Citation:
Edwards SV, Jennings WB, Shedlock AM. Phylogenetics of modern birds in the era of genomics. Proceeding of the Royal Society of London series. 2005;272 :979-992.
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Abstract:
In the 14 years since the first higher-level bird phylogenies based on DNA sequence data, avian
phylogenetics has witnessed the advent and maturation of the genomics era, the completion of the chicken
genome and a suite of technologies that promise to add considerably to the agenda of avian phylogenetics.
In this review, we summarize current approaches and data characteristics of recent higher-level bird studies
and suggest a number of as yet untested molecular and analytical approaches for the unfolding tree of life
for birds. A variety of comparative genomics strategies, including adoption of objective quality scores for
sequence data, analysis of contiguous DNA sequences provided by large-insert genomic libraries, and the
systematic use of retroposon insertions and other rare genomic changes all promise an integrated
phylogenetics that is solidly grounded in genome evolution. The avian genome is an excellent testing
ground for such approaches because of the more balanced representation of single-copy and repetitive
DNA regions than in mammals. Although comparative genomics has a number of obvious uses in avian
phylogenetics, its application to large numbers of taxa poses a number of methodological and
infrastructural challenges, and can be greatly facilitated by a ‘community genomics’ approach in which
the modest sequencing throughputs of single PI laboratories are pooled to produce larger, complementary
datasets. Although the polymerase chain reaction era of avian phylogenetics is far from complete, the
comparative genomics era—with its ability to vastly increase the number and type of molecular characters
and to provide a genomic context for these characters—will usher in a host of new perspectives and
opportunities for integrating genome evolution and avian phylogenetics.