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

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

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

BioGeoBEARS.Pygopodoidea

BioGeoBEARS distribution area matrix and MCC tree used

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

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

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

BEAST MCC tree Pygopodoidea

The MCC tree of the Pygopodoidea used for GeoSSE and BioGeoBEARS analyses

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

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