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Sexual Dichromatism Drives Diversification Within a Major Radiation of African Amphibians
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Description: A complete set of data and instructions required to replicate all analyses from this publication.
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Components
Species Tree Analyses
Complete set of input files, analysis instructions, and output files for species tree analysis using ASTRAL-III.
Supermatrix Phylogeny Using Species Tree Constraint
Contains alignment files and species tree partial constraint file used to generate a phylogeny of Afrobatrachia from a supermatrix using RAxML.
BEAST Divergence Dating using a Fixed Tree Topology
Instructions and data for running a BEAST analysis on a fixed tree topology, estimating branch lengths only.
BEAST for Bayesian Ancestral State Reconstruction
Data and instructions for running Bayesian ancestral trait reconstructions in BEAST using combinations of trait and clock models.
Trait-Dependent Diversification Analyses with Empirical Data
Instructions, scripts, and data for conducting both BiSSE and HiSSE analyses on empirical data (evolution of sexual dichromatism in Afrobatrachia).
Trait-Dependent Diversification Analyses with Simulated Data
Instructions, scripts, and data required to generate and filter trait simulation data, and conduct both BiSSE and HiSSE analyses on simulated data.
Alignments (Sequence Capture and GenBank)
Alignments of the sequence capture loci and GenBank loci.
Tree Files
Main tree files used for various analyses.
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