DOI: 10.5061/dryad.jn8nt
title: Data from: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

description: The increasing availability of complete genome data is facilitating the
 acquisition of phylogenomic datasets, but the process of obtaining
 orthologous sequences from other genomes and assembling multiple sequence
 alignments remains piecemeal and arduous. We designed software that
 performs these tasks and outputs anonymous loci (AL) or anchor loci
 (AE/UCE) datasets in ready-to-analyze formats. We demonstrate our program
 by applying it to the hominoids. Starting with human, chimpanzee, gorilla,
 and orangutan genomes, our software generated an exhaustive dataset of 292
 ALs (~1 kb each) in ~3 hours. Analyses of our AL dataset not only
 validated the program by yielding a portrait of hominoid evolution in
 agreement with previous studies, but the accuracy and precision of our
 estimated ancestral effective population sizes and speciation times
 represent improvements. We also used our program with a published set of
 512 vertebrate-wide AE 'probe' sequences to generate datasets
 consisting of 171 and 242 independent loci (~1 kb each) in 11 and 13
 minutes, respectively. The former dataset consisted of flanking sequences
 500 bp from adjacent AEs, while the latter contained sequences bordering
 AEs. Although our AE datasets produced the expected hominoid species tree,
 coalescent-based estimates of ancestral population sizes and speciation
 times based on these data were considerably lower than estimates from our
 AL dataset and previous studies. Accordingly, we suggest that loci
 subjected to direct or indirect selection may not be appropriate for
 coalescent-based methods. Complete in silico approaches, combined with the
 burgeoning genome databases, will accelerate the pace of phylogenomics.
description: AE171_data_filesThis folder contains AE171 data saved into different file formats: AE171_concatenated.phylip contains all 171 AE loci concatenated into a supermatrix for species tree analyses. AE171_fasta singles folder contains 171 AE loci as individual fasta-formatted files. AE171_multi.nexus file contains 171 AE loci together in a single nexus-formatted file with BEST and MrBayes commands for species tree analyses. AE171_multi.phylip file contains 171 AE loci together in a single phylip-formatted file (file used in BP&P2.2 analyses. AL171_nexus_singles folder contains 171 AE loci as individual nexus-formatted files.AE242_data_filesThis folder contains AE242 data saved into different file formats: AE242_concatenated.phylip contains all 242 AE loci concatenated into a supermatrix for species tree analyses. AE242_fasta singles folder contains 242 AE loci as individual fasta-formatted files. AE242_multi.nexus file contains 242 AE loci together in a single nexus-formatted file with BEST and MrBayes commands for species tree analyses. AE242_multi.phylip file contains 242 AE loci together in a single phylip-formatted file (file used in BP&P2.2 analyses. AL242_nexus_singles folder contains 242 AE loci as individual nexus-formatted files.AL292_data_filesThis folder contains AL292 data saved into different file formats: AL292_concatenated.phylip contains all 292 loci concatenated into a supermatrix for species tree analyses. AL292_fasta singles folder contains 292 single-copy, presumably neutral, and independent anonymous loci as individual fasta-formatted files. AL292_multi.nexus file contains 292 single-copy, presumably neutral, and independent anonymous loci together in a single nexus-formatted file with BEST and MrBayes commands for species tree analyses. AL292_multi.phylip file contains 292 single-copy, presumably neutral, and independent anonymous loci together in a single phylip-formatted file (file used in BP&P2.2 analyses. AL292_nexus_singles folder contains 292 single-copy, presumably neutral, and independent anonymous loci as individual nexus-formatted files.HKY208_data_filesThis folder contains HKY208 data saved into different file formats: HKY208_multi.phylip contains all 208 AL loci found in the AL292 dataset, which fit the HKY model of substitution. These HKY-only data were analyzed separately to evaluate the effects of model selection on our results. HKY208_nexus_singles folder contains 208 single-copy, presumably neutral, and independent anonymous loci that fit the HKY model as individual nexus-formatted files.