DOI: 10.5061/dryad.r43s0
title: Data from: Using phylogenomics to understand the link between biogeographic origins and regional diversification in ratsnakes

description: Globally distributed groups may show regionally distinct rates of
 diversification, where speciation is elevated given timing and sources of
 ecological opportunity. However, for most organisms, nearly complete
 sampling at genomic-data scales to reduce topological error in all regions
 is unattainable, thus hampering conclusions related to biogeographic
 origins and rates of diversification. We explore processes leading to the
 diversity of global ratsnakes and test several important hypotheses
 related to areas of origin and enhanced diversification upon colonizing
 new continents. We estimate species trees inferred from phylogenomic scale
 data (304 loci) while exploring several strategies that consider
 topological error from each individual gene tree. With a dated species
 tree, we examine taxonomy and test previous hypotheses that suggest the
 ratsnakes originated in the Old World (OW) and dispersed to New World
 (NW). Furthermore, we determine if dispersal to the NW represented a
 source of ecological opportunity, which should show elevated rates of
 species diversification. We show that ratsnakes originated in the OW
 during the mid-Oligocene and subsequently dispersed to the NW by the
 mid-Miocene; diversification was also elevated in a subclade of NW taxa.
 Finally, the optimal biogeographic region-dependent speciation model shows
 that the uptick in ratsnake diversification was associated with
 colonization of the NW. We consider several alternative explanations that
 account for regionally distinct diversification rates.
description: gene_fasta_87taxaGenes used to build the phylogenySpecies tree from MPESTTime-calibrated species tree using MPEST for topological inference and MCMCtree for the timetree_oldcal.treSpecies tree inferred using ASTRALrat_astral_II.tregene trees for each locusGene trees were built using Bayesian inference method with 1000 posterior probability trees saved in each file. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"rootedtrees-20170409T045003Z-001.zipbootstrap gene trees for each locusGene trees were built using maximum likelihood method with 1000 bootstrap gene trees saved in each file. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"bstree_1000-20170409T044850Z-001.zipmaximum likelihood gene tree for each locusThe gene tree for each locus inferred using Maximum likelihood method. These gene trees were used to calculate the among loci gene tree distance only. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"mltrees304.zipGene tree for each locus inferred using Bayesian inference methodThese gene trees were used to calculate the among loci gene tree distance only. For convenience, the species names of each tip were shorted with sequence code e.g. "I0066" for "Arizona_elegans". The bash scripts of converting the full species name and the sequence code are provided in "changetreetipnames.sh" and "changetreetipnames2.sh"ppcontrees.zipconvert full sequence code to full species nameThis is a bash script used to convert the tip names on species tree from sequence code to full species nameschangetreetipnames.shconvert sequence code to full species nameThis is a bash script used to convert the tip names on species tree from full species name to short sequence code.changetreetipnames2.sh