DOI: 10.5061/dryad.991p6
title: Data from: Mass turnover and recovery dynamics of a diverse Australian continental radiation

description: Trends in global and local climate history have been linked to observed
 macroevolutionary patterns across a variety of organisms. These climatic
 pressures may unilaterally or asymmetrically influence the evolutionary
 trajectory of clades. To test and compare signatures of changing global
 (Eocene-Oligocene boundary cooling) and continental (Miocene
 aridification) environments on a continental fauna, we investigated the
 macroevolutionary dynamics of one of Australia's most diverse endemic
 radiations, pygopodoid geckos. We generated a time-calibrated phylogeny
 (&gt;90% taxon coverage) to test whether (i) asymmetrical pygopodoid
 tree shape may be the result of mass turnover deep in the group's
 history, and (ii) how Miocene aridification shaped trends in biome
 assemblages. We find evidence of mass turnover in pygopodoids following
 the isolation of the Australian continental plate ∼30 million years ago,
 and in contrast, gradual aridification is linked to elevated speciation
 rates in the young arid zone. Surprisingly, our results suggest that
 invasion of arid habitats was not an evolutionary end point. Instead, arid
 Australia has acted as a source for diversity, with repeated outward
 dispersals having facilitated diversification of this group. This pattern
 contrasts trends in richness and distribution of other Australian
 vertebrates, illustrating the profound effects historical biome changes
 have on macroevolutionary patterns.
description: BEAST nuclear only
 operator file (xml)Operator xml file for
 our NUCLEAR ONLY analysis investigating divergence times of the
 Pygopodoidea. Run on CIPRES (phylo.org) using BEAST 1.8.3. Log files
 inspected using Tracer, and trees summarized using
 TreeAnnotator.Pygopodoidea.nuclear.all.300mil.xmlBEAST nDNA + mtDNA operator file (xml)Operator xml file for our NUCLEAR + MITOCHONDRIAL (total) analysis investigating divergence times of the Pygopodoidea. Run on CIPRES (phylo.org) using BEAST 1.8.3. Log files inspected using Tracer, and trees summarized using TreeAnnotator.Pygopodoidea.total.300mil.xmlBEAST alternative fossil calibration schemes operator files (xml)Operator xml files for our ALTERNATIVE FOSSIL CALIBRATION SCHEMES, used to test the robustness of fossil calibrations in our divergence time estimation of the Pygopodoidea. Run on CIPRES (phylo.org) using BEAST 1.8.3. Log files inspected using Tracer, and trees summarized using TreeAnnotator.Alternative Fossil Calibration Schemes.zipAlignments: mtDNA + nDNA COMBINED analysesAlignments used in the mtDNA+nDNA COMBINED analyses (BEAST). Folder includes separate gene alignments, as well as an interleaved file of all genes.mtDNA+nDNA.zipAlignments: nDNA for NUCLEAR ONLY analysesAlignments of NUCLEAR loci used for NUCLEAR ONLY analyses (BEAST). Folder includes individual locus alignments, as well as a single interleaved alignment file of all loci.nDNA.zipTESS: Mass Extinction Bayes factors GIFGIF (open in internet browser) of support for and timing of a mass extinction event across 100 posterior BEAST trees.Mass Extinction BF.gifTESS.Analysis Loop (R code)This R code provides the functions necessary to run a TESS analysis, investigating the timing and frequency of mass extinction and diversification shifts across a sample of trees, and then summarize the data. It also includes functions for model comparison among constant rate and variable rate models with and without mass extinction, using stepping stone sampling and Bayes factors for support.DRYAD.TESS.Analysis Loop.RTreePar R CodeThis is R code to run the TreePar analysis (optimizing the likelihood on speciation/extinction shifts). Also included is a loop for comparing TreePar models across a set of trees.DRYAD.Pygopodoidea.TreePar.RBioGeoBEARS.PygopodoideaBioGeoBEARS distribution area matrix and MCC tree used.DRYAD.BioGeoBEARS.Pygopodoidea.zipGeoSSE (R code & files)This folder includes the R code/functions to recreate our GeoSSE analyses on biome diversification/transition rates. Included are the 5 GeoSSE binary distribution coding files.DRYAD.GeoSSE.files.zipBEAST MCC tree PygopodoideaThe MCC tree of the Pygopodoidea used for GeoSSE and BioGeoBEARS analyses.Pygopodoidea.tre