Measurements

Measurements (in mm) for specimens used in principal components analysis of morphological variation in large-bodied Arthroleptis from Tanzania and neighboring countries

Measurement data

Measurements (in millimeters) of specimens used in morphometric analyses

Gastrotheca_Blackburn&Duelman2013

Nexus file containing aligned sequence data for four genes: 16S (mt), ND1 (mt), POMC (nuc), and RAG-1 (nuc). File also includes character sets and model settings for analysis

Multiple sequence alignment

Multiple sequence alignment of DNA sequence data for mitochondrial 16S ribosomal RNA gene

Alignment of Cardioglossa 16S sequences

Multiple alignment of mitochondrial DNA 16S sequences used for pairwise divergence calculations

Afrobatrachia_Sequence_Alignment

A nexus format sequence alignment of the five nuclear markers (FICD, KIAA2013, POMC, RAG1, TYR) and 16S data, along with relevant MrBayes style partitions and models defined. The alignment contains 186 taxa and 3700 bp

Blackburn&Rodel_Phrynobatrachus_schioetzi

Nexus file containing aligned mtDNA (12S, tRNA-Valine, 16S) for species of Phrynobatrachus

Power_Analyses_4_BayesTraitsScripts&Results

There are two python scripts used to execute BayesTraits on the subdirectories in the previous bundle, "BayesTraits_wrapper_ML.py" and "BayesTraits_wrapper_Bayesian.py". Each will automatically generate the independent and dependent model files required to run BayesTraits, and automatically access the tree file and BayesTraits executable in the subdirectory. It will run serial analyses across all the input files in a subdirectory, using the maximum likelihood version or Bayesian version with stepping stone sampling. Instructions and details are annotated at the top of those scripts. The results can be summarized using the relevant python script, bayesian ("Summary_bf_testing.py") or ml ("Summary_lr_testing.py") version. These will open the output files from each of the 500 analyses in a subdirectory and perform either likelihood ratio tests or bayes factors to compare the independent and dependent models for each input file. The output of these scripts for our set of analyses is provided in the directory "4_Results"

Power_Analyses_2_SimulationResults

The resulting output files from the previous step. The directory contains 500 files, each with independent simulations for characters 1-4 (note number of states varies across characters) across all taxa included

Afrobatrachia_Multi_Tree_SIMMAP

This directory contains character codings, a sample of trees (n=100) from BEAST run, and R script for performing stochastic character mapping (phytools) on multiple trees. To account for topological uncertainty, the simmap function is carried out with 100 replicates on each of 100 trees. The results are summarized across simulations for each character