biogeography

This repository contains the analysis for "Testing geology with biology: Plate tectonics and the diversification of microhylid frogs in the Papuan region"

History

2023-06-01 First release with data, code, results, and etc folders.

Overview

This repository supports the paper Hill et al (2023 in press), which tests hypotheses of biogeographical evolution in the hyperdiverse asterophryine frogs of the New Guinea region. A major idea is that plate tectonics can explain the hyperdiversity of these frogs by amplifying opportunities for dispersal and cladogenesis. We use DEC biogeographic models implemented in the R packages BioGeoBEARS and produce plots using ggplot2 and ggtree. See the code and data explainer provided in code/biogeog.html and the paper Hill et al (2023 in press) published in Integrative Organismal Biology.

Software requirements

This repository requires use of R, Quarto, Github and a reference manager for bibtex. A plain text editor is also necessary.

Repository structure

The description of the directory structure is as follows (Please see the README.md files in each folder for more details):

• All data is in the data folder or is referenced as a link to a publicly available file.
• All code is in the code folder. An explanation of all of the code is in the quarto file biogeog.qmd, and rendered for easy reading in biogeog.html (open the .html in a browser).
• All results (figures, tables, computed values) are saved into the results folder.
• Accessory files needed for the bibliography and styles are in the etc folder.
• The LaTeX file for the manuscript and its component parts are in the manuscript folder.
• See the various README.md files in those folders for some more information.

Reproducing the analysis

1. Run biogeog.R from the code folder
2. Run tree_plotting_DEC.R from the code folder (Figure 4)
3. Run genera_thru_time.R from the code folder (Figure 5)

Citations

(This study) Hill E.C., Gao D.F., Polhemus, D.A., Fraser C.J., Iova B., Allison A., and Butler M.A. (in press) Testing geology with biology: Plate tectonics and the diversification of microhylid frogs in the Papuan region. Integrative Organismal Biology.

Hill E.C., Fraser C.J., Gao D.F., Jarman M., Henry E.R., Iova B., Allison A., and Butler M.A. (2022) Resolving the deep phylogeny: Implications for Early Adaptive Radiation, Cryptic, and Present-day Ecological Diversity of Papuan Microhylid Frogs. Molecular Phylogenetics and Evolution. https://doi.org/10.1016/j.ympev.2022.107618

Hill E.C., Jarman M., Fraser C.J., Gao D.F., Henry E.R., Fisher, A.R., Iova B., Allison A., and Butler M.A. (2023) Molecular and phylogenetic datasets for the Asterophryinae frogs of New Guinea with additional data on lifestyle, geography, and elevation. Data in Brief. https://doi.org/10.1016/j.dib.2023.108987