Data from: In silico phylogenomics using complete genomes: a case study on the evolution of hominoids

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.