Welcome to the Early Bird Website

Website designed by Sushma Reddy and Edward Braun. Updated by Edward Braun on 11 May 2011

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.

Read More

Improving the Gamebird Tree of Life

Gamebirds (members of the order Galliformes) are some of the best-studied and most economically important birds. The Kimball-Braun lab has paid particular attention to resolving relationships within this order.  Publications focused on the order Galliformes include:

  • Kimball et al. 2011, Int J Evol Biol Article ID 423938 - evolution of sexually dimorphic traits [mt-nuc supermatrix tree]
  • Bonilla et al. 2010, MPE 56: 536-542 - comparison of phylogenetic signal in introns and 3' UTR [multilocus nuclear tree]
  • Kimball and Braun 2008, J Avian Biol 39: 438-445 -  support for a clade with erectile non-feathered traits [multilocus mt-nuc tree]
  • Cox et al. 2007, Auk 124: 71-84 - position of New World quail, a problematic group of gamebirds [multilocus mt-nuc tree]

The larger biological question and type of phylogenetic tree included in the publication (typically combined mitochondrial and nuclear matrices, often with little or no missing data).

Read More

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. Two recent papers (Braun et al. 2011, BMC Evol Biol in press; Han et al. 2011, Syst Biol 60:375-386) describe the accumulation of two specific RGCs (transposable element insertions and microinversions) over the avian tree of life. We demonstrate that both of these RGC types exhibit homoplasy, indicating they should be interpreted withcaution, just like any other type of character.

An ultrametric version of the Hackett et al. (2008) phylogeny  was used in both papers. This tree generated by non-parametric rate smoothing and it may be useful for studies that require an approximate clock.

Read More

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.

Read More

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.

Read More