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 (>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.
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.xml
BEAST 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.xml
BEAST 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.zip
Alignments: mtDNA + nDNA COMBINED analyses
Alignments used in the mtDNA+nDNA COMBINED analyses (BEAST). Folder includes separate gene alignments, as well as an interleaved file of all genes.
mtDNA+nDNA.zip
Alignments: nDNA for NUCLEAR ONLY analyses
Alignments 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.zip
TESS: Mass Extinction Bayes factors GIF
GIF (open in internet browser) of support for and timing of a mass extinction event across 100 posterior BEAST trees.
Mass Extinction BF.gif
TESS.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.R
TreePar R Code
This 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.R
BioGeoBEARS.Pygopodoidea
BioGeoBEARS distribution area matrix and MCC tree used.
DRYAD.BioGeoBEARS.Pygopodoidea.zip
GeoSSE (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.zip
BEAST MCC tree Pygopodoidea
The MCC tree of the Pygopodoidea used for GeoSSE and BioGeoBEARS analyses.
Pygopodoidea.tre