Suppl_alns

This folder contains three alignments: 'AMAS_j2013.fas', 'FcC_j2013.fas', and 'Phyut_j2013.nex' concatenated respectively by AMAS, FASconCAT-G, and Phyutility. The 'summary.txt' file contains summaries of these three alignments, as calculated by AMAS, showing that they are identical. 'FcC_info.xls' is the summary calculated on j2013 data set by FASconCAT-G

PhyloBayes Results

Results of all PhyloBayes analyses conducted in the study including Bayesien posterior densities and traces of selected parameters as well as consensus trees

PartitionFinder Results

Control files, data and results for all PartitionFinder analyses on concatenated matrices conducted in the study

Data Matrices

All concatenated matrices in PHYLIP and NEXUS formats. The names of the concatenated matrices correspond to Table 1

Jackknife

Results of 108-locus and 20-locus jackknife analyses. See Figure 3

OrthologID Output

Data partitions from OrthologID aligned and in NEXUS format. "full" dataset includes all orthologs recovered and "m27" includes only partitions present in at least 27 taxa

Partition Statistics

Spreadsheet containing data for all of the partition-specific statistics used to construct the various matrices described in the paper

Topology_tests

Results of Bayesian tests of topology carried out in MrBayes. Subfolder names correspond to alternative topologies tested. See Table 2 and manuscript text for explanations

Progressive Concatenation Data and Results

Matrices and RAxML result files from progressive concatenation analyses presented in order of slow- to fast-evolving loci

RAxML Concatenated

Data matrices and results from all RAxML analyses of concatenated datasets described in the stud