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A phylogeny of birds based on over 1,500 loci collected by target enrichment and high-throughput sequencing | | John E. McCormack
; Michael G. Harvey
; Brant C. Faircloth
; Nicholas G. Crawford
; Travis C. Glenn
; Robb T. Brumfield
; | | Date: |
5 Oct 2012 | | Abstract: | Evolutionary relationships among birds in Neoaves, a clade including 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 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 the 100% complete matrix
of 416 UCE loci was broadly 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 a sister relationship between bustards (Otididae) and
turacos (Musophagidae). This phylogeny bolsters support for monophyletic
waterbird and landbird clades and also strongly supports controversial
relationships 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. | | Source: | arXiv, 1210.1604 | | Services: | Forum | Review | PDF | Favorites | |
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