Welcome to the Early Bird Website

Website designed by Sushma Reddy and Edward Braun. Updated by Edward Braun on 5 March 2013

The “Early Bird” tree of life project, funded by the NSF Assembling the Tree of Life (AToL) program, is a large-scale, cooperative effort among five institutions in the U.S. to determine the evolutionary relationships among all major groups of birds. Although birds are well-studied in many ways, the relationships among avian orders (deep avian relationships) has been problematic and contentious.

Through the Early Bird project we have collected a large amount of sequence data from all major avian lineages.The Early Bird project characterized the utility of a number of regions in the nuclear genome for phylogenetic and populationgenetic studies. The project also supported a number of projects focused on the theory and practice of phylogenetics in birds and other organisms.

NSF support for the Early Bird AToL project is now complete, a number of participants in the project (Edward Braun, Michael Braun, Rebecca Kimball, Sushma Reddy, and Frederick Sheldon) remain committed to maintaining this web page and using it to disseminate information about avian phylogeny to the scientific community and the public.

Please send any feedback about this web site to Edward Braun.

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Testing Clades in the Avian Tree of Life

Relationships within specific groups of have been examined as part of the Early Bird project. Specific groups of interest include:

  • The Parrot-Passerine clade (Wang et al. 2012, MBE 29: 737-750).
  • Palaegnathae (Smith et al. 2013, Syst Biol, 62: 35-49
  • Galliformes (Cox et al. 2007, Auk 124: 71-84; Kimball and Braun 2008, J Avian Biol 39: 438-445; Bonilla et al. 2010, MPE 56: 536-542; Kimball et al. 2011, Int J Evol Biol Article ID 423938)

Many of these papers focus on using data that are independent of the large-scale Hackett et al. (2008) effort to test specific clades in the avian tree of life.

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Rare Genomic Changes and the Avian Tree of Life

Rare genomic changes (RGCs) are slowly accumulating mutations that exhibit substantially less homoplasy than nucleotide substitutions. As part of the Early Bird project we have examined the accumulation of indels (insertions and deletions; Yuri et al. 2013, Biology in press), microinversions (Braun et al. 2011, BMC Evol Biol 11:141), and transposable element insertions (Han et al. 2011, Syst Biol 60:375-386) during the avian evolution. We demonstrate that all of these RGC types exhibit homoplasy, indicating they should be interpreted with caution, just like any other type of character.

An ultrametric tree based upon the Hackett et al. (2008) phylogeny  was used in Braun et al. (2011) and Han et al. (2011). This tree generated by non-parametric rate smoothing and it may be useful for studies that require an approximate clock.

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Nuclear Loci for Avian Phylogenetics and Pop Gen

Primers for 36 nuclear loci developed for the Early Bird project (Kimball et al. 2009, MPE 50: 654-660), along with information about amplification conditions and the reliability of the primer sets in different avian groups. These primers are likely to prove useful for phylogenetic and population genetic studies.

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A Large-scale Avian Phylogenetic Tree


We have published an analysis of 19 loci from 169 avian species (Hackett et al. 2008, Science 320: 1763-1768), demonstrating that it is possible to resolve deep relationships among modern birds using large amounts of data.

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