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Avian genome research covers nearly all avian families

genome
A Eurasian Hoopoe offers food to its mate in a courtship ritual. Photographed at the Keoladeo-Ghana Bird Sanctuary, India by Christopher Ciccone

Scientists are well on their way to capturing a complete genetic portrait of the diversity of the world’s birds.

In the November 11 issue of the journal Nature, researchers reported on the genomes of 363 species of birds, including 267 that have been sequenced for the first time. The studied species represent more than 92 percent of the world’s avian families. The data from the study will advance research on the evolution of birds and aids in the conservation of threatened bird species.

“It might seem that having a genome for each bird family or species is a bit like stamp collecting, but this massive cooperative effort has given us a set of very important genomic resources for conservation,” says Rob Fleischer, one of the authors and head of the Smithsonian Conservation Biology Institute’s Center for Conservation Genomics. “For example, it provides a ready source of genetic markers useful to map population declines, identify kin, and reduce inbreeding when managing rescue populations of endangered species. Having the genomes simplifies the search for genes responsible for important survival traits such as resistance to deadly introduced diseases.”

Together, the data constitute a rich genomic resource that is now freely available to the scientific community. The release of the new genomes is a major milestone for the Bird 10,000 Genomes Project (B10K), an international collaboration organized by researchers at 10 institutions, including the Smithsonian’s National Museum of Natural History. It aims to sequence and share the genome of every avian species on the planet.

The B10K project is working in four phases. The first phase, completed a couple years ago, looked at avian orders. The second phase, which this new paper is about, is the family-level analysis. The process is currently underway for phase three — the genus-level analysis, and after that, phase four will look at individual species.

What genes say about species splits

Approximately 40% of the newly sequenced bird genomes were obtained using tissue samples preserved in the National Museum of Natural History’s Avian Genetic Resources Collection, which started in 1986 and has since become part of the Smithsonian’s Global Genome Initiative biorepository. Photo by Chip Clark/Smithsonian

We asked Fleischer if the work will help decide whether certain similar bird species or populations — Northern Cardinals in the Southwest and the East, for example — might be lumped or split based on genetics.

“The analysis in this particular paper concentrates primarily on one species from each avian family, so it does not directly address the question of species level taxonomy,” he explains. “But having genome sequences from multiple individuals and regions within a species or genus does provide us with a means to assess genetic differences among regional populations, subspecies, and suspected species. If the genomic sequences reveal very low levels of gene flow or hybridization among these subunits (say, the example of cardinals in the southwest isolated from those in the eastern U.S.), we can say there is support for their existence as distinct units and potentially split them. (But other differences other than the genomic ones usually also need to be taken into account to determine if the differences imply a species level split.)

“And the resources we obtain from having full genome sequences from a broad range of species across the avian class allow us to develop large numbers of genetic markers we can use instead of genomes to answer these taxonomic questions. The markers developed from one species often work in related species in the same genus or family. However, it is getting easier and less expensive to sequence whole genomes of individual birds, so the use of such markers may soon come to an end.

“And the ultimate goal of the B10k project is to sequence all >10k species of birds, so applying what we learn from one species to develop markers to study related species should not be necessary at that point.

“Answering questions about taxonomy and ‘evolutionarily significant units’ can be important for determining the units for conservation policy and action, and ultimately help to save avian diversity.”

A version of this article will be published in the January/February 2021 issue of BirdWatching magazine. 

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