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Avian phylogeny inferred from ultraconserved elements (free pdf)

Perhaps the most important contribution to higher-level avian
phylogenetics since Hackett et al. (2008). The paper uses 539,526 bp
from ultraconserved genomic elements (UCEs) and new methods for
inferring species trees from discordant gene trees (STAR, maximum
pseudo-likelihood) to resolve relationships among members of all major
and/or problematic neoavian lineages. Many groupings suggested by
previous phylogenomic studies are recovered with robust support by the
new set of analyses, including Mirandornithes (flamingos + grebes),
Strisores (hummingbirds, swifts, and nightjars), landbirds,
Aequornithes (waterbirds), Psittacopasserae (parrots + passerines),
Eufalconimorphae (parrots, passerines, and falcons), Afroaves, and
even something vaguely reminiscent of Metaves. The manuscript is going
to be published in _Systematic Biology_, but thanks to arXiv, it's
already freely available.

McCormack JE, Harvey MG, Faircloth BC, Crawford NG, Glenn TC,
Brumfield RT 2012 A phylogeny of birds based on over 1,500 loci
collected by target enrichment and high-throughput sequencing.

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

David Černý