DOI: 10.5061/dryad.sd080
title: Data from: A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing

description: Evolutionary relationships among birds in Neoaves, the clade comprising
 the vast majority of avian diversity, have vexed systematists due to the
 ancient, rapid radiation of numerous lineages. We applied a new
 phylogenomic approach to resolve relationships in Neoaves using target
 enrichment (sequence capture) and high-throughput sequencing of
 ultraconserved elements (UCEs) in avian genomes. We collected sequence
 data from UCE loci for 32 members of Neoaves and one outgroup (chicken)
 and analyzed data sets that differed in their amount of missing data. An
 alignment of 1,541 loci that allowed missing data was 87% complete and
 resulted in a highly resolved phylogeny with broad agreement between the
 Bayesian and maximum-likelihood (ML) trees. Although results from the 100%
 complete matrix of 416 UCE loci was similar, the Bayesian and ML trees
 differed to a greater extent in this analysis, suggesting that increasing
 from 416 to 1,541 loci led to increased stability and resolution of the
 tree. Novel results of our study include surprisingly close relationships
 between phenotypically divergent bird families, such as tropicbirds
 (Phaethontidae) and the sunbittern (Eurypygidae) as well as between
 bustards (Otididae) and turacos (Musophagidae). This phylogeny bolsters
 support for monophyletic waterbird and landbird clades and also strongly
 supports controversial results from previous studies, including the sister
 relationship between passerines and parrots and the non-monophyly of
 raptorial birds in the hawk and falcon families. Although significant
 challenges remain to fully resolving some of the deep relationships in
 Neoaves, especially among lineages outside the waterbirds and landbirds,
 this study suggests that increased data will yield an increasingly
 resolved avian phylogeny.
description: birds-contigs-assembled-from-uce-loci.fasta.gzUCE contigs assembled from raw reads collected using target enrichment.birds-lastz-matches-of-probes-to-contigs.lastz.tar.gzLASTZ matches of probes to species-specific contigs in contigs-assembled-from-uce-loci.fasta.gzbirds-matches-of-probes-to-contigs.sqlite.gzSQLITE database of LASTZ matches between assembled contigs in birds-contigs-assembled-from-uce-loci.fasta.gz and the UCE probes. This database is used to construct data sets containing loci that are shared across taxa and prep data for alignment. These data are derived from birds-lastz-matches-of-probes-to-contigs.lastz.tar.gz.birds-416-loci-alignments.tar.gzNexus formatted, complete (all taxa have data at all loci) alignments of 416 UCE loci enriched from birds.birds-416-loci-subs-models.txtSubstitution models estimated for 416 locus data set.birds-416-loci-mrbayes.gzNexus formatted, concatenated alignment of 416 UCE loci enriched from birds.birds-416-loci-cloudforest-output.tar.gzGenetrees and boostrap replicates generated from 416 loci using Cloudforest.birds-1541-loci-alignments.tar.gzNexus formatted, complete (all taxa have data at all loci) alignments of 1541 UCE loci enriched from birds.birds-1541-loci-subs-modelsSubstitution models estimated for 1541 locus data set.birds-1541-loci-mrbayes.gzNexus formatted, concatenated alignment of 1541 UCE loci enriched from birds.birds-416-loci-raxml.phylip.gzPhylip formatted, concatenated alignment of 416 UCE loci enriched from birds.birds-1541-loci-raxml.phylip.gzPhylip formatted, concatenated alignment of 1541 UCE loci enriched from birds.