RE: Avian phylogeny inferred from ultraconserved elements (free pdf)

["Thomas R. Holtz, Jr." <tholtz@umd.edu>]

Hmmm... Among the land bird clade, Falconidae is near the base of the 
Eufalconimorphae and Acciptridae + Cathartidae and owls at the base of whatever 
their big clade is called. With Aequornithes as their sister group, we have a 
cluster where "feeding on the flesh of vertebrates" seems to be the basal 
state, at least among extant forms.

Thomas R. Holtz, Jr.
Email: tholtz@umd.edu   Phone: 301-405-4084
Office: Centreville 1216                        
Senior Lecturer, Vertebrate Paleontology
Dept. of Geology, University of Maryland
http://www.geol.umd.edu/~tholtz/
Fax: 301-314-9661               

Faculty Director, Science & Global Change Program, College Park Scholars
http://www.geol.umd.edu/sgc
Fax: 301-314-9843

Mailing Address:        Thomas R. Holtz, Jr.
                        Department of Geology
                        Building 237, Room 1117
                        University of Maryland
                        College Park, MD 20742 USA

> -----Original Message-----
> From: owner-DINOSAUR@usc.edu [mailto:owner-DINOSAUR@usc.edu] On Behalf Of 
> David Cerný
> Sent: Monday, October 08, 2012 5:05 PM
> To: dinosaur@usc.edu
> Subject: 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.
> arXiv:1210.1604
> http://arxiv.org/pdf/1210.1604v1
> 
> 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.
> 
> --
> David Černý