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Sequence 363 Bird Species

Scientists from the Bird 10,000 Genomes Project have successfully sequenced and analyzed the genomes of a total of 363 bird species from 92.4% (218 out of 236) of avian families, including 267 bird species that have been sequenced for the first time.

Feng et al. report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analyzing 363 genomes from 92.4% of bird families. Image credit: Jon Fjeldsa / Josefin Stiller / University of Copenhagen.

Feng et al. report a substantial step towards the dense representation of avian phylogenetic and molecular diversity, by analyzing 363 genomes from 92.4% of bird families. Image credit: Jon Fjeldsa / Josefin Stiller / University of Copenhagen.

Since the first bird evolved more than 150 million years ago, its descendants have adapted to a vast range of ecological niches, giving rise to tiny, hovering hummingbirds, plunge-diving pelicans and showy birds-of-paradise.

Today, more than 10,000 species of birds live on the planet — and now scientists are well on their way to capturing a complete genetic portrait of that diversity.

The Bird 10,000 Genomes Project (B10K) aims to sequence and share the genome of every avian species on the planet.

Comparing genomes across bird families will enable researchers to explore how particular traits evolved in different birds, as well as to better understand evolution at the molecular level.

“B10K is probably the single most important project ever conducted in the study of birds,” said Dr. Gary Graves, curator of birds at the National Museum of Natural History.

“We’re not only hoping to learn about the phylogenetic relationships among the major branches of the tree of life of birds, but we’re providing an enormous amount of comparative data for the study of the evolution of vertebrates and life itself.”

The B10K consortium analyzed more than 17 trillion base pairs of DNA for the family-level phase of their project.

“Sequencing and analysis began in 2011, but the data represent several decades of work by field collectors and collections management staff who have collected and preserved birds from every continent,” Dr. Graves said.

The newly-sequenced genomes densely cover the bird tree of life: the 10,135 bird species are shown on a draft phylogeny that synthesizes taxonomic and phylogenetic information; in total, 363 species, covering 92.4% of all families, now have at least one genome assembly per sequenced family (purple branches); the gray arc marks the diverse Passeriformes radiation, with 6,063 species, of which 173 species have genome assemblies now; chicken (*) and zebra finch (**) are marked for orientation. Image credit: Feng et al., doi: 10.1038/s41586-020-2873-9.

The newly-sequenced genomes densely cover the bird tree of life: the 10,135 bird species are shown on a draft phylogeny that synthesizes taxonomic and phylogenetic information; in total, 363 species, covering 92.4% of all families, now have at least one genome assembly per sequenced family (purple branches); the gray arc marks the diverse Passeriformes radiation, with 6,063 species, of which 173 species have genome assemblies now; chicken (*) and zebra finch (**) are marked for orientation. Image credit: Feng et al., doi: 10.1038/s41586-020-2873-9.

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 Dr. Graves started in 1986 and has since become part of the Smithsonian’s Global Genome Initiative biorepository.

“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,” said Dr. Rob Fleischer, 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.”

“Through 34 years of field work and dozens of expeditions, we were able to get the stockpile of high-quality DNA that actually makes this project possible,” Dr. Graves said.

“Many of those resources were stored long before DNA sequencing technology had been developed, preserved for future analyses their collectors could not have imagined at the time.”

“It’s one of the many reasons why natural history museum collections and museum-based research programs are so important.”

The B10K team showed that the passerine birds, the largest extant order of bird species, possessed genomic features that differed from other bird groups. Their genomes also contain an additional copy of the growth hormone gene.

The songbirds, a group of Passeriformes, have lost a gene called cornulin, which might have contributed to the evolution of their diverse pure-tone vocalizations.

Dense genomic sampling also facilitated the detection of signals of natural selection down to the single-base level, which may not be possible with few genomes.

“Such detection power was only possible when the species were densely represented in the comparative genomic analyses,” said Dr. Guojie Zhang, a principal investigator on the B10K and head of the Villum Centre for Biodiversity Genomics at Department of Biology at the University of Copenhagen.

“These genomes allow us to explore the genomic variations among different bird groups and help to understand their diversification processes.”

The team’s paper was published in the journal Nature.

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S. Feng et al. 2020. Dense sampling of bird diversity increases power of comparative genomics. Nature 587, 252-257; doi: 10.1038/s41586-020-2873-9

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