Researchers from across the globe have helped sequence the genomes of 363 bird species as part of the Bird 10,000 Genome Project

Almost every bird family on Earth has now had its genome sequenced, according to a new study out today from the Bird 10,000 Genome Project (B10K), an initiative to sequence the genomes of all living bird species.

In this new study, published today in Nature, the B10K achieved this second milestone by releasing genomic resources for 363 bird species, or 92% of all all bird families, including 267 new genomes, and illustrated how these resources give improved resolution on genomic evolution analyses, or the process by which the genome changes over time.

This large international project is co-led by University of Copenhagen, China National Genebank at BGI-Shenzhen, the Smithsonian National Museum of Natural History, Rockefeller University and the Chinese Academy of Sciences, and includes researchers from across the globe, including the University of Colorado Boulder.

“This project represents a significant step forwards both for the study of avian evolutionary biology and for eukaryotic comparative genome datasets—it is the largest such dataset generated to date containing 363 bird genomes,” said Scott Taylor, an assistant professor in ecology and evolutionary biology at CU Boulder who, along with Dr. Irby Lovette from the Cornell Lab of Ornithology and Dr. Nancy Chen from the University of Rochester, provided the black-capped chickadee genome for the project

“It's hard to overstate how exciting this dataset and the insights that it will yield about avian evolution are. It has been really fun to be involved with the project.”

The large collaborative effort involved over 150 researchers from 125 institutions in 24 countries. To sequence the bird genomes, the project heavily relies on tissue samples stored in museums around the globe. The Smithsonian National Museum of Natural History, the Natural History Museum of Denmark, and the Louisiana State University Museum of Natural Science contributed the majority of the samples for the project. 

By working with these natural history museums, scientists were able to sequence genomes from rare and endangered birds, which will be important resources for conservation actions, according to the researchers.

“This B10K milestone would not have been possible without the proactive support of natural history museums and their vast resources of carefully documented genetic specimens,” said Gary Graves, curator of birds at the Smithsonian National Museum of Natural History in Washington D.C. “The relevance of museums to studies of genomic evolution and the diversification of life on Earth has never been greater.”

Peter Hosner, the current curator of birds at the Natural History Museum of Denmark, reflects: “Some genomes were derived from those tissue samples originally preserved in the early 1980s. The fact that these resources can now be used to generate whole genomes illustrates the foresight of those field biologists. This study demonstrates how investments in basic field work provide decades of research value, an important lesson in an era when nature is rapidly disappearing.”

Using this information, researchers were able to establish a new pipeline to analyze the unprecedented scale of genomic data, which revealed a detailed landscape of genomic sequence gains and losses across bird lineages. In particular, the study showed that the passerine birds, the largest extant order of bird species which includes more than half of all bird species, possessed genomic features that differed from other bird groups. 

Passerine genomes contain an additional copy of the growth hormone gene. Songbirds, a group of Passeriformes, on the other hand, lost that 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.

The genomes present an important resource for conservation biology and add to the growing number of genomes that can be compared to identify which genetic elements are shared and which differ across the Tree of Life. 

“There are still big open questions about the evolutionary relationships of birds; the new genomes play a key role in understanding bird diversification,” said Josefin Stiller from the Villum Centre for Biodiversity Genomics at the University of Copenhagen, who is leading the efforts to build a new evolutionary tree for all bird families.

Erich Jarvis, co-principal investigator on the B10K project, and professor at the Rockefeller University and Howard Hughes Medical Institute, agrees: 

“Having the full genetic diversity of birds will help us decipher the genetics of their diverse complex traits, such as flight, vocal learning, and high brain neuron densities”. 

Concurrently, the next phase of the project has started, which will take another leap to sequence genomes of species representing all 2,250 genera of birds. The B10K consortium is seeking worldwide collaborators on sample collection to fill the gaps in phylogenomic sequencing. 

“We are already making rapid progress in this new phase but are always on the lookout for missing species to include,” said Tom Gilbert at Copenhagen’s GLOBE Institute who is leading the push to expand the consortium. 

“We hope that teams across the world will be excited about the enormous range of possibilities that a genus level database of bird genomes has to offer and hope to hear from those that would like to join this exciting collaboration.”

This piece is adapted from a press release provided by the University of Copenhagen and the Smithsonian Institute.