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Genome Sequence Provides Clues to Pigeon Traits, Evolutionary History

NEW YORK (GenomeWeb News) – Most existing pigeon breeds trace their ancestry back thousands of years to sites in the Middle East, though racing pigeons share a closer-than-usual relationship with feral pigeon populations in North America, according to a genome sequencing study in the early, online edition of Science today.

Researchers from China, the US, Denmark, and Australia began their analyses by sequencing the genome of the domestic rock pigeon, Columba livia. Coupled with genome resequencing data on dozens more feral or domestic pigeons, this reference sequence helped in identifying almost 1.5 million SNPs that were subsequently used to discern phylogenetic relationships of the pigeon family tree.

The study also highlighted the potential for using pigeons for finding genes involved in specific traits of interest. In this case, for example, investigators tracked down a gene suspected of influencing the presence or absence of pigeon head crests — the sometimes-elaborate plumage that forms when feathers on the birds' heads and necks point up rather than down.

This gene, the ephrin receptor 2 gene EphB2, contained similar mutations in birds from all 22 crested pigeon breeds tested in the team's follow-up analyses, hinting that the head crest trait has been introduced into the pigeon lineage just once. Head crest-associated alterations in and around EphB2 were missing in the 57 pigeon breeds without crests that were examined.

"Our study of domestic rock pigeons illustrates how combining comparative genomics and population-based analyses forwards our understanding of genetic relationships and the genomic basis of traits," first author Michael Shapiro, a biologist based at the University of Utah, and his colleagues wrote.

The C. livia species includes pigeons belonging to hundreds of breeds with a wide range of physical features, ornamentation, behaviors, and vocal calls, the researchers said. And because the birds have been subjected to extensive breeding — often aimed at selecting for certain traits — the pigeon has the potential to serve as a useful model for delving into the genetics of those traits, they added.

Among pigeons' more noticeable features are head crests, found in 80 or more pigeon species. These are sometimes classified as manes, hoods, shells, or peaks depending on the precise shape formed by the head and neck feathers.

"Some [head crests] are small and pointed," Shapiro said in a statement. "Others look like a shell behind the head; some people think they look like mullets. They can be as extreme as an Elizabethan collar."

For the current study, the researchers looked for candidate genes related to head crest formation, as part of their broader study on pigeon genomics and phylogeny.

The team used Illumina's HiSeq 2000 instrument to generate sequences for a male pigeon from the "Danish tumbler" breed. After putting together a 1.1 billion-base reference genome from this data, the team went on to resequence 40 more C. livia pigeons at depths of eight to 26-fold coverage.

These resequenced birds included two feral pigeon representatives — one from Utah and another from Virginia — as well as 38 birds from three dozen domestic breeds.

Using 1.48 million variants found in the pigeon genomes, the researchers put together a pigeon phylogeny that largely underscores the Middle Eastern ancestry of modern-day pigeon breeds.

For instance, they demonstrated that short-beaked pigeons in the "owl breeds" shared particularly close genetic ties with breeds originating in Syria, Lebanon, and Egypt, while breeds historically linked to Iran and India tended to group together — a pattern that Shapiro said is "consistent with historical records of trade routes between those regions."

"People were not only trading goods along those routes," he added, "but probably also interbreeding their pigeons."

On the other hand, the investigators found that feral pigeons from the US clustered genetically with the racing pigeon breeds or "racing homers," suggesting the free birds may be descendents of fugitive homers that flew the coop.

In an effort to find genes related to head crest formation, meanwhile, the researchers resequenced eight pigeons with head crests, uncovering shared homozygous changes in EphB2 in all eight of the crested birds. The precise effect that this gene has on feather formation and growth remains to be determined, as do the additional genetic factors controlling the precise size and shape of head crests across the pigeon breeds.

Even so, the researchers saw head crest-associated signs of positive selection in and around EphB2 when they genotyped 61 birds belonging to 22 breeds known for having head crests and another 69 head crest-free birds from 57 breeds. And analyses of EphB2 data in other species suggested that crest-related changes to the gene likely curb the downstream activation of a receptor tyrosine kinase pathway.

Based on these data, the study's authors called EphB2 a "convincing candidate" in head crest formation. They also noted that the same approach used in the current study could yield information on genes involved in other derived pigeon traits.