refs.bib

@article {Ghodsi:2013bc,
author = {Ghodsi, Mohammadreza and Hill, Christopher M and Astrovskaya, Irina and Lin, Henry and Sommer, Dan D and Koren, Sergey and Pop, Mihai},
title = {{De novo likelihood-based measures for comparing genome assemblies.}},
journal = {BMC Research Notes},
year = {2013},
volume = {6},
xnumber = {1},
pages = {334},
month = aug
}

@article {Sturtevant:1913,
author = {Sturtevant, A. H.},
title = {The linear arrangement of six sex-linked factors in \textit{{Drosophila}}, as shown by their mode of association},
journal = {Journal of Experimental Zoology},
volume = {14},
xnumber = {1},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
xissn = {1097-010X},
xurl = {http://dx.xdoi.org/10.1002/jez.1400140104},
xdoi = {10.1002/jez.1400140104},
pages = {43--59},
year = {1913},
}

@article {Studer:2011,
author = {Studer, A. and Zhao, Q. and Ross-Ibarra, J. and Doebley, J.},
title = {Identificaiton of a functinal transposon insertion in the maize domestication gene \textit{tb1}},
journal = {Nature Genetics},
volume = {43},
xnumber = {1},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
xissn = {1097-010X},
xurl = {http://dx.xdoi.org/10.1002/jez.1400140104},
xdoi = {10.1002/jez.1400140104},
pages = {1160--1163},
year = {2011},
}

@article {Keeling:2008,
author = {Keeling, C. I. and Weisshaar, S. and Lin, R. P. C. and Bohlmann, J.},
title = {Functional plasticity of paralogous diterpene synthases involved in conifer defense},
journal = {Proceedings of the National Academy of Sciences USA},
volume = {105},
xnumber = {1},
xpublisher = {Wiley Subscription Services, Inc., A Wiley Company},
xissn = {1097-010X},
xurl = {http://dx.xdoi.org/10.1002/jez.1400140104},
xdoi = {10.1002/jez.1400140104},
pages = {1085--1090},
year = {2008},
}

@article {Pavy:2012,
author = {Pavy, N. and Pelgas, B. and Laroche, J. and Rigault, P. and Isabel, N. and Bousquet, J.},
title = {A spruce gene map infers ancient plant genome reshuffling and subsequent slow evolution in the gymnosperm lineage leading to extant conifers},
journal = {BMC Biology},
volume = {10},
xnumber = {1},
xpublisher = {Wiley Subscription Services, Inc., A Wiley Company},
xissn = {1097-010X},
xurl = {http://dx.xdoi.org/10.1002/jez.1400140104},
xdoi = {10.1002/jez.1400140104},
pages = {84},
year = {2012},
}

@article {Hausmann:2005,
author = {Hausmann, N. J. and Juenger, T. E. and Sen, S. and Stowe, K. A. and Dawson, T. E. and Simms, E. L.},
title = {Quantitative trait loci affecting $\delta^{13}${C} and response to differential water availability in \textit{Arabidopsis thaliana}},
journal = {Evolution},
volume = {59},
xnumber = {1},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
xissn = {1097-010X},
xurl = {http://dx.xdoi.org/10.1002/jez.1400140104},
xdoi = {10.1002/jez.1400140104},
pages = {81--96},
year = {2005},
}

@article {Moritsuka:2012,
author = {Moritsuka, E. and Histaka, Y. and Tamura, M. and Uchiyama, K. and Watanabe A. and Tsmura, Y. and Tachida, H.},
title = {Extended linkage disequilibrium in noncoding regions in a conifer, \textit{Cryptomeria japonica}},
journal = {Genetics},
volume = {190},
xnumber = {1},
publisher = {Wiley Subscription Services, Inc., A Wiley Company},
xissn = {1097-010X},
xurl = {http://dx.xdoi.org/10.1002/jez.1400140104},
xdoi = {10.1002/jez.1400140104},
pages = {1145--1148},
year = {2012},
}

@article {Limborg:2014,
author = {Limborg, M. T. and Waples, R. K. and Seeb, J. E. and Seeb, L. W.},
title = {Temporally isolated lineages of pink salmon reveal unique signatures of selection on distinct pools of standing genetic variation},
journal = {Journal of Heredity},
volume = {105},
pages = {741--751},
year = {2014},
}


@article {Mantel:1967,
author = {Mantel, N.},
title = {The detection of disease clustering and a generalized regression approach},
journal = {Cancer Research},
volume = {27},
xnumber = {2},
pages = {209--220},
year = {1967},
}

@article {Tani:2003,
author = {Tani, N. and Takahashi, T. and Iwata, H. and Mukai, Y. and Ujino-Ihara, T. and et al.},
title = {A consensus linkage map for Sugi (\textit{Cryptomeria japonica}) from two pedigrees, based on microsatellites and expressed sequence tags},
journal = {Genetics},
volume = {165},
pages = {1551--1568},
year = {2003},
}

@article {Scheet:2006,
author = {Scheet, P. and Stephens, M.},
title = {A fast and flexible statistical model for large-scale population genotype data: Applications to inferring missing genotypes and haplotypic phase},
journal = {American Journal of Human Genetics},
volume = {78},
xnumber = {2},
pages = {629--644},
year = {2006},
}

@article {Neves:2014,
author = {Neves, L. G. and Davis, J. M. and Barbazuk, W. B. and Kirst M.},
title = {A high-density gene map of loblolly pine (\textit{Pinus taeda} L.) based on exome sequence capture genotyping},
journal = {G3},
volume = {4},
xnumber = {2},
pages = {29--37},
year = {2014},
}

@article {Neale:2014,
author = {Neale, D. B. and Wegrzyn, J. L. and Stevens, K. A. and Zimin, A. V. and Puiu, D and et al.},
title = {Decoding the massive genome of loblolly pine using haploid {DNA} and novel assembly strategies},
journal = {Genome Biology},
volume = {15},
xnumber = {2},
pages = {R59},
year = {2014},
}

@article {Akerman:2014,
author = {Akerman, A. and Burger, R.},
title = {The consequences of gene flow for local adaptation and differentiation: a two-locus two-deme model},
journal = {Mathematical Biology},
volume = {68},
pages = {1135--1198},
year = {2014},
}

@article {Cheema:2009,
author = {Cheema, J. and Dicks, J.},
title = {Computational approaches and software tools for genetic linkage map estimation in plants},
journal = {Briefings in Bioinformatics},
volume = {10},
pages = {595--608},
year = {2009},
}

@article {Hackett:2003,
author = {Hackett, C. A. and Broadfoot, L. B.},
title = {Effects of genotyping errors, missing values and segregation distortion in molecular marker data on the construction of linkage maps},
journal = {Heredity},
volume = {90},
pages = {33--38},
year = {2003},
}

@article {Chakravarti:1991,
author = {Chakravarti, A. and Lasher, L. K. and Reefer, J. E.},
title = {A maximum-likelihood method for estimating genome length using genetic linkage data},
journal = {Genetics},
volume = {128},
pages = {175--182},
year = {1991},
}

@article {Lange:1982,
author = {Lange, K. and Boehnke, M.},
title = {How many polymorphic marker genes will it take to span the human genome?},
journal = {American Journal of Human Genetics},
volume = {128},
pages = {842--845},
year = {1982},
}

@article {Eckert:2012a,
author = {Eckert, Andrew J. and Dyer, Rodney J.},
title = {Defining the landscape of adaptive genetic diversity},
journal = {Molecular Ecology},
volume = {21},
xnumber = {12},
publisher = {Blackwell Publishing Ltd},
xissn = {1365-294X},
xurl = {http://dx.xdoi.org/10.1111/j.1365-294X.2012.05615.x},
xdoi = {10.1111/j.1365-294X.2012.05615.x},
pages = {2836--2838},
keywords = {adaptive traits, conifers, fitness landscape, genome-wide association, serotiny},
year = {2012},
}

@article {Kawecki:2004,
author = {Kawecki, Tadeusz J. and Ebert, Dieter},
title = {Conceptual issues in local adaptation},
journal = {Ecology Letters},
volume = {7},
xnumber = {12},
publisher = {Blackwell Science Ltd},
xissn = {1461-0248},
xurl = {http://dx.xdoi.org/10.1111/j.1461-0248.2004.00684.x},
xdoi = {10.1111/j.1461-0248.2004.00684.x},
pages = {1225--1241},
keywords = {Adaptive deme formation, adaptive evolution, coevolution, heterogeneous environments, gene flow, metapopulations, natural selection, population differentiation, reciprocal transplant, review},
year = {2004},
}

@article {Pannell:2013,
author = {Pannell, John R. and Fields, Peter D.},
title = {Evolution in subdivided plant populations: concepts, recent advances and future directions},
journal = {New Phytologist},
xissn = {1469-8137},
xurl = {http://dx.xdoi.org/10.1111/nph.12495},
xdoi = {10.1111/nph.12495},
year = {2013},
volume = {201},
pages = {417--432},
}

@article {Fisher:1918,
author = {Fisher, R. A.},
title = {The correlation between relatives on the supposition of Mendelian inheritance},
journal = {Transactions of the Royal Society of Edinburgh},
volume = {52},
pages = {399--433},
year = {1918},
}

@article {Hoffman:2008,
author = {Hoffmann, A. A. and Riesberg, L. H.},
title = {{Revisiting the impact of inversions in Evolution: From population genetic markers to drivers of adaptive shifts and speciation}},
journal = {Annual Review of Ecology, Evolution, and Systematics},
volume = {39},
pages = {21--42},
year = {2008},
}

@article {Mauricio:2001,
author ={Mauricio, Rodney},
title = {Mapping quantitative trait loci in plants: uses and caveats for evolutionary biology},
journal = {Nature Reviews Genetics},
volume = {2},
xnumber ={5},
xurl = {http://dx.xdoi.org/10.1038/35072085},
xdoi = {10.1038/35072085},
pages = {370--381},
year = {2001},
}

@article {Neale:2011,
author ={Neale, David B. and Kremer, Antoine},
title = {Forest tree genomics: growing resources and applications},
journal = {Nature Reviews Genetics},
volume = {12},
xnumber ={2},
xurl = {http://dx.xdoi.org/10.1038/nrg2931},
xdoi = {10.1038/nrg293},
pages = {111--122},
year = {2011},
}

@incollection{Ritland:2011,
author = {Ritland, Kermit and Krutovsky, Konstantin V. and Tsumura, Yoshihiko and Pelgas, Betty and Isabel, Nathalie and Bousquet, Jean},
title= {Genetic Mapping in Conifers},
editor={Plomion, Christophe and Bousquet, Jean and Kole, Chittaranjan},
booktitle = {Genetics, Genomics and Breeding of Conifers},
year = {2011},
address = {New York},
publisher = {CRC Press},
pages = {196--238},
}

@article {Ingvarsson:2011,
author = {Ingvarsson, Par K. and Street, Nathaniel R.},
title = {Association genetics of complex traits in plants},
journal = {New Phytologist},
volume = {189},
xnumber = {4},
publisher = {Blackwell Publishing Ltd},
xissn = {1469-8137},
xurl = {http://dx.xdoi.org/10.1111/j.1469-8137.2010.03593.x},
xdoi = {10.1111/j.1469-8137.2010.03593.x},
pages = {909--922},
keywords = {association mapping, complex traits, genetic architecture, genotyping, phenotyping},
year = {2011},
}

@article {Eckert:2013a,
author = {Eckert, Andrew J. and Wegrzyn, Jill Lee and Liechty, John D. and Lee, Jennifer M. and Cumbie, W. Patrick and Davis, John M. and Goldfarb, Barry and Loopstra, Carol A. and Palle, Sreenath R. and Quesada, Tania and Langley, Charles H. and Neale, David B.}, 
title = {The evolutionary genetics of the genes underlying phenotypic associations for loblolly pine (\textit{{Pinus} taeda}, {Pinaceae})},
year = {2013}, 
xdoi = {10.1534/genetics.113.157198}, 
xurl = {http://www.genetics.org/content/early/2013/10/07/genetics.113.157198.abstract}, 
journal = {Genetics},
volume = {112},
pages = {4--12},
}

@article {Anderson:2013a,
author = {Anderson, Jill T and Wagner, Maggie R and Rushworth, Catherine A and Prasad, Kasavajhala V S K and Mitchell-Olds, Thomas},
title = {The evolution of quantitative traits in complex environments},
journal = {Heredity},
xurl = {http://dx.xdoi.org/10.1038/hdy.2013.33},
xdoi = {10.1038/hdy.2013.33},
year = {2014},
volume = {195},
pages = {1353--1372},
}

@article {Anderson:2013b,
author = {Anderson, Jill T. and Lee, Cheng-Ruei and Rushworth, Catherine A. and Colautti, Robert I. and Mitchell-Olds, Thomas},
title = {Genetic trade-offs and conditional neutrality contribute to local adaptation},
journal = {Molecular Ecology},
volume = {22},
xnumber = {3},
publisher = {Blackwell Publishing Ltd},
xissn = {1365-294X},
xurl = {http://dx.xdoi.org/10.1111/j.1365-294X.2012.05522.x},
xdoi = {10.1111/j.1365-294X.2012.05522.x},
pages = {699--708},
year = {2013},
}

@article {Fournier-Level:2013,
author = {Fournier-Level, Alexandre and Wilczek, Amity M. and Cooper, Martha D. and Roe, Judith L. and Anderson, Jillian and Eaton, Deren and Moyers, Brook T. and Petipas, Renee H. and Schaeffer, Robert N. and Pieper, Bjorn and Reymond, Matthieu and Koornneef, Maarten and Welch, Stephen M. and Remington, David L. and Schmitt, Johanna},
title = {Paths to selection on life history loci in different natural environments across the native range of \textit{{Arabidopsis thaliana}}},
journal = {Molecular Ecology},
volume = {22},
xnumber = {13},
xissn = {1365-294X},
xurl = {http://dx.xdoi.org/10.1111/mec.12285},
xdoi = {10.1111/mec.12285},
pages = {3552--3566},
keywords = {adaptation, angiosperms, life history evolution, natural selection and contemporary evolution, phenotypic plasticity, quantitative genetics},
year = {2013},
}

@book {White:2007,
author = {White, Thomas L. and Adams, William T. and Neale, David B.},
title= {Forest genetics},
year = {2007},
address = {Cambridge},
publisher = {CABI Publishing},
}

@article {Alberto:2013,
author = {Alberto, Florian J. and Aitken, Sally N. and Alia, Ricardo and Gonzalez-Martinez, Santiago C. and Hanninen, Heikki and Kremer, Antoine and Lefevre, Francois and Lenormand, Thomas and Yeaman, Sam and Whetten, Ross and Savolainen, Outi},
title = {Potential for evolutionary responses to climate change - evidence from tree populations},
journal = {Global Change Biology},
volume = {19},
xnumber = {6},
xissn = {1365-2486},
xurl = {http://dx.xdoi.org/10.1111/gcb.12181},
xdoi = {10.1111/gcb.12181},
pages = {1645--1661},
keywords = {adaptive traits, conifers, local adaptation, natural selection, phenotypic plasticity, provenance trials, quantitative genetics},
year = {2013},
}

@article{Kirkpatrick:2006,
author = {Kirkpatrick, Mark and Barton, Nick}, 
title = {Chromosome inversions, local adaptation and speciation},
volume = {173}, 
xnumber = {1}, 
pages = {419-434}, 
year = {2006}, 
xdoi = {10.1534/genetics.105.047985}, 
xurl = {http://www.genetics.org/content/173/1/419.abstract}, 
xeprint = {http://www.genetics.org/content/173/1/419.full.pdf+html}, 
journal = {Genetics} 
}

@article {Yeaman:2011,
author = {Yeaman, Sam and Whitlock, Michael C.},
title = {The genetic architecture of adaptation under migration-selection balance},
journal = {Evolution},
volume = {65},
xnumber = {7},
publisher = {Blackwell Publishing Inc},
xissn = {1558-5646},
xurl = {http://dx.xdoi.org/10.1111/j.1558-5646.2011.01269.x},
xdoi = {10.1111/j.1558-5646.2011.01269.x},
pages = {1897--1911},
keywords = {Chromosomal inversions, genetic architecture, genomic islands of divergence, linkage, migrationâ€-selection balance, quantitative trait loci},
year = {2011},
}

@article{Yeaman:2013,
author = {Yeaman, Sam}, 
title = {Genomic rearrangements and the evolution of clusters of locally adaptive loci},
year = {2013}, 
xdoi = {10.1073/pnas.1219381110}, 
xurl = {http://www.pnas.org/content/early/2013/04/19/1219381110.abstract}, 
journal = {Proceedings of the National Academy of Sciences USA},
volume = {110},
pages = {E1743--E1751},
}

@article{Zerbino:2008bm,
author = {Zerbino, Daniel R and Birney, Ewan},
title = {{Velvet: algorithms for de novo short read assembly using de Bruijn graphs.}},
journal = {Genome Research},
year = {2008},
volume = {18},
number = {5},
pages = {821--829},
month = may
}

@article {Koboldt:2013,
author = {Koboldt, Daniel C. and Steinberg, Karyn Meltz and Larson, David E. and Wilson, Richard K. and Mardis, Elaine R.},
title = {The next-generation sequencing revolution and its impact on genomics},
journal = {Cell},
volume = {155},
xurl = {http://linkinghub.elsevier.com/retrieve/pii/S0092867413011410},
pages = {27--38},
year = {2013},
}

@article {Ahuja:2005,
author = {Ahuja, M. Raj and Neale, David B.},
title = {Evolution of genome size in conifers},
journal = {Silvae Genetica},
volume = {54},
pages = {126--137},
year = {2005},
}

@article{Mackay:2012,
year={2012},
issn={0167-4412},
journal={Plant Molecular Biology},
volume={80},
xnumber={6},
xdoi={10.1007/s11103-012-9961-7},
title={Towards decoding the conifer giga-genome},
xurl={http://dx.doi.org/10.1007/s11103-012-9961-7},
xpublisher={Springer Netherlands},
xkeywords={Conifers; Giga-genome sequencing; Functional genomics; Comparative genomics; Integrative studies},
author={Mackay, John and Dean, Jeffrey F. D. and Plomion, Christophe and Peterson, Daniel G. and Canovas, Francisco M. and Pavy, Nathalie and Ingvarsson, Par K. and Savolainen, Outi and Guevara, M. Angeles and Fluch, Silvia and Vinceti, Barbara and Abarca, Dolores and Diaz-Sala, Carmen and Cervera, Maria-Teresa},
pages={555-569},
xlanguage={English}
}


@article{Langmead:2012jh,
author = {Langmead, Ben and Salzberg, Steven L},
title = {{Fast gapped-read alignment with Bowtie 2.}},
journal = {Nature Methods},
year = {2012},
volume = {9},
xnumber = {4},
pages = {357--359},
month = apr
}

@article{Li:2009ka,
author = {Li, Heng and Handsaker, Bob and Subgroup, 1000 Genome Project Data Processing and {10}},
title = {{The Sequence Alignment/Map format and SAMtools.}},
journal = {Bioinformatics},
year = {2009},
volume = {25},
xnumber = {16},
pages = {2078--2079},
xmonth = aug
}

@article{Friedline:2012fm,
author = {Friedline, C J and Franklin, R B and McCallister, S L and Rivera, M C},
title = {{Bacterial assemblages of the eastern Atlantic Ocean reveal both vertical and latitudinal biogeographic signatures}},
journal = {Biogeosciences},
year = {2012},
volume = {9},
xnumber = {6},
pages = {2177--2193}
}

@article {Murray:1998,
author = {Murray, Brian G.},
title = {Nuclear {DNA} amounts in gymnosperms},
journal = {Annals of Botany},
volume = {82},
pages = {3--15},
year = {1998},
}

@article{Nystedt:2013,
author = {Nystedt, Bjorn and Street, Nathaniel R. and Wetterbom, Anna and Zuccolo, Andrea and Lin, Yao-Cheng and et al.},
title = {{The Norway spruce genome sequence and conifer genome evolution}},
journal = {Nature},
year = {2013},
volume = {497},
xnumber = {na},
pages = {579--584},
xdoi = {10.1038/nature12211}
}

@article{Martinez-Garcia:2013,
year={2013},
xissn={1614-2942},
journal={Tree Genetics and Genomes},
xdoi={10.1007/s11295-013-0646-4},
title={{Combination of multipoint maximum likelihood (MML) and regression mapping algorithms to construct a high-density genetic linkage map for loblolly pine (\textit{{Pinus taeda}} {L.})}},
xurl={http://dx.doi.org/10.1007/s11295-013-0646-4},
xpublisher={Springer Berlin Heidelberg},
xkeywords={High-density genetic map; Loblolly pine; Multipoint maximum likelihood algorithm; Regression mapping},
author={Martinez-Garcia, Pedro J. and Stevens, Kristian A. and Wegrzyn, Jill L. and Liechty, John and Crepeau, Marc and Langley, Charles H. and Neale, David B.},
xpages={1--7},
xlanguage={English},
volume = {9},
pages = {1529--1535},
}

@article{Eckert:2010a,
author = {Eckert, Andrew J. and van Heerwaarden, Joost and Wegrzyn, Jill L. and Nelson, C. Dana and Ross-Ibarra, Jeffrey and Gonzalez-Martinez, Santiago C. and Neale, David. B.}, 
title = {Patterns of population structure and environmental associations to aridity across the range of loblolly pine (\textit{{Pinus taeda}} {L.}, {Pinaceae})},
volume = {185}, 
xnumber = {3}, 
pages = {969--982}, 
year = {2010}, 
xdoi = {10.1534/genetics.110.115543}, 
xURL = {http://www.genetics.org/content/185/3/969.abstract}, 
journal = {Genetics} 
}

@article {Eckert:2010b,
author = {Eckert, Andrew J. and Bower, Andrew D. and Gonzalez-Martinez, Santiago C. and Wegrzyn, Jill L. and Coop, Graham and Neale, David B.},
title = {Back to nature: ecological genomics of loblolly pine (\textit{{Pinus taeda}}, {Pinaceae})},
journal = {Molecular Ecology},
volume = {19},
xnumber = {17},
publisher = {Blackwell Publishing Ltd},
xissn = {1365-294X},
xurl = {http://dx.doi.org/10.1111/j.1365-294X.2010.04698.x},
xdoi = {10.1111/j.1365-294X.2010.04698.x},
pages = {3789--3805},
xkeywords = {adaptation, ecological genomics, environmental gradients, Pinus taeda, population structure, single nucleotide polymorphisms},
year = {2010},
}

@article{Houle:2011,
title = {Measurement and Meaning in Biology},
author = {Houle, David and Pélabon, Christophe and  Wagner, Gunter P. and Hansen, Thomas F. },
journal = {The Quarterly Review of Biology},
volume = {86},
xnumber = {1},
pages = {3--34},
year = {2011},
}

@article {Cairney:2007,
author = {Cairney, John and Pullman, Gerald S.},
title = {The cellular and molecular biology of conifer embryogenesis},
journal = {New Phytologist},
volume = {176},
xnumber = {3},
xpublisher = {Blackwell Publishing Ltd},
xissn = {1469-8137},
xurl = {http://dx.doi.org/10.1111/j.1469-8137.2007.02239.x},
xdoi = {10.1111/j.1469-8137.2007.02239.x},
pages = {511--536},
xkeywords = {conifer, embryo, embryogenesis, female gametophyte, gene expression, gymnosperm, megagametophyte, molecular biology},
year = {2007},
}

@article{Tulsieram:1992,
title = {Singletree genetic linkage mapping in conifers using haploid {DNA} from megagametophytes},
author = {Tulsieram, L. K. and Glaubitz, J. C. and Kiss, G. and Carlson, J. E.},
journal = {Biotechnology},
volume = {10},
pages = {3--34},
year = {1992},
}

@article{Nelson:1993,
title = {A partial genetic linkage map of slash pine (\textit{{Pinus elliottii}} {Engelm.} var. \textit{elliottii}) based on random amplified polymorphic {DNA}},
author = {Nelson, C. Dana and Nance, Warren L. and Doudrick, Robert L.},
journal = {Theoretical and Applied Genetics},
volume = {87},
pages = {145--151},
year = {1993},
}

@article{Kubisiak:1996,
title = {Comparison of RAPD linkage maps constructed for a single longleaf pine from both haploid and diploid mapping populations},
author = {Kubisiak, Thomas L. and Nelson, C. Dana and Name, W. L. and Stine, M.},
journal = {Forest Genetics},
volume = {3},
pages = {203--211},
year = {1996},
}

@article{Kang:2010,
title = {{Near-saturated and complete genetic linkage map of black spruce (\textit{{Picea mariana}})}},
author = {Kang, Bum-Yong and Mann, Ishminder K. and Major, John E. and Rajora, Om P.},
journal = {BMC Genomics},
volume = {11},
pages = {515},
year = {2010},
}

@article{Achere:2004,
year={2004},
xissn={0040-5752},
journal={Theoretical and Applied Genetics},
volume={108},
xnumber={8},
xdoi={10.1007/s00122-004-1587-y},
title={A full saturated linkage map of \textit{{Picea abies}} including {AFLP, SSR, ESTP, 5S rDNA} and morphological markers},
xurl={http://dx.doi.org/10.1007/s00122-004-1587-y},
xpublisher={Springer-Verlag},
author={Achere, V. and Faivre-Rampant, P. and Jeandroz, S. and Besnard, G. and Markussen, T. and Aragones, A. and Fladung, M. and Ritter, E. and Favre, J.-M.},
pages={1602-1613},
xlanguage={English}
}

@article{Travis:1998,
year={1998},
journal={Theoretical and Applied Genetics},
volume={97},
title={A genetic linkage map of pinyon pine (\textit{{Pinus edulis}}) based on amplified fragment length polymorphisms},
author={Travis, S. E. and Ritland, K. and Whitham, T. G. and Keim, P.},
pages={871--880},
}

@article{Peterson:2012,
author = {Peterson, Brant K. and Weber, Jesse N. and Kay, Emily H. and Fisher, Heidi S. and Hoekstra, Hopi E.},
journal = {PLoS ONE},
title = {{Double digest RADseq: An inexpensive method for de novo SNP discovery and genotyping in model and non-model species}}, 
year = {2012},
pages = {e37135},
xdoi = {10.1371/journal.pone.0037135},
volume={7},
}

@article{Pfender:2011,
author={Pfender, W. F. and Saha, M. C. and Johnson, E. A. and Slabaugh, M. B.},
journal={Theoretical and Applied Genetics},
title={Mapping with {RAD} (restriction-site associated {DNA}) markers to rapidly identify {QTL} for stem rust resistance in \textit{{Lolium perenne}}}, 
year = {2011},
volume = {122},
pages={1467--1480},
xdoi={10.1007/s00122-011-1546-3},
}

@article{Ward:2013,
author = {Ward, Judson and Bhangoo, Jasbir and Fernandez-Fernandez, Felicidad and Moore, Patrick and Swanson, JD and Viola, Roberto and Velasco, Riccardo and Bassil, Nahla and Weber, Courtney and Sargent, Daniel},
title = {Saturated linkage map construction in \textit{{Rubus idaeus}} using genotyping by sequencing and genome-independent imputation},
journal = {BMC Genomics},
volume = {14},
year = {2013},
pages = {2},
}

@article {Parchman:2012,
author = {Parchman, Thomas L. and Gompert, Zachriah and Mudge, Joann and Schilkey, Faye D. and Benkman, Craig W. and Buerkle, C. Alex},
title = {Genome-wide association genetics of an adaptive trait in lodgepole pine},
journal = {Molecular Ecology},
volume = {21},
xnumber = {12},
xpublisher = {Blackwell Publishing Ltd},
xissn = {1365-294X},
xurl = {http://dx.doi.org/10.1111/j.1365-294X.2012.05513.x},
xdoi = {10.1111/j.1365-294X.2012.05513.x},
pages = {2991--3005},
xkeywords = {association mapping, next-generation sequencing, Pinus contorta, population genomics, serotiny},
year = {2012},
}

@article{Gernandt:2005,
title = {Phylogeny and classification of \textit{{Pinus}}},
author = {Gernandt, David S. and Lopez, Gretel Geada and Garcia, Sol Ortiz and Liston, Aaron},
journal = {Taxon},
volume = {54},
pages = {29--42},
year = {2005},
}

@article{Bailey:1970,
title = {Phytogeography and taxonomy of \textit{{Pinus}} subsection \textit{{Balfourianae}}},
author = {Bailey, D. K.},
journal = {Annals Missouri Botanical Garden},
volume = {57},
pages = {210--249},
year = {1970},
}

@article{Eckert:2006a,
title={Phylogeny, historical biogeography, and patterns of diversification for \textit{{Pinus}} ({Pinaceae}): Phylogenetic tests of fossil-based hypotheses},
author={Eckert, Andrew J. and Hall, Benjamin D.},
journal={Molecular Phylogenetics and Evolution},
volume={40},
xnumber={1},
pages={166--182},
year={2006},
xpublisher={Elsevier},
}

@article{Eckert:2008,
title={A phylogeographical analysis of the range disjunction for foxtail pine (\textit{{Pinus balfouriana}}, {Pinaceae}): the role of Pleistocene glaciation},
author={Eckert, Andrew J. and Tearse, Brandon R. and Hall, Benjamin D.},
journal={Molecular Ecology},
volume={17},
xnumber={8},
pages={1983--1997},
year={2008},
xpublisher={Wiley Online Library},
}

@article{Eckert:2006b,
title={Influence of substrate type and microsite availability on the persistence of foxtail pine (\textit{{Pinus balfouriana}}, Pinaceae) in the Klamath Mountains, California},
author={Eckert, Andrew J.},
journal={American Journal of Botany},
volume={93},
xnumber={11},
pages={1615--1624},
year={2006},
xpublisher={Botanical Soc America},
}

@article{Oline:2000,
title={Population and subspecific genetic differentiation in the foxtail pine (\textit{{Pinus balfouriana}})},
author={Oline, David K. and Mitton, Jeffry B. and Grant, Michael C.},
journal={Evolution},
volume={54},
pages={1813--1819},
year={2000},
}

@article{Morton:1955,
title={Sequential tests for the detection of linkage},
author={Morton, N. E.},
journal={American Journal of Human Genetics},
volume={7},
pages={277--318},
year={1955},
}

@article{Davey:2010,
author = {Davey, John W. and Blaxter, Mark L.}, 
title = {{RADSeq}: next-generation population genetics},
volume = {9}, 
xnumber = {5-6}, 
pages = {416--423}, 
year = {2010}, 
xdoi = {10.1093/bfgp/elq031}, 
xeprint = {http://bfg.oxfordjournals.org/content/9/5-6/416.full.pdf+html}, 
journal = {Briefings in Functional Genomics} 
}

@article{Mastrogiuseppe:1980,
title = {A study of \textit{{Pinus balfouriana}} {Grev.} \& {Balf.} ({Pinaceae})},
author = {Mastrogiuseppe, R. J. and Mastrogiuseppe, J. D.},
journal = {Systematic Botany},
volume={5},
pages = {86--104},
year={1980},
}

@article{Ellegren:2008,
author = {Ellegren, Hans and Sheldon, Ben C.},
journal = {Nature},
volume={452},
pages={169--175},
title={Genetic basis of fitness differences in natural populations},
year={2008},
}

@article{Stevison:2011,
author = {Stevison, Laurie S. and Hoehn, Kenneth B. and Noor, Mohamed A. F.},
journal = {Genome Biology and Evolution},
volume={3},
pages={830--841},
title={Effects of inversions on within- and between-species recombination and divergence},
year={2011},
}

@article{VanOoijen:2011,
author = {Van Ooijen, J. W.},
journal = {Genetics Research},
volume={93},
pages={343--349},
title={Multipoint maximum likelihood mapping in a full-sib family of an outbreeding species},
year={2011},
}

@article{Cartwright:2007,
author = {Cartwright, Dustin A. and Troggio, Michela and Velasco, Riccardo and Gutin, Alexander}, 
title = {Genetic mapping in the presence of genotyping errors},
volume = {176}, 
xnumber = {4}, 
pages = {2521-2527}, 
year = {2007}, 
xdoi = {10.1534/genetics.106.063982}, 
xabstract ={Genetic maps are built using the genotypes of many related individuals. Genotyping errors in these data sets can distort genetic maps, especially by inflating the distances. We have extended the traditional likelihood model used for genetic mapping to include the possibility of genotyping errors. Each individual marker is assigned an error rate, which is inferred from the data, just as the genetic distances are. We have developed a software package, called TMAP, which uses this model to find maximum-likelihood maps for phase-known pedigrees. We have tested our methods using a data set in Vitis and on simulated data and confirmed that our method dramatically reduces the inflationary effect caused by increasing the number of markers and leads to more accurate orders.}, 
xURL = {http://www.genetics.org/content/176/4/2521.abstract}, 
xeprint = {http://www.genetics.org/content/176/4/2521.full.pdf+html}, 
journal = {Genetics}, 
}

@article{Ward:1963,
author = {Ward, J. H. Jr.},
journal = {Journal of the American Statistical Association},
volume={58},
pages={236--244},
title={Hierarchical grouping to optimize an objective function},
year={1963},
}

@inbook{Kaufman:1987,
author = {Kaufman, L. and Rousseeuw, P. J.},
title= {Clustering by means of Medoids},
editor={Dodge, Y.},
booktitle = {{Statistical Data Analysis Based on the \textit{L{_1}}-Norm and Related Methods}},
year = {1987},
address = {Basel, Switzerland},
publisher = {Birkhauser Verlag},
xchapter = {na},
pages = {405--416},
}

@article{Sokal:1958,
author = {Sokal, R. and Michener, C.},
journal = {University of Kansas Science Bulletin},
volume={38},
pages={1409--1438},
title={A statistical method for evaluating systematic relationships},
year={1958},
}

@article{Antonovics:1970,
author = {Antonovics, J. and Bradshaw, A. D.},
journal = {Heredity},
volume={25},
pages={349--362},
title={{Evolution in closely adjacent plant populations VIII. Clinal patterns at a mine boundary}},
year={1970},
}

@article{Rousseeuw:1987,
author = {Rousseeuw, P. J.},
journal = {Journal of Computational and Applied Mathematics},
volume={20},
pages={53--65},
title={Silhouettes: A graphical aid to the interpretation and validation of cluster analysis},
year={1987},
}

@article{Kosambi:1944,
author = {Kosambi, D. D.},
journal = {Annals of Eugenics},
volume={12},
pages={172--175},
title={The estimation of map distance from recombination values},
year={1944},
}

@Manual{R:2013,
title = {R: A Language and Environment for Statistical Computing},
author = {{R Core Team}},
organization = {R Foundation for Statistical Computing},
address = {Vienna, Austria},
year = {2013},
url = {http://www.R-project.org},
}

@article{Hamming:1950,
author = {Hamming, R. W.},
journal = {Bell System Technical Journal},
volume={29},
pages={147--160},
title={Error detecting and error correcting codes},
year={1950},
}

@article{Morris:1978,
author = {Morris, R. W. and Spieth, P. T.},
journal = {Theoretical and Applied Genetics},
volume={51},
pages={217--222},
title={Sampling strategies for using female gametophytes to estimate heterozygosity in conifers},
year={1978},
}

@article{Wu:2008b,
author = {Wu, Y. and Close, T. J. and Lonardi, S.},
journal = {Computational Systems and Bioinformatics Conference},
volume={7},
pages={285--296},
title={On the accurate construction of consensus genetic maps},
year={2008},
}

@article{Spearman:1904,
author = {Spearman, C.},
journal = {American Journal of Psychology},
volume={15},
pages={72--101},
title={The proof and measurement of association between two things},
year={1904},
}

@article{Pool:2010,
author = {Pool, John E. and Hellmann, Ines and Jensen, Jeffrey D. and Nielsen, Rasmus},
journal = {Genome Research},
volume={20},
pages={291--300},
title={Population genetic inference from genomic sequence variation},
year={2010},
}

@article{Wu:2008a,
author = {Wu, Yonghui and Bhat, Prasanna R. and Close, Timothy J. and Lonardi, Stefano},
journal = {PLoS Genetics},
xpublisher = {Public Library of Science},
title = {Efficient and accurate construction of genetic linkage maps from the minimum spanning tree of a graph},
year = {2008},
volume = {4},
xurl = {http://dx.doi.org/10.1371%2Fjournal.pgen.1000212},
pages = {e1000212},
} 

@article{Willyard:2007,
author = {Willyard, A. and  Syring, J. and Gernandt, D. and Liston, A. and Cronn, R.},
title = {{Fossil calibration of molecular divergence in \textit{Pinus}: inferences for ages and mutation rates}},
journal = {Molecular Biology and Evolution},
year = {2007},
volume={24},
pages = {90--101},
}

@book{Nei:1987,
author = {Nei, M},
publisher = {Columbia University Press},
title = {Molecular Evolutionary Genetics},
year = {1987},
} 

@article{Eckert:2009,
author = {Eckert, A. J. and Pande, B. and Ersoz, E. S. and Wright, M. H. and Rashbrook,  V. K. and Nicolet, C. M. and Neale, D. B.},
journal = {Tree Genetics and Genomes},
title = {High-throughput genotyping and mapping of single nucleotide polymorphisms in loblolly pine ({Pinus taeda} L.)},
year = {2009},
volume = {5},
pages = {225--234},
} 


@article{Earl:2011gt,
author = {Earl, Dent and Bradnam, Keith and St John, John and Darling, Aaron and Lin, Dawei and Fass, Joseph and Yu, Hung On Ken and Buffalo, Vince and Zerbino, Daniel R and Diekhans, Mark and Nguyen, Ngan and Ariyaratne, Pramila Nuwantha and Sung, Wing-Kin and Ning, Zemin and Haimel, Matthias and Simpson, Jared T and Fonseca, Nuno A and Birol, {\'I}nan{\c c} and Docking, T Roderick and Ho, Isaac Y and Rokhsar, Daniel S and Chikhi, Rayan and Lavenier, Dominique and Chapuis, Guillaume and Naquin, Delphine and Maillet, Nicolas and Schatz, Michael C and Kelley, David R and Phillippy, Adam M and Koren, Sergey and Yang, Shiaw-Pyng and Wu, Wei and Chou, Wen-Chi and Srivastava, Anuj and Shaw, Timothy I and Ruby, J Graham and Skewes-Cox, Peter and Betegon, Miguel and Dimon, Michelle T and Solovyev, Victor and Seledtsov, Igor and Kosarev, Petr and Vorobyev, Denis and Ramirez-Gonzalez, Ricardo and Leggett, Richard and MacLean, Dan and Xia, Fangfang and Luo, Ruibang and Li, Zhenyu and Xie, Yinlong and Liu, Binghang and Gnerre, Sante and MacCallum, Iain and Przybylski, Dariusz and Ribeiro, Filipe J and Yin, Shuangye and Sharpe, Ted and Hall, Giles and Kersey, Paul J and Durbin, Richard and Jackman, Shaun D and Chapman, Jarrod A and Huang, Xiaoqiu and DeRisi, Joseph L and Caccamo, Mario and Li, Yingrui and Jaffe, David B and Green, Richard E and Haussler, David and Korf, Ian and Paten, Benedict},
title = {{Assemblathon 1: a competitive assessment of de novo short read assembly methods.}},
journal = {Genome Research},
year = {2011},
volume = {21},
number = {12},
pages = {2224--2241},
month = dec
}


@article{Bradnam:2013uu,
author = {Bradnam, Keith R and Fass, Joseph N and Alexandrov, Anton and Baranay, Paul and Bechner, Michael and  and Boisvert, S{\'e}bastien and Chapman, Jarrod A and Chapuis, Guillaume and Chikhi, Rayan and Chitsaz, Hamidreza and Chou, Wen-Chi and Corbeil, Jacques and Del Fabbro, Cristian and Docking, T Roderick and Durbin, Richard and Earl, Dent and Emrich, Scott and Fedotov, Pavel and Fonseca, Nuno A and Ganapathy, Ganeshkumar and Gibbs, Richard A and Gnerre, Sante and Godzaridis, {\'E}l{\'e}nie and Goldstein, Steve and Haimel, Matthias and Hall, Giles and Haussler, David and Hiatt, Joseph B and Ho, Isaac Y and Howard, Jason and Hunt, Martin and Jackman, Shaun D and Jaffe, David B and Jarvis, Erich and Jiang, Huaiyang and Kazakov, Sergey and Kersey, Paul J and Kitzman, Jacob O and Knight, James R and Koren, Sergey and Lam, Tak-Wah and Lavenier, Dominique and Laviolette, Fran{\c c}ois and Li, Yingrui and Li, Zhenyu and Liu, Binghang and Liu, Yue and Luo, Ruibang and MacCallum, Iain and MacManes, Matthew D and Maillet, Nicolas and Melnikov, Sergey and Vieira, Bruno Miguel and Naquin, Delphine and Ning, Zemin and Otto, Thomas D and Paten, Benedict and Paulo, Oct{\'a}vio S and Phillippy, Adam M and Pina-Martins, Francisco and Place, Michael and Przybylski, Dariusz and Qin, Xiang and Qu, Carson and Ribeiro, Filipe J and Richards, Stephen and Rokhsar, Daniel S and Ruby, J Graham and Scalabrin, Simone and Schatz, Michael C and Schwartz, David C and Sergushichev, Alexey and Sharpe, Ted and Shaw, Timothy I and Shendure, Jay and Shi, Yujian and Simpson, Jared T and Song, Henry and Tsarev, Fedor and Vezzi, Francesco and Vicedomini, Riccardo and Wang, Jun and Worley, Kim C and Yin, Shuangye and Yiu, Siu-Ming and Yuan, Jianying and Zhang, Guojie and Zhang, Hao and Zhou, Shiguo and Korf, Ian F},
title = {{Assemblathon 2: evaluating de novo methods of genome assembly in three vertebrate species}},
journal = {arXiv.org},
year = {2013},
eprint = {1301.5406v3},
eprinttype = {arxiv},
eprintclass = {q-bio.GN},
month = jan,
annote = {Additional files available at
  http://korflab.ucdavis.edu/Datasets/Assemblathon/Assemblathon2/Additional{\_}files/
  Major changes 1. Accessions for the 3 read data sets have now been included
  2. New file: spreadsheet containing details of all Study, Sample, Run, {\&}
  Experiment identifiers 3. Made miscellaneous changes to address reviewers
  comments. DOIs added to GigaDB datasets}
}

@article{Salzberg:2011fr,
author = {Salzberg, S L and Phillippy, A M and Yorke, J A and {13}},
title = {{GAGE: A critical evaluation of genome assemblies and assembly algorithms}},
journal = {Genome Research},
year = {2011},
pages = {--},
month = dec
}

@article{Altschul:1990vt,
author = {Altschul, S.F. and Gish, W. and Miller, W. and Myers, E.W. and Lipman, D.J.},
title = {{Basic local alignment search tool}},
journal = {Journal of Molecular Biology},
year = {1990},
volume = {215},
xnumber = {3},
pages = {403--410},
publisher = {Elsevier},
rating = {0},
date-added = {2011-11-15T17:04:28GMT},
date-modified = {2014-01-23T18:13:50GMT},
local-url = {file://localhost/Users/chris/Dropbox/Library.papers3/Files/22/2202D2E8-7D71-4B14-98A0-BB56DA6815FA.pdf},
file = {{2202D2E8-7D71-4B14-98A0-BB56DA6815FA.pdf:/Users/chris/Dropbox/Library.papers3/Files/22/2202D2E8-7D71-4B14-98A0-BB56DA6815FA.pdf:application/pdf}},
uri = {\url{papers3://publication/uuid/2CD9E70A-4A6D-4DC7-8B42-8C8BF4D61151}}
}

@article{Supek:2011bw,
author = {Supek, Fran and Bosnjak, Matko and Skunca, Nives and Smuc, Tomislav},
title = {{REVIGO summarizes and visualizes long lists of gene ontology terms.}},
journal = {PLoS ONE},
year = {2011},
volume = {6},
number = {7},
pages = {e21800--e21800},
month = jan
}

@article{Danecek:2011gz,
author = {Danecek, Petr and Auton, Adam and Abecasis, Goncalo and Albers, Cornelis A and Banks, Eric and DePristo, Mark A and Handsaker, Robert E and Lunter, Gerton and Marth, Gabor T and Sherry, Stephen T and McVean, Gilean and Durbin, Richard and {1000 Genomes Project Analysis Group}},
title = {{The variant call format and VCFtools.}},
journal = {Bioinformatics},
year = {2011},
volume = {27},
number = {15},
pages = {2156--2158},
month = aug
}