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New Phylogeny of Birds in PLoS ONE

From: Ben Creisler

A new paper in PLoS ONE that may be of interest:

John E. McCormack, Michael G. Harvey, Brant C. Faircloth, Nicholas G.
Crawford, Travis C. Glenn, Robb T. Brumfield (2013)
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target
Enrichment and High-Throughput Sequencing.
PLoS ONE 8(1): e54848.

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 were 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.