Code and data for article "Negative global-scale association between genetic diversity and speciation rates in mammals"

This is a little overview of the analyses performed for the manuscript submitted entitled "Negative global-scale association between genetic diversity and speciation rates in mammals".
OtherDataThis folder includes data from previously published articles and used for this project. It includes the available geographic coordinates for cyt b sequences, data from Upham et al. 2019 (DR tip speciation rates and used nuclear loci), the trait data and other nuclear datasets. Other Upham et a. 2019 files that were required to get ClaDS speciation rates are in 5.speciation_rate/inputs folder.
Figures_tableThis folder includes all the table, and main figures and supplementary figures used in the manuscript, both in pdf and png format. The folder Phylopics includes the phylopic svg files used in figure 1, and it includes link for each in PhylopicLinks.txt.
Scripts used in the analyses organized by folders1. Folder_per_family.R:* Extract GenBank sequence for a given family to get metadata per family using NCBI taxonomy database and prepare folders to parallelize SuperCrunch per family
2.nameMatching Scripts that improve how many sequences in GenBank can be matched into Upham et al. 2019 tree
3.superCrunch_family Scripts to run alignment of GenBank sequences per species
4.genetic_diversityScripts to get genetic diversity per species and the data used for analyses.
5.speciation_Rate Scripts to get speciation rates per species and the data used for analyses.
6.mutationRate Scripts to get mutation rates per species and the data used for analyses.
7.pgls Scripts to run PGLS analyses and the results.
8.bmlmScripts to run BMLM analyses and the results
Figures_v3.RmdRmarkdown file with code used to make all the figures, including some extra models mentioned in the manuscript. It also includes the code used to export the Source Data files used for each figure, versions of the used packages and exports the R working environment.
Output as HTML file Figures_v3.html that can be opened in a browser.
data.tar.xzSource data file with all the data used to make the figures.