A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

• DOI: 10.1371/journal.pone.0054848
• Publication Date: 2013-01-29T22:06:16Z
• Authors: John E. McCormack; Michael G. Harvey; Brant C. Faircloth; Nicholas G. Crawford; Travis C. Glenn; Robb T. Brumfield
• Keywords: Monophyly

Evolutionary relationships among birds in Neoaves, the clade comprising vast majority of avian diversity, have vexed systematists due to ancient, rapid radiation numerous lineages. We applied a new phylogenomic approach resolve Neoaves using target enrichment (sequence capture) and high-throughput sequencing ultraconserved elements (UCEs) genomes. collected sequence data from UCE loci for 32 members one outgroup (chicken) analyzed sets that differed their amount missing data. An alignment 1,541 allowed was 87% complete resulted highly resolved phylogeny with broad agreement between Bayesian maximum-likelihood (ML) trees. Although results 100% matrix 416 were similar, ML trees greater extent this analysis, suggesting increasing led increased stability resolution tree. Novel our study include surprisingly close phenotypically divergent bird families, such as tropicbirds (Phaethontidae) sunbittern (Eurypygidae) well bustards (Otididae) turacos (Musophagidae). This bolsters support monophyletic waterbird landbird clades also strongly supports controversial previous studies, including sister relationship passerines parrots non-monophyly raptorial hawk falcon families. significant challenges remain fully resolving some deep especially lineages outside waterbirds landbirds, suggests will yield an increasingly phylogeny.