title = {Markov Chain {M}onte {C}arlo Convergence Diagnostics: A Comparative
	Review},
  journal = {Journal of the American Statistical Association},
  year = {1996},
  volume = {91},
  pages = {883--904},
  url = {http://www.jstor.org/stable/2291683}
}

@BOOK{coyne04,
  title = {Speciation},
  publisher = {Sinauer Associates, Inc.},
  year = {2004},
  author = {J. A. Coyne and H. A. Orr},
  address = {Sunderland, Massachusetts}
}

@ARTICLE{Crottini2012,
  author = {Crottini, Angelica and Madsen, Ole and Poux, Celine and Strau\ss,
	Axel and Vieites, David R. and Vences, Miguel},
  title = {Vertebrate time-tree elucidates the biogeographic pattern of a major
	biotic change around the K--T boundary in Madagascar},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2012},
  volume = {109},
  pages = {5358-5363},
  number = {14}
}

@BOOK{crowson81,
  title = {The Biology of {C}oleoptera},
  publisher = {Academic Press},
  year = {1981},
  author = {R. A. Crowson},
  address = {London}
}

@ARTICLE{Cummings2003,
  author = {Cummings, Michael P. and Handley, Scott A. and Myers, Daniel S. and
	Reed, David L. and Rokas, Antonis and Winka, Katarina},
  title = {Comparing Bootstrap and Posterior Probability Values in the Four-Taxon
	Case},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {477-487},
  number = {4},
  doi = {10.1080/10635150390218213},
  eprint = {http://sysbio.oxfordjournals.org/content/52/4/477.full.pdf+html},
  url = {http://sysbio.oxfordjournals.org/content/52/4/477.abstract}
}

@ARTICLE{cummings05,
  author = {M. P. Cummings and A. Meyer},
  title = {Magic bullets and golden rules: {D}ata sampling in molecular phylogenetics},
  journal = Zoology,
  year = {2005},
  volume = {108},
  pages = {329--336}
}

@ARTICLE{cummings95,
  author = {M. P. Cummings and S. P. Otto and J. Wakeley},
  title = {Sampling properties of DNA sequence data in phylogenetic analysis},
  journal = MBE,
  year = {1995},
  volume = {12},
  pages = {814--822}
}

@ARTICLE{cunningham92,
  author = {C. W. Cunningham and N. W. Blackstone and L. W. Buss},
  title = {Evolution of king crabs from hermit crab ancestors},
  journal = {Nature},
  year = {1992},
  volume = {335},
  pages = {539--542}
}

@ARTICLE{Cusimano2010,
  author = {Cusimano, N. and Renner, S.S.},
  title = {Slowdowns in diversification rates from real phylogenies may not
	be real},
  journal = SYSB,
  year = {2010},
  volume = {59},
  pages = {458},
  number = {4},
  publisher = {Oxford University Press}
}

@ARTICLE{Cutler2000,
  author = {Cutler, David J.},
  title = {Estimating divergence times in the presence of an overdispersed molecular
	clock},
  journal = MBE,
  year = {2000},
  volume = {17},
  pages = {1647--1660}
}

@ARTICLE{Cutler2000a,
  author = {Cutler, David J.},
  title = {Understanding the overdispersed molecular clock},
  journal = {Genetics},
  year = {2000},
  volume = {154},
  pages = {1403--1417}
}

@ARTICLE{Darriba2013,
  author = {D. Darriba and A. J. Aberer and T. Flouri and T. A. Heath and F.
	Izquierdo-Carrasco and A. Stamatakis},
  title = {Boosting the performance of {B}ayesian divergence time estimation
	with the Phylogenetic Likelihood Library},
  journal = {IEEE 27th International Symposium on Parallel \& Distributed Processing},
  year = {2013},
  pages = {doi:10.1109/IPDPSW.2013.267}
}

@BOOK{darwin59,
  title = {On the {O}rigin of {S}pecies},
  publisher = {J. Murray},
  year = {1859},
  author = {C. Darwin},
  address = {London}
}

@ARTICLE{DasGupta2000,
  author = {DasGupta, B. and He, X. and Jiang, T. and Li, M. and Tromp, J. and
	Zhang, L.},
  title = {On computing the nearest neighbor interchange distance},
  year = {2000},
  volume = {55},
  pages = {125--143},
  booktitle = {Proc. DIMACS Workshop on Discrete Problems with Medical Applications}
}

@BOOK{Davis1984,
  title = {Methods of Numerical Integration Computer Science and Applied Mathematics},
  publisher = {Academic Press},
  year = {1984},
  author = {Davis, P.J. and Rabinowitz, P.}
}

@ARTICLE{Day1985,
  author = {Day, W.H.E.},
  title = {Optimal algorithms for comparing trees with labeled leaves},
  journal = {Journal of Classification},
  year = {1985},
  volume = {2},
  pages = {7--28},
  number = {1},
  publisher = {Springer}
}

@INPROCEEDINGS{dayhoff78,
  author = {M. O. Dayhoff and R. M. Schwartz and B. C. Orcutt},
  title = {A model of evolutionary change in proteins},
  booktitle = {Atlas of protein sequence and structure, Volume 5, Supplement 3},
  year = {1978},
  pages = {345--352},
  publisher = {National Biomedical Research Foundation}
}

@ARTICLE{debry92,
  author = {R. W. Debry},
  title = {The consistency of several phylogeny-inference methods under varying
	evolutionary rates},
  journal = MBE,
  year = {1992},
  volume = {9},
  pages = {537--551}
}

@ARTICLE{degnan06,
  author = {J. H. Degnan and N. A. Rosenberg},
  title = {Discordance of species trees with their most likely gene trees},
  journal = {PLoS Genetics},
  year = {2006},
  volume = {2},
  pages = {762--768}
}

@ARTICLE{degnan05,
  author = {J. H. Degnan and L. A. Salter},
  title = {Gene tree distributions under the coalescent process},
  journal = Evolution,
  year = {2005},
  volume = {59},
  pages = {24--37}
}

@ARTICLE{Dempster1977,
  author = {Dempster, A.P. and Laird, N.M. and Rubin, D.B. and others},
  title = {Maximum likelihood from incomplete data via the {EM} algorithm},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  year = {1977},
  volume = {39},
  pages = {1--38},
  number = {1},
  publisher = {Royal Statistical Society}
}

@ARTICLE{diaconis07,
  author = {P. Diaconis and S. Holmes and R. Montgomery},
  title = {Dynamical bias in the coin toss},
  journal = {SIAM Review},
  year = {2007},
  volume = {49},
  pages = {211--235}
}

@ARTICLE{dial89,
  author = {K. P. Dial and J. M. Marzluff},
  title = {Nonrandom Diversification within Taxonomic Assemblages},
  journal = SZ,
  year = {1989},
  volume = {38},
  pages = {26--37}
}

@ARTICLE{dickey71,
  author = {J. Dickey},
  title = {The weighted likelihood ratio, linear hypotheses on normal location
	parameters},
  journal = {The Annals of Statistics},
  year = {1971},
  volume = {42},
  pages = {204--223}
}

@ARTICLE{didier2012,
  author = {Didier, Gilles and Royer-Carenzi, Manuela and Laurin, Michel},
  title = {The reconstructed evolutionary process with the fossil record},
  journal = {Journal of Theoretical Biology},
  year = {2012},
  volume = {315},
  pages = {26--37}
}

@INPROCEEDINGS{dimmic04,
  author = {M. Dimic},
  title = {Models of protein evolution},
  booktitle = {Statistical Methods in Molecular Evolution},
  year = {2004},
  editor = {R. Nielsen},
  publisher = {Springer-Verlag}
}

@ARTICLE{dimmic02,
  author = {M. W. Dimmic and J. S. Rest and D. P. Mindell and D. Goldstein},
  title = {{RA}rt{REV}: {A}n amino acid substitution matrix for inference of
	retrovirus and reverse transcriptase phylogeny},
  journal = JME,
  year = {2002},
  volume = {55},
  pages = {65--73}
}

@ARTICLE{do05,
  author = {C. B. Do and M. S. P. Mahabhashyam and M. Brudno and S. Batzoglou},
  title = {{PROBCONS}: {P}robabilistic consistency-based multiple sequence alignment},
  journal = {Genome Research},
  year = {2005},
  volume = {15},
  pages = {330--340}
}

@ARTICLE{dongarra75,
  author = {J. J. Dongarra and B. S. Garbow},
  title = {Path chart and documentation for the {EISPACK} package of matrix
	eigensystem routines},
  journal = {Argonne National Laboratory Technical Memorandum},
  year = {1975},
  pages = {ANL-AMD-TM-250}
}

@INPROCEEDINGS{dongarra84,
  author = {J. J. Dongarra and G. W. Stewart},
  title = {{PROBCONS}: {P}robabilistic consistency-based multiple sequence alignment},
  booktitle = {Sources and Development of Mathematical Software},
  year = {1984},
  editor = {W. R. Cowell},
  pages = {20--48},
  publisher = {Prentice-Hall}
}

@ARTICLE{donoghue92,
  author = {M. J. Donoghue and J. W. Kadereit},
  title = {Walter Zimmermann and the growth of phylogenetic theory},
  journal = SYSB,
  year = {1992},
  volume = {41},
  pages = {74--85}
}

@ARTICLE{donoghue03,
  author = {Donoghue, Michael J. and Moore, Brian R.},
  title = {Toward an integrative historical biogeography},
  journal = {Integrative and Comparative Biology},
  year = {2003},
  volume = {43},
  pages = {261-270}
}

@ARTICLE{dorazio09,
  author = {R. M. Dorazio},
  title = {On selecting a prior for the precision parameter of the {D}irichlet
	process mixture models},
  journal = {Journal of Statistical Planning and Inference},
  year = {2009},
  volume = {139},
  pages = {3384--3390}
}

@ARTICLE{dornburg11,
  author = {A. Dornburg and J. M. Beaulieu and J. C. Oliver and T. J. Near},
  title = {Integrating Fossil Preservation Biases in the Selection of Calibrations
	for Molecular Divergence Time Estimation},
  journal = SYSB,
  year = {2011},
  volume = {60},
  pages = {519--527}
}

@ARTICLE{dornburg11b,
  author = {A. Dornburg and M. C. Brandley and M. R. McGowen and T. J. Near},
  title = {Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide
	Substitution and Divergence Time Estimates across Whales and Dolphins
	({M}ammalia: {C}etacea)},
  journal = MBE,
  year = {2011},
  volume = {doi:10.1093/molbev/msr228}
}

@ARTICLE{dosReis2012,
  author = {{dos Reis}, M. and Inoue, J. and Hasegawa, M. and Asher, R.J. and
	Donoghue, P.C.J. and Yang, Z.},
  title = {Phylogenomic datasets provide both precision and accuracy in estimating
	the timescale of placental mammal phylogeny},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2012},
  volume = {279},
  pages = {3491--3500},
  number = {1742}
}

@ARTICLE{dosReis2013,
  author = {{dos Reis}, M. and Yang, Z.},
  title = {The unbearable uncertainty of {B}ayesian divergence time estimation},
  journal = {Journal of Systematics and Evolution},
  year = {2012},
  volume = {51},
  pages = {30--43}
}

@ARTICLE{dosReis2011,
  author = {{dos Reis}, Mario and Yang, Ziheng},
  title = {Approximate Likelihood Calculation on a Phylogeny for {B}ayesian
	Estimation of Divergence Times},
  journal = MBE,
  year = {2011},
  volume = {28},
  pages = {2161-2172},
  number = {7}
}

@ARTICLE{Douady2003,
  author = {Douady, C.J. and Delsuc, F. and Boucher, Y. and Doolittle, W.F. and
	Douzery, E.J.P.},
  title = {Comparison of {B}ayesian and Maximum Likelihood Bootstrap Measures
	of Phylogenetic Reliability},
  journal = MBE,
  year = {2003},
  volume = {20},
  pages = {248--254},
  number = {2},
  publisher = {SMBE}
}

@ARTICLE{doyle93,
  author = {J. A. Doyle and M. J. Donoghue},
  title = {Phylogenies and angiosperm diversification},
  journal = {Paleobiology},
  year = {1993},
  volume = {19},
  pages = {141--167}
}

@BOOK{drucker59,
  title = {Landmarks of {T}omorrow},
  publisher = {Harper},
  year = {1959},
  author = {P. Drucker},
  address = {New York}
}

@BOOK{BEAST2book2014,
  title = {Bayesian evolutionary analysis with {BEAST} 2},
  publisher = {Cambridge University Press},
  year = {2014},
  author = {Alexei J. Drummond and Remco R. Bouckaert}
}

@ARTICLE{drummond06,
  author = {A. J. Drummond and S. Y. Ho and M. J. Phillips and A. Rambaut},
  title = {Relaxed phylogenetics and dating with confidence},
  journal = {PLoS Biology},
  year = {2006},
  volume = {4},
  pages = {e88}
}

@ARTICLE{Drummond2002,
  author = {Drummond, Alexei J. and Nicholls, Geoff K. and Rodrigo, Allen G.
	and Solomon, Wiremu},
  title = {Estimating Mutation Parameters, Population History and Genealogy
	Simultaneously From Temporally Spaced Sequence Data},
  journal = {Genetics},
  year = {2002},
  volume = {161},
  pages = {1307-1320},
  number = {3},
  eprint = {http://www.genetics.org/cgi/reprint/161/3/1307.pdf},
  url = {http://www.genetics.org/cgi/content/abstract/161/3/1307}
}

@ARTICLE{drummond2003,
  author = {Drummond, Alexei J and Pybus, Oliver G and Rambaut, Andrew and Forsberg,
	Roald and Rodrigo, Allen G},
  title = {Measurably evolving populations},
  journal = {Trends in Ecology \& Evolution},
  year = {2003},
  volume = {18},
  pages = {481--488},
  number = {9}
}

@ARTICLE{drummond07,
  author = {A. J. Drummond and A. Rambaut},
  title = {{BEAST}: {B}ayesian evolutionary analysis by sampling trees},
  journal = {BMC Evolutionary Biology},
  year = {2007},
  volume = {7},
  pages = {214}
}

@ARTICLE{drummond10,
  author = {A. J. Drummond and M. A. Suchard},
  title = {Bayesian random local clocks, or one rate to rule them all},
  journal = {BMC Biology},
  year = {2010},
  volume = {8},
  pages = {114}
}

@ARTICLE{Drummond2012,
  author = {Drummond, Alexei J. and Suchard, Marc A. and Xie, Dong and Rambaut,
	Andrew},
  title = {Bayesian Phylogenetics with {BEAU}ti and the {BEAST} 1.7},
  journal = MBE,
  year = {2012},
  volume = {29},
  pages = {1969-1973},
  number = {8}
}

@ARTICLE{Du2005,
  author = {Du, Z. and Lin, F. and Roshan, U.W.},
  title = {Reconstruction of large phylogenetic trees: A parallel approach},
  journal = {Computational Biology and Chemistry},
  year = {2005},
  volume = {29},
  pages = {273--280},
  number = {4},
  publisher = {Elsevier}
}

@ARTICLE{dunson09,
  author = {D. B. Dunson},
  title = {Nonparametric {B}ayes local partition models for random effects},
  journal = {Biometrika},
  year = {2009},
  volume = {96},
  pages = {249--262}
}

@BOOK{durbin98,
  title = {Biological {S}equence {A}nalysis},
  publisher = {Cambridge University Press},
  year = {1998},
  author = {R. Durbin and S. Eddy and A. Krogh and G. Mitchison},
  address = {Cambridge}
}

@INPROCEEDINGS{durrett04,
  author = {R. Durrett},
  title = {Evolution by genome rearrangement},
  booktitle = {Statistical Methods in Molecular Evolution},
  year = {2004},
  editor = {R. Nielsen},
  publisher = {Springer-Verlag}
}

@ARTICLE{eddy95,
  author = {S. R. Eddy and G. J. Mitchison and R. Durbin},
  title = {Maximum Discrimination Hidden {M}arkov Models of Sequence Consensus},
  journal = JComputBiol,
  year = {1995},
  volume = {2},
  pages = {9--23}
}

@ARTICLE{edgar04,
  author = {R. C. Edgar},
  title = {{MUSCLE}: {M}ultiple sequence alignment with high accuracy and high
	throughput},
  journal = {Nucleic Acids Research},
  year = {2004},
  volume = {32},
  pages = {1792--1797}
}

@ARTICLE{edwards96,
  author = {A. W. F. Edwards},
  title = {The origin and early development of the method of minimum evolution
	for the reconstruction of phylogenetic trees},
  journal = SYSB,
  year = {1996},
  volume = {45},
  pages = {79--91}
}

@BOOK{edwards72,
  title = {Likelihood},
  publisher = {Cambridge University Press},
  year = {1972},
  author = {A. W. F. Edwards},
  address = {Cambridge}
}

@ARTICLE{edwards70,
  author = {A. W. F. Edwards},
  title = {Estimation of the branch points of a branching diffusion process},
  journal = {Journal of the Royal Statistical Society B},
  year = {1970},
  volume = {32},
  pages = {155--174}
}

@ARTICLE{edwards66,
  author = {A. W. F. Edwards},
  title = {Studying human evolution by computer},
  journal = {New Scientist},
  year = {1966},
  volume = {30},
  pages = {438--440}
}

@INPROCEEDINGS{edwards64,
  author = {A. W. F. Edwards and L. L. Cavalli-Sforza},
  title = {Reconstruction of evolutionary trees},
  booktitle = {Phenetic and {P}hylogenetic {C}lassification},
  year = {1964},
  editor = {J. McNeill},
  publisher = {Systematics Association Publication}
}

@ARTICLE{edwards63,
  author = {A. W. F. Edwards and L. L. Cavalli-Sforza},
  title = {The reconstruction of evolution (Abstract)},
  journal = {Annals of Human Genetics},
  year = {1963},
  volume = {27},
  pages = {104--105}
}

@ARTICLE{edwards07,
  author = {S. V. Edwards and L. Liu and D. K. Pearl},
  title = {High-resolution species trees without concatenation},
  journal = PNAS,
  year = {2007},
  volume = {104},
  pages = {5936--5941}
}

@ARTICLE{efron96,
  author = {B. Efron and E. Halloran and S. Holmes},
  title = {Bootstrap confidence levels for phylogenetic trees},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {13429--13434}
}

@ARTICLE{Egan2006,
  author = {Mary G. Egan},
  title = {Support versus corroboration},
  journal = {Journal of Biomedical Informatics},
  year = {2006},
  volume = {39},
  pages = {72 - 85},
  number = {1},
  doi = {10.1016/j.jbi.2005.11.007},
  url = {http://www.sciencedirect.com/science/article/pii/S1532046405001322}
}

@ARTICLE{ehrlich90,
  author = {M. Ehrlich and X. Y. Zhang and N. M. Inamdar},
  title = {Spontaneous deamination of cytosine and 5-methylcytosine residues
	in {DNA} and replacement of 5-methylcytosine residues with cytosine
	residues},
  journal = {Mutat. Res.},
  year = {1990},
  volume = {238},
  pages = {277--286}
}

@ARTICLE{ElAdlouni2006,
  author = {El Adlouni, S. and Favre, A.C. and Bob{\'e}e, B.},
  title = {Comparison of methodologies to assess the convergence of {M}arkov
	chain {M}onte {C}arlo methods},
  journal = {Computational Statistics \& Data Analysis},
  year = {2006},
  volume = {50},
  pages = {2685--2701},
  number = {10},
  issn = {0167-9473},
  publisher = {Elsevier}
}

@BOOK{eldredge80,
  title = {Phylogenetic {P}atterns and the {E}volutionary {P}rocess},
  publisher = {Columbia University Press},
  year = {1980},
  author = {N. Eldredge and J. Cracraft},
  address = {New York}
}

@ARTICLE{elston71,
  author = {R. C. Elston and J. Stewart},
  title = {A general model for the genetic analysis of pedigree data},
  journal = {Human Heredity},
  year = {1971},
  volume = {21},
  pages = {523--542},
  number = {6}
}

@ARTICLE{Erixon2003,
  author = {Erixon, P. and Svennblad, B. and Britton, T. and Oxelman, B.},
  title = {Reliability of {B}ayesian posterior probabilities and bootstrap frequencies
	in phylogenetics},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {665},
  number = {5}
}

@ARTICLE{Erwin2011,
  author = {Erwin, D.H.},
  title = {Macroevolution: Dynamics of Diversity},
  journal = {Current Biology},
  year = {2011},
  volume = {21},
  pages = {R1000--R1001},
  number = {24},
  publisher = {Elsevier}
}

@ARTICLE{escobar95,
  author = {M. D. Escobar and M. West},
  title = {Bayesian density estimation and inference using mixtures},
  journal = {Journal of the American Statistical Association},
  year = {1995},
  volume = {90},
  pages = {577--588}
}

@ARTICLE{Etienne2009,
  author = {Etienne, R.S. and Apol, M.E.F.},
  title = {Estimating speciation and extinction rates from diversity data and
	the fossil record},
  journal = {Evolution},
  year = {2009},
  volume = {63},
  pages = {244--255},
  number = {1},
  publisher = {Wiley Online Library}
}

@ARTICLE{Etienne2012a,
  author = {Etienne, R.S. and Haegeman, B. and Stadler, T. and Aze, T. and Pearson,
	P.N. and Purvis, A. and Phillimore, A.B.},
  title = {Diversity-dependence brings molecular phylogenies closer to agreement
	with the fossil record},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2012},
  volume = {279},
  pages = {1300--1309},
  number = {1732},
  publisher = {The Royal Society}
}

@ARTICLE{Etienne2012,
  author = {Etienne, R.S. and Rosindell, J.},
  title = {Prolonging the past counteracts the pull of the present: protracted
	speciation can explain observed slowdowns in diversification},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {204--213},
  number = {2},
  publisher = {Oxford University Press}
}

@INPROCEEDINGS{ewens98,
  author = {W. J. Ewens and S. Tavar\'e},
  title = {The {E}wens sampling formula},
  booktitle = {Encyclopedia of Statistical Science},
  year = {1998},
  editor = {S. Kotz and C. B. Read and D. L. Banks},
  publisher = {Wiley, New York}
}

@ARTICLE{fan11,
  author = {Y. Fan and R. Wu and M.-H. Chen and L. Kuo and P. O. Lewis},
  title = {Choosing among Partition Models in {B}ayesian Phylogenetics},
  journal = MBE,
  year = {2011},
  volume = {28},
  pages = {523--532}
}

@ARTICLE{Farris1970,
  author = {Farris, J.S.},
  title = {Methods for Computing {W}agner Trees},
  journal = SZ,
  year = {1970},
  volume = {19},
  pages = {83--92},
  number = {1}
}

@ARTICLE{Farris1996,
  author = {Farris, J.S. and Albert, V.A. and Kallersjo, M. and Lipscomb, D.
	and Kluge, A.G.},
  title = {Parsimony jackknifing outperforms neighbor-joining},
  journal = {Cladistics},
  year = {1996},
  volume = {12},
  pages = {99--124},
  number = {2},
  publisher = {Blackwell Synergy}
}

@INPROCEEDINGS{farris83,
  author = {J. S. Farris},
  title = {The logical basis of phylogenetic analysis},
  booktitle = {Advances in {C}ladistics, {V}olume 2},
  year = {1983},
  editor = {N. I. Platnick and V. A. Funk},
  pages = {7--36},
  publisher = {Columbia University Press}
}

@ARTICLE{farris08,
  author = {J. S. Farris},
  title = {Parsimony and explanatory power},
  journal = {Cladistics},
  year = {2008},
  volume = {24},
  pages = {825--847}
}

@ARTICLE{farris73,
  author = {J. S. Farris},
  title = {A probability model for inferring evolutionary trees},
  journal = SZ,
  year = {1973},
  volume = {22},
  pages = {250--256}
}

@ARTICLE{farris70,
  author = {J. S. Farris},
  title = {Methods for computing Wagner trees},
  journal = SZ,
  year = {1970},
  volume = {19},
  pages = {83--92}
}

@ARTICLE{farris96,
  author = {J. S. Farris and V. A. Albert and M. K\"allersj\"o and D. Lipscomb
	and A. G. Kluge},
  title = {Parsimony jackknifing outperforms neighbor-joining},
  journal = {Cladistics},
  year = {1996},
  volume = {12},
  pages = {99--124}
}

@ARTICLE{Farris1970a,
  author = {Farris, James S. and Kluge, Arnold G. and Eckardt, Michael J.},
  title = {A Numerical Approach to Phylogenetic Systematics},
  journal = SZ,
  year = {1970},
  volume = {19},
  pages = {172--189},
  number = {2},
  url = {http://www.jstor.org/stable/2412452}
}

@INPROCEEDINGS{felsenstein88,
  author = {J. Felsenstein},
  title = {The detection of phylogeny},
  booktitle = {Prospects in {S}ystematics},
  year = {1988},
  editor = {D. L. Hawksworth},
  pages = {112--127},
  publisher = {Systematics Association and Clarendon Press}
}

@MISC{Felsenstein2005,
  author = {Felsenstein, J.},
  title = {{PHYLIP (phylogeny inference package) version 3.6}},
  year = {2005},
  journal = {Distributed by the author. Department of Genome Sciences, University
	of Washington, Seattle}
}

@BOOK{felsenstein04,
  title = {Inferring Phylogenies},
  publisher = {Sinauer Associates, Inc.},
  year = {2004},
  author = {J. Felsenstein},
  address = {Sunderland, Massachusetts}
}

@ARTICLE{felsenstein01,
  author = {J. Felsenstein},
  title = {The troubled growth of statistical phylogenetics},
  journal = SYSB,
  year = {2001},
  volume = {50},
  pages = {465--467}
}

@BOOK{felsenstein93,
  title = {{PHYLIP}: ({P}hylogeny {I}nference {P}ackage)},
  publisher = {University of Washington},
  year = {1993},
  author = {J. Felsenstein},
  address = {Seattle (USA)},
  note = {Available from: http://evolution.genetics.washington.edu/phylip.html}
}

@ARTICLE{Felsenstein1988,
  author = {Felsenstein,J},
  title = {Phylogenies from Molecular Sequences: Inference and Reliability},
  journal = {Annual Review of Genetics},
  year = {1988},
  volume = {22},
  pages = {521-565},
  number = {1},
  doi = {10.1146/annurev.ge.22.120188.002513},
  eprint = {http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.ge.22.120188.002513},
  url = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.ge.22.120188.002513}
}

@ARTICLE{felsenstein85a,
  author = {J. Felsenstein},
  title = {Confidence limits on phylogenies: {A}n approach using the bootstrap},
  journal = {Evolution},
  year = {1985},
  volume = {39},
  pages = {783--791}
}

@ARTICLE{felsenstein85b,
  author = {J. Felsenstein},
  title = {Phylogenies and the comparative method},
  journal = {The American Naturalist},
  year = {1985},
  volume = {125},
  pages = {1--15}
}

@ARTICLE{Felsenstein1984,
  author = {Felsenstein, Joseph},
  title = {Distance Methods for Inferring Phylogenies: A Justification},
  journal = {Evolution},
  year = {1984},
  volume = {38},
  pages = {16--24},
  number = {1},
  url = {http://www.jstor.org/stable/2408542}
}

@ARTICLE{Felsenstein1983,
  author = {Felsenstein, J.},
  title = {Parsimony in systematics: biological and statistical issues},
  journal = {Annual review of ecology and systematics},
  year = {1983},
  volume = {14},
  pages = {313--333},
  publisher = {JSTOR}
}

@ARTICLE{felsenstein81,
  author = {J. Felsenstein},
  title = {Evolutionary trees from {DNA} sequences: {A} maximum likelihood approach},
  journal = JME,
  year = {1981},
  volume = {17},
  pages = {368--376}
}

@ARTICLE{felsenstein78,
  author = {J. Felsenstein},
  title = {Cases in which parsimony and compatibility methods will be positively
	misleading},
  journal = SZ,
  year = {1978},
  volume = {27},
  pages = {401--411}
}

@ARTICLE{felsenstein73,
  author = {J. Felsenstein},
  title = {Maximum likelihood and minimum-steps methods for estimating evolutionary
	trees from data on discrete characters},
  journal = SZ,
  year = {1973},
  volume = {22},
  pages = {240--249}
}

@PHDTHESIS{felsenstein68,
  author = {J. Felsenstein},
  title = {Statistical inference and the estimation of phylogenies},
  school = {University of Chicago, Dept. of Zoology},
  year = {1968}
}

@ARTICLE{felsenstein96,
  author = {J. Felsenstein and G. A. Churchill},
  title = {A hidden {M}arkov model approach to variation among sites in rate
	of evolution},
  journal = MBE,
  year = {1996},
  volume = {13},
  pages = {93--104}
}

@ARTICLE{feng09,
  author = {C.-M. Feng and S. R. Manchester and Q.-Y. Xiang},
  title = {Phylogeny and biogeography of {A}langiaceae ({C}ornales) inferred
	from {DNA} sequences, morphology, and fossils},
  journal = MPE,
  year = {2009},
  volume = {51},
  pages = {201--214}
}

@ARTICLE{feng87,
  author = {D. F. Feng and R. F. Doolittle},
  title = {Progressive sequence alignment as a prerequisite to correct phylogenetic
	trees},
  journal = JME,
  year = {1987},
  volume = {25},
  pages = {351--360}
}

@ARTICLE{ferguson73,
  author = {T. S. Ferguson},
  title = {A {B}ayesian analysis of some nonparametric problems},
  journal = {Annals of Statistics},
  year = {1973},
  volume = {1},
  pages = {209--230}
}

@ARTICLE{ferrini2013,
  author = {Ferrini-Mundy, Joan},
  title = {Driven by Diversity},
  journal = {Science},
  year = {2013},
  volume = {340},
  pages = {278--278},
  number = {6130},
  publisher = {American Association for the Advancement of Science}
}

@ARTICLE{definetti37,
  author = {B. de Finetti},
  title = {le pr\'evision: ses lois logiques, ses sources subjectives},
  journal = {Ann. Inst. Poincare},
  year = {1937},
  volume = {7},
  pages = {1--68}
}

@BOOK{fisher25,
  title = {Statistical {M}ethods for {R}esearch {W}orkers},
  publisher = {Oliver and Boyd},
  year = {1925},
  author = {R. A. Fisher},
  address = {Edinburgh}
}

@ARTICLE{fisher22,
  author = {R. A. Fisher},
  title = {On the mathematical foundations of theoretical statistics},
  journal = {Philosophical Transactions of the Royal Society of London, A},
  year = {1922},
  volume = {222},
  pages = {309--368}
}

@ARTICLE{fisher21,
  author = {R. A. Fisher},
  title = {On the `probable error' of a coefficient of correlation deduced from
	a small sample},
  journal = {Metron, I},
  year = {1921},
  volume = {4},
  pages = {3--32}
}

@ARTICLE{fisher12,
  author = {R. A. Fisher},
  title = {On an absolute criterion for fitting frequency curves},
  journal = {Mess. Math.},
  year = {1912},
  volume = {41},
  pages = {155--160}
}

@ARTICLE{Fitch1967,
  author = {Fitch, W.M. and Margoliash, E.},
  title = {Construction of Phylogenetic Trees},
  journal = {Science},
  year = {1967},
  volume = {155},
  pages = {279--284},
  number = {3760}
}

@ARTICLE{fitch71,
  author = {W. M. Fitch},
  title = {Toward defining the course of evolution: {M}inimum change for a specific
	tree topology},
  journal = SZ,
  year = {1971},
  volume = {20},
  pages = {406--416}
}

@ARTICLE{fitch90,
  author = {W. M. Fitch and J. J. Beintema},
  title = {Correcting parsimonious trees for unseen nucleotide substitutions
	- the effect of dense branching as exemplified by {R}ibonuclease},
  journal = MBE,
  year = {1990},
  volume = {7},
  pages = {438--443}
}

@ARTICLE{fitch87,
  author = {W. M. Fitch and M. Bruschi},
  title = {The evolution of prokaryotic ferredoxins - with a general-method
	correcting for unobserved substitutions in less branched lineages},
  journal = MBE,
  year = {1987},
  volume = {4},
  pages = {381--394}
}

@ARTICLE{fitch97,
  author = {W. M. Fitch and R. M. Bush and C. A. Bender and N. J. Cox},
  title = {Long term trends in the evolution of {H(3)} {HA1} human influenza
	type {A}},
  journal = PNAS,
  year = {1997},
  volume = {94},
  pages = {7712--7718}
}

@ARTICLE{fitch67,
  author = {W. M. Fitch and E. Margoliash},
  title = {Construction of phylogenetic trees},
  journal = {Science},
  year = {1967},
  volume = {155},
  pages = {279--284}
}

@ARTICLE{FitzJohn2009,
  author = {FitzJohn, R.G. and Maddison, W.P. and Otto, S.P.},
  title = {Estimating trait-dependent speciation and extinction rates from incompletely
	resolved phylogenies},
  journal = SYSB,
  year = {2009},
  issn = {0039-7989}
}

@ARTICLE{Flegal2008,
  author = {Flegal, J.M. and Haran, M. and Jones, G.L.},
  title = {Markov chain {M}onte {C}arlo: Can we trust the third significant
	figure},
  journal = {Statistical Science},
  year = {2008},
  volume = {23},
  pages = {250--260},
  number = {2},
  publisher = {Institute of Mathematical Statistics}
}

@ARTICLE{Fleissner2005,
  author = {Fleissner, R. and Metzler, D. and von Haeseler, A.},
  title = {Simultaneous Statistical Multiple Alignment and Phylogeny Reconstruction},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {548--561},
  number = {4},
  publisher = {Taylor \& Francis}
}

@ARTICLE{flores93,
  author = {T. P. Flores and C. A. Orengo and D. S. Moss and J. M. Thornton},
  title = {Comparison of conformational characteristics in structurally similar
	protein pairs},
  journal = {Protein Science},
  year = {1993},
  volume = {2},
  pages = {1811--1826}
}

@ARTICLE{flouri2012,
  author = {Flouri, Tom{\'a}{\v{s}} and Stamatakis, Alexandros},
  title = {An improvement to {DPPD}iv},
  journal = {Technical Note},
  year = {2012}
}

@ARTICLE{fong11,
  author = {J. J. Fong and M. K. Fujita},
  title = {Evaluating phylogenetic informativeness and data-type usage for new
	protein-coding genes across {V}ertebrata},
  journal = MPE,
  year = {2011},
  volume = {61},
  pages = {300--307}
}

@ARTICLE{foote2001,
  author = {Foote, Michael},
  title = {Inferring temporal patterns of preservation, origination, and extinction
	from taxonomic survivorship analysis},
  journal = {Paleobiology},
  year = {2001},
  volume = {27},
  pages = {602--630},
  number = {4}
}

@ARTICLE{foote1996,
  author = {Foote, Mike},
  title = {On the probability of ancestors in the fossil record},
  journal = {Paleobiology},
  year = {1996},
  volume = {22},
  pages = {141--151}
}

@ARTICLE{foote1999,
  author = {Foote, Mike and Sepkoski, J John},
  title = {Absolute measures of the completeness of the fossil record},
  journal = {Nature},
  year = {1999},
  volume = {398},
  pages = {415--417},
  number = {6726}
}

@ARTICLE{Ford2009,
  author = {Ford, Daniel and Gernhard, Tanja and Matsen, Erick},
  title = {A method for investigating relative timing information on phylogenetic
	trees},
  journal = SYSB,
  year = {2009},
  volume = {58},
  pages = {167--183},
  number = {2}
}

@ARTICLE{forest2009,
  author = {Forest, F{\'e}lix},
  title = {Calibrating the Tree of Life: fossils, molecules and evolutionary
	timescales},
  journal = {Annals of Botany},
  year = {2009},
  volume = {104},
  pages = {789--794},
  number = {5}
}

@ARTICLE{forsberg03,
  author = {R. Forsberg and F. B. Christiansen},
  title = {A codon-based model of host-specific selection in parasites, with
	an application to the influenza virus},
  journal = MBE,
  year = {2003},
  volume = {20},
  pages = {1252--1259}
}

@MISC{Foster2003,
  author = {Foster, PG},
  title = {P4, A python package for phylogenetics},
  year = {2003},
  publisher = {Distributed by the author}
}

@ARTICLE{Foster2004,
  author = {Foster, Peter G.},
  title = {Modeling Compositional Heterogeneity},
  journal = SYSB,
  year = {2004},
  volume = {53},
  pages = {485-495},
  number = {3}
}

@ARTICLE{freitas04,
  author = {A. V. L. Freitas and K. S. Brown},
  title = {Phylogeny of the {N}ymphalidae ({L}epidoptera)},
  journal = SYSB,
  year = {2004},
  volume = {53},
  pages = {363--383}
}

@ARTICLE{friel2008,
  author = {Friel, Nial and Pettitt, Anthony N},
  title = {Marginal likelihood estimation via power posteriors},
  journal = {Journal of the Royal Statistical Society: Series B (Statistical Methodology)},
  year = {2008},
  volume = {70},
  pages = {589--607},
  number = {3}
}

@ARTICLE{fulton2010,
  author = {Fulton, Tara L and Strobeck, Curtis},
  title = {Multiple fossil calibrations, nuclear loci and mitochondrial genomes
	provide new insight into biogeography and divergence timing for true
	seals {(Phocidae, Pinnipedia)}},
  journal = {Journal of Biogeography},
  year = {2010},
  volume = {37},
  pages = {814--829},
  number = {5}
}

@ARTICLE{furnas84,
  author = {G. W. Furnas},
  title = {The generation of random, binary, unordered trees},
  journal = {Journal of Classification},
  year = {1984},
  volume = {1},
  pages = {187--233}
}

@ARTICLE{fusco1995,
  author = {Fusco, Giuseppe and Cronk, Quentin CB},
  title = {A new method for evaluating the shape of large phylogenies},
  journal = {Journal of Theoretical Biology},
  year = {1995},
  volume = {175},
  pages = {235--243},
  number = {2},
  publisher = {Elsevier}
}

@ARTICLE{Futuyma1987,
  author = {Futuyma, D.J.},
  title = {On the role of species in anagenesis},
  journal = {The American Naturalist},
  year = {1987},
  volume = {130},
  pages = {465--473},
  number = {3},
  publisher = {JSTOR}
}

@INPROCEEDINGS{gaffney79,
  author = {E. S. Gaffney},
  title = {An introduction to the logic of phylogeny reconstruction},
  booktitle = {Phylogenetic {A}nalysis and {P}aleontology},
  year = {1979},
  editor = {J. Cracraft and N. Eldredge},
  pages = {79--111},
  publisher = {Columbia University Press}
}

@BOOK{gallager63,
  title = {Low-density parity check codes},
  publisher = {MIT Press},
  year = {1963},
  author = {R. G. Gallager},
  address = {Cambridge, MA}
}

@ARTICLE{gallager62,
  author = {R. G. Gallager},
  title = {Low-density parity-check codes},
  journal = {IRE Transactions on Information Theory},
  year = {1962},
  volume = {8},
  pages = {21--28}
}

@ARTICLE{galtier07,
  author = {N. Galtier},
  title = {A model of horizontal gene transfer and the bacterial phylogeny problem},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {663--642}
}

@ARTICLE{galtier01,
  author = {N. Galtier},
  title = {Maximum-likelihood phylogenetic analysis under a covarion-like model},
  journal = MBE,
  year = {2001},
  volume = {18},
  pages = {866--873}
}

@ARTICLE{Gamerman1997,
  author = {Gamerman, D.},
  title = {Sampling from the posterior distribution in generalized linear mixed
	models},
  journal = {Statistics and Computing},
  year = {1997},
  volume = {7},
  pages = {57--68},
  number = {1},
  publisher = {Springer}
}

@BOOK{Gamerman2006,
  title = {Markov chain {M}onte {C}arlo: stochastic simulation for {B}ayesian
	inference},
  publisher = {Chapman \& Hall/CRC},
  year = {2006},
  author = {Gamerman, D. and Lopes, H.F.},
  isbn = {1584885874}
}

@ARTICLE{Ganapathy2003,
  author = {Ganapathy, G. and Ramachandran, V. and Warnow, T.},
  title = {Better Hill-Climbing Searches for Parsimony},
  journal = {Proceedings of the Third International Workshop on Algorithms in
	Bioinformatics (WABI)},
  year = {2003},
  volume = {2812},
  pages = {245--258},
  doi = {10.1007/b13243},
  publisher = {Springer}
}

@ARTICLE{gandolfo08,
  author = {M. A. Gandolfo and K. C. Nixon and W. L. Crepet},
  title = {Selection of fossils for calibration of molecular dating models},
  journal = {Annals of the Missouri Botanical Garden},
  year = {2008},
  volume = {95},
  pages = {34--42}
}

@ARTICLE{gao99,
  author = {F. Gao and E. Bailes and D. L. Robertson and Y. Chen and C. M. Rodenburg
	and S. F. Michael and L. B. Cummins and L. O. Arthur and M. Peeters
	and G. M. Shaw and P. M. Sharp and B. H. Hahn},
  title = {Origin of {HIV-1} in the chimpanzee {\it {P}an troglodytes troglodytes}},
  journal = {Nature},
  year = {1999},
  volume = {397},
  pages = {436--441}
}

@ARTICLE{gao92,
  author = {F. Gao and L. Yue and A. T. White and P. G. Pappas and J. Barchue
	and A. P. Hanson and B. M. Greene and P. M. Sharp and G. M. Shaw
	and B. H. Hahn BH},
  title = {Human infection by genetically diverse {SIVSM}-related {HIV-2} in
	{W}est {A}frica},
  journal = {Nature},
  year = {1992},
  volume = {358},
  pages = {495--499}
}

@ARTICLE{gatesy07,
  author = {J. Gatesy and R. DeSalle and N. Wahlberg},
  title = {How many genes should a systematist sample? {C}onflicting insights
	from a phylogenomic matrix characterized by replicated incongruence},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {355--363}
}

@ARTICLE{gaut95,
  author = {B. A. Gaut and P. O. Lewis},
  title = {Success of maximum likelihood in the four-taxon case},
  journal = MBE,
  year = {1995},
  volume = {12},
  pages = {152--162}
}

@ARTICLE{gaut94,
  author = {B. A. Gaut and B. S. Weir},
  title = {Detecting substitution-rate heterogeneity among regions of a nucleotide
	sequence},
  journal = MBE,
  year = {1994},
  volume = {11},
  pages = {620--629}
}

@ARTICLE{gaut11,
  author = {Gaut, Brandon and Yang, Liang and Takuno, Shohei and Eguiarte, Luis
	E.},
  title = {The Patterns and Causes of Variation in Plant Nucleotide Substitution
	Rates},
  journal = {Annual Review of Ecology, Evolution, and Systematics},
  year = {2011},
  volume = {42},
  pages = {245--266}
}

@ARTICLE{gauthier86,
  author = {J. Gauthier},
  title = {Saurischian monophyly and the origin of birds},
  journal = {Mem. Cal. Acad. Sci.},
  year = {1986},
  volume = {8},
  pages = {1--55}
}

@ARTICLE{gauthier88,
  author = {J. Gauthier and A. G. Kluge and T. Rowe},
  title = {Amniote phylogeny and the importance of fossils},
  journal = {Cladistics},
  year = {1988},
  volume = {4},
  pages = {105--209}
}

@ARTICLE{gavryushkina2014arxiv,
  author = {Gavryushkina, Alexandra and Welch, David and Stadler, Tanja and Drummond,
	Alexei},
  title = {Bayesian inference of sampled ancestor trees for epidemiology and
	fossil calibration},
  journal = {arXiv preprint arXiv:1406.4573},
  year = {2014}
}

@ARTICLE{gavryushkina2014,
  author = {Gavryushkina, Alexandra and Welch, David and Stadler, Tanja and Drummond,
	Alexei J},
  title = {Bayesian inference of sampled ancestor trees for epidemiology and
	fossil calibration},
  journal = {PLoS Computational Biology},
  year = {2014},
  volume = {10},
  pages = {e1003919},
  number = {12},
  publisher = {Public Library of Science}
}

@ARTICLE{gelfand05,
  author = {A. E. Gelfand and A. Kottas and S. N. MacEachern},
  title = {Bayesian nonparametric spatial modeling with {D}irichlet process
	mixing},
  journal = {Journal of the American Statistical Association},
  year = {2005},
  volume = {100},
  pages = {1021--1035}
}

@ARTICLE{Gelfand1990,
  author = {Gelfand, Alan E. and Smith, Adrian F. M.},
  title = {Sampling-Based Approaches to Calculating Marginal Densities},
  journal = {Journal of the American Statistical Association},
  year = {1990},
  volume = {85},
  pages = {398--409},
  number = {410},
  issn = {01621459},
  jstor_articletype = {primary_article},
  jstor_formatteddate = {Jun., 1990},
  publisher = {American Statistical Association},
  url = {http://www.jstor.org/stable/2289776}
}

@INPROCEEDINGS{gelman96,
  author = {A. Gelman},
  title = {Inference and monitoring convergence},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  year = {1996},
  editor = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  pages = {131--143},
  publisher = {Chapman and Hall}
}

@ARTICLE{Gelman2006,
  author = {Gelman, A.},
  title = {The Boxer, the Wrestler, and the Coin Flip},
  journal = {The American Statistician},
  year = {2006},
  volume = {60},
  pages = {146--150},
  number = {2},
  publisher = {ASA}
}

@ARTICLE{gelman98,
  author = {A. Gelman},
  title = {Simulating normalizing constants: {F}rom importance sampling to bridge
	sampling to path sampling},
  journal = {Statistical Science},
  year = {1998},
  volume = {13},
  pages = {163--185}
}

@BOOK{gelman95,
  title = {Bayesian Data Analysis},
  publisher = {Chapman and Hall/CRC},
  year = {1995},
  author = {A. Gelman and J. B. Carlin and H. S. Stern and D. B. Rubin},
  address = {Boca Raton}
}

@ARTICLE{gelman1998,
  author = {Gelman, Andrew and Meng, Xiao-Li},
  title = {Simulating normalizing constants: From importance sampling to bridge
	sampling to path sampling},
  journal = {Statistical science},
  year = {1998},
  pages = {163--185}
}

@ARTICLE{Gelman1992,
  author = {Gelman, A. and Rubin, D.B.},
  title = {A single series from the {G}ibbs sampler provides a false sense of
	security},
  journal = {Bayesian statistics},
  year = {1992},
  volume = {4},
  pages = {625--632},
  publisher = {Oxford University Press}
}

@ARTICLE{gelman92,
  author = {Gelman, Andrew and Rubin, Donald B},
  title = {Inference from iterative simulation using multiple sequences},
  journal = {Statistical science},
  year = {1992},
  pages = {457--472},
  publisher = {JSTOR}
}

@ARTICLE{Geman1984a,
  author = {Geman, S. and Geman, D.},
  title = {Stochastic relaxation, {G}ibbs distributions and the {B}ayesian restoration
	of images},
  journal = {Readings in Computer Vision: Issues, Problems, Principles, and Paradigms},
  year = {1984},
  pages = {564--584},
  publisher = {Morgan Kaufmann}
}

@ARTICLE{geman84,
  author = {S. Geman and D. Geman},
  title = {Stochastic relaxation, {G}ibbs distributions, and the {B}ayesian
	restoration of images},
  journal = {{IEEE} Transactions on Pattern Analysis and Machine Intelligence},
  year = {1984},
  volume = {6},
  pages = {721--741}
}

@ARTICLE{geraads2005,
  author = {Geraads, Denis and Kaya, Tanju and Mayda, Serdar and others},
  title = {Late Miocene large mammals from {Y}ulafli, {T}hrace region, {T}urkey,
	and their biogeographic implications},
  journal = {Acta Palaeontologica Polonica},
  year = {2005},
  volume = {50},
  pages = {523--544},
  number = {3}
}

@ARTICLE{gernhard08,
  author = {T. Gernhard},
  title = {The conditioned reconstructed process},
  journal = {Journal of Theoretical Biology},
  year = {2008},
  volume = {253},
  pages = {769--778}
}

@ARTICLE{geuten07,
  author = {W. Geuten and T. Massingham and P. Darius and E. Smets and N. Goldman},
  title = {Experimental design criteria in phylogenetics: {W}here to add taxa},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {609--622}
}

@INPROCEEDINGS{geyer99,
  author = {C. J. Geyer},
  title = {Likelihood inference for spatial point processes},
  booktitle = {Stochastic {G}eometry: {L}ikelihood and {C}omputation},
  year = {1999},
  editor = {O. E. Barndorff-Nielsen and W. S. Kendall and M. N. M. van Lieshout},
  pages = {79--140},
  publisher = {Chapman and Hall/CRC}
}

@INPROCEEDINGS{geyer91,
  author = {C. J. Geyer},
  title = {{M}arkov chain {M}onte {C}arlo maximum likelihood},
  booktitle = {Computing Science and Statistics: Proceedings of the 23rd Symposium
	on the Interface},
  year = {1991},
  editor = {E. M. Kerimidas},
  pages = {156--163},
  publisher = {Fairfax Station: Interface Foundation}
}

@ARTICLE{Geyer1992,
  author = {Geyer, Charles J.},
  title = {Practical {M}arkov Chain {M}onte {C}arlo},
  journal = {Statistical Science},
  year = {1992},
  volume = {7},
  pages = {473--483},
  number = {4},
  url = {http://www.jstor.org/stable/2246094}
}

@ARTICLE{gilbert86,
  author = {W. Gilbert},
  title = {The {RNA} world},
  journal = {Nature},
  year = {1986},
  volume = {319},
  pages = {618}
}

@BOOK{Gilks1996,
  title = {Markov Chain {M}onte {C}arlo in Practice},
  publisher = {Chapman \& Hall/CRC},
  year = {1996},
  author = {Gilks, W.R. and Richardson, S. and Spiegelhalter, DJ}
}

@ARTICLE{Gilks1994,
  author = {Gilks, WR and Thomas, A. and Spiegelhalter, DJ},
  title = {A language and program for complex {B}ayesian modelling},
  journal = {The Statistician},
  year = {1994},
  volume = {43},
  pages = {169--177},
  number = {1},
  publisher = {Blackwell Publishers}
}

@INPROCEEDINGS{gilks96b,
  author = {W. R. Gilks},
  title = {Full conditional distributions},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  year = {1996},
  editor = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  pages = {75--88},
  publisher = {Chapman and Hall}
}

@INPROCEEDINGS{gilks96c,
  author = {W. R. Gilks and G. O. Roberts},
  title = {Strategies for improving {MCMC}},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  year = {1996},
  editor = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  pages = {89--114},
  publisher = {Chapman and Hall}
}

@ARTICLE{gilks94,
  author = {W. R. Gilks and A. Thomas and D. J. Spiegelhalter},
  title = {A language and program for complex {B}ayesian modelling},
  journal = {The Statistician},
  year = {1994},
  volume = {43},
  pages = {169--177}
}

@ARTICLE{ginsburg1995,
  author = {Ginsburg, L and Morales, J},
  title = {\textit{{Z}aragocyon daamsi n. gen. sp. nov.}, U{}rsidae primitif
	du {M}ioc{\`e}ne inf{\'e}rieur d'{E}spagne},
  journal = {Comptes Rendus de l'Acad{\'e}mie des Sciences. S{\'e}rie 2. Sciences
	de la Terre et des Plan{\`e}tes},
  year = {1995},
  volume = {321},
  pages = {811--815},
  number = {9},
  publisher = {Elsevier}
}

@INPROCEEDINGS{ginsburg1998,
  author = {Ginsburg, L{\'e}onard and Morales, Jorge},
  title = {{Les Hemicyoninae (Ursidae, Carnivora, Mammalia) et les formes apparent{\'e}es
	du Mioc{\`e}ne inf{\'e}rieur et moyen d'Europe occidentale}},
  booktitle = {Annales de Pal{\'e}ontologie},
  year = {1998},
  volume = {84},
  number = {1},
  pages = {71--123},
  organization = {Elsevier}
}

@ARTICLE{gojobori82,
  author = {T. Gojobori and K. Ishii and M. Nei},
  title = {Estimation of average number of nucleotide substitutions when the
	rate of substitution varies with nucleotide},
  journal = JME,
  year = {1982},
  volume = {18},
  pages = {414--423}
}

@ARTICLE{Goldberg1991,
  author = {Goldberg, D.E. and Deb, K.},
  title = {A comparative analysis of selection schemes used in genetic algorithms},
  journal = {Foundations of Genetic Algorithms},
  year = {1991},
  volume = {1},
  pages = {69--93}
}

@ARTICLE{golding83,
  author = {G. B. Golding},
  title = {Estimates of {DNA} and protein sequence divergence: {A}n examination
	of some assumptions},
  journal = MBE,
  year = {1983},
  volume = {1},
  pages = {125--142}
}

@ARTICLE{goldman93,
  author = {N. Goldman},
  title = {Statistical tests of models of {DNA} substitution},
  journal = JME,
  year = {1993},
  volume = {36},
  pages = {182--198}
}

@ARTICLE{goldman90,
  author = {N. Goldman},
  title = {Maximum likelihood inference of phylogenetic trees with special reference
	to a {P}oisson process model of {DNA} substitution and to parsimony
	analyses},
  journal = SZ,
  year = {1990},
  volume = {39},
  pages = {345--361}
}

@ARTICLE{goldman96,
  author = {N. Goldman and J. Thorne and D. Jones},
  title = {Using evolutionary trees in protein secondary structure prediction
	and other comparative sequence analyses},
  journal = JMB,
  year = {1996},
  volume = {263},
  pages = {196--208}
}

@ARTICLE{Goldman1994,
  author = {Goldman, N. and Yang, Z.},
  title = {A codon-based model of nucleotide substitution for protein-coding
	{DNA} sequences},
  journal = MBE,
  year = {1994},
  volume = {11},
  pages = {725},
  number = {5}
}

@ARTICLE{goldman94,
  author = {N. Goldman and Z. Yang},
  title = {A codon-based model of nucleotide substitution for protein-coding
	{DNA} sequences},
  journal = MBE,
  year = {1994},
  volume = {11},
  pages = {725--736}
}

@ARTICLE{goldstein06,
  author = {R. N. Goldstein},
  title = {Architectural design and the collaborative research environment},
  journal = {Cell},
  year = {2006},
  volume = {127},
  pages = {243--246}
}

@ARTICLE{goloboff03,
  author = {P. A. Goloboff},
  title = {Parsimony, likelihood, and simplicity},
  journal = {Cladistics},
  year = {2003},
  volume = {19},
  pages = {91--103}
}

@BOOK{golub83,
  title = {Matrix {C}omputations},
  publisher = {Johns Hopkins University Press},
  year = {1983},
  author = {G. H. Golub and C. F. Van Loan},
  address = {Baltimore, Maryland}
}

@ARTICLE{gotoh82,
  author = {O. Gotoh},
  title = {An improved algorithm for matching biological sequences},
  journal = JMB,
  year = {1982},
  volume = {162},
  pages = {705--708}
}

@PHDTHESIS{Gowri-Shankar2006,
  author = {Gowri-Shankar, Vivek},
  title = {{RNA} Phylogenetic Inference with Heterogeneous substitution models},
  school = {University of Manchester},
  year = {2006}
}

@ARTICLE{Gowri-Shankar2007,
  author = {Gowri-Shankar, V. and Rattray, M.},
  title = {A Reversible Jump Method for {B}ayesian Phylogenetic Inference with
	a Nonhomogeneous Substitution Model},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {1286},
  number = {6}
}

@ARTICLE{graham00,
  author = {M. Graham and J. Kennedy and C. Hand},
  title = {A comparison of set-based and graph-based visualisations of overlapping
	classification hierarchies},
  journal = {Proceedings of Advanced Visual Interfaces},
  year = {2000},
  pages = {41--50}
}

@ARTICLE{Grant2008,
  author = {Grant, Taran and Kluge, Arnold G.},
  title = {Clade support measures and their adequacy},
  journal = {Cladistics},
  year = {2008},
  volume = {24},
  pages = {1051--1064},
  number = {6},
  doi = {10.1111/j.1096-0031.2008.00231.x},
  publisher = {Blackwell Publishing Ltd},
  url = {http://dx.doi.org/10.1111/j.1096-0031.2008.00231.x}
}

@ARTICLE{grantham74,
  author = {R. Grantham},
  title = {Amino acid difference formula to help explain protein evolution},
  journal = {Science},
  year = {1974},
  volume = {185},
  pages = {862--864}
}

@ARTICLE{graur04,
  author = {D. Graur and W. Martin},
  title = {Reading the entrails of chickens: {M}olecular timescales of evolution
	and the illusion of precision},
  journal = {Trends in Genetics},
  year = {2004},
  volume = {20},
  pages = {80--86}
}

@ARTICLE{graybeal98,
  author = {A. Graybeal},
  title = {Is it better to add taxa or characters to a difficult phylogenetic
	problem?},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {9--17}
}

@ARTICLE{graybeal94,
  author = {A. Graybeal},
  title = {Evaluating the phylogenetic utility of genes: {A} search for genes
	informative about deep divergences among vertebrates},
  journal = SYSB,
  year = {1994},
  volume = {43},
  pages = {174--193}
}

@ARTICLE{Green1995,
  author = {Green, P.J.},
  title = {Reversible jump {M}arkov chain {M}onte {C}arlo computation and {B}ayesian
	model determination},
  journal = {Biometrika},
  year = {1995},
  volume = {82},
  pages = {711},
  number = {4}
}

@INPROCEEDINGS{green03,
  author = {P. J. Green},
  title = {Trans-dimensional {M}arkov chain {M}onte {C}arlo},
  booktitle = {Highly {S}tructured {S}tochastic {S}ystems},
  year = {2003},
  editor = {P. J. Green and N. L. Hjort and S. Richardson},
  pages = {179--198},
  publisher = {Oxford University Press}
}

@ARTICLE{green95,
  author = {P. J. Green},
  title = {Reversible jump {MCMC} computation and {B}ayesian model determination},
  journal = {Biometrika},
  year = {1995},
  volume = {82},
  pages = {771--732}
}

@ARTICLE{green08,
  author = {R. E. Green and A.-S. Malaspinas and J. Krause and A. W. Briggs and
	P. L. F. Johnson and C. Uhler and M. Meyer and J. M. Good and T.
	Maricic and U. Stenzel and K. Pr\"ufer and M. Siebauer and H. A.
	Burbano and M. Ronan and J. M. Rothberg and M. Egholm and P. Rudan
	and D. Brajkovi\'c and \u{Z}. Ku\'can and I. Gu\u{s}i\'c and M. Wikstr\"om
	and L. Laakkonen and J. Kelso and M. Slatkin and S. P\"a\"abo},
  title = {A complete Neandertal mitochondrial genome sequence determined by
	high-throughput sequencing},
  journal = {Cell},
  year = {2008},
  volume = {134},
  pages = {416--426}
}

@ARTICLE{greider85,
  author = {C. W. Greider and E. H. Blackburn},
  title = {Identification of a specific telomere terminal transferase activity
	in {T}etrahymena extracts},
  journal = {Cell},
  year = {1985},
  volume = {43},
  pages = {405--413}
}

@ARTICLE{griffiths1994,
  author = {Griffiths, RC and Tavare, Simon},
  title = {Simulating probability distributions in the coalescent},
  journal = {Theoretical Population Biology},
  year = {1994},
  volume = {46},
  pages = {131--159},
  number = {2},
  publisher = {Elsevier}
}

@ARTICLE{gu95,
  author = {X. Gu and Y. -X. Fu and W.-H. Li},
  title = {Maximum likelihood estimation of the heterogeneity of substitution
	rates among nucleotide sites},
  journal = MBE,
  year = {1995},
  volume = {12},
  pages = {546--557}
}

@ARTICLE{Guindon2010,
  author = {Guindon, St\'{e}phane},
  title = {Bayesian Estimation of Divergence Times from Large Sequence Alignments},
  journal = MBE,
  year = {2010},
  volume = {27},
  pages = {1768-1781},
  number = {8}
}

@ARTICLE{Guindon2003,
  author = {Guindon, Stephane and Gascuel, Olivier},
  title = {A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies
	by Maximum Likelihood},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {696--704},
  number = {5},
  url = {http://www.jstor.org/stable/3651071}
}

@ARTICLE{guindon04,
  author = {S. Guindon and A. G. Rodrigo and K. A. Dyer and J. P. Huelsenbeck},
  title = {Modeling the site-specific variation of selection patterns along
	lineages},
  journal = PNAS,
  year = {2004},
  volume = {101},
  pages = {12957--12962}
}

@ARTICLE{gusfield02,
  author = {D. Gusfield},
  title = {Partition-distance: {A} problem and class of perfect graphs arising
	in clustering},
  journal = {Information Processing Letters},
  year = {2002},
  volume = {82},
  pages = {159--164}
}

@INPROCEEDINGS{gutell96,
  author = {R. R. Gutell},
  title = {Comparative sequence analysis and the structure of {16S} and {23S}
	{rRNA}},
  booktitle = {Ribosomal RNA: Structure, Evolution, Processing and Function in Protein
	Biosynthesis},
  year = {1996},
  editor = {A. E. Dahlberg and R. A. Zimmermann},
  pages = {111--128},
  publisher = {CRC Press}
}

@ARTICLE{gutell02,
  author = {R. R. Gutell and J. C. Lee and J. J. Cannone},
  title = {The accuracy of ribosomal {RNA} comparative structure models},
  journal = {Current Opinion in Structural Biology},
  year = {2002},
  volume = {12},
  pages = {301--310}
}

@ARTICLE{guyer91,
  author = {C. Guyer and J. B. Slowinski},
  title = {Comparisons of observed phylogenetic topologies with null expectations
	among three monophyletic lineages},
  journal = {Evolution},
  year = {1991},
  volume = {45},
  pages = {340--350}
}

@ARTICLE{hohna2014P1,
  author = {H{\"o}hna, Sebastian},
  title = {Likelihood Inference of Non-Constant Diversification Rates with Incomplete
	Taxon Sampling},
  journal = {PloS One},
  year = {2014},
  volume = {9},
  pages = {e84184},
  number = {1},
  publisher = {Public Library of Science}
}

@ARTICLE{hohna2013time,
  author = {H{\"o}hna, Sebastian},
  title = {The time-dependent reconstructed evolutionary process with a key-role
	for mass-extinction events},
  journal = {arXiv preprint arXiv:1312.2392},
  year = {2013}
}

@ARTICLE{Hohna2012,
  author = {H{\"o}hna, Sebastian and Drummond, Alexei J},
  title = {Guided Tree Topology Proposals for {B}ayesian Phylogenetic Inference},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {1--11},
  number = {1},
  publisher = {Oxford University Press}
}

@ARTICLE{hohna2011,
  author = {H{\"o}hna, Sebastian and Stadler, Tanja and Ronquist, Fredrik and
	Britton, Tom},
  title = {Inferring speciation and extinction rates under different sampling
	schemes},
  journal = MBE,
  year = {2011},
  volume = {28},
  pages = {2577--2589},
  number = {9}
}

@ARTICLE{hoehnaGM2014,
  author = {H\"{o}hna, Sebastian and Heath, Tracy A. and Boussau, Bastien and
	Landis, Michael J. and Ronquist, Fredrik and Huelsenbeck, John P.},
  title = {Probabilistic Graphical Model Representation in Phylogenetics},
  journal = SYSB,
  year = {2014},
  volume = {63},
  pages = {753-771},
  number = {5},
  doi = {10.1093/sysbio/syu039}
}

@PHDTHESIS{Hohna2009,
  author = {Sebastian H\"ohna},
  title = {New Efficient Algorithms for {B}ayesian Phylogenetic Inference Using
	{M}arkov Chain {M}onte {C}arlo},
  school = {The Universtiy of Auckland},
  year = {2009},
  type = {Master Thesis},
  address = {The University of Auckland, Department of Computer Science, Private
	Bag 92019, Auckland, New Zealand.},
  month = {February}
}

@CONFERENCE{Hohna2008,
  author = {H\"ohna, S. and Defoin-Platel, M. and Drummond, A.J.},
  title = {Clock-constrained tree proposal operators in {B}ayesian phylogenetic
	inference},
  booktitle = {8th IEEE International Conference on BioInformatics and BioEngineering,
	2008. BIBE 2008},
  year = {2008},
  pages = {1--7}
}

@ARTICLE{hohna11,
  author = {H\"ohna, Sebastian and Stadler, Tanja and Ronquist, Fredrik and Britton,
	Tom},
  title = {Inferring Speciation and Extinction Rates under Different Sampling
	Schemes},
  journal = MBE,
  year = {2011},
  volume = {28},
  pages = {2577-2589},
  number = {9}
}

@BOOK{haeckel66,
  title = {Generelle {M}orphologie der {O}rganismen: {A}llgemeine {G}rundzuge
	der organischen {F}ormen-{W}issenschaft, mechanisch begrundet durch
	die von {C}harles {D}arwin reformirte {D}escendenz-{T}heorie},
  publisher = {Georg Riemer},
  year = {1866},
  author = {E. Haeckel},
  address = {Berlin}
}

@ARTICLE{hafner94,
  author = {M. S. Hafner and P. D. Sudman and F. X. Villablanca and T. A. Spradling
	and J. W. Demastes and S. A. Nadler},
  title = {Disparate rates of molecular evolution in cospeciating hosts and
	parasites},
  journal = {Science},
  year = {1994},
  volume = {265},
  pages = {1087--1090}
}

@ARTICLE{hahn00,
  author = {B. H. Hahn and G. M. Shaw and K. M. de Cock and P. M. Sharp},
  title = {{AIDS} as a zoonosis: {S}cientific and public health implications},
  journal = {Science},
  year = {2000},
  volume = {287},
  pages = {607--614}
}

@ARTICLE{hall06,
  author = {B. G. Hall},
  title = {Simple and accurate estimation of ancestral protein sequences},
  journal = PNAS,
  year = {2006},
  volume = {103},
  pages = {5431--5436}
}

@BOOK{Hamilton1994,
  title = {Time series analysis},
  publisher = {Cambridge Univ Press},
  year = {1994},
  author = {Hamilton, J.D.},
  volume = {10}
}

@BOOK{Hammersley1964,
  title = {Monte {C}arlo methods},
  publisher = {Methuen},
  year = {1964},
  author = {Hammersley, J.M. and Handscomb, D.C.}
}

@ARTICLE{harshman03,
  author = {J. Harshman and C. J. Huddleston and J. P. Bollback and T. J. Parsons
	and M. J. Braun},
  title = {True and false {G}harials: {A} nuclear gene phylogeny of {C}rocodylia},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {386--402}
}

@ARTICLE{Hart1968,
  author = {Hart, PE and Nilsson, NJ and Raphael, B.},
  title = {A Formal Basis for the Heuristic Determination of Minimum Cost Paths},
  journal = {Systems Science and Cybernetics, IEEE Transactions on},
  year = {1968},
  volume = {4},
  pages = {100--107},
  number = {2}
}

@ARTICLE{hartigan73,
  author = {J. A. Hartigan},
  title = {Minimum mutation fits to a given tree},
  journal = {Biometrics},
  year = {1973},
  volume = {29},
  pages = {53--65}
}

@ARTICLE{hartmann10,
  author = {K. Hartmann and D. Wong and T. Stadler},
  title = {Sampling trees from evolutionary models},
  journal = SYSB,
  year = {2010},
  volume = {59},
  pages = {465--476}
}

@ARTICLE{Harvey1994,
  author = {Harvey, Paul H. and May, Robert M. and Nee, Sean},
  title = {Phylogenies Without Fossils},
  journal = {Evolution},
  year = {1994},
  volume = {48},
  pages = {523--529},
  number = {3},
  url = {http://www.jstor.org/stable/2410466}
}

@BOOK{harvey91,
  title = {The {C}omparative {M}ethod in {E}volutionary {B}iology},
  publisher = {Oxford University Press},
  year = {1991},
  author = {P. H. Harvey and M. D. Pagel},
  address = {Oxford}
}

@ARTICLE{hasegawa91,
  author = {M. Hasegawa and J. Horai},
  title = {Time of the deepest root for polymorphism in human mitochondrial
	{DNA}},
  journal = JME,
  year = {1991},
  volume = {32},
  pages = {37--42}
}

@ARTICLE{hasegawa89,
  author = {M. Hasegawa and H. Kishino and T. Yano},
  title = {Estimation of branching dates among primates by molecular clocks
	of nuclear {DNA} which slowed down in {H}ominoidea},
  journal = {Journal of Human Evolution},
  year = {1989},
  volume = {18},
  pages = {461--476}
}

@ARTICLE{hasegawa85,
  author = {M. Hasegawa and H. Kishino and T. Yano},
  title = {Dating the human-ape splitting by a molecular clock of mitochondrial
	{DNA}},
  journal = JME,
  year = {1985},
  volume = {22},
  pages = {160--174}
}

@ARTICLE{hasegawa84,
  author = {M. Hasegawa and T. Yano and H. Kishino},
  title = {A new molecular clock of mitochondrial {DNA} and the evolution of
	{H}ominoids},
  journal = {Proc. Japan Acad. Ser. B},
  year = {1984},
  volume = {60},
  pages = {95--98}
}

@ARTICLE{Hastings1970,
  author = {Hastings, W. K.},
  title = {Monte {C}arlo Sampling Methods Using {M}arkov Chains and Their Applications},
  journal = {Biometrika},
  year = {1970},
  volume = {57},
  pages = {97--109},
  number = {1},
  publisher = {Biometrika Trust},
  url = {http://www.jstor.org/stable/2334940}
}

@ARTICLE{hastings70,
  author = {W. K. Hastings},
  title = {Monte {C}arlo sampling methods using {M}arkov chains and their applications},
  journal = {Biometrika},
  year = {1970},
  volume = {57},
  pages = {97--109}
}

@ARTICLE{hayasaka88,
  author = {K. Hayasaka and T. Gojobori and S. Horai},
  title = {Molecular phylogeny and evolution of primate mitochondrial {DNA}},
  journal = MBE,
  year = {1988},
  volume = {5},
  pages = {626--644}
}

@ARTICLE{heard92,
  author = {S. B. Heard},
  title = {Patterns in tree balance among cladistic, phenetic, and randomly
	generated phylogenetic trees},
  journal = Evolution,
  year = {1992},
  volume = {46},
  pages = {1818--1826}
}

@ARTICLE{heath12,
  author = {T. A. Heath},
  title = {A hierarchical {B}ayesian model for calibrating estimates of species
	divergence times},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {793--809}
}

@ARTICLE{heath08b,
  author = {T. A. Heath and S. M. Hedtke and D. M. Hillis},
  title = {Taxon sampling and the accuracy of phylogenetic analyses},
  journal = {Journal of Systematics and Evolution},
  year = {2008},
  volume = {46},
  pages = {239--257}
}

@ARTICLE{heath11,
  author = {T. A. Heath and M. T. Holder and J. P. Huelsenbeck},
  title = {A {D}irichlet process prior for estimating lineage-specific substitution
	rates},
  journal = MBE,
  year = {2012},
  volume = {29},
  pages = {939--255}
}

@ARTICLE{heath2013fossilized,
  author = {Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja},
  title = {The fossilized birth-death process for coherent calibration of divergence-time
	estimates},
  journal = PNAS,
  year = {2014},
  volume = {111},
  pages = {E2957--E2966}
}

@ARTICLE{heath2013fossilizedarXiv,
  author = {Heath, Tracy A and Huelsenbeck, John P and Stadler, Tanja},
  title = {The Fossilized Birth-Death Process: A Coherent Model of Fossil Calibration
	for Divergence Time Estimation},
  journal = {arXiv preprint arXiv:1310.2968},
  year = {2013}
}

@INCOLLECTION{HeathMoore2013,
  author = {T. A. Heath and B. R. Moore},
  title = {Bayesian inference of species divergence times},
  booktitle = {Bayesian Phylogenetics: Methods, Algorithms, and Applications},
  publisher = {Chapman \& Hall/CRC},
  year = {2014},
  editor = {M.-H. Chen and L. Kuo and P. O. Lewis},
  series = {Chapman \& Hall/CRC Mathematical and Computational Biology},
  pages = {277--318},
  address = {Boca Raton, FL}
}

@ARTICLE{heath08,
  author = {T. A. Heath and D. J. Zwickl and J. Kim and D. M. Hillis},
  title = {Taxon sampling affects inferences of macroevolutionary processes
	from phylogenetic trees},
  journal = SYSB,
  year = {2008},
  volume = {57},
  pages = {160--166}
}

@ARTICLE{hedges04,
  author = {S. B. Hedges and S. Kumar},
  title = {Precision of molecular time estimates},
  journal = {Trends in Genetics},
  year = {2004},
  volume = {20},
  pages = {242--247}
}

@ARTICLE{hedtke06,
  author = {S. M. Hedtke and T. M. Townsend and D. M. Hillis},
  title = {Resolution of phylogenetic conflict in large data sets by increased
	taxon sampling},
  journal = SYSB,
  year = {2006},
  volume = {55},
  pages = {522--529}
}

@ARTICLE{heerwagen04,
  author = {J. H. Heerwagen and K. Kampschoer and K. M. Powell and V. Loftness},
  title = {Collaborative knowledge work environments},
  journal = {Building Research \& Information},
  year = {2004},
  volume = {32},
  pages = {510--528}
}

@article{heibl2008phyloch,
  author = {C. Heibl},
  title  = {PHYLOCH: {R} language tree plotting tools and interfaces to diverse phylogenetic software packages},
  pages   = {\url{http://www.christophheibl.de/Rpackages.html}},
year = {2008}
}

@ARTICLE{Heidelberger1983,
  author = {Heidelberger, P. and Welch, P.D.},
  title = {Simulation run length control in the presence of an initial transient},
  journal = {Operations Research},
  year = {1983},
  volume = {31},
  pages = {1109--1144},
  number = {6},
  publisher = {JSTOR}
}

@INPROCEEDINGS{hein01,
  author = {J. Hein},
  title = {An Algorithm for Statistical Alignment of Sequences Related by a
	Binary Tree},
  booktitle = {Pacific Symposium on Biocomputing},
  year = {2001},
  editor = {R. B. Altman and A. K. Dunker and L. Hunter and K. Lauderdale and
	T. E. Klein},
  pages = {179--190},
  address = {Singapore},
  publisher = {World Scientific}
}

@ARTICLE{hein03,
  author = {J. Hein and J. L. Jensen and C. N. S. Pedersen},
  title = {{R}ecursions for statistical multiple alignment},
  journal = PNAS,
  year = {2003},
  volume = {100},
  pages = {14960--14965},
  number = {25},
  month = {Dec}
}

@ARTICLE{hein00,
  author = {J. Hein and C. Wiuf and B. Knudsen and M. B. Moller and G. Wibling},
  title = {Statistical alignment: {C}omputational properties, homology testing
	and goodness-of-fit},
  journal = JMB,
  year = {2000},
  volume = {302},
  pages = {265--279}
}

@ARTICLE{heizmann1980,
  author = {E Heizmann and L Ginsburg and C Bulot},
  title = {\textit{{P}rosansanosmilus peregrinus}, ein neuer machairodontider
	{F}elidae aus dem {M}ioz\"{a}n {D}eutschlands und {F}rankreichs},
  journal = {Stuttgarter Beitr. Naturk. B},
  year = {1980},
  volume = {58},
  pages = {1--27}
}

@ARTICLE{Heled2010,
  author = {Heled, J. and Drummond, A.J.},
  title = {Bayesian inference of species trees from multilocus data},
  journal = MBE,
  year = {2010},
  volume = {27},
  pages = {570},
  number = {3},
  publisher = {SMBE}
}

@ARTICLE{heleddrummond2013,
  author = {Heled, Joseph and Drummond, Alexei J},
  title = {Calibrated birth-death phylogenetic time-tree priors for {B}ayesian
	inference},
  journal = {arXiv preprint arXiv:1311.4921},
  year = {2013}
}

@ARTICLE{heled12,
  author = {J. Heled and A. J. Drummond},
  title = {Calibrated tree priors for relaxed phylogenetics and divergence time
	estimation},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {138--149}
}

@ARTICLE{heled10,
  author = {J. Heled and A. J. Drummond},
  title = {Bayesian inference of species trees from multilocus data},
  journal = MBE,
  year = {2010},
  volume = {27},
  pages = {570--580}
}

@ARTICLE{hendy93,
  author = {M. D. Hendy and D. Penny},
  title = {Spectral analysis of phylogenetic data},
  journal = {Journal of Classification},
  year = {1993},
  volume = {10},
  pages = {5--24}
}

@ARTICLE{henikoff92,
  author = {S. Henikoff and J. G. Henikoff},
  title = {Amino acid substitution matrices from protein blocks},
  journal = PNAS,
  year = {1992},
  volume = {89},
  pages = {10915--10919}
}

@BOOK{hennig69,
  title = {Die {S}tammesgeschichte der {I}nsekten},
  publisher = {Kramer},
  year = {1969},
  author = {W. Hennig},
  address = {Frankfurt}
}

@BOOK{hennig66,
  title = {Phylogenetic {S}ystematics},
  publisher = {University of Illinois Press},
  year = {1966},
  author = {W. Hennig},
  address = {Urbana}
}

@BOOK{hennig50,
  title = {Grundzuge einer {T}heorie der {P}hylogenetischen {S}ystematik},
  publisher = {Deutscher Zentralverlag},
  year = {1950},
  author = {W. Hennig},
  address = {Berlin}
}

@ARTICLE{herman00,
  author = {I. Herman and G. Melancon and M. S. Marshall},
  title = {Graph visualization and navigation in information visualization:
	{A} survey},
  journal = {IEEE Transactions on Visualization and Computer Graphics},
  year = {2000},
  volume = {6},
  pages = {24--43}
}

@ARTICLE{hess94,
  author = {S. T. Hess and J. D. Blake and R. D. Blake},
  title = {Wide variations in neighbor-dependent substitution rates},
  journal = JMB,
  year = {1994},
  volume = {236},
  pages = {1022--1033}
}

@ARTICLE{Hey1992,
  author = {Hey, J.},
  title = {Using phylogenetic trees to study speciation and extinction},
  journal = {Evolution},
  year = {1992},
  volume = {46},
  pages = {627--640},
  publisher = {JSTOR}
}

@ARTICLE{hey07,
  author = {J. Hey and R. Nielsen},
  title = {Integration with the {F}elsenstein equation for improved {M}arkov
	chain {M}onte {C}arlo methods in population genetics},
  journal = PNAS,
  year = {2007},
  volume = {104},
  pages = {2785--2790}
}

@ARTICLE{higgins88,
  author = {D. G. Higgins and P. M. Sharp},
  title = {{CLUSTAL}---a package for performing multiple sequence alignment
	on a microcomputer},
  journal = {Gene},
  year = {1988},
  volume = {73},
  pages = {237--244}
}

@ARTICLE{Hillis2005,
  author = {Hillis, D.M. and Heath, T.A. and John, K.S.},
  title = {Analysis and Visualization of Tree Space},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {471--482},
  number = {3},
  publisher = {Taylor \& Francis}
}

@INPROCEEDINGS{hillis94,
  author = {D. M. Hillis},
  title = {Homology in molecular biology},
  booktitle = {Homology: {T}he {H}ierarchical {B}asis of {C}omparative {B}iology},
  year = {1994},
  editor = {B. K. Hall},
  pages = {339--368},
  publisher = {Academic Press}
}

@ARTICLE{hillis98,
  author = {D. M. Hillis},
  title = {Taxonomic sampling, phylogenetic accuracy, and investigator bias},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {3--8}
}

@ARTICLE{hillis96,
  author = {D. M. Hillis},
  title = {Inferring complex phylogenies},
  journal = {Nature},
  year = {1996},
  volume = {383},
  pages = {130--131}
}

@ARTICLE{Himmelmann2009,
  author = {Himmelmann, Lin and Metzler, Dirk},
  title = {TreeTime: an extensible C++ software package for {B}ayesian phylogeny
	reconstruction with time-calibration},
  journal = BI,
  year = {2009},
  volume = {25},
  pages = {2440-2441},
  number = {18}
}

@ARTICLE{hitchcock03,
  author = {D. Hitchcock},
  title = {A history of the {M}etropolis-{H}astings algorithm},
  journal = {The American Statistician},
  year = {2003},
  volume = {57},
  pages = {254--257}
}

@ARTICLE{ho2008,
  author = {Ho, Simon YW and Saarma, Urmas and Barnett, Ross and Haile, James
	and Shapiro, Beth},
  title = {The effect of inappropriate calibration: three case studies in molecular
	ecology},
  journal = {PLoS One},
  year = {2008},
  volume = {3},
  pages = {e1615},
  number = {2}
}

@ARTICLE{ho07,
  author = {S. Y. W. Ho},
  title = {Calibrating molecular estimates of substitution rates and divergence
	times in birds},
  journal = {Journal of Avian Biology},
  year = {2007},
  volume = {38},
  pages = {409--414}
}

@ARTICLE{ho11,
  author = {S. Y. W. Ho and R. Lanfear and L. Bromham and M. J. Phillips and
	J. Soubrier and A. G. Rodrigo and A. Cooper},
  title = {Time-dependent rates of molecular evolution},
  journal = {Molecular Ecology},
  year = {2011},
  volume = {20},
  pages = {3087--3101}
}

@ARTICLE{ho09,
  author = {S. Y. W. Ho and M. J. Phillips},
  title = {Accounting for calibration uncertainty in phylogenetic estimation
	of evolutionary divergence times},
  journal = SYSB,
  year = {2009},
  volume = {58},
  pages = {367--380}
}

@ARTICLE{hoffmeister2014,
  author = {Hoffmeister, Mart\'{i}n Ch\'{a}vez and Brice\~{n}o, Jorge D Carrillo
	and Nielsen, Sven N},
  title = {The Evolution of Seabirds in the {H}umboldt Current: New Clues from
	the {P}liocene of {C}entral {C}hile},
  journal = {PloS One},
  year = {2014},
  volume = {9},
  pages = {e90043},
  number = {3},
  publisher = {Public Library of Science}
}

@ARTICLE{hogeweg84,
  author = {P. Hogeweg and P. Hesper},
  title = {The alignment of sets of sequences and the construction of phyletic
	trees: {A}n integrated method},
  journal = JME,
  year = {1984},
  volume = {20},
  pages = {175--186}
}

@ARTICLE{Holder2003,
  author = {Holder, M. and Lewis, P.O.},
  title = {Phylogeny estimation: traditional and {B}ayesian approaches},
  journal = {Nature Reviews Genetics},
  year = {2003},
  volume = {4},
  pages = {275},
  number = {4},
  publisher = {Nature Publishing Group}
}

@ARTICLE{holder10,
  author = {M. T. Holder and P. O. Lewis and D. L. Swofford},
  title = {The {A}kaike information criterion will not choose the no common
	mechanism model},
  journal = SYSB,
  year = {2010},
  volume = {59},
  pages = {477--485},
  number = {4}
}

@ARTICLE{holman05,
  author = {E. W. Holman},
  title = {Nodes in phylogenetic trees: {T}he relation between imbalance and
	number of descendent species},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {895--899}
}

@ARTICLE{holmes07,
  author = {I. Holmes},
  title = {{P}hylocomposer and {P}hylodirector: {A}nalysis and {V}isualization
	of {T}ransducer {I}ndel {M}odels},
  journal = BI,
  year = {2007},
  month = {Sep}
}

@ARTICLE{holmes05,
  author = {I. Holmes},
  title = {Accelerated probabilistic inference of {RNA} structure evolution},
  journal = BMCBI,
  year = {2005},
  volume = {6},
  number = {73}
}

@ARTICLE{holmes05b,
  author = {I. Holmes},
  title = {Using evolutionary {E}xpectation {M}aximization to estimate indel
	rates},
  journal = BI,
  year = {2005},
  volume = {21},
  pages = {2294--2300},
  number = {10}
}

@ARTICLE{holmes04,
  author = {I. Holmes},
  title = {A probabilistic model for the evolution of {RNA} structure},
  journal = BMCBI,
  year = {2004},
  volume = {5},
  number = {166}
}

@ARTICLE{holmes03,
  author = {I. Holmes},
  title = {Using guide trees to construct multiple-sequence evolutionary {HMM}s},
  journal = BI,
  year = {2003},
  volume = {19 Suppl. 1},
  pages = {i147--157}
}

@ARTICLE{holmes01,
  author = {I. Holmes and W. J. Bruno},
  title = {Evolutionary {HMM}s: {A} {B}ayesian approach to multiple alignment},
  journal = BI,
  year = {2001},
  volume = {17},
  pages = {803--820},
  number = {9}
}

@ARTICLE{holmes98,
  author = {I. Holmes and R. Durbin},
  title = {Dynamic programming alignment accuracy},
  journal = JCB,
  year = {1998},
  volume = {5},
  pages = {493--504},
  number = {3}
}

@UNPUBLISHED{holmes02a,
  author = {I. Holmes and G. M. Rubin},
  title = {Pairwise {RNA} structure comparison using stochastic context-free
	grammars},
  note = {Pacific Symposium on Biocomputing, 2002},
  year = {2002}
}

@ARTICLE{holmes02b,
  author = {I. Holmes and G. M. Rubin},
  title = {An {E}xpectation {M}aximization algorithm for training hidden substitution
	models},
  journal = JMB,
  year = {2002},
  volume = {317},
  pages = {757--768},
  number = {5}
}

@ARTICLE{horner19,
  author = {W. G. Horner},
  title = {A new method of solving numerical equations of all orders, by continuous
	approximation},
  journal = {Philosophical Transactions of the Royal Society of London},
  year = {1819},
  volume = {109},
  pages = {308--335}
}

@BOOK{howson93,
  title = {Scientific {R}easoning: {T}he {B}ayesian {A}pproach, {S}econd {E}dition},
  publisher = {Open Court},
  year = {1993},
  author = {C. Howson and P. Urbach},
  address = {Chicago}
}

@ARTICLE{Hudelot2003,
  author = {Hudelot, C. and Gowri-Shankar, V. and Jow, H. and Rattray, M. and
	Higgs, P.G.},
  title = {{RNA}-based phylogenetic methods: application to mammalian mitochondrial
	{RNA} sequences},
  journal = {Molecular Phylogenetics and Evolution},
  year = {2003},
  volume = {28},
  pages = {241--252},
  number = {2},
  publisher = {Elsevier}
}

@ARTICLE{hudson90,
  author = {R. R. Hudson},
  title = {Gene genealogies and the coalescent process},
  journal = {Oxford Surveys in Evolutionary Biology},
  year = {1990},
  volume = {7},
  pages = {1--44}
}

@ARTICLE{Huelsenbeck2002,
  author = {Huelsenbeck, JP and Larget, B. and Miller, RE and Ronquist, F.},
  title = {Potential Applications and Pitfalls of {B}ayesian Inference of Phylogeny},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {673--688},
  number = {5},
  publisher = {Taylor and Francis Ltd}
}

@ARTICLE{huelsenbeck02a,
  author = {J. P. Huelsenbeck},
  title = {Testing a covariotide model of DNA substitution},
  journal = MBE,
  year = {2002},
  volume = {19},
  pages = {698--707}
}

@ARTICLE{huelsenbeck98,
  author = {J. P. Huelsenbeck},
  title = {Systematic bias in phylogenetic analysis: {I}s the {S}trepsiptera
	problem solved?},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {519--537}
}

@ARTICLE{huelsenbeck97b,
  author = {J. P. Huelsenbeck},
  title = {Is the {F}elsenstein zone a fly trap?},
  journal = SYSB,
  year = {1997},
  volume = {46},
  pages = {69--74}
}

@ARTICLE{huelsenbeck95a,
  author = {J. P. Huelsenbeck},
  title = {Performance of phylogenetic methods in simulation},
  journal = SYSB,
  year = {1995},
  volume = {44},
  pages = {17--48}
}

@ARTICLE{huelsenbeck95b,
  author = {J. P. Huelsenbeck},
  title = {The robustness of two phylogenetic methods: {F}our taxon simulations
	reveal a slight superiority of maximum likelihood over neighbor joining},
  journal = MBE,
  year = {1995},
  volume = {12},
  pages = {843--849}
}

@ARTICLE{huelsenbeck08a,
  author = {J. P. Huelsenbeck and C. An\'e and B. Larget and F. Ronquist},
  title = {A {B}ayesian perspective on a non-parsimonious parsimony model},
  journal = SYSB,
  year = {2008},
  volume = {57},
  pages = {406--419}
}

@ARTICLE{huelsenbeck07a,
  author = {J. P. Huelsenbeck and P. Andolfatto},
  title = {Inference of population structure under a {D}irichlet process model},
  journal = {Genetics},
  year = {2007},
  volume = {175},
  pages = {1787--1802}
}

@ARTICLE{huelsenbeck01a,
  author = {J. P. Huelsenbeck and J. P. Bollback},
  title = {Empirical and hierarchical {B}ayesian estimation of ancestral states},
  journal = SYSB,
  year = {2001},
  volume = {50},
  pages = {351--366}
}

@ARTICLE{huelsenbeck02b,
  author = {J. P. Huelsenbeck and J. P. Bollback and A. M. Levine},
  title = {Inferring the root of a phylogenetic tree},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {32--43}
}

@ARTICLE{huelsenbeck96b,
  author = {J. P. Huelsenbeck and J. J. Bull},
  title = {A likelihood ratio test for detection of conflicting phylogenetic
	signal},
  journal = SYSB,
  year = {1996},
  volume = {45},
  pages = {92--98}
}

@ARTICLE{huelsenbeck96c,
  author = {J. P. Huelsenbeck and J. J. Bull and C. W. Cunningham},
  title = {Combining data in phylogenetic analysis},
  journal = {Trends in Ecology and Evolution},
  year = {1996},
  volume = {11},
  pages = {152--158}
}

@ARTICLE{huelsenbeck04c,
  author = {J. P. Huelsenbeck and K. Dyer},
  title = {Bayesian estimation of positively selected sites},
  journal = JME,
  year = {2004},
  volume = {58},
  pages = {661--672}
}

@ARTICLE{huelsenbeck93,
  author = {J. P. Huelsenbeck and D. M. Hillis},
  title = {Success of phylogenetic methods in the four-taxon case},
  journal = SYSB,
  year = {1993},
  volume = {42},
  pages = {247--264}
}

@ARTICLE{huelsenbeck96d,
  author = {J. P. Huelsenbeck and D. M. Hillis and R. Nielsen},
  title = {A likelihood-ratio test of monophyly},
  journal = SYSB,
  year = {1996},
  volume = {45},
  pages = {546--558}
}

@ARTICLE{huelsenbeck02c,
  author = {J. P. Huelsenbeck and N. S. Imennov},
  title = {Geographic origin of human mitochondrial {DNA}: {A}ccommodating phylogenetic
	uncertainty and model comparison},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {155--165}
}

@ARTICLE{huelsenbeck06,
  author = {J. P. Huelsenbeck and S. Jain and S. W. D. Frost and S. L. Kosakovsky
	Pond},
  title = {A {D}irichlet process model for detecting positive selection in protein-coding
	{DNA} sequences},
  journal = PNAS,
  year = {2006},
  volume = {103},
  pages = {6263--6268}
}

@ARTICLE{huelsenbeck08b,
  author = {J. P. Huelsenbeck and P. Joyce and C. Lakner and F. Ronquist},
  title = {Bayesian analysis of amino acid substitution models},
  journal = PROCROYB,
  year = {2008},
  volume = {363},
  pages = {3941--3953}
}

@ARTICLE{huelsenbeck96a,
  author = {J. P. Huelsenbeck and M. Kirkpatrick},
  title = {Do phylogenetic methods produce trees with biased shapes?},
  journal = {Evolution},
  year = {1996},
  volume = {50},
  pages = {1418--1424}
}

@ARTICLE{huelsenbeck03b,
  author = {J. P. Huelsenbeck and K. M. Lander},
  title = {Frequent inconsistency of parsimony under a simple model of cladogenesis},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {641--648}
}

@ARTICLE{huelsenbeck04d,
  author = {J. P. Huelsenbeck and B. Larget and M. E. Alfaro},
  title = {Bayesian phylogenetic model selection using reversible jump {M}arkov
	chain {M}onte {C}arlo},
  journal = MBE,
  year = {2004},
  volume = {21},
  pages = {1123--1133}
}

@ARTICLE{huelsenbeck00a,
  author = {J. P. Huelsenbeck and B. Larget and D. L. Swofford},
  title = {A compound {P}oisson process for relaxing the molecular clock},
  journal = {Genetics},
  year = {2000},
  volume = {154},
  pages = {1879--1892}
}

@ARTICLE{huelsenbeck99,
  author = {J. P. Huelsenbeck and R. Nielsen},
  title = {Effect of non-independent substitution on phylogenetic accuracy},
  journal = SYSB,
  year = {1999},
  volume = {48},
  pages = {317--328}
}

@ARTICLE{huelsenbeck03,
  author = {J. P. Huelsenbeck and R. Nielsen and J. P. Bollback},
  title = {Stochastic mapping of morphological characters},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {131--158}
}

@ARTICLE{huelsenbeck04b,
  author = {J. P. Huelsenbeck and B. Rannala},
  title = {Frequentist properties of {B}ayesian posterior probabilities of phylogenetic
	trees under simple and complex substitution models},
  journal = SYSB,
  year = {2004},
  volume = {53},
  pages = {904--913}
}

@ARTICLE{huelsenbeck97a,
  author = {J. P. Huelsenbeck and B. Rannala},
  title = {Phylogenetic methods come of age: {T}esting hypotheses in an evolutionary
	context},
  journal = {Science},
  year = {1997},
  volume = {276},
  pages = {227--232}
}

@ARTICLE{huelsenbeck00b,
  author = {J. P. Huelsenbeck and B. Rannala and B. Larget},
  title = {A {B}ayesian framework for the analysis of cospeciation},
  journal = {Evolution},
  year = {2000},
  volume = {54},
  pages = {353--364}
}

@INPROCEEDINGS{huelsenbeck05,
  author = {J. P. Huelsenbeck and F. Ronquist},
  title = {Bayesian analysis of molecular evolution using {MrBayes}},
  booktitle = {Statistical Methods in Molecular Evolution},
  year = {2005},
  editor = {R. Nielsen},
  pages = {183--232},
  publisher = {Springer-Verlag}
}

@ARTICLE{huelsenbeck01c,
  author = {J. P. Huelsenbeck and F. Ronquist},
  title = {{MRBAYES}: {B}ayesian inference of phylogenetic trees},
  journal = BI,
  year = {2001},
  volume = {17},
  pages = {754--755}
}

@ARTICLE{huelsenbeck01b,
  author = {J. P. Huelsenbeck and F. Ronquist and R. Nielsen and J. Bollback},
  title = {{B}ayesian inference of phylogeny and its impact on evolutionary
	biology},
  journal = {Science},
  year = {2001},
  volume = {294},
  pages = {2310--2314}
}

@ARTICLE{huelsenbeck07b,
  author = {J. P. Huelsenbeck and M. Suchard},
  title = {A Nonparametric Method for Accommodating and Testing Across-Site
	Rate Variation},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {975--987}
}

@ARTICLE{hug07,
  author = {L. A. Hug and A. J. Roger},
  title = {The impact of fossils and taxon sampling on ancient molecular dating
	analyses},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {1889--1897}
}

@ARTICLE{hugall07,
  author = {A. F. Hugall and R. Foster and M. S. Y. Lee},
  title = {Calibration choice, rate smoothing, and the pattern of tetrapod diversification
	according to the long nuclear gene {RAG}-1},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {543--63}
}

@ARTICLE{hugall07b,
  author = {A. F. Hugall and M. S. Y. Lee},
  title = {The likelihood node density effect and consequences for evolutionary
	studies of molecular rates},
  journal = Evolution,
  year = {2007},
  volume = {61},
  pages = {2293--2307}
}

@BOOK{hull88,
  title = {Science as a {P}rocess. {A}n {E}volutionary {A}ccount of the {S}ocial
	and {C}onceptual {D}evelopment of {S}cience},
  publisher = {University of Chicago Press},
  year = {1988},
  author = {D. L. Hull},
  address = {Chicago}
}

@ARTICLE{hunt07,
  author = {T. Hunt and J. Bergsten and Z. Levkanicova and A. Papadopoulou and
	O. St. John and R. Wild and P. M. Hammond and D. Ahrens and M. Balke
	and M. S. Caterino and J. G\'omez-Zurita and I. Ribera and T. G.
	Barraclough and M. Bocakova and L. Bocak and A. P. Vogler},
  title = {A comprehensive phylogeny of {B}eetles reveals the evolutionary origins
	of a superradiation},
  journal = {Science},
  year = {2007},
  volume = {318},
  pages = {1913--1916}
}

@ARTICLE{hurtado2009,
  author = {Hurtado, Sylvia and Cabrera, Nolan L and Lin, Monica H and Arellano,
	Lucy and Espinosa, Lorelle L},
  title = {Diversifying science: Underrepresented student experiences in structured
	research programs},
  journal = {Research in Higher Education},
  year = {2009},
  volume = {50},
  pages = {189--214},
  number = {2}
}

@ARTICLE{hurtado2008,
  author = {Hurtado, Sylvia and Eagan, M Kevin and Cabrera, Nolan L and Lin,
	Monica H and Park, Julie and Lopez, Miguel},
  title = {Training future scientists: Predicting first-year minority student
	participation in health science research},
  journal = {Research in Higher Education},
  year = {2008},
  volume = {49},
  pages = {126--152},
  number = {2}
}

@ARTICLE{hutchinson12,
  author = {M. N. Hutchinson and A. Skinner and M. S. Y. Lee},
  title = {\textit{Tikiguania} and the antiquity of squamate reptiles (lizards
	and snakes)},
  journal = {Biology Letters},
  year = {2012},
  volume = {doi:10.1098/rsbl.2011.1216}
}

@ARTICLE{ihaka96,
  author = {R. Ihaka and R. Gentleman},
  title = {R: {A} Language for data analysis and graphics},
  journal = {Journal of Computational and Graphical Statistics},
  year = {1996},
  volume = {5},
  pages = {299--314}
}

@ARTICLE{inoue10,
  author = {J. Inoue and P. C. Donoghue and Z. Yang},
  title = {The Impact of the Representation of Fossil Calibrations on {B}ayesian
	Estimation of Species Divergence Times},
  journal = SYSB,
  year = {2010},
  volume = {59},
  pages = {74--89}
}

@ARTICLE{jackman99,
  author = {T. R. Jackman and A. Larson and K. de Queiroz and J. B. Losos},
  title = {Phylogenetic relationshiops ad tempo of early diversification in
	{\it {A}nolis} lizards},
  journal = SYSB,
  year = {1999},
  volume = {48},
  pages = {254--285}
}

@ARTICLE{jadwiszczak2001,
  author = {Jadwiszczak, Piotr},
  title = {Body size of {E}ocene {A}ntarctic penguins},
  journal = {Polish Polar Research},
  year = {2001},
  volume = {22},
  pages = {147--158},
  number = {2}
}

@ARTICLE{jain99,
  author = {R. Jain and M. Rivera and J. Lake},
  title = {Horizontal gene transfer among genomes: {T}he complexity hypothesis},
  journal = PNAS,
  year = {1999},
  volume = {96},
  pages = {3801--3806}
}

@ARTICLE{jain02,
  author = {R. Jain and M. Rivera and J. Moore and J. Lake},
  title = {Horizontal gene transfer in microbial genome evolution},
  journal = {Theoretical Population Biology},
  year = {2002},
  volume = {61},
  pages = {489--495}
}

@ARTICLE{jain07,
  author = {S. Jain and R. M. Neal},
  title = {Splitting and merging components of a nonconjugate {D}irichlet process
	mixture model},
  journal = {Bayesian analysis},
  year = {2007},
  volume = {2},
  pages = {445--473}
}

@ARTICLE{jain04,
  author = {S. Jain and R. M. Neal},
  title = {A split-merge {M}arkov chain {M}onte {C}arlo procedure for the {D}irichlet
	process mixture model},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2004},
  volume = {13},
  pages = {158--182}
}

@ARTICLE{jara07,
  author = {A. Jara and M. J. Garcia-Zattera and E. Lesaffre},
  title = {A {D}irichlet Process Mixture Model for the Analysis of Correlated
	Binary Responses},
  journal = {Computational Statistics and Data Analysis},
  year = {2007},
  volume = {51},
  pages = {5402--5415}
}

@INPROCEEDINGS{jefferies79,
  author = {R. P. S. Jefferies},
  title = {The origin of chordates --- a methodological essay},
  booktitle = {The {O}rigin of {M}ajor {I}nvertebrate {G}roups},
  year = {1979},
  editor = {M. R. House},
  pages = {443--477},
  publisher = {Academic Press}
}

@BOOK{jeffreys61,
  title = {Theory of {P}robability},
  publisher = {Oxford University Press},
  year = {1961},
  author = {H. Jeffreys},
  address = {Oxford}
}

@ARTICLE{jeffreys35,
  author = {H. Jeffreys},
  title = {Some tests of significance, treated by the theory of probability},
  journal = {Proceedings of the Cambridge Philosophy Society},
  year = {1935},
  volume = {31},
  pages = {203--222}
}

@ARTICLE{Jensen1995,
  author = {Jensen, C.S. and Kj{\ae}rulff, U. and Kong, A.},
  title = {Blocking {G}ibbs sampling in very large probabilistic expert systems},
  journal = {International Journal of Human Computer Studies},
  year = {1995},
  volume = {42},
  pages = {647--666},
  number = {6},
  publisher = {Citeseer}
}

@ARTICLE{jermann95,
  author = {T. M. Jermann and J. G. Opitz and J. Stackhouse and S. A. Benner
	},
  title = {Reconstructing the evolutionary history of the artiodactyl ribonuclease
	superfamily},
  journal = {Nature},
  year = {1995},
  volume = {374},
  pages = {108--110}
}

@ARTICLE{jin2007,
  author = {Jin, Changzhu and Ciochon, Russell L and Dong, Wei and Hunt, Robert
	M and Liu, Jinyi and Jaeger, Marc and Zhu, Qizhi},
  title = {The first skull of the earliest giant panda},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2007},
  volume = {104},
  pages = {10932--10937},
  number = {26}
}

@ARTICLE{jin91,
  author = {L. Jin and M. Nei},
  title = {Relative efficiencies of the maximum-parsimony and distance-matrix
	methods of phylogeny construction for restriction data},
  journal = MBE,
  year = {1991},
  volume = {8},
  pages = {356--365}
}

@ARTICLE{jin90,
  author = {L. Jin and M. Nei},
  title = {Limitations of the evolutionary parsimony method of phylogenetic
	analysis},
  journal = MBE,
  year = {1990},
  volume = {7},
  pages = {82--102}
}

@ARTICLE{jones92,
  author = {D. T. Jones and W. R. Taylor and J. M. Thornton},
  title = {The rapid generation of mutation data matrices from protein sequences},
  journal = {Computer Applications in the Biosciences (CABIOS)},
  year = {1992},
  volume = {8},
  pages = {275--282}
}

@ARTICLE{jones96,
  author = {D. T. Jones and J. M. Thornton},
  title = {Potential energy functions for threading},
  journal = {Curr. Opin. Struct. Biol.},
  year = {1996},
  volume = {6},
  pages = {210--216}
}

@ARTICLE{Jones2004,
  author = {Jones, G.L.},
  title = {On the {M}arkov chain central limit theorem},
  journal = {Probability surveys},
  year = {2004},
  volume = {1},
  pages = {299--320},
  issn = {1549-5787},
  publisher = {IMS and ISI/Bernoulli Society}
}

@ARTICLE{Jones2006,
  author = {Jones, G.L. and Haran, M. and Caffo, B.S. and Neath, R.},
  title = {Fixed-width output analysis for {M}arkov chain {M}onte {C}arlo},
  journal = {Journal of the American Statistical Association},
  year = {2006},
  volume = {101},
  pages = {1537--1547},
  number = {476},
  issn = {0162-1459},
  publisher = {ASA}
}

@ARTICLE{Jordan2004,
  author = {Jordan, M.I.},
  title = {Graphical Models},
  journal = {Statistical Science},
  year = {2004},
  volume = {19},
  pages = {140--155},
  number = {1},
  publisher = {JSTOR}
}

@ARTICLE{jordan04,
  author = {M. I. Jordan},
  title = {Graphical models},
  journal = {Statistical Science},
  year = {2004},
  volume = {19},
  pages = {140--155}
}

@BOOK{joset93,
  title = {Prokaryotic {G}enetics},
  publisher = {Blackwell Scientific Publications},
  year = {1993},
  author = {F. Joset and J. Guespin-Michel},
  address = {Oxford}
}

@ARTICLE{Jow2002,
  author = {Jow, H. and Hudelot, C. and Rattray, M. and Higgs, P. G.},
  title = {Bayesian Phylogenetics Using an {RNA} Substitution Model Applied
	to Early Mammalian Evolution},
  journal = MBE,
  year = {2002},
  volume = {19},
  pages = {1591-1601},
  number = {9},
  eprint = {http://mbe.oxfordjournals.org/cgi/reprint/19/9/1591.pdf},
  url = {http://mbe.oxfordjournals.org/cgi/content/abstract/19/9/1591}
}

@ARTICLE{Jukes1969,
  author = {Jukes, TH and Cantor, CR},
  title = {Evolution of protein molecules},
  journal = {Mammalian Protein Metabolism},
  year = {1969},
  volume = {3},
  pages = {21--132}
}

@INPROCEEDINGS{jukes69,
  author = {T. H. Jukes and C. R. Cantor},
  title = {Evolution of protein molecules},
  booktitle = {Mammalian {P}rotein {M}etabolism},
  year = {1969},
  editor = {H. N. Munro},
  pages = {21--123},
  address = {New York},
  publisher = {Academic Press}
}

@ARTICLE{kashyap74,
  author = {R. L. Kashyap and S. Subas},
  title = {Statistical estimation of parameters in a phylogenetic tree using
	a dynamic model of the substitutional process},
  journal = {Journal of Theoretical Biology},
  year = {1974},
  volume = {47},
  pages = {75-101}
}

@ARTICLE{kass95,
  author = {R. E. Kass and A. E. Raftery},
  title = {Bayes factors},
  journal = {Journal of the American Statistical Association},
  year = {1995},
  volume = {90},
  pages = {773--795}
}

@ARTICLE{kathirithamby98,
  author = {J. Kathirithamby},
  title = {Introductory remarks},
  journal = {International Journal of Insect Morphology and Embryology},
  year = {1998},
  volume = {27},
  pages = {1--2}
}

@ARTICLE{kathirithamby89,
  author = {J. Kathirithamby},
  title = {A review of the order {S}trepsiptera},
  journal = {Systematic Entomology},
  year = {1989},
  volume = {14},
  pages = {41--92}
}

@ARTICLE{kathirithamby78,
  author = {J. Kathirithamby},
  title = {The effects of stylopisation on the sexual development of {{\it Javesella
	dubia}} ({K}irschbaum) ({H}omoptera: {D}elphacidae)},
  journal = {Biological Journal of the Linnean Society},
  year = {1978},
  volume = {10},
  pages = {163--179}
}

@ARTICLE{katoh02,
  author = {K. Katoh and K. Misawa and K. Kuma and T. Miyata},
  title = {{MAFFT}: {A} novel method for rapid multiple sequence alignment based
	on fast {F}ourier transform},
  journal = {Nucleic Acids Research},
  year = {2002},
  volume = {30},
  pages = {3059--3066}
}

@ARTICLE{katoh2013,
  author = {Katoh, Kazutaka and Standley, Daron M},
  title = {{MAFFT} multiple sequence alignment software version 7: improvements
	in performance and usability},
  journal = MBE,
  year = {2013},
  volume = {30},
  pages = {772--780},
  number = {4}
}

@ARTICLE{kawahara09,
  author = {R. Kawahara and M. Miya and K. Mabuchi and T. J Near and N. Nishida},
  title = {Stickleback phylogenies resolved: {E}vidence from mitochondrial genomes
	and 11 nuclear genes},
  journal = MPE,
  year = {2009},
  volume = {50},
  pages = {401--404}
}

@ARTICLE{Keith2004,
  author = {Keith, J.M. and Kroese, D.P. and Bryant, D.},
  title = {A Generalized {M}arkov Sampler},
  journal = {Methodology and Computing in Applied Probability},
  year = {2004},
  volume = {6},
  pages = {29--53},
  number = {1},
  publisher = {Springer}
}

@ARTICLE{keller99,
  author = {M. P. Keller and B. A. Seifried and P. F. Chance},
  title = {Molecular evolution of the {CMT1A-REP} region: {A} human- and chimpanzee-specific
	repeat},
  journal = MBE,
  year = {1999},
  volume = {16},
  pages = {1019--1026}
}

@ARTICLE{kellis03,
  author = {M. Kellis and N. Patterson and M. Endrizzi and B. Birren and E. S.
	Lander},
  title = {Sequencing and comparison of yeast species to identify genes and
	regulatory elements},
  journal = {Nature},
  year = {2003},
  volume = {423},
  pages = {241--254}
}

@ARTICLE{Kendall1949,
  author = {Kendall, David G.},
  title = {Stochastic Processes and Population Growth},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  year = {1949},
  volume = {11},
  pages = {230--282},
  number = {2},
  url = {http://www.jstor.org/stable/2984078}
}

@ARTICLE{Kendall1948,
  author = {Kendall, David G.},
  title = {On the Generalized "Birth-and-Death" Process},
  journal = {The Annals of Mathematical Statistics},
  year = {1948},
  volume = {19},
  pages = {1--15},
  number = {1},
  url = {http://www.jstor.org/stable/2236051}
}

@ARTICLE{kendall48,
  author = {D. G. Kendall},
  title = {On the generalized ``birth-and-death'' process},
  journal = {Annals of Mathematical Statistics},
  year = {1948},
  volume = {19},
  pages = {1--15}
}

@ARTICLE{kidd71,
  author = {K. K. Kidd and L. A. Sgaramella-Zonta},
  title = {Phylogenetic analysis: {C}oncepts and methods},
  journal = {American Journal of Human Genetics},
  year = {1971},
  volume = {23},
  pages = {235--252}
}

@ARTICLE{kim98b,
  author = {J. Kim},
  title = {Large-scale phylogenies and measuring the performance of phylogenetic
	estimators},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {43--60}
}

@ARTICLE{kim08,
  author = {J. Kim and M. J. Sanderson},
  title = {Penalized likelihood phylogenetic inference: {B}ridging the parsimony-likelihood
	gap},
  journal = SYSB,
  year = {2008},
  volume = {57},
  pages = {665--674}
}

@ARTICLE{kimura81,
  author = {M. Kimura},
  title = {Estimation of evolutionary distances between homologous nucleotide
	sequences},
  journal = PNAS,
  year = {1981},
  volume = {78},
  pages = {454--458}
}

@ARTICLE{kimura80,
  author = {M. Kimura},
  title = {A simple method for estimating evolutionary rates of base substitutions
	through comparative studies of nucleotide sequences},
  journal = JME,
  year = {1980},
  volume = {16},
  pages = {111--120}
}

@INPROCEEDINGS{kingman82c,
  author = {J. F. C. Kingman},
  title = {On the genealogy of large populations},
  booktitle = {Essays in {S}tatistical {S}cience: {P}apers in {H}onour of {P. A.
	P. M}oran, Journal of Applied Probability, Special Volume 19A},
  year = {1982},
  editor = {J. Gani and E. J. Hannan},
  pages = {27--43},
  publisher = {Applied Probability Trust}
}

@INPROCEEDINGS{kingman82b,
  author = {J. F. C. Kingman},
  title = {Exchangeability and the evolution of large populations},
  booktitle = {Exchangeability in {P}robability and {S}tatistics},
  year = {1982},
  editor = {G. Koch and F. Spizzichino},
  pages = {97--112},
  publisher = {North-Holland}
}

@ARTICLE{Kingman1982,
  author = {Kingman, J. F. C.},
  title = {On the Genealogy of Large Populations},
  journal = {Journal of Applied Probability},
  year = {1982},
  volume = {19},
  pages = {27--43},
  url = {http://www.jstor.org/stable/3213548}
}

@ARTICLE{kingman82a,
  author = {J. F. C. Kingman},
  title = {The coalescent},
  journal = {Stochastic Processes and their Applications},
  year = {1982},
  volume = {13},
  pages = {235--248}
}

@ARTICLE{kinzelbach71,
  author = {R. K. Kinzelbach},
  title = {Morphologische Befunde an F{\"a}cherfl{\"u}glern und ihre phylogenetische
	bedeutung ({I}nsecta: {S}trepsiptera)},
  journal = {Zoologica},
  year = {1971},
  volume = {119},
  pages = {1--256}
}

@ARTICLE{kirkpatrick93,
  author = {M. Kirkpatrick and M. Slatkin},
  title = {Searching for evolutionary patterns in the shape of a phylogenetic
	tree},
  journal = {Evolution},
  year = {1993},
  volume = {47},
  pages = {1171--1181}
}

@ARTICLE{kishino90b,
  author = {H. Kishino and M. Hasegawa},
  title = {Converting distance to time: {A}pplication to human evolution},
  journal = {Methods in Enzymology},
  year = {1990},
  volume = {183},
  pages = {550--570}
}

@ARTICLE{kishino90,
  author = {H. Kishino and T. Miyata and M. Hasegawa},
  title = {Maximum likelihood inference of protein phylogeny and the origin
	of chloroplasts},
  journal = JME,
  year = {1990},
  volume = {31},
  pages = {151--160}
}

@ARTICLE{kishino01,
  author = {H. Kishino and J. L. Thorne and W. Bruno},
  title = {Performance of a divergence time estimation method under a probabilistic
	model of rate evolution},
  journal = MBE,
  year = {2001},
  volume = {18},
  pages = {352--361}
}

@ARTICLE{Kloek1978,
  author = {Kloek, T. and van Dijk, H.K.},
  title = {Bayesian Estimates of Equation System Parameters: An Application
	of Integration by {M}onte {C}arlo},
  journal = {Econometrica},
  year = {1978},
  volume = {46},
  pages = {1--19},
  number = {1}
}

@ARTICLE{klosterman06,
  author = {P. S. Klosterman and A. V. Uzilov and Y. R. Bendana and R. K. Bradley
	and S. Chao and C. Kosiol and N. Goldman and I. Holmes},
  title = {{XRate}: {A} fast prototyping, training and annotation tool for phylo-grammars},
  journal = BMCBI,
  year = {2006},
  volume = {7},
  number = {428}
}

@ARTICLE{kluge98,
  author = {A. G. Kluge},
  title = {Total evidence or taxonomic congruence: {C}ladistics or consensus
	classification},
  journal = {Cladistics},
  year = {1998},
  volume = {14},
  pages = {151--158}
}

@ARTICLE{kluge97a,
  author = {A. G. Kluge},
  title = {Testability and the refutation and corroboration of cladistic hypotheses},
  journal = {Cladistics},
  year = {1997},
  volume = {13},
  pages = {81--96}
}

@ARTICLE{kluge89,
  author = {A. G. Kluge},
  title = {A concern for evidence and a phylogenetic hypothesis of relationships
	among {E}picarates ({B}oidae, {S}erpentes)},
  journal = SZ,
  year = {1989},
  volume = {14},
  pages = {151--158}
}

@ARTICLE{kluge69,
  author = {A. G. Kluge and J. S. Farris},
  title = {Quantitative phyletics and the evolution of anurans},
  journal = SZ,
  year = {1969},
  volume = {18},
  pages = {1--32}
}

@ARTICLE{kluge93,
  author = {A. G. Kluge and A. J. Wolf},
  title = {Cladistics: {W}hat's in a word?},
  journal = {Cladistics},
  year = {1993},
  volume = {9},
  pages = {183--199}
}

@ARTICLE{knudsen03,
  author = {B. Knudsen and M. Miyamoto},
  title = {Sequence Alignments and Pair Hidden {M}arkov Models Using Evolutionary
	History},
  journal = JME,
  year = {2003},
  volume = {333},
  pages = {453--460},
  number = {2}
}

@ARTICLE{kodandaramaiah10,
  author = {U. Kodandaramaiah},
  title = {Tectonic calibrations in molecular dating},
  journal = {Current Zoology},
  year = {2010},
  volume = {57},
  pages = {116--124},
  number = {1}
}

@BOOK{Koller2009,
  title = {Probabilistic Graphical Models: Principles and Techniques},
  publisher = {The MIT Press},
  year = {2009},
  author = {Koller, D. and Friedman, N.},
  address = {Cambridge, MA USA}
}

@BOOK{kolmogorov33,
  title = {Grundbegriffe der {W}ahrscheinlichkeitsrechnung},
  publisher = {Springer-Verlag},
  year = {1933},
  author = {A. N. Kolmogorov},
  address = {Berlin}
}

@ARTICLE{konings87,
  author = {D. A. Konings and P. Hogeweg and B. Hesper},
  title = {Evolution of the primary and secondary structures of {E1a} m{RNA}s
	of the adenovirus},
  journal = MBE,
  year = {1987},
  volume = {4},
  pages = {300--314}
}

@ARTICLE{kosiol07,
  author = {Carolin Kosiol and Ian Holmes and Nick Goldman},
  title = {An empirical codon model for protein sequence evolution},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {1464--1479}
}

@ARTICLE{krause2008,
  author = {Krause, Johannes and Unger, Tina and No{\c{c}}on, Aline and Malaspinas,
	Anna-Sapfo and Kolokotronis, Sergios-Orestis and Stiller, Mathias
	and Soibelzon, Leopoldo and Spriggs, Helen and Dear, Paul H and Briggs,
	Adrian W and others},
  title = {Mitochondrial genomes reveal an explosive radiation of extinct and
	extant bears near the {M}iocene-{P}liocene boundary},
  journal = {BMC Evolutionary Biology},
  year = {2008},
  volume = {8},
  pages = {220},
  number = {1},
  publisher = {BioMed Central Ltd}
}

@INPROCEEDINGS{kraut90,
  author = {R. E. Kraut and C. Egido and J. Galegher},
  title = {Patterns of contact and communication in scientific research collaboration},
  booktitle = {Intellectual {T}eamwork},
  year = {1990},
  editor = {R. E. Kraut and C. Egido},
  publisher = {Earlbaum, Hillsdale}
}

@ARTICLE{krogh97,
  author = {A. Krogh},
  title = {Two methods for improving performance of a {HMM} and their application
	for gene finding},
  journal = {Proc. Int. Conf. Intell. Syst. Mol. Biol.},
  year = {1997},
  volume = {5},
  pages = {179--186}
}

@ARTICLE{kruspe07,
  author = {M. Kruspe and P. F. Stadler},
  title = {{P}rogressive multiple sequence alignments from triplets},
  journal = BMCBI,
  year = {2007},
  volume = {8},
  pages = {254}
}

@ARTICLE{Kschischang2001,
  author = {Kschischang, F.R. and Frey, B.J. and Loeliger, H.-A.},
  title = {Factor graphs and the sum-product algorithm},
  journal = {Information Theory, IEEE Transactions on},
  year = {2001},
  volume = {47},
  pages = {498 -519},
  number = {2}
}

@ARTICLE{ksepka2010,
  author = {Ksepka, Daniel T and Clarke, Julia A},
  title = {The basal penguin ({A}ves: {S}phenisciformes) \textit{{P}erudyptes
	devriesi} and a phylogenetic evaluation of the penguin fossil record},
  journal = {Bulletin of the American Museum of Natural History},
  year = {2010},
  volume = {337},
  pages = {1--77},
  number = {1},
  publisher = {BioOne}
}

@ARTICLE{ksepka2012,
  author = {Ksepka, Daniel T and Fordyce, R Ewan and Ando, Tatsuro and Jones,
	Craig M},
  title = {New fossil penguins ({A}ves, {S}phenisciformes) from the {O}ligocene
	of {N}ew {Z}ealand reveal the skeletal plan of stem penguins},
  journal = {Journal of Vertebrate Paleontology},
  year = {2012},
  volume = {32},
  pages = {235--254},
  number = {2}
}

@ARTICLE{Kuhner1994,
  author = {Kuhner, M.K. and Felsenstein, J.},
  title = {A simulation comparison of phylogeny algorithms under equal and unequal
	evolutionary rates},
  journal = MBE,
  year = {1994},
  volume = {11},
  pages = {459--468},
  number = {3}
}

@ARTICLE{kuhner94,
  author = {M. Kuhner and J. Felsenstein},
  title = {A simulation comparison of phylogeny algorithms under equal and unequal
	evolutionary rates},
  journal = MBE,
  year = {1994},
  volume = {11},
  pages = {459--468}
}

@ARTICLE{kuhner95,
  author = {M. Kuhner and J. Yamato and J. Felsenstein},
  title = {Estimating effective population size and mutation rate from sequence
	data using {M}etropolis-{H}astings sampling},
  journal = {Genetics},
  year = {1995},
  volume = {140},
  pages = {1421--1430}
}

@ARTICLE{Kuhner2006,
  author = {Kuhner, Mary K.},
  title = {{LAMARC} 2.0: maximum likelihood and {B}ayesian estimation of population
	parameters},
  journal = BI,
  year = {2006},
  volume = {22},
  pages = {768-770},
  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/6/768}
}

@ARTICLE{Kuhner2007,
  author = {Kuhner, Mary K. and Smith, Lucian P.},
  title = {Comparing Likelihood and {B}ayesian Coalescent Estimation of Population
	Parameters},
  journal = {Genetics},
  year = {2007},
  volume = {175},
  pages = {155-165},
  number = {1},
  url = {http://www.genetics.org/cgi/content/abstract/175/1/155}
}

@ARTICLE{kullback51,
  author = {S. Kullback and R. A. Leibler},
  title = {On information and sufficiency},
  journal = {Annals of Mathematical Statistics},
  year = {1951},
  volume = {22},
  pages = {79--86}
}

@ARTICLE{Kuo1998,
  author = {Kuo, Lynn and Mallick, Bani},
  title = {Variable Selection for Regression Models},
  journal = {Sankhy\={a}: The Indian Journal of Statistics, Series B (1960-2002)},
  year = {1998},
  volume = {60},
  pages = {65--81},
  number = {1},
  publisher = {Springer on behalf of the Indian Statistical Institute}
}

@ARTICLE{lake91,
  author = {J. A. Lake},
  title = {The order of sequence alignment can bias the selection of tree topology},
  journal = MBE,
  year = {1991},
  volume = {8},
  pages = {378--385}
}

@ARTICLE{lakner08,
  author = {C. Lakner and P. van der Mark and J. P. Huelsenbeck and B. Larget
	and F. Ronquist},
  title = {Efficiency of {MCMC} proposals in {B}ayesian phylogenetics},
  journal = SYSB,
  year = {2008},
  pages = {86--103}
}

@ARTICLE{Lakner2008,
  author = {Lakner, Clemens and van der Mark, Paul and Huelsenbeck, John P. and
	Larget, Bret and Ronquist, Frederik},
  title = {Efficiency of {M}arkov Chain {M}onte {C}arlo Tree Proposals in {B}ayesian
	Phylogenetics},
  journal = SYSB,
  year = {2008},
  volume = {57},
  pages = {86--103},
  number = {1},
  publisher = {Taylor \& Francis}
}

@ARTICLE{lamping95,
  author = {J. Lamping and R. Rao and P. Pirolli},
  title = {A focus+context technique based on hyperbolic geometry for visualizing
	large hierarchies},
  journal = {Proceedings of Human Factors in Computing Systems},
  year = {1995},
  pages = {401--408}
}

@ARTICLE{lanave84,
  author = {C. Lanave and G. Preparata and C. Saccone and G. Serio},
  title = {A new method for calculating evolutionary substitution rates},
  journal = JME,
  year = {1984},
  volume = {20},
  pages = {86--93}
}

@ARTICLE{landis2013,
  author = {Landis, Michael J and Matzke, Nicholas J and Moore, Brian R and Huelsenbeck,
	John P},
  title = {Bayesian analysis of biogeography when the number of areas is large},
  journal = {Systematic biology},
  year = {2013},
  pages = {789--804},
  publisher = {Oxford University Press}
}

@ARTICLE{lanfear2010,
  author = {Lanfear, Robert and Welch, John J and Bromham, Lindell},
  title = {Watching the clock: studying variation in rates of molecular evolution
	between species},
  journal = {Trends in Ecology \& Evolution},
  year = {2010},
  volume = {25},
  pages = {495--503},
  number = {9}
}

@BOOK{laplace12,
  title = {Th{\'e}orie {A}nalytique des {P}robabilit{\'e}s},
  publisher = {Unknown Publisher},
  year = {1812},
  author = {P. S. Laplace},
  address = {Paris}
}

@ARTICLE{laplace74,
  author = {P. S. Laplace},
  title = {M{\'e}moire sur la probabilit{\'e} des causes le {\'ev\`e}nemens},
  journal = {M{\'e}moires de l'Acad{\'e}mie Royale des Sciences Present{\'e}s
	par Divers Savans},
  year = {1774},
  volume = {6},
  pages = {621--656}
}

@ARTICLE{Larget1999,
  author = {Larget, B and Simon, DL},
  title = {Markov Chain {M}onte {C}arlo Algorithms for the {B}ayesian Analysis
	of Phylogenetic Trees},
  journal = MBE,
  year = {1999},
  volume = {16},
  pages = {750-759},
  number = {6},
  eprint = {http://mbe.oxfordjournals.org/cgi/reprint/16/6/750.pdf},
  url = {http://mbe.oxfordjournals.org}
}

@ARTICLE{larget98,
  author = {B. Larget and D. Simon},
  title = {Faster likelihood calculations on trees},
  journal = {Technical Report 98-02, Department of Mathematics and Computer Science,
	Duquesne University, Pittsburgh, Pennsylvania},
  year = {1998}
}

@ARTICLE{larget99,
  author = {B. Larget and D. L. Simon},
  title = {Markov chain {M}onte {C}arlo algorithms for the {B}ayesian analysis
	of phylogenetic trees},
  journal = MBE,
  year = {1999},
  volume = {16},
  pages = {750--759}
}

@ARTICLE{larget05,
  author = {B. Larget and D. L. Simon and J. B. Kadane},
  title = {A {B}ayesian analysis of metazoan mitochondrial genome arrangements},
  journal = MBE,
  year = {2005},
  volume = {22},
  pages = {486--495}
}

@ARTICLE{larsen93,
  author = {N. Larsen and C. Zwieb},
  title = {The signal recognition particle database (SRPDB)},
  journal = {Nucleic Acids Research},
  year = {1993},
  volume = {21},
  pages = {3019--3020}
}

@ARTICLE{larsson2007,
  author = {Larsson, Hans CE and Sues, Hans-Dieter},
  title = {Cranial osteology and phylogenetic relationships of \textit{{H}amadasuchus
	rebouli} ({C}rocodyliformes: {M}esoeucrocodylia) from the {C}retaceous
	of {M}orocco},
  journal = {Zoological Journal of the Linnean Society},
  year = {2007},
  volume = {149},
  pages = {533--567},
  number = {4},
  publisher = {Wiley Online Library}
}

@ARTICLE{lartillot2013,
  author = {Lartillot, Nicolas},
  title = {Interaction between Selection and Biased Gene Conversion in Mammalian
	Protein-Coding Sequence Evolution Revealed by a Phylogenetic Covariance
	Analysis},
  journal = MBE,
  year = {2013},
  volume = {30},
  pages = {356--368},
  number = {2},
  publisher = {SMBE}
}

@ARTICLE{Lartillot2006,
  author = {Lartillot, N.},
  title = {Conjugate {G}ibbs Sampling for {B}ayesian Phylogenetic Models},
  journal = {Journal of Computational Biology},
  year = {2006},
  volume = {13},
  pages = {1701--1722},
  number = {10},
  publisher = {Mary Ann Liebert, Inc. 2 Madison Avenue Larchmont, NY 10538 USA}
}

@ARTICLE{lartillot2012,
  author = {Lartillot, Nicolas and Delsuc, Fr{\'e}d{\'e}ric},
  title = {Joint reconstruction of divergence times and life-history evolution
	in placental mammals using a phylogenetic covariance model},
  journal = {Evolution},
  year = {2012},
  volume = {66},
  pages = {1773--1787},
  number = {6},
  publisher = {Wiley Online Library}
}

@ARTICLE{Lartillot2009,
  author = {Lartillot, N. and Lepage, T. and Blanquart, S.},
  title = {PhyloBayes 3: a {B}ayesian software package for phylogenetic reconstruction
	and molecular dating},
  journal = BI,
  year = {2009},
  volume = {25},
  pages = {2286},
  number = {17},
  publisher = {Oxford Univ Press}
}

@ARTICLE{lartillot06,
  author = {N. Lartillot and H. Philippe},
  title = {Computing {B}ayes factors using Theromodynamic integration},
  journal = SYSB,
  year = {2006},
  volume = {55},
  pages = {195--207}
}

@ARTICLE{lartillot04,
  author = {N. Lartillot and H. Philippe},
  title = {A {B}ayesian mixture model for across-site heterogeneities in the
	amino-acid replacement process},
  journal = MBE,
  year = {2004},
  volume = {21},
  pages = {1095--1109}
}

@ARTICLE{lartillot2011,
  author = {Lartillot, Nicolas and Poujol, Rapha{\"e}l},
  title = {A phylogenetic model for investigating correlated evolution of substitution
	rates and continuous phenotypic characters},
  journal = MBE,
  year = {2011},
  volume = {28},
  pages = {729--744},
  number = {1}
}

@BOOK{Lauritzen1996,
  title = {Graphical Models},
  publisher = {Oxford University Press, USA},
  year = {1996},
  author = {Lauritzen, S.L.}
}

@BOOK{lauritzen96,
  title = {Graphical Models},
  publisher = {Clarendon Press},
  year = {1996},
  author = {S. L. Lauritzen},
  address = {Oxford}
}

@ARTICLE{lavine99,
  author = {M. Lavine and M. J. Schervish},
  title = {Bayes factors: {W}hat they are and what they are not},
  journal = {American Statistician},
  year = {1999},
  volume = {53},
  pages = {119--122}
}

@ARTICLE{lawrence99,
  author = {J. Lawrence},
  title = {Gene transfer, speciation and the evolution of bacterial genomes},
  journal = {Current Opinions in Microbiology},
  year = {1999},
  volume = {2},
  pages = {519--523}
}

@ARTICLE{lawrence97,
  author = {J. Lawrence and H. Ochman},
  title = {Amelioration of bacterial genomes: {R}ates of change and exchange},
  journal = JME,
  year = {1997},
  volume = {44},
  pages = {383--397}
}

@ARTICLE{lecointre93,
  author = {G. Lecointre and H. Philippe and H. L. Van Le and H. Le Guyader},
  title = {Species sampling has a major impact on phylogenetic inference},
  journal = MPE,
  year = {1993},
  volume = {2},
  pages = {205--224}
}

@ARTICLE{lee09,
  author = {M. S. Y. Lee and P. M. Oliver and M. N. Hutchinson},
  title = {Phylogenetic uncertainty and molecular clock calibrations: {A} case
	study of legless lizards ({P}ygopodidae, {G}ekkota)},
  journal = MPE,
  year = {2009},
  volume = {50},
  pages = {661--666}
}

@ARTICLE{leitner97,
  author = {T. Leitner and S. Kumar and J. Albert},
  title = {Tempo and mode of nucleotide substitutions in {\it gag} and {\it
	env} gene fragments in human immunodeficiency virus type 1 populations
	with a known transmission history},
  journal = {Journal of Virology},
  year = {1997},
  volume = {71},
  pages = {4761--4770}
}

@ARTICLE{lemey09,
  author = {P. Lemey and A. Rambaut and A. J. Drummond and M. A. Suchard},
  title = {Bayesian Phylogeography Finds Its Roots},
  journal = {PLoS Computational Biology},
  year = {2009},
  volume = {5},
  pages = {e1000520}
}

@ARTICLE{Lemmon2009,
  author = {Lemmon, Alan R. and Brown, Jeremy M. and Stanger-Hall, Kathrin and
	Lemmon, Emily Moriarty},
  title = {The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by
	Maximum Likelihood and {B}ayesian Inference},
  journal = SYSB,
  year = {2009},
  volume = {58},
  pages = {130-145},
  number = {1}
}

@ARTICLE{lemmon04,
  author = {A. R. Lemmon and E. C. Moriarty},
  title = {The importance of proper model assumption in {B}ayesian phylogenetics},
  journal = SYSB,
  year = {2004},
  volume = {53},
  pages = {265--277}
}

@ARTICLE{lepage07,
  author = {T. Lepage and D. Bryant and H. Philippe and N. Lartillot},
  title = {A general comparison of relaxed molecular clock models},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {2669--2680}
}

@ARTICLE{lepage06,
  author = {T. Lepage and S. Lawi and P. Tupper and D. Bryant},
  title = {Continuous and tractable models for the variation of evolutionary
	rates},
  journal = {Mathematical Biosciences},
  year = {2006},
  volume = {199},
  pages = {216--233}
}

@ARTICLE{Lewis2005,
  author = {Lewis, P.O. and Holder, M.T. and Holsinger, K.E.},
  title = {Polytomies and {B}ayesian Phylogenetic Inference},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {241--253},
  number = {2}
}

@ARTICLE{lewis01,
  author = {P. O. Lewis},
  title = {A likelihood approach to estimating phylogeny from discrete morphological
	character data},
  journal = SYSB,
  year = {2001},
  volume = {50},
  pages = {913--925}
}

@ARTICLE{lewis98,
  author = {P. O. Lewis},
  title = {A genetic algorithm for maximum-likelihood phylogeny inference using
	nucleotide sequence data},
  journal = MBE,
  year = {1998},
  volume = {15},
  pages = {277--283}
}

@PHDTHESIS{li96,
  author = {S. Li},
  title = {Phylogenetic tree construction using {M}arkov chain {M}onte {C}arlo},
  school = {Ohio State University},
  year = {1996}
}

@ARTICLE{li00,
  author = {S. Li and H. Doss and D. Pearl},
  title = {Phylogenetic tree reconstruction using {M}arkov chain {M}onte {C}arlo},
  journal = {Journal of the American Statistical Society},
  year = {2000},
  volume = {95},
  pages = {493--508}
}

@ARTICLE{Li2000a,
  author = {Li, Shuying and Pearl, Dennis K. and Doss, Hani},
  title = {Phylogenetic Tree Construction Using {M}arkov Chain {M}onte {C}arlo},
  journal = {Journal of the American Statistical Association},
  year = {2000},
  volume = {95},
  pages = {493--508},
  number = {450},
  publisher = {American Statistical Association},
  url = {http://www.jstor.org/stable/2669394}
}

@ARTICLE{li93,
  author = {W. -H. Li},
  title = {Unbiased estimation of the rates of synonymous and nonsynonymous
	substitution},
  journal = JME,
  year = {1993},
  volume = {36},
  pages = {96--99}
}

@ARTICLE{li90,
  author = {W. H. Li and M. Gouy and P. M. Sharp and C. O'Huigin and Y.-W. Yang},
  title = {Molecular phylogeny of rodentia, lagomorpha, primates, artiodactyla,
	and carnivora and molecular clocks},
  journal = PNAS,
  year = {1990},
  volume = {87},
  pages = {6703--6707}
}

@ARTICLE{li85,
  author = {W. -H. Li and C. -I Wu and C. -C Luo},
  title = {A new method for estimating synonymous and nonsynonymous rates of
	nucleotide substitution considering the relative likelihood of nucleotide
	and codon changes},
  journal = MBE,
  year = {1985},
  volume = {2},
  pages = {150--174}
}

@ARTICLE{li12,
  author = {W. L. S. Li and A. J. Drummond},
  title = {Model averaging and {B}ayes factor calculation of relaxed molecular
	clocks in {B}ayesian phylogenetics},
  journal = MBE,
  year = {2012},
  volume = {29},
  pages = {751--761}
}

@BOOK{linnaeus58,
  title = {Systema naturae. {R}egnum animale},
  publisher = {British Museum},
  year = {1758},
  author = {C. Linnaeus},
  address = {London}
}

@ARTICLE{Liow2010,
  author = {Liow, L.H. and Quental, T.B. and Marshall, C.R.},
  title = {When Can Decreasing Diversification Rates Be Detected with Molecular
	Phylogenies and the Fossil Record?},
  journal = SYSB,
  year = {2010},
  volume = {59},
  pages = {646},
  number = {6},
  publisher = {Oxford University Press}
}

@BOOK{Liu2001,
  title = {Monte {C}arlo Strategies in Scientific Computing},
  publisher = {Springer},
  year = {2001},
  author = {Liu, J.S.}
}

@ARTICLE{Liu1996a,
  author = {Liu, J.S.},
  title = {Metropolized independent sampling with comparisons to rejection sampling
	and importance sampling},
  journal = {Statistics and Computing},
  year = {1996},
  volume = {6},
  pages = {113--119},
  number = {2},
  publisher = {Springer}
}

@ARTICLE{Liu1994,
  author = {Liu, J.S.},
  title = {The Collapsed {G}ibbs Sampler in {B}ayesian Computations With Applications
	to a Gene Regulation Problem},
  journal = {Journal of the American Statistical Association},
  year = {1994},
  volume = {89},
  pages = {958--966},
  number = {427},
  publisher = {American Statistical Association}
}

@BOOK{liu01,
  title = {Monte {C}arlo strategies in scientific computing},
  publisher = {Springer},
  year = {2001},
  author = {J. S. Liu},
  address = {New York}
}

@ARTICLE{Liu1996,
  author = {Liu, Jun S.},
  title = {Peskun's theorem and a modified discrete-state {G}ibbs sampler},
  journal = {Biometrika},
  year = {1996},
  volume = {83},
  pages = {681-682},
  number = {3},
  doi = {10.1093/biomet/83.3.681},
  eprint = {http://biomet.oxfordjournals.org/cgi/reprint/83/3/681.pdf},
  url = {http://biomet.oxfordjournals.org/cgi/content/abstract/83/3/681}
}

@ARTICLE{liu96,
  author = {J. S. Liu},
  title = {Nonparametric hierarchical {B}ayes via sequential imputations},
  journal = {Annals of Statistics},
  year = {1996},
  volume = {3},
  pages = {911--930}
}

@ARTICLE{Liu2007,
  author = {Liang Liu and Dennis K Pearl},
  title = {Species Trees from Gene Trees: Reconstructing {B}ayesian Posterior
	Distributions of a Species Phylogeny Using Estimated Gene Tree Distributions},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {504--514},
  number = {3}
}

@ARTICLE{lloyd12,
  author = {G. T. Lloyd and J. R. Young and A. B. Smith},
  title = {Taxonomic structure of the fossil record is shaped by sampling bias},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {80--89}
}

@ARTICLE{lockhart96,
  author = {P. J. Lockhart and A. W. D. Larkum and M. A. Steel and P. J. Waddell
	and D. Penny},
  title = {Evolution of chlorophyll and bacteriochlorophyll: {T}he problem of
	invariant sites in sequence analysis},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {1930--1934}
}

@ARTICLE{loreille2001,
  author = {Loreille, Odile and Orlando, Ludovic and Patou-Mathis, Maryl{\`e}ne
	and Philippe, Michel and Taberlet, Pierre and H{\"a}nni, Catherine},
  title = {Ancient {DNA} analysis reveals divergence of the cave bear, \textit{{U}rsus
	spelaeus}, and brown bear, \textit{{U}rsus arctos}, lineages},
  journal = {Current Biology},
  year = {2001},
  volume = {11},
  pages = {200--203},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{losos98,
  author = {J. B. Losos and T. R. Jackman and A. Larson and D. de Queiroz and
	L. Rodr\'iguez-Schettino},
  title = {Contingency and determinism in replicated adaptive radiations of
	island lizards},
  journal = {Science},
  year = {1998},
  volume = {279},
  pages = {2115--2118}
}

@ARTICLE{lukoschek12,
  author = {V. Lukoschek and J. S. Keogh and J. C. Avise},
  title = {Evaluating fossil calibrations for dating phylogenies in light of
	rates of molecular evolution: {A} comparison of three approaches},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {22--43}
}

@ARTICLE{Lunn2009,
  author = {Lunn, David and Spiegelhalter, David and Thomas, Andrew and Best,
	Nicky},
  title = {The {BUGS} project: Evolution, critique and future directions},
  journal = {Statistics in Medicine},
  year = {2009},
  volume = {28},
  pages = {3049--3067},
  number = {25}
}

@ARTICLE{lunn00,
  author = {D. J. Lunn and A. Thomas and N. Best and D. Spiegelhalter},
  title = {Win{BUGS} --- a {B}ayesian modelling framework: {C}oncepts, structure,
	and extensibility},
  journal = {Statistics and Computing},
  year = {2000},
  volume = {10},
  pages = {325--337}
}

@ARTICLE{lunter07,
  author = {G. A. Lunter},
  title = {{{H}{M}{M}o{C}--a compiler for hidden {M}arkov models}},
  journal = BI,
  year = {2007},
  volume = {23},
  pages = {2485--2487},
  number = {18},
  month = {Sep}
}

@INCOLLECTION{lunter04,
  author = {G. A. Lunter and A. J. Drummond and I. Mikl\'{o}s and J. Hein},
  title = {Statistical Alignment: {R}ecent Progress, New Applications, and Challenges},
  booktitle = {Statistical methods in Molecular Evolution},
  publisher = {Springer Verlag},
  year = {2004},
  editor = {R. Nielsen},
  series = {Series in Statistics in Health and Medicine}
}

@ARTICLE{Lunter2005,
  author = {Lunter, G. and Miklos, I. and Drummond, A. and Jensen, J.L. and Hein,
	J.},
  title = {Bayesian coestimation of phylogeny and sequence alignment},
  journal = {BMC Bioinformatics},
  year = {2005},
  volume = {6},
  pages = {83},
  number = {1},
  publisher = {BioMed Central}
}

@ARTICLE{luo07,
  author = {R. Luo and A. L. Hipp and B. Larget},
  title = {A {B}ayesian model of {AFLP} marker evolution and phylogenetic inference},
  journal = {Statistical Applications in Genetics and Molecular Biology},
  year = {2007},
  volume = {6},
  pages = {1}
}

@ARTICLE{luo09,
  author = {R. Luo and B. Larget},
  title = {Modeling substitution and indel processes for {AFLP} marker evolution
	and phylogenetic inference},
  journal = {The Annals of Applied Statistics},
  year = {2009},
  volume = {1},
  pages = {222--248}
}

@ARTICLE{lutzoni00,
  author = {F. Lutzoni and P. Wagner and V. Reeb and S. Zoller},
  title = {Integrating ambiguously aligned regions of {DNA} sequences in phylogenetic
	analysis without violating positional homology},
  journal = SYSB,
  year = {2000},
  volume = {49},
  pages = {628--651}
}

@TECHREPORT{Muller1992,
  author = {Peter M{\"u}ller},
  title = {Alternatives to the {G}ibbs sampling scheme},
  institution = {Tech. report, Institute of Statistics and Decision Sciences, Duke
	University},
  year = {1992}
}

@ARTICLE{muller2004,
  author = {M\"{u}ller, Peter and Quintana, Fernando A.},
  title = {Nonparametric {B}ayesian Data Analysis},
  journal = {Statistical Science},
  year = {2004},
  volume = {19},
  pages = {pp. 95-110},
  number = {1},
  language = {English},
  publisher = {Institute of Mathematical Statistics}
}

@ARTICLE{maddison91,
  author = {D. R. Maddison},
  title = {The discovery and importance of multiple islands of most-parsimonious
	trees},
  journal = SZ,
  year = {1991},
  volume = {40},
  pages = {315--328}
}

@ARTICLE{maddison92,
  author = {D. R. Maddison and M. Ruvolo and D. L. Swofford},
  title = {Geographic origins of human mitochondrial {DNA} phylogenetic inference
	from control region sequences},
  journal = SYSB,
  year = {1992},
  volume = {41},
  pages = {111--124}
}

@ARTICLE{Maddison2007,
  author = {Maddison, W.P. and Midford, P.E. and Otto, S.P.},
  title = {Estimating a binary character's effect on speciation and extinction},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {701},
  number = {5},
  issn = {1063-5157}
}

@ARTICLE{maddison97,
  author = {W. P. Maddison},
  title = {Gene trees in species trees},
  journal = SYSB,
  year = {1997},
  volume = {46},
  pages = {523--536}
}

@ARTICLE{maddison89,
  author = {W. P. Maddison},
  title = {Reconstructing character evolution on polytomous cladograms},
  journal = {Cladistics},
  year = {1989},
  volume = {5},
  pages = {365--377}
}

@ARTICLE{maddison06b,
  author = {W. P. Maddison and L. L. Knowles},
  title = {Inferring phylogeny despite incomplete lineage sorting},
  journal = SYSB,
  year = {2006},
  volume = {55},
  pages = {21--30}
}

@ARTICLE{maddison06,
  author = {W. P. Maddison and D. R. Maddison},
  title = {Mesquite: {A} modular system for evolutionary analysis, {V}ersion
	1.12},
  year = {2006},
  url = {http://mesquiteproject.org}
}

@ARTICLE{maeta98,
  author = {Y. Maeta and K. Takahashi and N. Shimada},
  title = {Host body size as a factor determining the egg complement of {S}trepsiptera,
	an insect parasite},
  journal = {International Journal of Insect Morphology and Embryology},
  year = {1998},
  volume = {27},
  pages = {27--37}
}

@ARTICLE{magallon09,
  author = {S. Magall\'on},
  title = {Using Fossils to Break Long Branches in Molecular Dating: {A} Comparison
	of Relaxed Clocks Applied to the Origin of Angiosperms},
  journal = SYSB,
  year = {2009},
  volume = {59},
  pages = {384--399}
}

@ARTICLE{maguire52,
  author = {B. A. Maguire and E. S. Pearson and A. H. A. Wynn},
  title = {The time intervals between industrial accidents},
  journal = {Biometrika},
  year = {1952},
  volume = {39},
  pages = {168--180}
}

@BOOK{malecot48,
  title = {Les {M}ath\'ematiques Dt {H}\'er\'edit\'e},
  publisher = {Masson et Cie},
  year = {1948},
  author = {G. Mal\'ecot},
  address = {Paris}
}

@ARTICLE{marshall08,
  author = {C. R. Marshall},
  title = {A simple method for bracketing absolute divergence times on molecular
	phylogenies using multiple fossil calibration points},
  journal = {The American Naturalist},
  year = {2008},
  volume = {171},
  pages = {726--742}
}

@ARTICLE{marshall1997,
  author = {Marshall, Charles R},
  title = {Confidence intervals on stratigraphic ranges with nonrandom distributions
	of fossil horizons},
  journal = {Paleobiology},
  year = {1997},
  volume = {23},
  number = {2}
}

@ARTICLE{marshall1994,
  author = {Marshall, Charles R},
  title = {Confidence intervals on stratigraphic ranges: {P}artial relaxation
	of the assumption of randomly distributed fossil horizons},
  journal = {Paleobiology},
  year = {1994},
  pages = {459--469}
}

@ARTICLE{marshall90,
  author = {C. R. Marshall},
  title = {Confidence intervals on stratigraphic ranges},
  journal = {Paleobiology},
  year = {1990},
  volume = {16},
  pages = {1--10}
}

@ARTICLE{marshall06,
  author = {D. C. Marshall and C. Simon and T. R. Buckley},
  title = {Accurate branch length estimation in partitioned {B}ayesian analyses
	requires accommodation of among-partition rate variation and attention
	to branch length priors},
  journal = SYSB,
  year = {2006},
  volume = {55},
  pages = {993--1003}
}

@ARTICLE{mathews99,
  author = {D. H. Mathews and J. Sabina and M. Zuker and D. H. Turner},
  title = {Expanded sequence dependence of thermodynamic parameters improves
	prediction of {RNA} secondary structure},
  journal = JMB,
  year = {1999},
  volume = {288},
  pages = {911--940}
}

@ARTICLE{mathews06,
  author = {D. H. Mathews and D. H. Turner},
  title = {Prediction of {RNA} secondary structure by free energy minimization},
  journal = {Current Opinion in Structural Biology},
  year = {2006},
  volume = {16},
  pages = {270--278}
}

@ARTICLE{mathews02,
  author = {D. H. Mathews and D. H. Turner},
  title = {Dynalign: {A}n algorithm for finding the secondary structure common
	to two RNA sequences},
  journal = JMB,
  year = {2002},
  volume = {317},
  pages = {191--203}
}

@ARTICLE{Matsen2005,
  author = {Frederick A. Matsen},
  title = {A geometric approach to tree shape statistics},
  journal = {Arxiv preprint q-bio/0512009},
  year = {2005},
  url = {http://www.citebase.org/abstract?id=oai:arXiv.org:q-bio/0512009}
}

@INPROCEEDINGS{matsuda96,
  author = {H. Matsuda},
  title = {Protein phylogenetic inference using maximum likelihood with a genetic
	algorithm},
  booktitle = {Pacific {S}ymposium on {B}iocomputing},
  year = {1996},
  editor = {L. Hunter and T. E. Klein},
  pages = {512--523},
  publisher = {World Scientific}
}

@PHDTHESIS{mau96,
  author = {B. Mau},
  title = {Bayesian phylogenetic inference via {M}arkov chain {M}onte {C}arlo
	methods},
  school = {University of Wisconsin},
  year = {1996}
}

@ARTICLE{Mau1997,
  author = {Mau, Bob and Newton, Michael A.},
  title = {Phylogenetic Inference for Binary Data on Dendograms Using {M}arkov
	Chain {M}onte {C}arlo},
  journal = {Journal of Computational and Graphical Statistics},
  year = {1997},
  volume = {6},
  pages = {122--131},
  number = {1},
  url = {http://www.jstor.org/stable/1390728}
}

@ARTICLE{mau97,
  author = {B. Mau and M. A. Newton},
  title = {Phylogenetic inference for binary data on dendograms using {M}arkov
	chain {M}onte {C}arlo},
  journal = {Journal of Computational and Graphical Statistics},
  year = {1997},
  volume = {6},
  pages = {122--131}
}

@ARTICLE{mau99,
  author = {B. Mau and M. A. Newton and B. Larget},
  title = {Bayesian phylogenetic inference via {M}arkov chain {M}onte {C}arlo
	methods},
  journal = {Biometrics},
  year = {1999},
  volume = {55},
  pages = {1--12}
}

@ARTICLE{Mau1999,
  author = {Mau, B. and Newton, M.A. and Larget, B.},
  title = {Bayesian Phylogenetic Inference via {M}arkov Chain {M}onte {C}arlo
	Methods},
  journal = {Biometrics},
  year = {1999},
  volume = {55},
  pages = {1--12},
  number = {1},
  publisher = {JSTOR}
}

@ARTICLE{Mayrose2005,
  author = {Mayrose, I. and Mitchell, A. and Pupko, T.},
  title = {Site-Specific Evolutionary Rate Inference: Taking Phylogenetic Uncertainty
	into Account},
  journal = {Journal of Molecular Evolution},
  year = {2005},
  volume = {60},
  pages = {345--353},
  number = {3},
  publisher = {Springer}
}

@ARTICLE{mcauliffe06,
  author = {J. D. McAuliffe and D. M. Blei and M. I. Jordan},
  title = {Nonparametric empirical {B}ayes for the {D}irichlet process mixture
	model},
  journal = {Statistics and Computing},
  year = {2006},
  volume = {16},
  pages = {5--14}
}

@ARTICLE{mcguire07,
  author = {J. A. McGuire and C. C. Witt and D. L. Altshuler and J. V. Remsen},
  title = {Phylogenetic systematics and biogeography of hummingbirds: {B}ayesian
	and maximum likelihood analyses of partitioned data and selection
	of an appropriate partitioning strategy},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {837--856}
}

@ARTICLE{mckeown92,
  author = {M. McKeown},
  title = {Alternative m{RNA} splicing},
  journal = {Annual Review of Cell Biology},
  year = {1992},
  volume = {8},
  pages = {133--155}
}

@ARTICLE{melefors93,
  author = {O. Melefors and M. W. Hentze},
  title = {Translational regulation by m{RNA}/protein interactions in eukaryotic
	cells: {F}erritin and beyond},
  journal = {BioEssays},
  year = {1993},
  volume = {15},
  pages = {85--90}
}

@ARTICLE{meredith2011,
  author = {Meredith, Robert W and Hekkala, Evon R and Amato, George and Gatesy,
	John},
  title = {A phylogenetic hypothesis for \textit{{C}rocodylus} ({C}rocodylia)
	based on mitochondrial {DNA}: Evidence for a trans-{A}tlantic voyage
	from {A}frica to the {N}ew {W}orld},
  journal = {Molecular Phylogenetics and Evolution},
  year = {2011},
  volume = {60},
  pages = {183--191},
  number = {1},
  publisher = {Elsevier}
}

@ARTICLE{Meredith2011mammal,
  author = {Meredith, Robert W. and Jane\v{c}ka, Jan E. and Gatesy, John and
	Ryder, Oliver A. and Fisher, Colleen A. and Teeling, Emma C. and
	Goodbla, Alisha and Eizirik, Eduardo and Sim\~{a}o, Taiz L. L. and
	Stadler, Tanja and Rabosky, Daniel L. and Honeycutt, Rodney L. and
	Flynn, John J. and Ingram, Colleen M. and Steiner, Cynthia and Williams,
	Tiffani L. and Robinson, Terence J. and Burk-Herrick, Angela and
	Westerman, Michael and Ayoub, Nadia A. and Springer, Mark S. and
	Murphy, William J.},
  title = {Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction
	on Mammal Diversification},
  journal = {Science},
  year = {2011},
  volume = {334},
  pages = {521-524},
  number = {6055}
}

@ARTICLE{messier97,
  author = {W. Messier and C. B. Stewart},
  title = {Episodic adaptive evolution of primate lysozymes},
  journal = {Nature},
  year = {1997},
  volume = {385},
  pages = {151--154}
}

@ARTICLE{metropolis53,
  author = {N. Metropolis and A. W. Rosenbluth and M. N. Rosenbluth and A. H.
	Teller and E. Teller},
  title = {Equation of state calculations by fast computing machines},
  journal = {Journal of Chemical Physics},
  year = {1953},
  volume = {21},
  pages = {1087--1092}
}

@ARTICLE{metzker02,
  author = {M. L. Metzker and D. P. Mindell and X. M. Liu and R. G. Ptak and
	R. A. Gibbs and D. M. Hillis},
  title = {Molecular evidence of {HIV}-1 transmission in a criminal case},
  journal = PNAS,
  year = {2002},
  volume = {99},
  pages = {14292--14297}
}

@ARTICLE{meyer04,
  author = {I. M. Meyer and R. Durbin},
  title = {Gene structure conservation aids similarity based gene prediction},
  journal = NAR,
  year = {2004},
  volume = {32},
  pages = {776--783},
  number = {2}
}

@ARTICLE{michel00,
  author = {F. Michel and M. Costa and I. Massire and E. Westhof},
  title = {Modeling {RNA} tertiary structure from patterns of sequence variation},
  journal = {Methods Enzymology},
  year = {2000},
  volume = {317},
  pages = {491--510}
}

@ARTICLE{miklos04,
  author = {I. Mikl\'{o}s and G. Lunter and I. Holmes},
  title = {A long indel model for evolutionary sequence alignment},
  journal = MBE,
  year = {2004},
  volume = {21},
  pages = {529--540},
  number = {3}
}

@ARTICLE{miller88,
  author = {W. Miller and E. W. Myers},
  title = {Sequence comparison with concave weighting functions},
  journal = BMB,
  year = {1988},
  volume = {50},
  pages = {97--120}
}

@ARTICLE{minin08,
  author = {V. N. Minin and M. A. Suchard},
  title = {Counting labeled transitions in continuous-time {M}arkov models of
	evolution},
  journal = {Journal of Mathematical Biology},
  year = {2008},
  volume = {56},
  pages = {391--412}
}

@ARTICLE{Minka2008,
  author = {Minka, T. and Winn, J.},
  title = {Gates: A graphical notation for mixture models},
  year = {2008},
  publisher = {Citeseer}
}

@ARTICLE{Mira2001,
  author = {Mira, A.},
  title = {Ordering and improving the performance of {M}onte {C}arlo {M}arkov
	chains},
  journal = {Statistical Science},
  year = {2001},
  pages = {340--350},
  keywords = {MCMC, Convergence, Asymptotic Variance, Speed of Convergence},
  publisher = {Institute of Mathematical Statistics}
}

@ARTICLE{Mira1999,
  author = {Mira, A. and Geyer, C.J.},
  title = {Ordering {M}onte {C}arlo {M}arkov chains},
  journal = {School of Statistics, University of Minnesota},
  year = {1999},
  keywords = {Convergence, MCMC, Asymptotic Variance, Speed of Convergence}
}

@ARTICLE{mitchison99,
  author = {G. J. Mitchison},
  title = {A probabilistic treatment of phylogeny and sequence alignment},
  journal = JME,
  year = {1999},
  volume = {49},
  pages = {11-22},
  number = {1}
}

@ARTICLE{miyake71,
  author = {T. Miyake and I. Haruna and T. Shiba and Y. H. Itoh and K. Yamane
	and I. Watanabe},
  title = {Grouping of {RNA} phages based on template specificity of their {RNA}
	replicases},
  journal = PNAS,
  year = {1971},
  volume = {68},
  pages = {2022--2024}
}

@ARTICLE{miyamoto85,
  author = {M. M. Miyamoto},
  title = {Consensus cladograms and general classifications},
  journal = {Cladistics},
  year = {1985},
  volume = {1},
  pages = {186--189}
}

@ARTICLE{miyata80,
  author = {T. Miyata and T. Yasunaga},
  title = {Molecular evolution of m{RNA}: {A} method for estimating evolutionary
	rates of synonymous and amino acid substitutions from homologous
	nucleotide sequences and its application},
  journal = JME,
  year = {1980},
  volume = {16},
  pages = {23--36}
}

@ARTICLE{mohri00,
  author = {M. Mohri and F. Pereira and M. Riley},
  title = {Weighted Finite-State Transducers in Speech Recognition},
  journal = {ISCA ITRW Automatic Speech Recognition},
  year = {2000},
  pages = {97--106}
}

@ARTICLE{moler78,
  author = {C. Moler and C. Van Loan},
  title = {Nineteen dubious ways to compute the exponential of a matrix},
  journal = {SIAM Review},
  year = {1978},
  volume = {20},
  pages = {801--836}
}

@ARTICLE{montoya2001,
  author = {Montoya, P and Alcal{\'a}, L and Morales, J},
  title = {\textit{{I}ndarctos} ({U}rsidae, {M}ammalia) from the {S}panish {T}urolian
	({U}pper {M}iocene)},
  journal = {Scripta Geologica},
  year = {2001},
  volume = {122},
  pages = {123--151}
}

@ARTICLE{mooers95,
  author = {A. O. Mooers},
  title = {Tree balance and tree completeness},
  journal = Evolution,
  year = {1995},
  volume = {49},
  pages = {379--384}
}

@INPROCEEDINGS{moore04,
  author = {B. R. Moore and K. M. A. Chan and M. J. Donoghue},
  title = {Detecting diversification rate variation in supertrees},
  booktitle = {Phylogenetic Supertrees: Combining Information to Reveal the Tree
	of Life},
  year = {2004},
  editor = {O. R. P. Bininda-Emonds},
  pages = {487--533},
  publisher = {Kluwer Academic Press}
}

@ARTICLE{moore09,
  author = {Moore, Brian R. and Donoghue, Michael J.},
  title = {A {B}ayesian approach for evaluating the impact of historical events
	on rates of diversification},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2009},
  volume = {106},
  pages = {4307-4312},
  number = {11}
}

@ARTICLE{moore2014,
  author = {Moore, Brian R and McGuire, Jim and Ronquist, Fredrik and Huelsenbeck,
	John P},
  title = {Bayesian Analysis of Partitioned Data},
  journal = {arXiv preprint arXiv:1409.0906},
  year = {2014}
}

@INPROCEEDINGS{Moran1958,
  author = {Moran, PAP},
  title = {Random processes in genetics},
  booktitle = {Mathematical Proceedings of the Cambridge Philosophical Society},
  year = {1958},
  volume = {54},
  number = {01},
  pages = {60--71},
  organization = {Cambridge Univ Press}
}

@ARTICLE{moreau11,
  author = {C. S. Moreau and C. D. Bell},
  title = {Fossil cross-validation of the dated ant phylogeny ({H}ymenoptera:
	{F}ormicidae)},
  journal = {Entomologica Americana},
  year = {2011},
  volume = {117},
  pages = {22--27}
}

@ARTICLE{Moret2005,
  author = {Moret, BME},
  title = {Computational Challenges from the Tree of Life},
  journal = {Proc. 7th SIAM Workshop on Algorithm Engineering \& Experiments (ALENEX•À?05)},
  year = {2005},
  booktitle = {Proc. 7th SIAM Workshop on Algorithm Engineering \& Experiments (ALENEX•À?05)}
}

@ARTICLE{morgenstern99,
  author = {B. Morgenstern},
  title = {{DIALIGN} 2: {i}mprovement of the segment-to-segment approach to
	multiple sequence alignment},
  journal = BI,
  year = {1999},
  volume = {15},
  pages = {211--218}
}

@ARTICLE{morlon10,
  author = {H. Morlon},
  title = {Inferring the Dynamics of Diversification: {A} Coalescent Approach},
  journal = {PLoS Biology},
  year = {2010},
  volume = {8},
  pages = {e1000493}
}

@ARTICLE{Morlon2011,
  author = {Morlon, H. and Parsons, T.L. and Plotkin, J.B.},
  title = {Reconciling molecular phylogenies with the fossil record},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2011},
  volume = {108},
  pages = {16327--16332},
  number = {39},
  publisher = {National Acad Sciences}
}

@ARTICLE{Morlon2010,
  author = {Morlon, H. and Potts, M.D. and Plotkin, J.B.},
  title = {Inferring the dynamics of diversification: a coalescent approach},
  journal = {PLoS Biology},
  year = {2010},
  volume = {8},
  pages = {e1000493},
  number = {9},
  publisher = {Public Library of Science}
}

@ARTICLE{Morrison1996,
  author = {Morrison, D.A.},
  title = {Phylogenetic tree-building},
  journal = {International Journal for Parasitology},
  year = {1996},
  volume = {26},
  pages = {589--617},
  number = {6},
  publisher = {Elsevier}
}

@ARTICLE{morrison97,
  author = {D. A. Morrison and J. T. Ellis},
  title = {Effects of nucleotide sequence alignment on phylogeny estimation:
	{A} case study of {18S} {rDNAs} of {\it {A}picomplexa}},
  journal = MBE,
  year = {1997},
  volume = {14},
  pages = {428--441}
}

@ARTICLE{Mossel2005,
  author = {Elchanan Mossel and Eric Vigoda},
  title = {Phylogenetic MCMC Algorithms Are Misleading on Mixtures of Trees},
  journal = {Science},
  year = {2005},
  volume = {309},
  pages = {2207-2209},
  optmonth = {September},
  optnumber = {5744},
  optpages = {2207 - 2209},
  optvolume = {309},
  url = {http://www.sciencemag.org/cgi/content/abstract/309/5744/2207}
}

@ARTICLE{moyle06,
  author = {R. G. Moyle and J. Cracraft and M. Laim and J. Nais and F. H. Sheldon},
  title = {Reconsideration of the phylogenetic relationships of the enigmatic
	{B}ornean {B}ristlehead ({\it {P}ityriasis gymnocephala)}},
  journal = MPE,
  year = {2006},
  volume = {39},
  pages = {893--898}
}

@ARTICLE{mugridge00,
  author = {N. B. Mugridge and D. A. Morrison and T. Jakel and A. R. Heckeroth
	and A. M. Tenter and A. M. Johnson},
  title = {Effects of sequence alignment and structural domains of ribosomal
	{DNA} on phylogeny reconstruction for the {P}rotozoan family {S}arcocystidae},
  journal = MBE,
  year = {2000},
  volume = {17},
  pages = {1842--1853}
}

@ARTICLE{Mulcahy2012,
  author = {Mulcahy, Daniel G and Noonan, Brice P and Moss, Travis and Townsend,
	Ted M and Reeder, Tod W and Sites Jr, Jack W and Wiens, John J},
  title = {Estimating divergence dates and evaluating dating methods using phylogenomic
	and mitochondrial data in squamate reptiles},
  journal = MPE,
  year = {2012},
  volume = {65},
  pages = {974--991},
  number = {3}
}

@ARTICLE{muller00,
  author = {T. Muller and M. Vingron},
  title = {Modeling amino acid replacement},
  journal = JCB,
  year = {2000},
  volume = {7},
  pages = {761--776}
}

@ARTICLE{munch08,
  author = {K. Munch and W. Boomsmsa and J. P. Huelsenbeck and E. Willerslev
	and R. Nielsen},
  title = {Statistical assignment of environmental {DNA} sequence},
  journal = SYSB,
  year = {2008},
  volume = {57},
  pages = {750--757}
}

@ARTICLE{murphy01,
  author = {W. J. Murphy and E. Eizirik and S. J. O'Brien and O. Madsen and M.
	Scally and C. Douady and E. Teeling and O. A. Ryder and M. Stanhope
	and W. W. De Jong and M. S. Springer},
  title = {Resolution of the early placental mammal radiation using {B}ayesian
	phylogenetics},
  journal = {Science},
  year = {2001},
  volume = {294},
  pages = {2348--2351}
}

@ARTICLE{muse94,
  author = {S. V. Muse and B. S. Gaut},
  title = {A likelihood approach for comparing synonymous and nonsynonymous
	nucleotide substitution rates with application to the chloroplast
	genome},
  journal = MBE,
  year = {1994},
  volume = {11},
  pages = {715--724}
}

@ARTICLE{muse92,
  author = {S. V. Muse and B. S. Weir},
  title = {Testing for equality of evolutionary rates},
  journal = {Genetics},
  year = {1992},
  volume = {132},
  pages = {269--276}
}

@ARTICLE{Mykland1995,
  author = {Mykland, P. and Tierney, L. and Yu, B.},
  title = {Regeneration in {M}arkov Chain Samplers},
  journal = {Journal of the American Statistical Association},
  year = {1995},
  volume = {90},
  number = {429},
  publisher = {American Statistical Association}
}

@ARTICLE{nagda1998,
  author = {Nagda, Biren A and Gregerman, Sandra R and Jonides, John and {von
	Hippel}, William and Lerner, Jennifer S},
  title = {Undergraduate Student-Faculty Research Partnerships Affect Student
	Retention},
  journal = {Review of Higher Education},
  year = {1998},
  volume = {22},
  pages = {55--72},
  number = {1}
}

@BOOK{NSFURMdata,
  title = {Women, Minorities, and Persons with Disabilities in Science and Engineering:
	2013},
  year = {2013},
  author = {{National Science Foundation} and {National Center for Science and
	Engineering Statistics}},
  note = {Arlington, VA},
  booktitle = {Special Report NSF 13-304},
  url = {http://www.nsf.gov/statistics/wmpd/}
}

@ARTICLE{navidi91,
  author = {W. C. Navidi and G. A. Churchill and A. von Haeseler},
  title = {Methods for inferring phylogenies from nucleic acid sequence data
	by using maximum likelihood and linear invariants},
  journal = MBE,
  year = {1991},
  volume = {8},
  pages = {128--143}
}

@BOOK{Neal1993,
  title = {Probabilistic Inference Using {M}arkov Chain {M}onte {C}arlo Methods},
  publisher = {Department of Computer Science, University of Toronto},
  year = {1993},
  author = {Neal, R.M.}
}

@ARTICLE{neal00,
  author = {R. M. Neal},
  title = {Markov chain sampling methods for {D}irichlet process mixture models},
  journal = {Journal of Computational and Graphical Statistics},
  year = {2000},
  volume = {9},
  pages = {249--265}
}

@ARTICLE{near05,
  author = {T. J. Near and P. A. Meylan and H. B. Shaffer},
  title = {Assessing concordance of fossil calibration points in molecular clock
	studies: {A}n example using turtles},
  journal = {The American Naturalist},
  year = {2005},
  volume = {165},
  pages = {137--146}
}

@ARTICLE{Nee2006,
  author = {Nee, S.},
  title = {Birth-death models in macroevolution},
  journal = {Annu. Rev. Ecol. Evol. Syst.},
  year = {2006},
  volume = {37},
  pages = {1--17},
  publisher = {Annual Reviews}
}

@ARTICLE{Nee1994a,
  author = {Nee, S. and Holmes, E.C. and May, R.M. and Harvey, P.H.},
  title = {Extinction rates can be estimated from molecular phylogenies},
  journal = {Philosophical Transactions: Biological Sciences},
  year = {1994},
  volume = {344},
  pages = {77--82},
  number = {1307},
  publisher = {The Royal Society}
}

@ARTICLE{nee94b,
  author = {S. Nee and E. C. Holmes and R. M. May and P. H. Harvey},
  title = {Extinction rates can be estimated from molecular phylogenies},
  journal = PHTRANSRB,
  year = {1994},
  volume = {344},
  pages = {77--82}
}

@ARTICLE{nee94,
  author = {S. Nee and R. M. May and P. H. Harvey},
  title = {The reconstructed evolutionary process},
  journal = PHTRANSRB,
  year = {1994},
  volume = {344},
  pages = {305--311}
}

@ARTICLE{needleman70,
  author = {S. B. Needleman and C. D. Wunsch},
  title = {A General Method Applicable to the Search for Similarities in the
	Amino Acid Sequence of Two Proteins},
  journal = JMB,
  year = {1970},
  volume = {48},
  pages = {443--453}
}

@INPROCEEDINGS{nei91,
  author = {M. Nei},
  title = {Relative efficiencies of different tree-making methods for molecular
	data},
  booktitle = {Phylogenetic {A}nalysis of {DNA} {S}equences},
  year = {1991},
  editor = {M. M. Miyamoto and J. Cracraft},
  pages = {90--128},
  publisher = {Oxford University Press}
}

@ARTICLE{nei86,
  author = {M. Nei and T. Gojobori},
  title = {Simple methods for estimating the numbers of synonymous and nonsynonymous
	nucleotide substitutions},
  journal = MBE,
  year = {1986},
  volume = {3},
  pages = {418--426}
}

@ARTICLE{nei83,
  author = {M. Nei and F. Tajima and Y. Tateno},
  title = {Accuracy of estimated phylogenetic trees from molecular data. {II}.
	{G}ene frequency data},
  journal = JME,
  year = {1983},
  volume = {19},
  pages = {153--170}
}

@ARTICLE{Neumann1951,
  author = {von Neumann, J.},
  title = {Various techniques used in connection with random digits},
  journal = {Applied Math Series},
  year = {1951},
  volume = {12},
  pages = {36--38}
}

@ARTICLE{newton94,
  author = {M. A. Newton and A. E. Raftery},
  title = {Approximate {B}ayesian inference by the weighted likelihood bootstrap},
  journal = {Journal of the Royal Statistical Society, B},
  year = {1994},
  volume = {56},
  pages = {3--48}
}

@INPROCEEDINGS{newton99,
  author = {M. Newton and B. Mau and B. Larget},
  title = {Markov chain {M}onte {C}arlo for the {B}ayesian analysis of evolutionary
	trees from aligned molecular sequences},
  booktitle = {Statistics in {M}olecular {B}iology and {G}enetics},
  year = {1999},
  editor = {F. Seillier-Moseiwitch},
  pages = {143--162},
  publisher = {IMS Lecture Notes-Monograph Series, Volume 33}
}

@ARTICLE{Newton1994,
  author = {Newton, M.A. and Raftery, A.E.},
  title = {Approximate {B}ayesian inference with the weighted likelihood bootstrap},
  journal = {Journal of the Royal Statistical Society, Series B},
  year = {1994},
  volume = {56},
  pages = {3--48},
  number = {1}
}

@INPROCEEDINGS{neyman71,
  author = {J. Neyman},
  title = {Molecular studies of evolution: {A} source of novel statistical problems},
  booktitle = {Statistical Decision Theory and Related Topics},
  year = {1971},
  editor = {S. S. Gupta and J. Yackel},
  pages = {1--27},
  publisher = {Academic Press}
}

@ARTICLE{neyman48,
  author = {J. Neyman and E. L. Scott},
  title = {Consistent estimates based on partially consistent observations},
  journal = {Econometrica},
  year = {1948},
  volume = {16},
  pages = {1--32}
}

@ARTICLE{Nickle2003,
  author = {Nickle, D.C. and Jensen, M.A. and Shriner, D. and Brodie, S.J. and
	Frenkel, L.M. and Mittler, J.E. and Mullins, J.I.},
  title = {Evolutionary indicators of human immunodeficiency virus type 1 reservoirs
	and compartments},
  journal = {Journal of virology},
  year = {2003},
  volume = {77},
  pages = {5540--5546},
  number = {9},
  publisher = {Am Soc Microbiol}
}

@ARTICLE{nielsen02,
  author = {R. Nielsen},
  title = {Mapping mutations on phylogenies},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {729--739}
}

@ARTICLE{nielsen97,
  author = {R. Nielsen},
  title = {Site-by-site estimation of the rate of evolution and the correlation
	of rates in mitochondrial {DNA}},
  journal = SYSB,
  year = {1997},
  volume = {46},
  pages = {346--353}
}

@ARTICLE{nielsen98,
  author = {R. Nielsen and Z. Yang},
  title = {Likelihood models for detecting positively selected amino acid sites
	and applications to the {HIV-1} envelope gene},
  journal = {Genetics},
  year = {1998},
  volume = {148},
  pages = {929--93}
}

@ARTICLE{Nordborg2001,
  author = {Nordborg, M.},
  title = {Coalescent theory},
  journal = {Handbook of Statistical Genetics},
  year = {2001},
  pages = {179--212}
}

@ARTICLE{Nordborg1997,
  author = {Nordborg, M.},
  title = {Structured Coalescent Processes on Different Time Scales},
  journal = {Genetics},
  year = {1997},
  volume = {146},
  pages = {1501-1514},
  number = {4},
  eprint = {http://www.genetics.org/cgi/reprint/146/4/1501.pdf},
  url = {http://www.genetics.org/cgi/content/abstract/146/4/1501}
}

@ARTICLE{notredame00,
  author = {C. Notredame and D. G. Higgins and J. Heringa},
  title = {T-Coffee: {A} novel method for fast and accurate multiple sequence
	alignment},
  journal = JMB,
  year = {2000},
  volume = {302},
  pages = {205--217}
}

@ARTICLE{nowak2013,
  author = {Nowak, Michael D and Smith, Andrew B and Simpson, Carl and Zwickl,
	Derrick J},
  title = {A Simple Method for Estimating Informative Node Age Priors for the
	Fossil Calibration of Molecular Divergence Time Analyses},
  journal = {PloS One},
  year = {2013},
  volume = {8},
  pages = {e66245},
  number = {6},
  publisher = {Public Library of Science}
}

@ARTICLE{Nye2008,
  author = {Nye, T.},
  title = {Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies},
  journal = SYSB,
  year = {2008},
  volume = {57},
  pages = {785--794},
  number = {5},
  publisher = {Taylor and Francis Ltd}
}

@ARTICLE{nylander04,
  author = {J. A. A. Nylander and F. Ronquist and J. P. Huelsenbeck and J. L.
	Nieves Aldrey},
  title = {Bayesian phylogenetic analysis of combined data},
  journal = SYSB,
  year = {2004},
  volume = {53},
  pages = {47--67}
}

@ARTICLE{Nylander2008,
  author = {Nylander, J.A.A. and Wilgenbusch, J.C. and Warren, D.L. and Swofford,
	D.L.},
  title = {AWTY (are we there yet?): a system for graphical exploration of MCMC
	convergence in {B}ayesian phylogenetics},
  journal = BI,
  year = {2008},
  volume = {24},
  pages = {581},
  number = {4},
  publisher = {Oxford Univ Press}
}

@ARTICLE{odonell59,
  author = {C. A. O'Donell},
  title = {Convolvulaceas argentinas},
  journal = {Lilloa},
  year = {1959},
  volume = {29},
  pages = {87--343}
}

@ARTICLE{oaks2011,
  author = {Oaks, Jamie R},
  title = {A time-calibrated species tree of crocodylia reveals a recent radiation
	of the true crocodiles},
  journal = {Evolution},
  year = {2011},
  volume = {65},
  pages = {3285--3297},
  number = {11},
  publisher = {Wiley Online Library}
}

@ARTICLE{Oh1992,
  author = {Oh, M.S. and Berger, J.O.},
  title = {Adaptive importance sampling in {M}onte {C}arlo integration},
  journal = {Journal of Statistical Computation and Simulation},
  year = {1992},
  volume = {41},
  pages = {143--168},
  number = {3},
  publisher = {Taylor \& Francis}
}

@ARTICLE{ooyen79,
  author = {A. van Ooyen and J. van den Berg and N. Mantel and C. Weissmann},
  title = {Comparison of total sequence of a cloned rabbit $\beta$-globin gene
	and its flanking regions with a homologous mouse sequence},
  journal = {Science},
  year = {1979},
  volume = {206},
  pages = {337--344}
}

@INPROCEEDINGS{orbanz2010,
  author = {P. Orbanz and Y.W. Teh},
  title = {Bayesian Nonparametric Models},
  booktitle = {Encyclopedia of {M}achine {L}earning},
  year = {2010},
  editor = {C. Sammut and G. I. Webb},
  publisher = {Springer}
}

@ARTICLE{otha93,
  author = {T. Otha},
  title = {Pattern of nucleotide substitutions in growth hormone-{P}rolactin
	gene family: {A} paradigm for evolution by gene duplication},
  journal = {Genetics},
  year = {1993},
  volume = {134},
  pages = {1271--1276}
}

@ARTICLE{ou92,
  author = {C. -Y. Ou and C. A. Ciesielski and G. Myers and C. I. Bandea and
	C. -C. Luo and B. T. M. Korber and J. I. Mullins and G. Schochetman
	and R. L. Berkelman and A. N. Economou and J. J. Witte and L. J.
	Furman and G. A. Satten and K. A. MacInnes and J. W. Curran and H.
	W. Jaffe},
  title = {Molecular epidemiology of {HIV} transmission in a dental practice},
  journal = {Science},
  year = {1992},
  volume = {256},
  pages = {1165-1171}
}

@BOOK{owen43,
  title = {Lectures on the {C}omparative {A}natomy and {P}hysiology of the {I}nvertebrate
	{A}nimals, delivered at the {R}oyal {C}ollege of {S}urgeons},
  publisher = {Longman, Brown, Green, and Longmans},
  year = {1843},
  author = {R. Owen},
  address = {London}
}

@ARTICLE{page01,
  author = {S. L. Page and M. Goodman},
  title = {Catarrhine phylogeny: noncoding {DNA} evidence for a diphyletic origin
	of the mangabeys and for a human-chimpanzee clade},
  journal = MPE,
  year = {2001},
  volume = {18},
  pages = {14--25}
}

@ARTICLE{pagel99,
  author = {M. Pagel},
  title = {The maximum likelihood approach to reconstructing ancestral character
	states of discrete characters on phylogenies},
  journal = SYSB,
  year = {1999},
  volume = {48},
  pages = {612--622}
}

@INPROCEEDINGS{pagel05,
  author = {M. Pagel and A. Meade},
  title = {Mixture models in phylogenetic inference},
  booktitle = {Mathematics of Evolution and Phylogeny},
  year = {2005},
  editor = {O. Gascuel},
  pages = {121--142},
  publisher = {Oxford University Press}
}

@ARTICLE{Pagel2005,
  author = {Pagel, M. and Meade, A.},
  title = {Mixture models in phylogenetic inference},
  journal = {Mathematics of Evolution and Phylogeny},
  year = {2005},
  pages = {121},
  publisher = {Oxford University Press, USA}
}

@ARTICLE{pagel04,
  author = {M. Pagel and A. Meade},
  title = {A phylogenetic mixture model for detecting pattern-heterogeneity
	in gene sequence or character-state data},
  journal = SYSB,
  year = {2004},
  volume = {53},
  pages = {571--581}
}

@ARTICLE{palumbi89,
  author = {S. R. Palumbi},
  title = {Rates of molecular evolution and the function of nucleotide positions
	free to vary},
  journal = JME,
  year = {1989},
  volume = {29},
  pages = {180--187}
}

@ARTICLE{pamilo93,
  author = {P. Pamilo and N. O. Bianchi},
  title = {Evolution of the {Z}fx and {Z}fv genes: {R}ates and interdependence
	between the genes},
  journal = MBE,
  year = {1993},
  volume = {10},
  pages = {271--281}
}

@ARTICLE{pamilo88,
  author = {P. Pamilo and M. Nei},
  title = {Relationships between gene trees and species trees},
  journal = MBE,
  year = {1988},
  volume = {5},
  pages = {568--583}
}

@ARTICLE{Parham2012,
  author = {Parham, James F. and Donoghue, Philip C. J. and Bell, Christopher
	J. and Calway, Tyler D. and Head, Jason J. and Holroyd, Patricia
	A. and Inoue, Jun G. and Irmis, Randall B. and Joyce, Walter G. and
	Ksepka, Daniel T. and Patan\'{e}, Jos\'{e} S. L. and Smith, Nathan
	D. and Tarver, James E. and van Tuinen, Marcel and Yang, Ziheng and
	Angielczyk, Kenneth D. and Greenwood, Jenny M. and Hipsley, Christy
	A. and Jacobs, Louis and Makovicky, Peter J. and M\"{u}ller, Johannes
	and Smith, Krister T. and Theodor, Jessica M. and Warnock, Rachel
	C. M. and Benton, Michael J.},
  title = {Best Practices for Justifying Fossil Calibrations},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {346-359},
  number = {2}
}

@INPROCEEDINGS{patterson82,
  author = {C. Patterson},
  title = {Morphological Characters and Homology},
  booktitle = {Problems of {P}hylogenetic {R}econstruction},
  year = {1982},
  editor = {K. A. Joysey and A. B. Friday},
  pages = {21-74},
  publisher = {Academic Press}
}

@ARTICLE{patterson88,
  author = {C. Patterson},
  title = {Homology in classical and molecular biology},
  journal = MBE,
  year = {1988},
  volume = {5},
  pages = {603--625}
}

@BOOK{Pawitan2001,
  title = {In all likelihood: statistical modelling and inference using likelihood},
  publisher = {Oxford University Press, USA},
  year = {2001},
  author = {Pawitan, Y.},
  isbn = {0198507658}
}

@ARTICLE{peacock75,
  author = {D. Peacock and D. Boulter},
  title = {Use of amino acid sequence data in phylogeny and evaluation of methods
	using computer simulation},
  journal = JMB,
  year = {1975},
  volume = {95},
  pages = {513--527}
}

@BOOK{Pearl1988,
  title = {Probabilistic reasoning in intelligent systems: networks of plausible
	inference},
  publisher = {Morgan Kaufmann},
  year = {1988},
  author = {Pearl, J.}
}

@ARTICLE{pella06,
  author = {J. Pella and M. Masuda},
  title = {The {G}ibbs and split-merge sampler for population mixture analysis
	from genetic data with incomplete baselines},
  journal = {Can. J. Fish. Aquat. Sci.},
  year = {2006},
  volume = {63},
  pages = {576--596}
}

@ARTICLE{peltz92,
  author = {S. W. Peltz and A. Jacobson},
  title = {m{RNA} stability: in trans-it},
  journal = {Current Opinion in Cell Biology},
  year = {1992},
  volume = {4},
  pages = {979--983}
}

@ARTICLE{Peskun1973,
  author = {Peskun, P. H.},
  title = {Optimum {M}onte-{C}arlo sampling using {M}arkov chains},
  journal = {Biometrika},
  year = {1973},
  volume = {60},
  pages = {607-612},
  number = {3},
  doi = {10.1093/biomet/60.3.607},
  eprint = {http://biomet.oxfordjournals.org/cgi/reprint/60/3/607.pdf},
  url = {http://biomet.oxfordjournals.org/cgi/content/abstract/60/3/607}
}

@ARTICLE{pettigrew94,
  author = {J. D. Pettigrew},
  title = {Flying {DNA}},
  journal = SZ,
  year = {1994},
  volume = {40},
  pages = {277--280}
}

@ARTICLE{pettigrew91a,
  author = {J. D. Pettigrew},
  title = {Wings or brain? {C}onvergent evolution in the origin of bats},
  journal = SZ,
  year = {1991},
  volume = {40},
  pages = {199--216}
}

@ARTICLE{pettigrew91b,
  author = {J. D. Pettigrew},
  title = {A fruitful wrong hypothesis? {R}esponse to {B}aker, {N}ovacek, and
	{S}immons},
  journal = SZ,
  year = {1991},
  volume = {40},
  pages = {231--239}
}

@ARTICLE{pettigrew86,
  author = {J. D. Pettigrew},
  title = {Flying primates? {M}egabats have the advanced pathway from eye to
	midbrain},
  journal = {Science},
  year = {1986},
  volume = {231},
  pages = {1304--1306}
}

@ARTICLE{philippe94,
  author = {H. Philippe and E. Douzery},
  title = {The pitfalls of molecular phylogeny based on four species, as illustrated
	by the cetacea/artiodactyla relationships},
  journal = {Journal of Mammalian Evolution},
  year = {1994},
  volume = {2},
  pages = {133--152}
}

@ARTICLE{Phillimore2008,
  author = {Phillimore, A.B. and Price, T.D.},
  title = {Density-dependent cladogenesis in birds},
  journal = {PLoS biology},
  year = {2008},
  volume = {6},
  pages = {e71},
  number = {3},
  publisher = {Public Library of Science}
}

@ARTICLE{Pickett2005,
  author = {Kurt M. Pickett and Christopher P. Randle},
  title = {Strange bayes indeed: uniform topological priors imply non-uniform
	clade priors},
  journal = {Molecular Phylogenetics and Evolution},
  year = {2005},
  volume = {34},
  pages = {203 - 211},
  number = {1},
  doi = {10.1016/j.ympev.2004.09.001},
  issn = {1055-7903},
  keywords = {Bayesian phylogenetics},
  url = {http://www.sciencedirect.com/science/article/pii/S1055790304002817}
}

@ARTICLE{piras2007,
  author = {Piras, Paolo and Delfino, Massimo and Del Favero, Letizia and Kotsakis,
	Tassos},
  title = {Phylogenetic position of the crocodylian \textit{{M}egadontosuchus
	arduini} and \textit{tomistomine} palaeobiogeography},
  journal = {Acta Palaeontologica Polonica},
  year = {2007},
  volume = {52},
  pages = {315},
  number = {2}
}

@ARTICLE{pitman02,
  author = {J. Pitman},
  title = {Combinatorial stochastic processes},
  journal = {Technical Report 621, University of California at Berkeley, lecture
	notes for St. Flour Summer School},
  year = {2002}
}

@ARTICLE{plaisant02,
  author = {C. Plaisant and J. Grosjean and B. B. Bederson},
  title = {{SpaceTree}: {S}upporting exploration in large node link tree, design
	evolution and empirical evaluation},
  journal = {Proceedings of the Information Visualization Symposium},
  year = {2002},
  pages = {57--64}
}

@ARTICLE{Plummer2006,
  author = {Plummer, M. and Best, N. and Cowles, K. and Vines, K.},
  title = {{CODA}: Convergence diagnosis and output analysis for {MCMC}},
  journal = {R News},
  year = {2006},
  volume = {6},
  pages = {7--11}
}

@ARTICLE{poe03,
  author = {S. Poe},
  title = {Evaluation of the strategy of long-branch subdivision to improve
	the accuracy of phylogenetic methods},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {423--428}
}

@ARTICLE{poe98a,
  author = {S. Poe},
  title = {The effect of taxonomic sampling on accuracy of phylogeny estimation:
	{T}est case of a known phylogeny},
  journal = MBE,
  year = {1998},
  volume = {15},
  pages = {1086--1090}
}

@ARTICLE{poe98b,
  author = {S. Poe},
  title = {Sensitivity of phylogeny estimation to taxonomic sampling},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {18--31}
}

@ARTICLE{poe99,
  author = {S. Poe and D. L. Swofford},
  title = {Taxon sampling revisited},
  journal = Nature,
  year = {1999},
  volume = {398},
  pages = {299--300}
}

@ARTICLE{Poff2010,
  author = {Poff, N.L. and Richter, B.D. and Arthington, A.H. and Bunn, S.E.
	and Naiman, R.J. and Kendy, E. and Acreman, M. and Apse, C. and Bledsoe,
	B.P. and Freeman, M.C. and others},
  title = {The ecological limits of hydrologic alteration (ELOHA): a new framework
	for developing regional environmental flow standards},
  journal = {Freshwater Biology},
  year = {2010},
  volume = {55},
  pages = {147--170},
  number = {1},
  publisher = {Wiley Online Library}
}

@ARTICLE{pollock00,
  author = {D. D. Pollock and W. J. Bruno},
  title = {Assessing an unknown evolutionary process: {E}ffect of increasing
	site-specific knowledge through taxon addition},
  journal = MBE,
  year = {2000},
  volume = {17},
  pages = {1854--1858}
}

@ARTICLE{pollock99,
  author = {D. D. Pollock and W. R. Taylor and N. Goldman},
  title = {Coevolving protein residues: {M}aximum likelihood identification
	and relationship to structure},
  journal = JMB,
  year = {1999},
  volume = {287},
  pages = {187--198}
}

@ARTICLE{pollock02,
  author = {D. D. Pollock and D. J. Zwickl and J. A. McGuire and D. M. Hillis},
  title = {Increased taxon sampling is advantageous for phylogenetic inference},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {664--671}
}

@ARTICLE{pond05,
  author = {S. L. Kosakovsky Pond and S. D. W. Frost and S. V. Muse},
  title = {Hyphy: hypothesis testing using phylogenies},
  journal = BI,
  year = {2005},
  volume = {21},
  pages = {676--679}
}

@ARTICLE{pond04,
  author = {S. L. Kosakovsky Pond and S. V. Muse},
  title = {Column sorting: {R}apid calculation of the phylogenetic likelihood},
  journal = SYSB,
  year = {2004},
  volume = {50},
  pages = {685--692}
}

@ARTICLE{popovic04,
  author = {L. Popovic},
  title = {Asymptotic genealogy of a critical branching process},
  journal = {Annals of Applied Probability},
  year = {2004},
  volume = {14},
  pages = {2120--2148}
}

@BOOK{popper83,
  title = {Realism and the {A}im of {S}cience. [{V}ol. 1. of the {P}ostscript
	to {T}he {L}ogic of {S}cientific {D}iscovery]},
  publisher = {Routledge},
  year = {1983},
  author = {K. R. Popper},
  address = {London}
}

@BOOK{popper59,
  title = {The {L}ogic of {S}cientific {D}iscovery},
  publisher = {Basic Books},
  year = {1959},
  author = {K. R. Popper},
  address = {New York}
}

@ARTICLE{poux08,
  author = {C. Poux and O. Madsen and J. Glos and W. W. de Jong and M. Vences},
  title = {Molecular phylogeny and divergence times of {M}alagasy tenrecs: {I}nfluence
	of data partitioning and taxon sampling on dating analyses},
  journal = {BMC Evolutionary Biology},
  year = {2008},
  volume = {8},
  pages = {102}
}

@BOOK{press92,
  title = {Numerical {R}ecipes in {C}},
  publisher = {Cambridge University Press},
  year = {1992},
  author = {W. H. Press and S. A. Teukolsky and W. T. Vetterling and B. P. Flannery},
  address = {Cambridge}
}

@ARTICLE{pritchard00,
  author = {J. K. Pritchard and M. Stephens and P. Donnelly},
  title = {Inference of population structure using multilocus genotype data},
  journal = {Genetics},
  year = {2000},
  volume = {155},
  pages = {945--959}
}

@ARTICLE{Purvis2008,
  author = {Purvis, A.},
  title = {Phylogenetic approaches to the study of extinction},
  journal = {Annual Review of Ecology, Evolution, and Systematics},
  year = {2008},
  volume = {39},
  pages = {301--319},
  publisher = {Annual Reviews}
}

@ARTICLE{purvis2002,
  author = {Purvis, Andy and Agapow, Paul-Michael},
  title = {Phylogeny imbalance: {T}axonomic level matters},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {844--854},
  number = {6},
  publisher = {Oxford University Press}
}

@ARTICLE{Pybus2000,
  author = {O G Pybus and P H Harvey},
  title = {Testing macro-evolutionary models using incomplete molecular phylogenies},
  journal = {Proc Biol Sci},
  year = {2000},
  volume = {267},
  pages = {2267--72},
  number = {1459}
}

@ARTICLE{pyron11,
  author = {R. A. Pyron},
  title = {Divergence Time Estimation Using Fossils as Terminal Taxa and the
	Origins of {Lissamphibia}},
  journal = SYSB,
  year = {2011},
  volume = {60},
  pages = {466--481}
}

@ARTICLE{dequeiroz94,
  author = {K. de Queiroz and J. Gauthier},
  title = {Toward a phylogenetic system of biological nomenclature},
  journal = {Trends in Ecology and Evolution},
  year = {1994},
  volume = {9},
  pages = {27--31}
}

@ARTICLE{dequeiroz92,
  author = {K. de Queiroz and J. Gauthier},
  title = {Phylogenetic taxonomy},
  journal = {Annual Review of Ecology and Systematics},
  year = {1992},
  volume = {23},
  pages = {449--480}
}

@ARTICLE{dequeiroz90,
  author = {K. de Queiroz and J. Gauthier},
  title = {Phylogeny as a central principle in taxonomy: {P}hylogenetic definitions
	of taxon names},
  journal = SZ,
  year = {1990},
  volume = {39},
  pages = {307--322}
}

@ARTICLE{Quental2010,
  author = {Quental, T.B. and Marshall, C.R.},
  title = {Diversity dynamics: {M}olecular phylogenies need the fossil record},
  journal = {Trends in Ecology \& Evolution},
  year = {2010},
  volume = {25},
  pages = {434--441},
  publisher = {Elsevier}
}

@ARTICLE{Quental2009,
  author = {Quental, T.B. and Marshall, C.R.},
  title = {Extinction during evolutionary radiations: reconciling the fossil
	record with molecular phylogenies},
  journal = {Evolution},
  year = {2009},
  volume = {63},
  pages = {3158--3167},
  number = {12},
  publisher = {Wiley Online Library}
}

@ARTICLE{Quesenberry1964,
  author = {Quesenberry, C. P. and Hurst, D. C.},
  title = {Large Sample Simultaneous Confidence Intervals for Multinomial Proportions},
  journal = {Technometrics},
  year = {1964},
  volume = {6},
  pages = {191--195},
  number = {2},
  publisher = {American Statistical Association and American Society for Quality},
  url = {http://www.jstor.org/stable/1266151}
}

@ARTICLE{Rabosky2009a,
  author = {Rabosky, D.L.},
  title = {Ecological limits and diversification rate: alternative paradigms
	to explain the variation in species richness among clades and regions},
  journal = {Ecology letters},
  year = {2009},
  volume = {12},
  pages = {735--743},
  number = {8},
  publisher = {Wiley Online Library}
}

@ARTICLE{Rabosky2009b,
  author = {Rabosky, D.L.},
  title = {Ecological limits on clade diversification in higher taxa},
  journal = {The American Naturalist},
  year = {2009},
  volume = {173},
  pages = {662--674},
  publisher = {JSTOR}
}

@ARTICLE{Rabosky2006,
  author = {Rabosky, D.L.},
  title = {Likelihood methods for detecting temporal shifts in diversification
	rates},
  journal = {Evolution},
  year = {2006},
  volume = {60},
  pages = {1152--1164},
  number = {6},
  publisher = {Wiley Online Library}
}

@ARTICLE{Rabosky2009,
  author = {Rabosky, D.L. and Lovette, I.J.},
  title = {Problems detecting density-dependent diversification on phylogenies:
	reply to Bokma},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2009},
  volume = {276},
  pages = {995},
  number = {1659},
  publisher = {The Royal Society}
}

@ARTICLE{Rabosky2008,
  author = {Rabosky, D.L. and Lovette, I.J.},
  title = {Explosive evolutionary radiations: decreasing speciation or increasing
	extinction through time?},
  journal = {Evolution},
  year = {2008},
  volume = {62},
  pages = {1866--1875},
  number = {8},
  publisher = {Wiley Online Library}
}

@ARTICLE{rabosky2014,
  author = {Rabosky, Daniel L},
  title = {Automatic detection of key innovations, rate shifts, and diversity-dependence
	on phylogenetic trees},
  journal = {PloS One},
  year = {2014},
  volume = {9},
  pages = {e89543},
  number = {2},
  publisher = {Public Library of Science}
}

@ARTICLE{Rabosky2010a,
  author = {Rabosky, Daniel L},
  title = {Extinction rates should not be estimated from molecular phylogenies},
  journal = {Evolution; international journal of organic evolution},
  year = {2010},
  volume = {64},
  pages = {1816-1824}
}

@ARTICLE{Rabosky2009c,
  author = {Rabosky, Daniel L.},
  title = {Heritability of Extinction Rates Links Diversification Patterns in
	Molecular Phylogenies and Fossils},
  journal = SYSB,
  year = {2009},
  volume = {58},
  pages = {629-640},
  number = {6}
}

@ARTICLE{Rabosky2010,
  author = {Rabosky, Daniel L. and Alfaro, Michael E.},
  title = {Evolutionary Bangs and Whimpers: Methodological Advances and Conceptual
	Frameworks for Studying Exceptional Diversification},
  journal = SYSB,
  year = {2010},
  volume = {59},
  pages = {615-618},
  number = {6},
  doi = {10.1093/sysbio/syq061},
  eprint = {http://sysbio.oxfordjournals.org/content/59/6/615.full.pdf+html},
  url = {http://sysbio.oxfordjournals.org/content/59/6/615.short}
}

@INPROCEEDINGS{raftery96,
  author = {A. Raftery},
  title = {Hypothesis testing and model selection},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  year = {1996},
  editor = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  pages = {163--187},
  publisher = {Chapman and Hall}
}

@ARTICLE{Raftery1992,
  author = {Raftery, A.E. and Lewis, S.},
  title = {How many iterations in the {G}ibbs sampler},
  journal = {Bayesian Statistics},
  year = {1992},
  volume = {4},
  pages = {763--773},
  number = {2},
  publisher = {Citeseer}
}

@ARTICLE{ragan01,
  author = {M. Ragan},
  title = {Detection of lateral gene transfer among microbial genomes},
  journal = {Current Opinion in Genetics and Development},
  year = {2001},
  volume = {11},
  pages = {620--626}
}

@ARTICLE{Ragan1992,
  author = {Ragan, MA},
  title = {Phylogenetic inference based on matrix representation of trees},
  journal = {Molecular Phylogenetics and Evolution},
  year = {1992},
  volume = {1},
  pages = {53--8},
  number = {1}
}

@ARTICLE{rambaut98,
  author = {A. Rambaut and L. Bromham},
  title = {Estimating divergence dates from molecular sequences},
  journal = MBE,
  year = {1998},
  volume = {15},
  pages = {442--448}
}

@BOOK{rambaut09,
  title = {Tracer v1.5},
  publisher = {Institute of Evolutionary Biology, University of Edinburgh},
  year = {2009},
  author = {A. Rambaut and A. J. Drummond},
  address = {Edinburgh (United Kingdom)},
  note = {Available from: http://beast.bio.ed.ac.uk/Tracer}
}

@ARTICLE{Rambaut1997,
  author = {Rambaut, Andrew and Grass, Nicholas C.},
  title = {{Seq-Gen: an application for the {M}onte {C}arlo simulation of DNA
	sequence evolution along phylogenetic trees}},
  journal = {Comput. Appl. Biosci.},
  year = {1997},
  volume = {13},
  pages = {235--238},
  doi = {10.1093/bioinformatics/13.3.235},
  eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/13/3/235.pdf},
  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/13/3/235}
}

@ARTICLE{rambaut97,
  author = {A. Rambaut and N. C. Grassly},
  title = {{Seq-Gen}: an application for the {M}onte {C}arlo simulation of {DNA}
	sequence evolution along phylogenetic trees},
  journal = {Computer Applications in the Biosciences},
  year = {1997},
  volume = {13},
  pages = {235--238}
}

@ARTICLE{Rambaut1996,
  author = {Rambaut, Andrew and Grassly, Nicholas C. and Nee, Sean and Harvey,
	Paul H.},
  title = {{Bi-De}: an application for simulating phylogenetic processes},
  journal = {Comput. Appl. Biosci.},
  year = {1996},
  volume = {12},
  pages = {469-471},
  number = {6},
  doi = {10.1093/bioinformatics/12.6.469},
  eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/12/6/469.pdf},
  url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/12/6/469}
}

@ARTICLE{Randle2010,
  author = {Randle, Christopher P. and Pickett, Kurt M.},
  title = {The conflation of ignorance and knowledge in the inference of clade
	posteriors},
  journal = {Cladistics},
  year = {2010},
  volume = {26},
  pages = {550--559},
  number = {5},
  doi = {10.1111/j.1096-0031.2009.00301.x},
  issn = {1096-0031},
  publisher = {Blackwell Publishing Ltd},
  url = {http://dx.doi.org/10.1111/j.1096-0031.2009.00301.x}
}

@ARTICLE{Rannala2002,
  author = {Rannala, Bruce},
  title = {Identifiability of Parameters in MCMC {B}ayesian Inference of Phylogeny},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {754-760},
  number = {5}
}

@ARTICLE{rannala98,
  author = {B. Rannala and J. P. Huelsenbeck and Z. Yang and R. Nielsen},
  title = {Taxon sampling and the accuracy of large phylogenies},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {702--719}
}

@ARTICLE{rannala07,
  author = {B. Rannala and Z. Yang},
  title = {Inferring speciation times under an episodic molecular clock},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {453--466}
}

@ARTICLE{Rannala2007,
  author = {Rannala, Bruce and Yang, Ziheng},
  title = {Inferring Speciation Times under an Episodic Molecular Clock},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {453-466},
  number = {3},
  doi = {10.1080/10635150701420643},
  eprint = {http://sysbio.oxfordjournals.org/content/56/3/453.full.pdf+html},
  url = {http://sysbio.oxfordjournals.org/content/56/3/453.abstract}
}

@ARTICLE{rannala2003,
  author = {Rannala, Bruce and Yang, Ziheng},
  title = {Bayes estimation of species divergence times and ancestral population
	sizes using {DNA} sequences from multiple loci},
  journal = {Genetics},
  year = {2003},
  volume = {164},
  pages = {1645--1656},
  number = {4},
  publisher = {Genetics Soc America}
}

@ARTICLE{rannala96,
  author = {B. Rannala and Z. Yang},
  title = {Probability distribution of molecular evolutionary trees: {A} new
	method of phylogenetic inference},
  journal = JME,
  year = {1996},
  volume = {43},
  pages = {304--311}
}

@ARTICLE{raup74,
  author = {D. M. Raup and S. J. Gould},
  title = {Stochastic simulation and evolution of morphology---towards a nomothetic
	paleontology},
  journal = SZ,
  year = {1974},
  volume = {23},
  pages = {305--322}
}

@ARTICLE{raup73,
  author = {D. M. Raup and S. J. Gould and T. J. M. Schopf and D. S. Simberloff},
  title = {Stochastic models of phylogeny and the evolution of diversity},
  journal = {Journal of Geology},
  year = {1973},
  volume = {81},
  pages = {525--542}
}

@MANUAL{RDevelopmentCoreTeam2009,
  title = {R: A Language and Environment for Statistical Computing},
  author = {{R Development Core Team}},
  organization = {R Foundation for Statistical Computing},
  address = {Vienna, Austria},
  year = {2009},
  url = {http://www.R-project.org}
}

@ARTICLE{Redelings2005,
  author = {Redelings, B.D. and Suchard, M.A.},
  title = {Joint {B}ayesian Estimation of Alignment and Phylogeny},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {401--418},
  number = {3},
  publisher = {Taylor \& Francis}
}

@ARTICLE{redelings07,
  author = {B. D. Redelings and M. A. Suchard},
  title = {Incorporating indel information into phylogeny estimation for rapidly
	emerging pathogens},
  journal = {BMC Evolutionary Biology},
  year = {2007},
  volume = {7},
  pages = {40}
}

@ARTICLE{redelings05,
  author = {B. D. Redelings and M. A. Suchard},
  title = {Joint {B}ayesian estimation of alignment and phylogeny},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {401--418}
}

@ARTICLE{ree2005,
  author = {Ree, Richard H and Moore, Brian R and Webb, Campbell O and Donoghue,
	Michael J},
  title = {A likelihood framework for inferring the evolution of geographic
	range on phylogenetic trees},
  journal = EVO,
  year = {2005},
  volume = {59},
  pages = {2299--2311},
  number = {11}
}

@ARTICLE{revell2012phytools,
  author = {Revell, Liam J},
  title = {{phytools}: an {R} package for phylogenetic comparative biology (and
	other things)},
  journal = {Methods in Ecology and Evolution},
  year = {2012},
  volume = {3},
  pages = {217--223},
  number = {2},
  publisher = {Wiley Online Library}
}

@ARTICLE{ribeiro98,
  author = {S. Ribeiro and G. B. Golding},
  title = {The mosaic nature of the eukaryotic nucleus},
  journal = MBE,
  year = {1998},
  volume = {7},
  pages = {779--788}
}

@BOOK{rice95,
  title = {Mathematical {S}tatistics and {D}ata {A}nalysis},
  publisher = {Duxbury Press},
  year = {1995},
  author = {J. A. Rice},
  address = {Belmont, California}
}

@ARTICLE{ritland87,
  author = {K. Ritland and M. T. Clegg},
  title = {Evolutionary analysis of plant {DNA} sequences},
  journal = {American Naturalist},
  year = {1987},
  volume = {130},
  pages = {S74--S100}
}

@ARTICLE{robbins18,
  author = {R. B. Robbins},
  title = {Some applications of mathematics to breeding problems, {II}},
  journal = {Genetics},
  year = {1918},
  volume = {3},
  pages = {73--92}
}

@BOOK{Robert1998,
  title = {Discretization and {MCMC} convergence assessment},
  publisher = {Springer Verlag},
  year = {1998},
  author = {Robert, C.P.},
  isbn = {0387985913}
}

@BOOK{robert02,
  title = {Monte {C}arlo {S}tatistical {M}ethods},
  publisher = {Springer},
  year = {2002},
  author = {C. P. Robert and G. Casella},
  address = {New York}
}

@ARTICLE{Roberts1997,
  author = {G. O. Roberts and S. K. Sahu},
  title = {Updating Schemes, Correlation Structure, Blocking and Parameterization
	for the {G}ibbs Sampler},
  journal = {Journal of the Royal Statistical Society: Series B (Methodological)},
  year = {1997},
  volume = {59},
  pages = {291-317},
  number = {2},
  doi = {10.1111/1467-9868.00070},
  url = {http://dx.doi.org/10.1111/1467-9868.00070}
}

@ARTICLE{Robinson1979,
  author = {Robinson, DF and Foulds, LR},
  title = {Comparison of weighted labelled trees},
  journal = {Combinatorial mathematics, VI (Proc. Sixth Austral. Conf., Univ.
	New England, Armidale, 1978), Lecture Notes in Mathematics},
  year = {1979},
  volume = {748},
  pages = {119--126}
}

@INPROCEEDINGS{robinson79,
  author = {D. F. Robinson and L. R. Foulds},
  title = {Comparison of weighted labelled trees},
  booktitle = {Combinatorial Mathematics VI. Proceedings of the Sixth Australian
	Conference on Combinatorial Mathematics, Armidale, Australia, August
	1978},
  year = {1979},
  editor = {A. F. Horadam and W. D. Wallis},
  pages = {119--126},
  publisher = {Springer-Verlag}
}

@ARTICLE{robinson81,
  author = {D. F. Robinson and L. R. Foulds},
  title = {Comparison of phylogenetic trees},
  journal = {Mathematical Biosciences},
  year = {1981},
  volume = {53},
  pages = {131--147}
}

@ARTICLE{robinson03,
  author = {D. M. Robinson and D. T. Jones and H. Kishino and N. Goldman and
	J. L. Thorne},
  title = {Protein evolution with dependence among codons due to tertiary structure},
  journal = MBE,
  year = {2003},
  volume = {20},
  pages = {1692--1704}
}

@ARTICLE{robinson98,
  author = {M. Robinson and M. Gouy and C. Gautier and D. Mouchiroud},
  title = {Sensitivity of the relative-rate test to taxonomic sampling},
  journal = MBE,
  year = {1998},
  volume = {15},
  pages = {1091--1098}
}

@ARTICLE{rodrigo2003,
  author = {Rodrigo, Allen G and Goode, Matthew and Forsberg, Roald and Ross,
	Howard A and Drummond, Alexei},
  title = {Inferring evolutionary rates using serially sampled sequences from
	several populations},
  journal = MBE,
  year = {2003},
  volume = {20},
  pages = {2010--2018},
  number = {12}
}

@ARTICLE{rodrigue05,
  author = {N. Rodrigue and N. Lartillot and D. Bryant and H. Philippe},
  title = {Site interdependence attributed to tertiary structure in amino acid
	sequence evolution},
  journal = {Gene},
  year = {2005},
  volume = {347},
  pages = {207--217}
}

@ARTICLE{rodrigue08,
  author = {N. Rodrigue and H. Philippe and N. Lartillot},
  title = {Uniformization for sampling realizations of {M}arkov processes: {A}pplications
	to {B}ayesian implementations of codon substitution models},
  journal = BI,
  year = {2008},
  volume = {24},
  pages = {56--62}
}

@ARTICLE{rodriguez90,
  author = {F. Rodriguez and J. F. Oliver and A. Marin and J. R. Medina},
  title = {The general stochastic model of nucleotide substitutions},
  journal = {Journal of Theoretical Biology},
  year = {1990},
  volume = {142},
  pages = {485--501}
}

@ARTICLE{rogers97,
  author = {J. S. Rogers},
  title = {On the consistency of maximum likelihood estimation of phylogenetic
	trees from nucleotide sequences},
  journal = SYSB,
  year = {1997},
  volume = {46},
  pages = {354--357}
}

@ARTICLE{rogers98,
  author = {J. S. Rogers and D. L. Swofford},
  title = {A fast method for approximating maximum likelihoods of phylogenetic
	trees from nucleotide sequences},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {77--89}
}

@ARTICLE{rohl04,
  author = {C. A. Rohl and C. E. Strauss and K. M. Misura and D. Baker},
  title = {Protein structure prediction using {R}osetta},
  journal = {Methods of Enzymology},
  year = {2004},
  volume = {383},
  pages = {66--93}
}

@ARTICLE{rokas05,
  author = {A. Rokas and D. Kruger and S. B. Carroll},
  title = {Animal evolution and the molecular signature of radiations compressed
	in time},
  journal = Science,
  year = {2005},
  volume = {310},
  pages = {1933--1938}
}

@ARTICLE{rokas03,
  author = {A. Rokas and B. L. Williams and N. King and S. B. Carroll},
  title = {Genome-scale approaches to resolving incongruence in molecular phylogenies},
  journal = Nature,
  year = {2003},
  volume = {425},
  pages = {798--804}
}

@ARTICLE{Ronquist1996,
  author = {Ronquist, Fredrik},
  title = {Matrix Representation of Trees, Redundancy, and Weighting},
  journal = SYSB,
  year = {1996},
  volume = {45},
  pages = {247--253},
  number = {2},
  issn = {10635157},
  jstor_articletype = {primary_article},
  jstor_formatteddate = {Jun., 1996},
  publisher = {Taylor \& Francis, Ltd. for the Society of Systematic Biologists},
  url = {http://www.jstor.org/stable/2413617}
}

@ARTICLE{Ronquist2010,
  author = {Ronquist, F. and Deans, A.R.},
  title = {Bayesian phylogenetics and its influence on insect systematics},
  journal = {Annual review of entomology},
  year = {2010},
  volume = {55},
  pages = {189--206},
  publisher = {Annual Reviews}
}

@ARTICLE{Ronquist2003,
  author = {Ronquist, F. and Huelsenbeck, J.P.},
  title = {{MrBayes} 3: {B}ayesian phylogenetic inference under mixed models},
  journal = BI,
  year = {2003},
  volume = {19},
  pages = {1572--1574},
  number = {12},
  publisher = {Oxford Univ Press}
}

@MISC{Ronquist2005,
  author = {Ronquist, F. and Huelsenbeck, J.P. and van der Mark, P.},
  title = {{MrBayes 3.1 manual}},
  year = {2005}
}

@ARTICLE{ronquist03,
  author = {F. Ronquist and J. P. Huelsenbeck},
  title = {MrBayes 3: {B}ayesian phylogenetic inference under mixed models},
  journal = BI,
  year = {2003},
  volume = {19},
  pages = {1572--1574}
}

@INPROCEEDINGS{ronquist04,
  author = {F. Ronquist and J. P. Huelsenbeck and T. Britton},
  title = {Bayesian supertrees},
  booktitle = {Phylogenetic supertrees: Combining information to reveal the tree
	of life, Computational Biology, Volume 4},
  year = {2004},
  editor = {O. Bininda-Emonds},
  pages = {193--224},
  publisher = {Kluwer Academic Publishers, The Netherlands}
}

@ARTICLE{ronquist11,
  author = {F. Ronquist and S. Klopfstein and L. Vilhelmsen and S. Schulmeister
	and D. L. Murray and A. P. Rasnitsyn},
  title = {A total-evidence approach to dating with fossils, applied to the
	early radiation of the {H}ymenoptera},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {973--999}
}

@ARTICLE{ronquist06,
  author = {F. Ronquist and B. Larget and J. P. Huelsenbeck and J. B. Kadane
	and D. Simon and P. van der Mark},
  title = {Comment on `{P}hylogenetic {MCMC} algorithms are misleading on mixtures
	of trees},
  journal = {Science},
  year = {2006},
  volume = {312},
  pages = {367}
}

@INPROCEEDINGS{ronquist09,
  author = {F. Ronquist and P. van der Mark and J. P. Huelsenbeck},
  title = {Bayesian analysis of molecular evolution using {MrBayes}},
  booktitle = {The Phylogenetic Handbook: A Practical Approach to Phylogenetic Analysis
	and Hypothesis Testing, Second Edition},
  year = {2009},
  editor = {P. Lemey and M. Salemi and A. M. Vandamme},
  pages = {1--1},
  publisher = {Cambridge University Press}
}

@ARTICLE{Ronquist2012,
  author = {Ronquist, Fredrik and Teslenko, Maxim and van der Mark, Paul and
	Ayres, Daniel L. and Darling, Aaron and H\"ohna, Sebastian and Larget,
	Bret and Liu, Liang and Suchard, Marc A. and Huelsenbeck, John P.},
  title = {MrBayes 3.2: Efficient {B}ayesian Phylogenetic Inference and Model
	Choice Across a Large Model Space},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {539-542},
  number = {3}
}

@ARTICLE{rosenberg03,
  author = {M. S. Rosenberg and S. Kumar},
  title = {Taxon sampling, bioinformatics, and phylogenomics},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {119--124}
}

@ARTICLE{rosenberg01,
  author = {M. S. Rosenberg and S. Kumar},
  title = {Incomplete taxon sampling is not a problem for phylogenetic inference},
  journal = PNAS,
  year = {2001},
  volume = {98},
  pages = {10751--10756}
}

@INPROCEEDINGS{Roshan2004,
  author = {Roshan, U. and Moret, B.M.E. and Williams, T.L. and Warnow, T.},
  title = {Performance of supertree methods on various dataset decompositions},
  booktitle = {Phylogenetic supertrees: Combining information to reveal the tree
	of life, Computational Biology, Volume 4},
  year = {2004},
  editor = {O. Bininda-Emonds},
  pages = {301--328},
  publisher = {Kluwer Academic Pub}
}

@ARTICLE{Rosindell2010,
  author = {Rosindell, J. and Cornell, S.J. and Hubbell, S.P. and Etienne, R.S.},
  title = {Protracted speciation revitalizes the neutral theory of biodiversity},
  journal = {Ecology letters},
  year = {2010},
  volume = {13},
  pages = {716--727},
  number = {6},
  publisher = {Wiley Online Library}
}

@ARTICLE{ross02,
  author = {H. A. Ross and A. G. Rodrigo},
  title = {Immune-mediated positive selection drives {H}uman {I}mmunodeficiency
	{V}irus {T}ype 1 molecular variation and predicts disease duration},
  journal = {Journal of Virology},
  year = {2002},
  volume = {76},
  pages = {11715--11720}
}

@ARTICLE{rougemont07,
  author = {J. Rougemont and B. Nyffeler and S. E. Antonarakis},
  title = {Early history of mammals is elucidated with the {ENCODE} multiple
	species sequencing data},
  journal = {PLoS Genetics},
  year = {2007},
  volume = {3},
  pages = {e2}
}

@ARTICLE{Roure2013,
  author = {Roure, B\'{e}atrice and Baurain, Denis and Philippe, Herv\'{e}},
  title = {Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic
	Data Sets},
  journal = MBE,
  year = {2013},
  volume = {30},
  pages = {197-214},
  number = {1}
}

@ARTICLE{ruane10,
  author = {S. Ruane and R. A. Pyron and F. T. Burbrink},
  title = {Phylogenetic relationships of the {C}retaceous frog \textit{{B}eelzebufo}
	from {M}adagascar and the placement of fossil constraints based on
	temporal and phylogenetic evidence},
  journal = {Journal of Evolutionary Biology},
  year = {2010},
  volume = {24},
  pages = {274--285}
}

@ARTICLE{Rubin1981,
  author = {Rubin, D.B.},
  title = {The {B}ayesian bootstrap},
  journal = {The Annals of Statistics},
  year = {1981},
  volume = {9},
  pages = {130--134},
  number = {1},
  publisher = {Institute of Mathematical Statistics}
}

@BOOK{Rubinstein1981,
  title = {Simulation and the {M}onte {C}arlo Method},
  publisher = {John Wiley \& Sons, Inc. New York, NY, USA},
  year = {1981},
  author = {Rubinstein, R.Y.}
}

@BOOK{russell16,
  title = {Form and {F}unction},
  publisher = {J. Murray},
  year = {1916},
  author = {E. S. Russell},
  address = {London}
}

@ARTICLE{russell97,
  author = {R. B. Russell and M. A. Saqi and R. A. Sayle and P. A. Bates and
	M. J. Sternberg},
  title = {Recognition of analogous and homologous protein folds: analysis of
	sequence and structure conservation},
  journal = JMB,
  year = {1997},
  volume = {269},
  pages = {423--439}
}

@ARTICLE{rutschmann07,
  author = {F. Rutschmann and T. Eriksson and K. Abu Salim and E. Conti},
  title = {Assessing calibration uncertainty in molecular dating: the assignment
	of fossils to alternative calibration points},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {591--608}
}

@ARTICLE{rzhetsky95,
  author = {A. Rzhetsky},
  title = {Estimating substitution rates in ribosomal {RNA} genes},
  journal = {Genetics},
  year = {1995},
  volume = {141},
  pages = {771--783}
}

@CONFERENCE{Rzhetsky2001,
  author = {Rzhetsky, A. and Morozov, P.},
  title = {Markov chain {M}onte {C}arlo computation of confidence intervals
	for substitution-rate variation in proteins},
  booktitle = {Pac Symp Biocomput},
  year = {2001},
  volume = {6},
  pages = {203--214}
}

@ARTICLE{sackin72,
  author = {M. J. Sackin},
  title = {``Good'' and ``bad'' phenograms},
  journal = SZ,
  year = {1972},
  volume = {21},
  pages = {225--226}
}

@ARTICLE{Saitou1989,
  author = {Saitou, N and Imanishi, T},
  title = {Relative Efficiencies of the {Fitch-Margoliash}, Maximum-Parsimony,
	Maximum-Likelihood, Minimum-Evolution, and Neighbor-joining Methods
	of Phylogenetic Tree Construction in Obtaining the Correct Tree},
  journal = MBE,
  year = {1989},
  volume = {6},
  pages = {514-525},
  number = {5},
  eprint = {http://mbe.oxfordjournals.org/cgi/reprint/6/5/514.pdf},
  url = {http://mbe.oxfordjournals.org}
}

@ARTICLE{saitou87,
  author = {N. Saitou and M. Nei},
  title = {The neighbor-joining method: {A} new method for reconstructing phylogenetic
	trees},
  journal = MBE,
  year = {1987},
  volume = {4},
  pages = {406--425}
}

@ARTICLE{salichos2013,
  author = {Salichos, Leonidas and Rokas, Antonis},
  title = {Inferring ancient divergences requires genes with strong phylogenetic
	signals},
  journal = {Nature},
  year = {2013},
  volume = {497},
  pages = {327--331}
}

@ARTICLE{salisbury01,
  author = {B. A. Salisbury and J. H. Kim},
  title = {Ancestral state estimation and taxon sampling density},
  journal = SYSB,
  year = {2001},
  volume = {50},
  pages = {557--564}
}

@ARTICLE{salisbury2006,
  author = {Salisbury, Steven W and Molnar, Ralph E and Frey, Eberhard and Willis,
	Paul MA},
  title = {The origin of modern crocodyliforms: new evidence from the {C}retaceous
	of {A}ustralia},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2006},
  volume = {273},
  pages = {2439--2448},
  number = {1600},
  publisher = {The Royal Society}
}

@ARTICLE{Sanderson1998,
  author = {Sanderson, M.J. and Purvis, A. and Henze, C.},
  title = {Phylogenetic supertrees: Assembling the trees of life},
  journal = {Trends in Ecology \& Evolution},
  year = {1998},
  volume = {13},
  pages = {105--109},
  number = {3},
  publisher = {Elsevier}
}

@ARTICLE{Sanderson2003,
  author = {Sanderson, Michael J.},
  title = {{r8s}: inferring absolute rates of molecular evolution and divergence
	times in the absence of a molecular clock},
  journal = BI,
  year = {2003},
  volume = {19},
  pages = {301-302},
  number = {2},
  doi = {10.1093/bioinformatics/19.2.301},
  eprint = {http://bioinformatics.oxfordjournals.org/content/19/2/301.full.pdf+html},
  url = {http://bioinformatics.oxfordjournals.org/content/19/2/301.abstract}
}

@ARTICLE{sanderson02,
  author = {M. J. Sanderson},
  title = {Estimating absolute rates of molecular evolution and divergence times:
	a penalized likelihood approach},
  journal = MBE,
  year = {2002},
  volume = {19},
  pages = {101--109}
}

@ARTICLE{sanderson97,
  author = {M. J. Sanderson},
  title = {A nonparametric approach to estimating divergence times in the absence
	of rate constancy},
  journal = MBE,
  year = {1997},
  volume = {14},
  pages = {1218--1231}
}

@ARTICLE{sanderson94,
  author = {M. J. Sanderson and M. J. Donoghue},
  title = {Shifts in diversification rate with the origin of angiosperms},
  journal = Science,
  year = {1994},
  volume = {264},
  pages = {1590--1593}
}

@ARTICLE{sanderson2004,
  author = {Sanderson, Michael J and Thorne, Jeffrey L and Wikstr{\"o}m, Niklas
	and Bremer, K{\aa}re},
  title = {Molecular evidence on plant divergence times},
  journal = {American Journal of Botany},
  year = {2004},
  volume = {91},
  pages = {1656--1665},
  number = {10}
}

@ARTICLE{sanderson00,
  author = {M. J. Sanderson and M. F. Wojciechowski},
  title = {Improved bootstrap confidence limits in large-scale phylogenies with
	an example from {N}eo-{A}stragalus ({L}eguminosae)},
  journal = SYSB,
  year = {2000},
  volume = {49},
  pages = {671--685}
}

@ARTICLE{sansom2013,
  author = {Sansom, Robert S and Gabbott, Sarah E and Purnell, Mark A},
  title = {Atlas of vertebrate decay: {A} visual and taphonomic guide to fossil
	interpretation},
  journal = {Palaeontology},
  year = {2013},
  volume = {56},
  pages = {457--474},
  number = {3}
}

@ARTICLE{santiago02,
  author = {M. L. Santiago and C. M. Rodenburg and S. Kamenya and F. Bibollet-Ruche
	and F. Gao and E. Bailes and S. Meleth and S. Soong and J. M. Kilby
	and Z. Moldoveanu and B. Fahey and M. N. Muller and A. Ayouba and
	E. Nerrienet and H. M. McClure and J. L. Heeney and A. E. Pusey and
	D. A. Collins and C. Boesch and R. W. Wrangham and J. Goodall and
	P. M. Sharp and G. M. Shaw and B. H. Hahn},
  title = {{SIVcpz} in wild chimpanzees },
  journal = {Science},
  year = {2002},
  volume = {295},
  pages = {465}
}

@ARTICLE{satta00,
  author = {Y. Satta and J. Klein and N. Takahata},
  title = {{DNA} archives and our nearest relative: The trichotomy problem revisited},
  journal = MPE,
  year = {2000},
  volume = {14},
  pages = {259--275}
}

@ARTICLE{sauquet2013,
  author = {Sauquet, Herv{\'e}},
  title = {A practical guide to molecular dating},
  journal = {Comptes Rendus Palevol},
  year = {2013},
  volume = {12},
  pages = {355--367},
  number = {6}
}

@ARTICLE{Sauquet2012,
  author = {Sauquet, Hervé and Ho, Simon Y. W. and Gandolfo, Maria A. and Jordan,
	Gregory J. and Wilf, Peter and Cantrill, David J. and Bayly, Michael
	J. and Bromham, Lindell and Brown, Gillian K. and Carpenter, Raymond
	J. and Lee, Daphne M. and Murphy, Daniel J. and Sniderman, J. M.
	Kale and Udovicic, Frank},
  title = {Testing the Impact of Calibration on Molecular Divergence Times Using
	a Fossil-Rich Group: The Case of Nothofagus (Fagales)},
  journal = SYSB,
  year = {2012},
  volume = {61},
  pages = {289-313},
  number = {2}
}

@ARTICLE{savage83,
  author = {H. M. Savage},
  title = {The shape of evolution: {S}ystematic tree topology},
  journal = {Biological Journal of the Linnean Society},
  year = {1983},
  volume = {20},
  pages = {225--244}
}

@ARTICLE{savolainen00,
  author = {V. Savolainen and M. W. Chase and S. B. Hoot and C. M. Morton and
	D. E. Soltis and C. Bayer and M. F. Fay and A. De Bruijn and S. Sullivan
	and Q. L. Qiu},
  title = {Phylogenetics of flowering plants based upon a combined analysis
	of plastid atpB and rbc{L} gene sequences},
  journal = SYSB,
  year = {2000},
  volume = {49},
  pages = {306--362}
}

@ARTICLE{savolainen02,
  author = {V. Savolainen and S. B. Heard and M. P. Powell and T. J. Davies and
	A. O. Mooers},
  title = {Is cladogenesis heritable?},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {835--843}
}

@ARTICLE{schoniger95,
  author = {M. Sch{\"o}niger and A. von Haeseler},
  title = {Performance of the maximum likelihood, neighbor joining, and maximum
	parsimony methods when sequence sites are not independent},
  journal = SYSB,
  year = {1995},
  volume = {44},
  pages = {533--547}
}

@ARTICLE{schoniger94,
  author = {M. Sch{\"o}niger and A. von Haeseler},
  title = {A stochastic model and the evolution of autocorrelated DNA sequences},
  journal = MPE,
  year = {1994},
  volume = {3},
  pages = {240--247}
}

@ARTICLE{schluter95,
  author = {D. Schluter},
  title = {Uncertainty in ancient phylogenies},
  journal = {Nature},
  year = {1995},
  volume = {377},
  pages = {108--109}
}

@ARTICLE{schluter97,
  author = {D. Schluter and T. Price and A. {\O}. Mooers and D. Ludwig},
  title = {Likelihood of ancestor states in adaptive radiation},
  journal = {Evolution},
  year = {1997},
  volume = {51},
  pages = {1699--1711}
}

@ARTICLE{schroder70,
  author = {E. Schr{\"o}der},
  title = {Vier combinatorische probleme},
  journal = {Zeitschrift f{\"u}r Mathematik und Physik},
  year = {1870},
  volume = {15},
  pages = {361--376}
}

@ARTICLE{schultz99,
  author = {T. R. Schultz and G. A. Churchill},
  title = {The role of subjectivity in reconstructing ancestral character states:
	{A} {B}ayesian approach to unknown rates, states, and transformation
	asymmetries},
  journal = SYSB,
  year = {1999},
  volume = {48},
  pages = {651--664}
}

@ARTICLE{schwartz05,
  author = {A. S. Schwartz and E. W. Myers and L. Pachter},
  title = {Alignment metric accuracy},
  journal = {http://arxiv.org/abs/q-bio.QM/0510052},
  year = {2005}
}

@ARTICLE{schwartz07,
  author = {A. S. Schwartz and L. Pachter},
  title = {Multiple alignment by sequence annealingThe evolution of dinosaurs},
  journal = BI,
  year = {2007},
  volume = {23},
  pages = {e24--e29}
}

@ARTICLE{Seary1997,
  author = {Seary, A. and Richards, W.},
  title = {The Physics of Networks},
  journal = {INSNA Sunbelt XVII, San Diego, February},
  year = {1997},
  pages = {13--17}
}

@ARTICLE{Semple2000,
  author = {Charles Semple and Mike Steel},
  title = {A supertree method for rooted trees},
  journal = {Discrete Applied Mathematics},
  year = {2000},
  volume = {105},
  pages = {147 - 158},
  number = {1-3},
  doi = {DOI: 10.1016/S0166-218X(00)00202-X},
  url = {http://www.sciencedirect.com/science/article/B6TYW-4118F15-B/2/ded03d5ea4d8818efabc4e98c5f25735}
}

@ARTICLE{sereno99,
  author = {P. C. Sereno},
  title = {The evolution of dinosaurs},
  journal = {Science},
  year = {1999},
  volume = {284},
  pages = {2137--2147}
}

@ARTICLE{shankarappa99,
  author = {R. Shankarappa and R. B. Margolick and S. J. Gange and A. G. Rodrigo
	and D. Upchurch and H. Farzadegan and P. Gupta and C. R. Rinaldoand
	G. H. Learn and X. He and X. L. Huang and J. I. Mullins},
  title = {Consistent viral evolutionary changes associated with progression
	of {HIV-1} infection},
  journal = {Journal of Virology},
  year = {1999},
  volume = {73},
  pages = {10489--10502}
}

@ARTICLE{shao90,
  author = {K. T. Shao and R. R. Sokal},
  title = {Tree balance},
  journal = SZ,
  year = {1990},
  volume = {39},
  pages = {266--276}
}

@ARTICLE{Shapiro2004,
  author = {Shapiro, Beth and Drummond, Alexei J. and Rambaut, Andrew and Wilson,
	Michael C. and Matheus, Paul E. and Sher, Andrei V. and Pybus, Oliver
	G. and Gilbert, M. Thomas P. and Barnes, Ian and Binladen, Jonas
	and Willerslev, Eske and Hansen, Anders J. and Baryshnikov, Gennady
	F. and Burns, James A. and Davydov, Sergei and Driver, Jonathan C.
	and Froese, Duane G. and Harington, C. Richard and Keddie, Grant
	and Kosintsev, Pavel and Kunz, Michael L. and Martin, Larry D. and
	Stephenson, Robert O. and Storer, John and Tedford, Richard and Zimov,
	Sergei and Cooper, Alan},
  title = {Rise and Fall of the {B}eringian {S}teppe Bison},
  journal = {Science},
  year = {2004},
  volume = {306},
  pages = {1561-1565},
  number = {5701}
}

@ARTICLE{shapiro11,
  author = {B. Shapiro and S. Y. W Ho and A. J. Drummond and M. A. Suchard and
	O. G. Pybus and A. Rambaut},
  title = {A {B}ayesian Phylogenetic Method to Estimate Unknown Sequence Ages},
  journal = MBE,
  year = {2011},
  volume = {28},
  pages = {879-887}
}

@ARTICLE{Shapiro2006,
  author = {Shapiro, B. and Rambaut, A. and Drummond, A.J.},
  title = {Choosing appropriate substitution models for the phylogenetic analysis
	of protein-coding sequences},
  journal = MBE,
  year = {2006},
  volume = {23},
  pages = {7},
  number = {1},
  publisher = {SMBE}
}

@ARTICLE{shapiro06,
  author = {B. Shapiro and A. Rambaut and A. J. Drummond},
  title = {Choosing appropriate substitution models for the phylogenetic analysis
	of protein-coding sequences},
  journal = MBE,
  year = {2006},
  volume = {23},
  pages = {7-9}
}

@INPROCEEDINGS{shapiro75,
  author = {L. Shapiro and I. Bendis},
  title = {{RNA} phages of bacteria other than {E}. coli},
  booktitle = {{RNA} {P}hages},
  year = {1975},
  editor = {N. D. Zinder},
  pages = {397--410},
  publisher = {Cold Spring Harbor Laboratory}
}

@ARTICLE{sharp01,
  author = {P. M. Sharp and E. Bailes and R. R. Chaudhuri and C. M. Rodenburg
	and M. O. Santiago and B. H. Hahn},
  title = {The origins of acquired immune deficiency syndrome viruses: {W}here
	and when?},
  journal = PHTRANSRB,
  year = {2001},
  volume = {356},
  pages = {867--876}
}

@ARTICLE{siddall97,
  author = {M. E. Siddall and A. G. Kluge},
  title = {Probabilism and phylogenetic inference},
  journal = {Cladistics},
  year = {1997},
  volume = {13},
  pages = {313--336}
}

@ARTICLE{sierwald01,
  author = {P. Sierwald and W. A. Shear and R. M. Shelley and J. E. Bond},
  title = {Millipede phylogeny revisited in the light of the enigmatic order
	{S}iphoniulida},
  journal = {Journal of Zoological Systematics and Evolutionary Research},
  year = {2001},
  volume = {41},
  pages = {87--99}
}

@ARTICLE{signor1982,
  author = {Signor, Philip W and Lipps, Jere H},
  title = {Sampling bias, gradual extinction patterns and catastrophes in the
	fossil record},
  journal = {Geological Society of America Special Paper},
  year = {1982},
  volume = {190},
  pages = {291--296}
}

@ARTICLE{Simmons2004,
  author = {Simmons, M.P. and Pickett, K.M. and Miya, M.},
  title = {How meaningful are {B}ayesian support values?},
  journal = MBE,
  year = {2004},
  volume = {21},
  pages = {188},
  number = {1},
  publisher = {SMBE}
}

@MISC{simon01,
  author = {D. Simon and B. Larget},
  title = {Bayesian Analysis in Molecular Biology and Evolution {(BAMBE)}},
  howpublished = {http://www.mathcs.duq.edu/larget/bambe.html},
  year = {2001}
}

@ARTICLE{sinsheimer03,
  author = {J. S. Sinsheimer and M. A. Suchard and K. S. Dorman and F. Fang and
	R. E. Weiss},
  title = {Are you my mother? {B}ayesian phylogenetic inference of recombination
	among putative parental strains},
  journal = {Applied Bioinformatics},
  year = {2003},
  volume = {2},
  pages = {131--144}
}

@ARTICLE{slater2012,
  author = {Slater, Graham J and Harmon, Luke J and Alfaro, Michael E},
  title = {Integrating fossils with molecular phylogenies improves inference
	of trait evolution},
  journal = {Evolution},
  year = {2012},
  volume = {66},
  pages = {3931--3944},
  number = {12}
}

@ARTICLE{slatkin91,
  author = {M. Slatkin and R. R. Hudson},
  title = {Pairwise comparisons of mitochondrial DNA sequences in stable and
	exponentially growing populations},
  journal = {Genetics},
  year = {1991},
  volume = {129},
  pages = {555--562}
}

@ARTICLE{slatkin97a,
  author = {M. Slatkin and B. Rannala},
  title = {Estimating the age of alleles by use of intraallelic variability},
  journal = {American Journal of Human Genetics},
  year = {1997},
  volume = {60},
  pages = {447--458}
}

@ARTICLE{slatkin97b,
  author = {M. Slatkin and B. Rannala},
  title = {The sampling distribution of disease-associated alleles},
  journal = {Genetics},
  year = {1997},
  volume = {147},
  pages = {1855--1861}
}

@ARTICLE{Smith1993,
  author = {Smith, AFM and Roberts, GO},
  title = {Bayesian computation via the {G}ibbs sampler and related {M}arkov
	chain {M}onte {C}arlo methods},
  journal = {Journal of the Royal Statistical Society. Series B (Methodological)},
  year = {1993},
  volume = {55},
  pages = {3--23},
  number = {1},
  issn = {0035-9246},
  publisher = {JSTOR}
}

@ARTICLE{smith2001,
  author = {Smith, Andrew B},
  title = {Large--scale heterogeneity of the fossil record: {I}mplications for
	{P}hanerozoic biodiversity studies},
  journal = {Philosophical Transactions of the Royal Society of London. Series
	B: Biological Sciences},
  year = {2001},
  volume = {356},
  pages = {351--367},
  number = {1407}
}

@ARTICLE{Smith2007,
  author = {Smith, B.J.},
  title = {{boa}: An {R} package for {MCMC} output convergence assessment and
	posterior inference},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {21},
  pages = {1--37},
  number = {11},
  publisher = {American Statistical Association}
}

@MANUAL{Smith2004,
  title = {{Bayesian output analysis program}},
  author = {Smith, B.},
  year = {2004},
  publisher = {The University of Iowa College of Public Health, Iowa City}
}

@ARTICLE{smith07,
  author = {B. J. Smith},
  title = {boa: {A}n {R} package for {MCMC} output convergence assessment and
	posterior inference},
  journal = {Journal of Statistical Software},
  year = {2007},
  volume = {21},
  pages = {1--37}
}

@ARTICLE{smith81,
  author = {B. J. Smith and M. S. Waterman},
  title = {Identification of Common Molecular Subsequences},
  journal = JMB,
  year = {1981},
  volume = {147},
  pages = {195--197}
}

@ARTICLE{Smith2008,
  author = {S. A. Smith and M. J. Donoghue},
  title = {Rates of molecular evolution are linked to life history in flowering
	plants},
  journal = {Science},
  year = {2008},
  volume = {322},
  pages = {86--89}
}

@ARTICLE{Smith2012,
  author = {Smith, Stephen A. and O'Meara, Brian C.},
  title = {treePL: divergence time estimation using penalized likelihood for
	large phylogenies},
  journal = BI,
  year = {2012},
  volume = {28},
  pages = {2689-2690},
  number = {20},
  doi = {10.1093/bioinformatics/bts492},
  eprint = {http://bioinformatics.oxfordjournals.org/content/28/20/2689.full.pdf+html},
  url = {http://bioinformatics.oxfordjournals.org/content/28/20/2689.abstract}
}

@ARTICLE{smith05,
  author = {S. A. Smith and P. R. Stephens and J. J. Wiens},
  title = {Replicate patterns of species richness, historical biogeography,
	and phylogeny in {H}olarctic treefrogs},
  journal = {Evolution},
  year = {2005},
  volume = {59},
  pages = {2433--2450}
}

@BOOK{Sneath1973,
  title = {Numerical taxonomy},
  publisher = {Springer},
  year = {1973},
  author = {Sneath, P.H.A. and Sokal, R.R.}
}

@ARTICLE{snel99,
  author = {B. Snel and P. Bork and M. Huynen},
  title = {Genome phylogeny based on gene content},
  journal = {Nature Genetics},
  year = {1999},
  volume = {21},
  pages = {108--110}
}

@ARTICLE{sokal58,
  author = {R. R. Sokal and C. D. Michener},
  title = {A statistical method for evaluating systematic relationships},
  journal = {University of Kansas Science Bulletin},
  year = {1958},
  volume = {28},
  pages = {1409--1438}
}

@BOOK{sokal69,
  title = {Biometry},
  publisher = {W. H. Freeman and Company},
  year = {1969},
  author = {R. R. Sokal and F. J. Rohlf},
  address = {New York}
}

@BOOK{sokal63,
  title = {Principles of {N}umerical {T}axonomy},
  publisher = {W. H. Freeman},
  year = {1963},
  author = {R. R. Sokal and P. H. A. Sneath},
  address = {San Francisco}
}

@ARTICLE{sparks04,
  author = {J. S. Sparks and W. L. Smith},
  title = {Phylogeny and Biogeography of Cichlid Fishes ({T}eleostei: {P}erciformes:
	{C}ichlidae)},
  journal = {Cladistics},
  year = {2004},
  volume = {20},
  pages = {501--517}
}

@ARTICLE{stadler11,
  author = {T. Stadler},
  title = {Simulating trees on a fixed number of extant species},
  journal = SYSB,
  year = {2011},
  volume = {60},
  pages = {668--675}
}

@ARTICLE{Stadler2011,
  author = {Stadler, Tanja},
  title = {Mammalian phylogeny reveals recent diversification rate shifts},
  journal = PNAS,
  year = {2011},
  volume = {108},
  pages = {6187-6192},
  number = {15}
}

@ARTICLE{stadler10,
  author = {T. Stadler},
  title = {Sampling-through-time in birth-death trees},
  journal = {Journal of Theoretical Biology},
  year = {2010},
  volume = {267},
  pages = {396--404}
}

@MANUAL{Stadler2010,
  title = {TreeSim: Simulating trees under the birth-death model},
  author = {Tanja Stadler},
  year = {2010},
  note = {R package version 1.0},
  url = {http://CRAN.R-project.org/package=TreeSim}
}

@ARTICLE{Stadler2010a,
  author = {Stadler, T.},
  title = {Sampling-through-time in birth-death trees},
  journal = {Journal of Theoretical Biology},
  year = {2010},
  publisher = {Elsevier}
}

@ARTICLE{stadler09,
  author = {T. Stadler},
  title = {On incomplete sampling under birth-death models and connections to
	the sampling-based coalescent},
  journal = {Journal of Theoretical Biology},
  year = {2009},
  volume = {261},
  pages = {58--66}
}

@ARTICLE{stadlerbonhoeffer2013,
  author = {Stadler, Tanja and Bonhoeffer, Sebastian},
  title = {Uncovering epidemiological dynamics in heterogeneous host populations
	using phylogenetic methods},
  journal = {Philosophical Transactions of the Royal Society B: Biological Sciences},
  year = {2013},
  volume = {368},
  pages = {20120198},
  number = {1614}
}

@ARTICLE{Stadler2013,
  author = {Stadler, Tanja and K\"{u}hnert, Denise and Bonhoeffer, Sebastian
	and Drummond, Alexei J.},
  title = {Birth--death skyline plot reveals temporal changes of epidemic spread
	in {HIV} and hepatitis {C} virus ({HCV})},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2013},
  volume = {110},
  pages = {228-233},
  number = {1}
}

@ARTICLE{Stadler012,
  author = {Stadler, Tanja and Kouyos, Roger and von Wyl, Viktor and Yerly, Sabine
	and B\"{o}ni, J\"{u}rg and B\"{u}rgisser, Philippe and Klimkait,
	Thomas and Joos, Beda and Rieder, Philip and Xie, Dong and G{\"u}nthard,
	Huldrych F. and Drummond, Alexei J. and Bonhoeffer, Sebastian and
	the Swiss HIV Cohort Study},
  title = {Estimating the Basic Reproductive Number from Viral Sequence Data},
  journal = MBE,
  year = {2012},
  volume = {29},
  pages = {347-357},
  number = {1}
}

@ARTICLE{StadlerYang2013,
  author = {Stadler, Tanja and Yang, Ziheng},
  title = {Dating phylogenies with sequentially sampled tips},
  journal = SYSB,
  year = {2013},
  doi = {10.1093/sysbio/syt030}
}

@ARTICLE{stamatakis05,
  author = {A. Stamatakis and T. Ludwig and H. Meier},
  title = {{RAxML-III}: {A} fast program for maximum likelihood based inference
	of large phylogenetic tress},
  journal = BI,
  year = {2005},
  volume = {21},
  pages = {456--463}
}

@BOOK{stanton86,
  title = {Constructive {C}ombinatorics},
  publisher = {Springer-Verlag},
  year = {1986},
  author = {D. Stanton and D. White},
  address = {New York}
}

@ARTICLE{steel88,
  author = {M. A. Steel},
  title = {Loss of information from genetic distances},
  journal = {Nature},
  year = {1988},
  volume = {336},
  pages = {118}
}

@ARTICLE{steel04,
  author = {M. A. Steel and D. Penny},
  title = {Two further links between {MP} ad {ML} under the {P}oisson model},
  journal = {Applied Mathematics Letters},
  year = {2004},
  volume = {17},
  pages = {785--790}
}

@ARTICLE{steel93a,
  author = {M. A. Steel and D. Penny},
  title = {Parsimony, likelihood, and the role of models in molecular phylogenetics},
  journal = MBE,
  year = {2000},
  volume = {17},
  pages = {839--850}
}

@ARTICLE{steel93,
  author = {M. A. Steel and D. Penny},
  title = {Distributions of tree comparison metrics --- some new results},
  journal = SYSB,
  year = {1993},
  volume = {42},
  pages = {126--141}
}

@ARTICLE{steel93b,
  author = {M. A. Steel and D. Penny},
  title = {Distributions of tree comparison metrics---some new results},
  journal = SYSB,
  year = {1993},
  volume = {42},
  pages = {126--141}
}

@ARTICLE{Steel2007,
  author = {Steel, M. and Matsen, F.A.},
  title = {The {B}ayesian ``star paradox'' persists for long finite sequences},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {1075},
  number = {4},
  publisher = {SMBE}
}

@INPROCEEDINGS{stephens03,
  author = {M. Stephens},
  title = {Inference under the coalescent},
  booktitle = {Handbook of {S}tatistical {G}enetics, 2nd {E}dition},
  year = {2003},
  editor = {D. J. Balding and M. Bishop and C. Cannings},
  pages = {636--661},
  publisher = {John Wiley \& Sons}
}

@ARTICLE{stephens00,
  author = {M. Stephens},
  title = {Dealing with label-switching in mixture models},
  journal = {Journal of the Royal Statistics Society, Series B },
  year = {2000},
  volume = {62},
  pages = {795--809}
}

@INPROCEEDINGS{stewart99,
  author = {W. J. Stewart},
  title = {Numerical methods for computing stationary distributions of finite
	irreducible {M}arkov chains},
  booktitle = {Advances in Computational Probability},
  year = {1999},
  editor = {W. Grassmann},
  publisher = {Kluwer Academic Publishers}
}

@ARTICLE{stoye98,
  author = {J. Stoye},
  title = {Multiple sequence alignment with the divide-and-conquer method},
  journal = {Gene},
  year = {1998},
  volume = {211},
  pages = {GC45--GC56}
}

@ARTICLE{Straatsma1986,
  author = {Straatsma, TP and Berendsen, HJC and Stam, AJ},
  title = {Estimation of statistical errors in molecular simulation calculations},
  journal = {Molecular Physics},
  year = {1986},
  volume = {57},
  pages = {89--95},
  number = {1},
  publisher = {Taylor \& Francis}
}

@ARTICLE{strauss89,
  author = {Strauss, David and Sadler, Peter M},
  title = {Classical confidence intervals and {B}ayesian probability estimates
	for ends of local taxon ranges},
  journal = {Mathematical Geology},
  year = {1989},
  volume = {21},
  pages = {411--427},
  number = {4}
}

@ARTICLE{Strimmer1997,
  author = {Strimmer, K and Goldman, N and von Haeseler, A},
  title = {Bayesian Probabilities and Quartet Puzzling},
  journal = MBE,
  year = {1997},
  volume = {14},
  pages = {210-211},
  number = {2},
  eprint = {http://mbe.oxfordjournals.org/cgi/reprint/14/2/210.pdf},
  url = {http://mbe.oxfordjournals.org}
}

@ARTICLE{Strimmer1996,
  author = {Strimmer, K. and von Haeseler, A.},
  title = {Quartet Puzzling: A Quartet Maximum-Likelihood Method for Reconstructing
	Tree Topologies},
  journal = MBE,
  year = {1996},
  volume = {13},
  pages = {964},
  number = {7},
  publisher = {SMBE}
}

@ARTICLE{strimmer96,
  author = {K. Strimmer and A. von Haeseler},
  title = {Quartet puzzling: {A} quartet maximum likelihood method for reconstructing
	tree topologies},
  journal = MBE,
  year = {1996},
  volume = {13},
  pages = {964--969}
}

@ARTICLE{subramanian2013,
  author = {Subramanian, Sankar and Beans-Pic{\'o}n, Gabrielle and Swaminathan,
	Siva K and Millar, Craig D and Lambert, David M},
  title = {Evidence for a recent origin of penguins},
  journal = {Biology letters},
  year = {2013},
  volume = {9},
  pages = {20130748},
  number = {6},
  publisher = {The Royal Society}
}

@ARTICLE{suchard05,
  author = {M. A. Suchard},
  title = {Stochastic models for horizontal gene transfer: taking a random walk
	through tree space},
  journal = {Genetics},
  year = {2005},
  volume = {170},
  pages = {419--431}
}

@ARTICLE{suchard03b,
  author = {M. A. Suchard and C. M. R. Kitchen and J. S. Sinsheimer and R. E.
	Weiss},
  title = {Hierarchical phylogenetic models for analyzing multipartite sequence
	data},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {649--664}
}

@ARTICLE{suchard06,
  author = {M. A. Suchard and B. D. Redelings},
  title = {{Bali-Phy}: simultaneous {B}ayesian estimation of alignment and phylogeny},
  journal = BI,
  year = {2006},
  volume = {22},
  pages = {2047--2048}
}

@ARTICLE{suchard03a,
  author = {M. A. Suchard and R. E. Weiss and K. S. Dorman and J. S. Sinsheimer},
  title = {Inferring spatial phylogenetic variation along nucleotide sequences:
	{A} multiple changepoint model},
  journal = {Journal of the American Statistics Association},
  year = {2003},
  volume = {98},
  pages = {427--437}
}

@ARTICLE{suchard02,
  author = {M. A. Suchard and R. E. Weiss and K. S. Dorman and J. S. Sinsheimer},
  title = {Oh brother, where art thou? {A} {B}ayes factor test for recombination
	with uncertain heritage},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {715--728}
}

@ARTICLE{Suchard2003,
  author = {Suchard, Marc A. and Weiss, Robert E. and Sinsheimer, Janet S.},
  title = {Testing a Molecular Clock without an Outgroup: Derivations of Induced
	Priors on Branch-Length Restrictions in a {B}ayesian Framework},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {48-54},
  number = {1}
}

@ARTICLE{suchard01,
  author = {M. A. Suchard and R. E. Weiss and J. S. Sinsheimer},
  title = {Bayesian selection of continuous-time {M}arkov chain evolutionary
	models},
  journal = MBE,
  year = {2001},
  volume = {18},
  pages = {1001--1013}
}

@ARTICLE{Suchard2005,
  author = {Suchard, M.A. and Weiss, R.E. and Sinsheimer, J.S.},
  title = {Models for estimating Bayes factors with applications to phylogeny
	and tests of monophyly},
  journal = {Biometrics},
  year = {2005},
  volume = {61},
  pages = {665--673},
  number = {3},
  publisher = {Wiley Online Library}
}

@ARTICLE{sukumaran10,
  author = {J. Sukumaran and M. T. Holder},
  title = {Dendro{P}y: {A} {P}ython library for phylogenetic computing},
  journal = BI,
  year = {2010},
  volume = {26},
  pages = {1569--1571}
}

@ARTICLE{sullivan05,
  author = {J. Sullivan and P. Joyce},
  title = {Model selection in phylogenetics},
  journal = {Annual Review of Ecology, Evolution, and Systematics},
  year = {2005},
  volume = {36},
  pages = {445--466}
}

@ARTICLE{sullivan01,
  author = {J. Sullivan and D. L. Swofford},
  title = {Should we use model-based methods for phylogenetic inference when
	we know that assumptions about among-site rate variation and nucleotide
	substitution pattern are violated?},
  journal = SYSB,
  year = {2001},
  volume = {50},
  pages = {723--729}
}

@ARTICLE{sullivan99,
  author = {J. Sullivan and D. L. Swofford and G. J. P. Naylor},
  title = {The effect of taxon sampling on estimating rate heterogeneity parameters
	of maximum-likelihood models},
  journal = MBE,
  year = {1999},
  volume = {16},
  pages = {1347--1356}
}

@ARTICLE{Svennblad2006,
  author = {Svennblad, B. and Erixon, P. and Oxelman, B. and Britton, T.},
  title = {Fundamental differences between the methods of maximum likelihood
	and maximum posterior probability in phylogenetics},
  journal = SYSB,
  year = {2006},
  volume = {55},
  pages = {116},
  number = {1}
}

@ARTICLE{Swendsen1987,
  author = {Swendsen, Robert H. and Wang, Jian-Sheng},
  title = {Nonuniversal critical dynamics in {M}onte {C}arlo simulations},
  journal = {Phys. Rev. Lett.},
  year = {1987},
  volume = {58},
  pages = {86--88},
  number = {2},
  month = {Jan},
  doi = {10.1103/PhysRevLett.58.86},
  numpages = {2},
  publisher = {American Physical Society}
}

@ARTICLE{Swofford1991,
  author = {Swofford, D.L.},
  title = {When are phylogeny estimates from molecular and morphological data
	incongruent},
  journal = {Phylogenetic Analysis of DNA Sequences},
  year = {1991},
  pages = {295--333},
  publisher = {Oxford University Press}
}

@BOOK{swofford98,
  title = {{PAUP*}: {P}hylogenetic {A}nalysis {U}sing {P}arsimony and {O}ther
	{M}ethods},
  publisher = {Sinauer Associates, Inc.},
  year = {1998},
  author = {D. L. Swofford},
  address = {Sunderland, Massachusetts}
}

@INPROCEEDINGS{swofford92,
  author = {D. L. Swofford and W. P. Maddison},
  title = {Parsimony, character-state reconstructions, and evolutionary inferences},
  booktitle = {Systematics, historical ecology, and North American freshwater fishes},
  year = {1992},
  editor = {R. L. Mayden},
  pages = {186--223},
  publisher = {Stanford University Press}
}

@INPROCEEDINGS{swofford96,
  author = {D. L. Swofford and G. Olsen and P. Waddell and D. M. Hillis},
  title = {Phylogenetic inference},
  booktitle = {Molecular Systematics, 2nd edition},
  year = {1996},
  editor = {D. M. Hillis and C. Moritz and B. Mable},
  pages = {407--511},
  publisher = {Sinauer Associates, Inc.}
}

@ARTICLE{swofford01,
  author = {D. L. Swofford and P. J. Waddell and J. P. Huelsenbeck and P. G.
	Foster and P. O. Lewis and J. S. Rogers},
  title = {Bias in phylogenetic estimation and its relevance to the choice between
	parsimony and likelihood methods},
  journal = SYSB,
  year = {2001},
  volume = {50},
  pages = {525--539}
}

@ARTICLE{syvanen94,
  author = {M. Syvanen},
  title = {Horizontal gene transfer: evidence and possible consequences},
  journal = {Annual Review of Genetics},
  year = {1994},
  volume = {28},
  pages = {237--261}
}

@ARTICLE{szollHosi2012,
  author = {Sz{\"o}ll{\H{o}}si, Gergely J and Boussau, Bastien and Abby, Sophie
	S and Tannier, Eric and Daubin, Vincent},
  title = {Phylogenetic modeling of lateral gene transfer reconstructs the pattern
	and relative timing of speciations},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2012},
  volume = {109},
  pages = {17513--17518},
  number = {43},
  publisher = {National Acad Sciences}
}

@ARTICLE{tajima93,
  author = {F. Tajima},
  title = {Simple methods for testing molecular clock hypothesis},
  journal = {Genetics},
  year = {1993},
  volume = {135},
  pages = {599--607}
}

@ARTICLE{Tamura2012,
  author = {Tamura, Koichiro and Battistuzzi, Fabia Ursula and Billing-Ross,
	Paul and Murillo, Oscar and Filipski, Alan and Kumar, Sudhir},
  title = {Estimating divergence times in large molecular phylogenies},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2012},
  url = {http://www.pnas.org/content/early/2012/10/31/1213199109.abstract}
}

@ARTICLE{tamura93,
  author = {K. Tamura and M. Nei},
  title = {Estimation of the number of nucleotide substitutions in the control
	region of mitochondrial DNA in humans and chimpanzees},
  journal = MBE,
  year = {1993},
  volume = {10},
  pages = {512--526}
}

@ARTICLE{tarnas98,
  author = {C. Tarnas and R. Hughey},
  title = {{R}educed space hidden {M}arkov model training},
  journal = BI,
  year = {1998},
  volume = {14},
  pages = {401--406},
  number = {5},
  month = {Jun}
}

@ARTICLE{tateno82,
  author = {Y. Tateno and M. Nei and F. Tajima},
  title = {Accuracy of estimated phylogenetic trees from molecular data. {I}.
	{D}istantly related species},
  journal = JME,
  year = {1982},
  volume = {18},
  pages = {387--404}
}

@ARTICLE{Tavare1986,
  author = {Tavar{\'e}, S.},
  title = {Some probabilistic and statistical problems in the analysis of DNA
	sequences},
  journal = {Some Mathematical Questions in Biology•À?DNA Sequence Analysis},
  year = {1986},
  volume = {17},
  pages = {57--86}
}

@ARTICLE{tavare86,
  author = {S. Tavar{\'e}},
  title = {Some probabilistic and statistical problems on the analysis of {DNA}
	sequences},
  journal = {Lectures in Mathematics in the Life Sciences},
  year = {1986},
  volume = {17},
  pages = {57--86}
}

@ARTICLE{Taylor2004,
  author = {Taylor, Derek J. and Piel, William H.},
  title = {An Assessment of Accuracy, Error, and Conflict with Support Values
	from Genome-Scale Phylogenetic Data},
  journal = MBE,
  year = {2004},
  volume = {21},
  pages = {1534-1537},
  number = {8},
  doi = {10.1093/molbev/msh156},
  eprint = {http://mbe.oxfordjournals.org/content/21/8/1534.full.pdf+html},
  url = {http://mbe.oxfordjournals.org/content/21/8/1534.abstract}
}

@ARTICLE{Taylor2005,
  author = {Jesse E. Taylor and Bette T. Korber},
  title = {HIV-1 intra-subtype superinfection rates: estimates using a structured
	coalescent with recombination},
  journal = {Infection, Genetics and Evolution},
  year = {2005},
  volume = {5},
  pages = {85 - 95},
  number = {1},
  doi = {DOI: 10.1016/j.meegid.2004.07.001},
  url = {http://www.sciencedirect.com/science/article/B6W8B-4D1MX6T-1/2/62e9082238a5fc98173cc59f0d84d4c5}
}

@ARTICLE{teh06,
  author = {Y. W. Teh and M. I. Jordan and M. J. Beal and D. M. Blei},
  title = {Hierarchical {D}irichlet processes},
  journal = {Journal of the American Statistical Association},
  year = {2006},
  volume = {101},
  pages = {1566--1581}
}

@MISC{revbayesWeb,
  author = {{The RevBayes Development Team}},
  title = {{RevBayes}: Bayesian phylogenetic inference using probabilistic graphical
	models and an interpreted language},
  howpublished = {\url{http://revbayes.github.io}}
}

@ARTICLE{thomas00,
  author = {A. Thomas and N. Best and D. Spiegelhalter},
  title = {Win{BUGS} --- A {B}ayesian modelling framework: {C}oncepts, structure,
	and extensibility},
  journal = {Statistics and Computing},
  year = {2000},
  volume = {10},
  pages = {325--337}
}

@BOOK{thompson75,
  title = {Human {E}volutionary {T}rees},
  publisher = {Cambridge University Press},
  year = {1975},
  author = {E. A. Thompson},
  address = {Cambridge, England}
}

@ARTICLE{thompson94,
  author = {J. D. Thompson and D. G. Higgins and T. J. Gibson},
  title = {Clustal-{W}---improving the sensitivity of progressive multiple alignment
	through sequence weighting, position-specific gap penalties and weight
	matrix choice},
  journal = {Nucleic Acids Research},
  year = {1994},
  volume = {22},
  pages = {4673--4680}
}

@TECHREPORT{Thompson2010,
  author = {Thompson, M.B.},
  title = {A comparison of methods for computing autocorrelation time},
  institution = {Department of Statistics, University of Toronto},
  year = {2010},
  journal = {Arxiv preprint arXiv:1011.0175}
}

@INPROCEEDINGS{thorne04,
  author = {J. Thorne},
  title = {{B}ayesian calibration of the molecular clock},
  booktitle = {Statistical Methods in Molecular Evolution},
  year = {2004},
  editor = {R. Nielsen},
  publisher = {Springer-Verlag}
}

@ARTICLE{thorne02,
  author = {J. Thorne and H. Kishino},
  title = {Divergence time and evolutionary rate estimation with multilocus
	data},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {689--702}
}

@ARTICLE{thorne98,
  author = {J. Thorne and H. Kishino and I. S. Painter},
  title = {Estimating the rate of evolution of the rate of molecular evolution},
  journal = MBE,
  year = {1998},
  volume = {15},
  pages = {1647--1657}
}

@INPROCEEDINGS{thorne05,
  author = {J. L. Thorne and H. Kishino},
  title = {Estimation of divergence times from molecular sequence data},
  booktitle = {Statistical {M}ethods in {M}olecular {E}volution},
  year = {2005},
  editor = {R. Nielsen},
  pages = {235--256},
  address = {New York},
  publisher = {Springer}
}

@ARTICLE{thorne92,
  author = {J. L. Thorne and H. Kishino and J. Felsenstein},
  title = {Inching Toward Reality: an Improved Likelihood Model of Sequence
	Evolution},
  journal = JME,
  year = {1992},
  volume = {34},
  pages = {3--16}
}

@ARTICLE{thorne91,
  author = {J. L. Thorne and H. Kishino and J. Felsenstein},
  title = {An Evolutionary Model for Maximum Likelihood Alignment of {DNA} Sequences},
  journal = JME,
  year = {1991},
  volume = {33},
  pages = {114--124}
}

@ARTICLE{Thorpe1982,
  author = {Thorpe,J P},
  title = {The Molecular Clock Hypothesis: Biochemical Evolution, Genetic Differentiation
	and Systematics},
  journal = {Annual Review of Ecology and Systematics},
  year = {1982},
  volume = {13},
  pages = {139-168},
  number = {1},
  doi = {10.1146/annurev.es.13.110182.001035},
  eprint = {http://arjournals.annualreviews.org/doi/pdf/10.1146/annurev.es.13.110182.001035},
  url = {http://arjournals.annualreviews.org/doi/abs/10.1146/annurev.es.13.110182.001035}
}

@INPROCEEDINGS{tierney96,
  author = {L. Tierney},
  title = {Introduction to general state-space {M}arkov chain theory},
  booktitle = {Markov {C}hain {M}onte {C}arlo in {P}ractice},
  year = {1996},
  editor = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  pages = {59--74},
  publisher = {Chapman and Hall}
}

@ARTICLE{Tierney1998,
  author = {Tierney, Luke},
  title = {A Note on Metropolis-Hastings Kernels for General State Spaces},
  journal = {The Annals of Applied Probability},
  year = {1998},
  volume = {8},
  pages = {1--9},
  number = {1},
  publisher = {Institute of Mathematical Statistics},
  url = {http://www.jstor.org/stable/2667233}
}

@ARTICLE{Tierney1994,
  author = {Tierney, Luke},
  title = {Markov Chains for Exploring Posterior Distributions},
  journal = {The Annals of Statistics},
  year = {1994},
  volume = {22},
  pages = {1701--1728},
  number = {4},
  publisher = {Institute of Mathematical Statistics},
  url = {http://www.jstor.org/stable/2242477}
}

@ARTICLE{tierney94,
  author = {L. Tierney},
  title = {{Markov} chains for exploring posterior distributions (with discussion)},
  journal = {Annals of Statistics},
  year = {1994},
  volume = {22},
  pages = {1701--1762}
}

@ARTICLE{Tierney1999,
  author = {Tierney, L. and Mira, A.},
  title = {Some Adaptive {M}onte {C}arlo Methods for {B}ayesian Inference},
  journal = {Statistics in Medicine},
  year = {1999},
  volume = {18},
  pages = {2507--2515},
  number = {1718}
}

@ARTICLE{tuffley98,
  author = {C. Tuffley and M. Steel},
  title = {Modeling the covarion hypothesis of nucleotide substitution},
  journal = {Mathematical Biosciences},
  year = {1998},
  volume = {147},
  pages = {63--91}
}

@ARTICLE{tuffley97,
  author = {C. Tuffley and M. Steel},
  title = {Links between maximum likelihood and maximum parsimony under a simple
	model of site substitution},
  journal = {Bulletin of Mathematical Biology},
  year = {1997},
  volume = {59},
  pages = {581--607}
}

@ARTICLE{turner2005,
  author = {Turner, Alan H and Calvo, Jorge O},
  title = {A new sebecosuchian crocodyliform from the {L}ate {C}retaceous of
	{P}atagonia},
  journal = {Journal of Vertebrate Paleontology},
  year = {2005},
  volume = {25},
  pages = {87--98},
  number = {1},
  publisher = {Taylor \& Francis}
}

@ARTICLE{underhill00,
  author = {P. A. Underhill and P. Shen and A. A. Lin and L. Jin and G. Passarino
	and W. H. Yang and E. Kauffman and B. Bonn\'e-Tamir and J. Bertranpetit
	and P. Francalacci and M. Ibrahim and T. Jenkins and J. R. Kidd and
	S. Q. Mehdi and M. T. Seielstad and R. S. Wells and A. Piazza and
	R. W. Davis and M. W. Feldman and L. L. Cavalli-Sforza and P. J.
	Oefner},
  title = {Y chromosome sequence variation and the history of human populations},
  journal = {Nature Genetics},
  year = {2000},
  volume = {26},
  pages = {358--361}
}

@ARTICLE{uzzell71,
  author = {T. Uzzell and K. W. Corbin},
  title = {Fitting discrete probability distributions to evolutionary events},
  journal = {Science},
  year = {1971},
  volume = {172},
  pages = {1089--1096}
}

@ARTICLE{valentine2006,
  author = {Valentine, James W. and Jablonski, David and Kidwell, Susan and Roy,
	Kaustuv},
  title = {Assessing the fidelity of the fossil record by using marine bivalves},
  journal = {Proceedings of the National Academy of Sciences},
  year = {2006},
  volume = {103},
  pages = {6599-6604},
  number = {17},
  doi = {10.1073/pnas.0601264103}
}

@ARTICLE{Valladares2007,
  author = {Valladares, F. and Gianoli, E. and G{\'o}mez, J.M.},
  title = {Ecological limits to plant phenotypic plasticity},
  journal = {New Phytologist},
  year = {2007},
  volume = {176},
  pages = {749--763},
  number = {4},
  publisher = {Wiley Online Library}
}

@ARTICLE{vendetti08,
  author = {C. Vendetti and A. Meade and M. Pagel},
  title = {Phylogenetic mixture models can reduce node-density artifacts},
  journal = SYSB,
  year = {2008},
  volume = {58},
  pages = {286--293}
}

@ARTICLE{verdinelli95,
  author = {I. Verdinelli and L. Wasserman},
  title = {Computing {B}ayes factors using a generalization of the {S}avageÐ{D}ickey
	density ratio},
  journal = {Journal of the American Statistical Association},
  year = {1995},
  volume = {90},
  pages = {614--618}
}

@ARTICLE{vigilant91,
  author = {L. Vigilant and M. Stoneking and H. Harpending and K. Hawkes and
	A. C. Wilson},
  title = {African populations and the evolution of human mitochondrial {DNA}},
  journal = {Science},
  year = {1991},
  volume = {253},
  pages = {1503--1507}
}

@ARTICLE{vingron97,
  author = {M. Vingron and A. von Haeseler},
  title = {Towards integration of multiple alignment and phylogenetic tree construction},
  journal = JCB,
  year = {1997},
  volume = {4},
  pages = {23--34}
}

@ARTICLE{Vos2004,
  author = {Vos, R.A. and Mooers, A.{\O}. and Bininda-Emonds, ORP},
  title = {Reconstructing divergence times for supertrees},
  journal = {Phylogenetic supertrees: Combining information to reveal the tree
	of life},
  year = {2004},
  pages = {281--299}
}

@ARTICLE{Waddell2002,
  author = {Waddell, P.J. and Kishino, H. and Ota, R.},
  title = {Very Fast Algorithms for Evaluating the Stability of {ML} and {B}ayesian
	Phylogenetic Trees from Sequence Data},
  journal = {Genome Informatics},
  year = {2002},
  volume = {13},
  pages = {82--92}
}

@ARTICLE{wagner2000,
  author = {Wagner, Peter J},
  title = {Likelihood tests of hypothesized durations: {D}etermining and accommodating
	biasing factors},
  journal = {Paleobiology},
  year = {2000},
  volume = {26},
  pages = {431--449},
  number = {3}
}

@ARTICLE{wagner2013,
  author = {Wagner, Peter J and Marcot, Jonathan D},
  title = {Modelling distributions of fossil sampling rates over time, space
	and taxa: {A}ssessment and implications for macroevolutionary studies},
  journal = {Methods in Ecology and Evolution},
  year = {2013},
  volume = {4},
  pages = {703--713},
  number = {8}
}

@ARTICLE{Wang1990,
  author = {{Wang}, J.-S. and {Swendsen}, R.~H.},
  title = {Cluster {M}onte {C}arlo algorithms},
  journal = {Physica A Statistical Mechanics and its Applications},
  year = {1990},
  volume = {167},
  pages = {565-579},
  month = sep,
  adsnote = {Provided by the SAO/NASA Astrophysics Data System},
  adsurl = {http://adsabs.harvard.edu/abs/1990PhyA..167..565W},
  doi = {10.1016/0378-4371(90)90275-W}
}

@BOOK{wang1994,
  title = {{Phylogenetic Systematics of the Hesperocyoninae (Carnivora, Canidae)}},
  year = {1994},
  author = {Wang, Xiaoming},
  volume = {221},
  booktitle = {Bulletin of the AMNH}
}

@BOOK{wang1999,
  title = {{Phylogenetic Systematics of the Borophaginae (Carnivora, Canidae)}},
  year = {1999},
  author = {Wang, Xiaoming and Tedford, Richard H and Taylor, Beryl E},
  volume = {243},
  booktitle = {Bulletin of the AMNH}
}

@ARTICLE{warnock2015,
  author = {Warnock, Rachel CM and Parham, James F and Joyce, Walter G and Lyson,
	Tyler R and Donoghue, Philip CJ},
  title = {Calibration uncertainty in molecular dating analyses: there is no
	substitute for the prior evaluation of time priors},
  journal = {Proceedings of the Royal Society B: Biological Sciences},
  year = {2015},
  volume = {282},
  pages = {20141013},
  number = {1798}
}

@ARTICLE{warnock12,
  author = {R. C. M. Warnock and Z. Yang and P. C. J. Donoghue},
  title = {Exploring the uncertainty in the calibration of the molecular clock},
  journal = {Biology Letters},
  year = {2012},
  volume = {8},
  pages = {156--159}
}

@ARTICLE{Waterman1978,
  author = {Waterman, MS and Smith, TF},
  title = {On the similarity of dendrograms},
  journal = {Journal of Theoretical Biology},
  year = {1978},
  volume = {73},
  pages = {732},
  number = {789-800}
}

@ARTICLE{weir2008,
  author = {Weir, J.T. and Schluter, D.},
  title = {Calibrating the avian molecular clock},
  journal = {Molecular Ecology},
  year = {2008},
  volume = {17},
  pages = {2321--2328},
  number = {10}
}

@ARTICLE{weiss1999,
  author = {Weiss, Robert E and Marshall, Charles R},
  title = {The uncertainty in the true end point of a fossil's stratigraphic
	range when stratigraphic sections are sampled discretely},
  journal = {Mathematical Geology},
  year = {1999},
  volume = {31},
  pages = {435--453},
  number = {4}
}

@ARTICLE{welch2005,
  author = {Welch, John J and Bromham, Lindell},
  title = {Molecular dating when rates vary},
  journal = {Trends in Ecology \& Evolution},
  year = {2005},
  volume = {20},
  pages = {320--327},
  number = {6}
}

@ARTICLE{welch05,
  author = {Welch, John J. and Fontanillas, Eric and Bromham, Lindell},
  title = {Molecular Dates for the ``Cambrian Explosion'': The Influence of
	Prior Assumptions},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {672--678}
}

@INPROCEEDINGS{west94,
  author = {M. West and P. M\"uller and M. D. Escobar},
  title = {Hierarchical priors and mixture models, with application in regression
	and density estimation},
  booktitle = {Aspects of Uncertainty: A Tribute to D. V. Lindley},
  year = {1994},
  editor = {A. F. M. Smith and P. Freeman},
  pages = {363--386},
  publisher = {Wiley, Chichester, UK}
}

@ARTICLE{westneat05,
  author = {M. W. Westneat and M. E. Alfaro},
  title = {Phylogenetic relationships and evolutionary history of the reef fish
	family {L}abridae},
  journal = MPE,
  year = {2005},
  volume = {36},
  pages = {370--390}
}

@ARTICLE{Wheeler2010,
  author = {Wheeler, W.C.},
  title = {Distinctions between optimal and expected support},
  journal = {Cladistics},
  year = {2010},
  volume = {26},
  pages = {657Ð663},
  publisher = {Wiley Online Library}
}

@ARTICLE{wheeler90,
  author = {W. C. Wheeler},
  title = {Nucleic acid sequence phylogeny and random outgroups},
  journal = {Cladistics},
  year = {1990},
  volume = {6},
  pages = {363--368}
}

@ARTICLE{Wheeler2008,
  author = {Wheeler, Ward C. and Pickett, Kurt M.},
  title = {Topology-Bayes versus Clade-Bayes in Phylogenetic Analysis},
  journal = MBE,
  year = {2008},
  volume = {25},
  pages = {447-453},
  number = {2},
  eprint = {http://mbe.oxfordjournals.org/content/25/2/447.full.pdf+html},
  url = {http://mbe.oxfordjournals.org/content/25/2/447.abstract}
}

@ARTICLE{whelan07,
  author = {S. Whelan},
  title = {New approaches to phylogenetic tree search and their application
	to large numbers of protein alignments},
  journal = SYSB,
  year = {2007},
  volume = {56},
  pages = {727--740}
}

@ARTICLE{whelan03,
  author = {S. Whelan and P. de Bakker and N. Goldman},
  title = {Pandit: {A} database of protein and associated nucleotide domains
	with inferred trees},
  journal = BI,
  year = {2003},
  volume = {19},
  pages = {1556--1563}
}

@ARTICLE{whelan06,
  author = {S. Whelan and P. de Bakker and E. Quevillon and N. Rodriguez and
	N. Goldman},
  title = {{PANDIT}: {A}n evolution-centric database of protein and associated
	nucleotide domains with inferred trees},
  journal = {Nucleic Acids Research},
  year = {2006},
  volume = {34},
  pages = {D327--D331}
}

@ARTICLE{whelan01,
  author = {S. Whelan and N. Goldman},
  title = {A general empirical model of protein evolution derived from multiple
	protein familes using a maximum likelihood approach},
  journal = MBE,
  year = {2001},
  volume = {18},
  pages = {691--699}
}

@ARTICLE{whiting97,
  author = {M. F. Whiting and J. A. Carpenter and Q. D. Wheeler and W. C. Wheeler},
  title = {The {S}trepsiptera problem: {P}hylogeny of the holometabolous insect
	orders inferred from {18S} and {28S} ribosomal {DNA} sequences and
	morphology},
  journal = SYSB,
  year = {1997},
  volume = {46},
  pages = {1--68}
}

@ARTICLE{whiting94,
  author = {M. F. Whiting and W. C. Wheeler},
  title = {Insect homeotic transformation},
  journal = {Nature},
  year = {1994},
  volume = {368},
  pages = {696}
}

@ARTICLE{wiens09,
  author = {J. J. Wiens},
  title = {Paleontology, Genomics, and Combined-Data Phylogenetics: Can Molecular
	Data Improve Phylogeny Estimation for Fossil Taxa?},
  journal = SYSB,
  year = {2009},
  volume = {58},
  pages = {87--99}
}

@ARTICLE{wiens05,
  author = {J. J. Wiens and J. W. Fetzner and C. L. Parinson and T. W. Reeder},
  title = {Hylid frog phylogeny and sampling strategies for speciose clades},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {719--748}
}

@ARTICLE{wiens10,
  author = {J. J. Wiens and C. A. Kuczynski and T. Townsend and T. W. Reeder
	and D. G. Mulcahy and J. W. Sites},
  title = {Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile
	Phylogeny: Molecular Data Change the Placement of Fossil Taxa},
  journal = SYSB,
  year = {2010},
  volume = {59},
  pages = {674--688}
}

@ARTICLE{Wiens2011,
  author = {Wiens, John J. and Morrill, Matthew C.},
  title = {Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations
	and Empirical Data},
  journal = SYSB,
  year = {2011},
  volume = {60},
  pages = {719-731},
  number = {5}
}

@ARTICLE{wiens98,
  author = {J. J. Wiens and M. R. Servedio},
  title = {Phylogenetic analysis and intraspecific variation: {P}erformance
	of parsimony, likelihood, and distance methods},
  journal = SYSB,
  year = {1998},
  volume = {47},
  pages = {228--253}
}

@BOOK{wiley81,
  title = {Phylogenetics: {T}he {T}heory and {P}ractice of {P}hylogenetic {S}ystematics},
  publisher = {John Wiley and Sons},
  year = {1981},
  author = {E. O. Wiley},
  address = {New York}
}

@ARTICLE{wiley75,
  author = {E. O. Wiley},
  title = {Karl {R}. {P}opper, systematics, and classification: {A} reply to
	{W}alter {B}ock and other evolutionary taxonomists},
  journal = SYSB,
  year = {1975},
  volume = {24},
  pages = {233--243}
}

@ARTICLE{wilkinson11,
  author = {R. D. Wilkinson and M. E. Steiper and C. Soligo and R. D. Martin
	and Z. Yang and S. Tavar\'e},
  title = {Dating Primate Divergences through an Integrated Analysis of Palaeontological
	and Molecular Data},
  journal = SYSB,
  year = {2011},
  volume = {60},
  pages = {16--31}
}

@ARTICLE{wilks38,
  author = {S. S. Wilks},
  title = {The large-sample distribution of the likelihood ratio for testing
	composite hypotheses},
  journal = {Ann. Math. Statist.},
  year = {1938},
  volume = {9},
  pages = {554--560}
}

@ARTICLE{williams71,
  author = {W. T. Williams and H. T. Clifford},
  title = {On the comparison of two classifications of the same set of elements},
  journal = {Taxon},
  year = {1971},
  volume = {20},
  pages = {519--522}
}

@ARTICLE{Wilson2003,
  author = {Wilson, I.J. and Weale, M.E. and Balding, D.J.},
  title = {Inferences from {DNA} data: population histories, evolutionary processes
	and forensic match probabilities},
  journal = {Journal of the Royal Statistical Society: Series A (Statistics in
	Society)},
  year = {2003},
  volume = {166},
  pages = {155--188},
  publisher = {Blackwell Synergy}
}

@ARTICLE{Wilson1998,
  author = {Wilson, Ian J. and Balding, David J.},
  title = {Genealogical Inference From Microsatellite Data},
  journal = {Genetics},
  year = {1998},
  volume = {150},
  pages = {499-510},
  eprint = {http://www.genetics.org/cgi/reprint/150/1/499.pdf},
  url = {http://www.genetics.org/cgi/content/abstract/150/1/499}
}

@ARTICLE{wimmer02,
  author = {R. Wimmer and S. Kirsch and G. A. Rappold and W. Schempp},
  title = {Direct evidence for the {\it {H}omo-{P}an} clade},
  journal = {Chromosome Research},
  year = {2002},
  volume = {10},
  pages = {55--61}
}

@INPROCEEDINGS{woese93,
  author = {C. R. Woese and N. R. Pace},
  title = {Probing {RNA} structure, function, and history by comparative analysis},
  booktitle = {The RNA World},
  year = {1993},
  editor = {R. F. Gesteland and J. F. Atkins},
  pages = {91--117},
  publisher = {Cold Spring Harbor Laboratory Press}
}

@MASTERSTHESIS{wong06,
  author = {K. M. Wong},
  title = {A systematic analysis of multiple alignment variability using common
	phylogenetic estimation parameters},
  school = {University of California, San Diego},
  year = {2006}
}

@ARTICLE{wong08,
  author = {K. M. Wong and M. A. Suchard and J. P. Huelsenbeck},
  title = {Alignment uncertainty and genomic analysis},
  journal = {Science},
  year = {2008},
  volume = {319},
  pages = {473--476}
}

@ARTICLE{Wood01032013,
  author = {Wood, Hannah Marie and Matzke, Nicholas J. and Gillespie, Rosemary
	G. and Griswold, Charles E.},
  title = {Treating Fossils as Terminal Taxa in Divergence Time Estimation Reveals
	Ancient Vicariance Patterns in the Palpimanoid Spiders},
  journal = SYSB,
  year = {2013},
  volume = {62},
  pages = {264-284},
  number = {2}
}

@ARTICLE{wright51,
  author = {S. Wright},
  title = {The genetical structure of populations},
  journal = {Ann. Eugen.},
  year = {1951},
  volume = {15},
  pages = {323--354}
}

@ARTICLE{wuCH2013,
  author = {Wu, Chieh-Hsi and Suchard, Marc A. and Drummond, Alexei J.},
  title = {Bayesian Selection of Nucleotide Substitution Models and Their Site
	Assignments},
  journal = MBE,
  year = {2013},
  volume = {30},
  pages = {669-688},
  number = {3}
}

@ARTICLE{Xia2011,
  author = {Xuhua Xia and Qun Yang},
  title = {A distance-based least-square method for dating speciation events},
  journal = {Molecular Phylogenetics and Evolution},
  year = {2011},
  volume = {59},
  pages = {342 - 353},
  number = {2},
  doi = {10.1016/j.ympev.2011.01.017},
  issn = {1055-7903},
  url = {http://www.sciencedirect.com/science/article/pii/S1055790311000443}
}

@ARTICLE{xiang06,
  author = {Q. Y. Xiang and D. T. Thomas and W. Zhang and S. R. Manchester and
	Z. Murrell},
  title = {Species level phylogeny of the genus {\it {C}ornus} ({C}ornaceae)
	based on molecular and morphological evidence --- implications for
	taxonomy and {T}ertiary intercontinental migration},
  journal = {Taxon},
  year = {2006},
  volume = {55},
  pages = {9--30}
}

@ARTICLE{xiang08,
  author = {Q. Y. Xiang and J. L. Thorne and T. K. Seo and W. H. Zhang and D.
	T. Thomas and R. E. Ricklefs},
  title = {Rates of nucleotide substitution in {C}ornaceae ({C}ornales) ---
	pattern of variation and underlying causal factors},
  journal = MPE,
  year = {2008},
  volume = {49},
  pages = {327--342}
}

@ARTICLE{xie11,
  author = {W. Xie and P. O. Lewis and Y. Fan and L. Kuo and M.-H. Chen},
  title = {Improving marginal likelihood estimation for {B}ayesian phylogenetic
	model selection},
  journal = SYSB,
  year = {2011},
  volume = {60},
  pages = {150--160}
}

@INPROCEEDINGS{yang04,
  author = {Z. Yang},
  title = {Detecting positive selection using {PAML}},
  booktitle = {Statistical Methods in Molecular Evolution},
  year = {2004},
  editor = {R. Nielsen},
  publisher = {Springer-Verlag}
}

@ARTICLE{Yang2008,
  author = {Yang, Z.},
  title = {Empirical evaluation of a prior for {B}ayesian phylogenetic inference},
  journal = {Phil. Trans. R. Soc. B},
  year = {2008},
  volume = {363},
  pages = {4031--4039},
  publisher = {Citeseer}
}

@ARTICLE{Yang2007,
  author = {Yang, Z.},
  title = {Fair-balance paradox, star-tree paradox, and {B}ayesian phylogenetics},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {1639},
  number = {8},
  publisher = {SMBE}
}

@ARTICLE{Yang2007a,
  author = {Yang, Ziheng},
  title = {{PAML} 4: Phylogenetic Analysis by Maximum Likelihood},
  journal = MBE,
  year = {2007},
  volume = {24},
  pages = {1586-1591},
  number = {8},
  doi = {10.1093/molbev/msm088},
  eprint = {http://mbe.oxfordjournals.org/cgi/reprint/24/8/1586.pdf},
  url = {http://mbe.oxfordjournals.org/cgi/content/abstract/24/8/1586}
}

@ARTICLE{yang04a,
  author = {Z. Yang},
  title = {A heuristic rate smoothing procedure for maximum likelihood estimation
	of species divergence times},
  journal = {Acta Zoologica Sinica},
  year = {2004},
  volume = {50},
  pages = {645--656}
}

@ARTICLE{yang97a,
  author = {Z. Yang},
  title = {{PAML}: {A} program package for phylogenetic analysis by maximum
	likelihood},
  journal = {Computer Applications in BioSciences},
  year = {1997},
  volume = {13},
  pages = {555--556}
}

@ARTICLE{yang96a,
  author = {Z. Yang},
  title = {Maximum-likelihood models for combined analyses of multiple sequence
	data},
  journal = JME,
  year = {1996},
  volume = {42},
  pages = {587--596}
}

@ARTICLE{yang96b,
  author = {Z. Yang},
  title = {Phylogenetic analysis using parsimony and likelihood methods},
  journal = JME,
  year = {1996},
  volume = {42},
  pages = {294--307}
}

@ARTICLE{yang95a,
  author = {Z. Yang},
  title = {A space-time process model for the evolution of {DNA} sequences},
  journal = {Genetics},
  year = {1995},
  volume = {139},
  pages = {993--1005}
}

@ARTICLE{yang94a,
  author = {Z. Yang},
  title = {Maximum likelihood phylogenetic estimation from {DNA} sequences with
	variable rates over sites: {A}pproximate methods},
  journal = JME,
  year = {1994},
  volume = {39},
  pages = {306--314}
}

@ARTICLE{yang94b,
  author = {Z. Yang},
  title = {Estimating the pattern of nucleotide substitution},
  journal = JME,
  year = {1994},
  volume = {39},
  pages = {105--111}
}

@ARTICLE{yang93,
  author = {Z. Yang},
  title = {Maximum likelihood estimation of phylogeny from {DNA} sequences when
	substitution rates differ over sites},
  journal = MBE,
  year = {1993},
  volume = {10},
  pages = {1396--1401}
}

@ARTICLE{yang95b,
  author = {Z. Yang and N. Goldman and A. E. Friday},
  title = {Maximum likelihood trees from {DNA} sequences: {A} peculiar statistical
	estimation problem},
  journal = SYSB,
  year = {1995},
  volume = {44},
  pages = {384--399}
}

@ARTICLE{yang95c,
  author = {Z. Yang and S. Kumar and M. Nei},
  title = {A new method for inference of ancestral nucleotide and amino acid
	sequences},
  journal = {Genetics},
  year = {1995},
  volume = {141},
  pages = {1641--1650}
}

@ARTICLE{yang02,
  author = {Z. Yang and R. Nielsen},
  title = {Codon-substitution models for detecting molecular adaptation at individual
	sites along specific lineages},
  journal = MBE,
  year = {2002},
  volume = {19},
  pages = {908--917}
}

@ARTICLE{yang00,
  author = {Z. Yang and R. Nielsen and N. Goldman and A. M. K. Pedersen},
  title = {Codon-substitution models for heterogeneous selection pressure},
  journal = {Genetics},
  year = {2000},
  volume = {155},
  pages = {431--449}
}

@ARTICLE{yang98,
  author = {Z. Yang and R. Nielsen and M. Hasegawa},
  title = {Models of amino acid substitution and applications to mitochondrial
	protein evolution},
  journal = MBE,
  year = {1998},
  volume = {15},
  pages = {1600--1611}
}

@ARTICLE{yang06,
  author = {Z. Yang and B. Rannala},
  title = {Bayesian estimation of species divergence times under a molecular
	clock using multiple fossil calibrations with soft bounds},
  journal = MBE,
  year = {2006},
  volume = {23},
  pages = {212--226}
}

@ARTICLE{Yang2005,
  author = {Yang, Z. and Rannala, B.},
  title = {Branch-length prior influences {B}ayesian posterior probability of
	phylogeny},
  journal = SYSB,
  year = {2005},
  volume = {54},
  pages = {455--470},
  number = {3}
}

@ARTICLE{yang97b,
  author = {Z. Yang and B. Rannala},
  title = {{B}ayesian phylogenetic inference using {DNA} sequences: {A} {Markov}
	chain {Monte {C}arlo} method},
  journal = MBE,
  year = {1997},
  volume = {14},
  pages = {717--724}
}

@ARTICLE{yang03,
  author = {Z. Yang and A. D. Yoder},
  title = {Comparison of likelihood and {B}ayesian methods for estimating divergence
	times using multiple gene loci and calibration points, with application
	to a radiation of cute-looking mouse lemur species},
  journal = SYSB,
  year = {2003},
  volume = {52},
  pages = {705--716}
}

@ARTICLE{yeldandi91,
  author = {A. V. Yeldandi and V. Yeldandi and S. Kumar and C. V. Murthy and
	X. D. Wang and K. Alvares and M. S. Rao and J. K. Reddy},
  title = {Molecular evolution of the urate oxidase-encoding gene in hominoid
	primates: nonsense mutations},
  journal = {Gene},
  year = {1991},
  volume = {109},
  pages = {281--284}
}

@ARTICLE{yoder00,
  author = {A. D. Yoder and Z. Yang},
  title = {Estimation of primate speciation dates using local molecular clocks},
  journal = MBE,
  year = {2000},
  volume = {17},
  pages = {1081--1090}
}

@ARTICLE{yu06,
  author = {J. Yu and J. L. Thorne},
  title = {Dependence among sites in {RNA} evolution},
  journal = MBE,
  year = {2006},
  volume = {23},
  pages = {1525--1537}
}

@ARTICLE{yule24,
  author = {G. U. Yule},
  title = {A mathematical theory of evolution, based on the conclusions of {Dr.
	J. C. Wills, F. R. S.}},
  journal = {Philosophical Transactions of the Royal Society of London, Biology},
  year = {1924},
  volume = {213},
  pages = {21--87}
}

@ARTICLE{zani00,
  author = {P. A. Zani},
  title = {The comparative evolution of lizard claw and toe morphology and clinging
	performance},
  journal = {Journal of Evolutionary Biology},
  year = {2000},
  volume = {13},
  pages = {316--325}
}

@ARTICLE{zanotto96,
  author = {P. M. Zanotto and E. A. Gould and G. F. Gao and P. H. Harvey and
	E. C. Holmes},
  title = {Population dynamics of flaviviruses revealed by molecular phylogenies},
  journal = PNAS,
  year = {1996},
  volume = {93},
  pages = {548--553}
}

@ARTICLE{zhang97,
  author = {J. Zhang and M. Nei},
  title = {Accuracies of ancestral amino acid sequences inferred by the parsimony,
	likelihood, and distance methods},
  journal = JME,
  year = {1997},
  volume = {44},
  pages = {5139--5146}
}

@ARTICLE{zhao02,
  author = {Z. Zhao and E. Boerwinkle},
  title = {Neighboring-nucleotide effects on single nucleotide polymorphisms:
	{A} study of 2.6 million polymorphisms across the human genome},
  journal = {Genome Research},
  year = {2002},
  volume = {12},
  pages = {1679--1686}
}

@INPROCEEDINGS{zimmerman31,
  author = {W. Zimmerman},
  title = {Arbeitsweise der botanischen {P}hylogenetik und anderer {G}ruppierungswissenschaften},
  booktitle = {Handbuch der biologischen {A}rbeitsmethoden},
  year = {1931},
  editor = {E. Abderhalden},
  pages = {941--1053},
  publisher = {Urban and Schwarzenberg, Berlin}
}

@INPROCEEDINGS{zuckerkandl62,
  author = {E. Zuckerkandl and L. Pauling},
  title = {Molecular disease, evolution, and genetic heterogeneity},
  booktitle = {Horizons in Biochemistry},
  year = {1962},
  editor = {M. Kasha and B. Pullman},
  pages = {189--225},
  publisher = {Academic Press, New York}
}

@ARTICLE{Zuckerkandl1965,
  author = {Zuckerkandl, E. and Pauling, L.},
  title = {Evolutionary divergence and convergence in proteins},
  journal = {Evolving Genes and Proteins},
  year = {1965},
  pages = {97--166}
}

@ARTICLE{zuker89,
  author = {M. Zuker},
  title = {On Finding All Suboptimal Foldings of an {RNA} Molecule},
  journal = {Science},
  year = {1989},
  volume = {244},
  pages = {48--52}
}

@ARTICLE{zwickl06,
  author = {D. J. Zwickl},
  title = {Genetic algorithm approaches for the phylogenetic analyses of large
	biological sequence datasets under the maximum likelihood criterion},
  journal = {Ph.D. dissertation, The University of Texas at Austin},
  year = {2006},
  volume = {www.bio.utexas.edu/faculty/antisense/garli/Garli.html}
}

@ARTICLE{zwickl02,
  author = {D. J. Zwickl and D. M. Hillis},
  title = {Increased taxon sampling greatly reduces phylogenetic error},
  journal = SYSB,
  year = {2002},
  volume = {51},
  pages = {588--598}
}

@ARTICLE{zwickl04,
  author = {D. J. Zwickl and M. T. Holder},
  title = {Model parameterization, prior distributions, and the general time-reversible
	model in {B}ayesian phylogenetics},
  journal = SYSB,
  year = {2004},
  volume = {53},
  pages = {877--888}
}

@BOOK{gilks96a,
  title = {Markov chain {M}onte {C}arlo in practice},
  publisher = {Chapman and Hall/CRC},
  year = {1996},
  editor = {W. R. Gilks and S. Richardson and D. J. Spiegelhalter},
  address = {Boca Raton}
}

@BOOK{jordan99,
  title = {Learning in graphical models},
  publisher = {MIT Press},
  year = {1999},
  editor = {M. I. Jordan},
  address = {Cambridge, MA}
}

@MISC{penguinBlog,
  title = {March of the Fossil Penguins},
  howpublished = {\url{https://fossilpenguins.wordpress.com}}
}

@MISC{revbayesGH,
  title = {The RevBayes GitHub Repository},
  howpublished = {\url{https://github.com/revbayes/revbayes}}
}

@Article{Vaughan2017,
  author  = {Vaughan, Timothy Glenn},
  title   = {{IcyTree}: Rapid browser-based visualization for phylogenetic trees and networks},
  journal = {Bioinformatics},
  year    = {2017},
  pages   = {in press},
  doi     = {https://doi.org/10.1093/bioinformatics/btx155},
}