New bird genomes give insight into evolution of genomic diversity

The Bird 10,000 Genome Project (B10K) is a large international project 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. In a study published today in Nature, the B10K achieved its family phase milestone releasing genomic resources for 363 bird species including 267 new genomes, and illustrating how these resources give improved resolution on genomic evolution analyses.

The paper also established 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. The study showed that the passerine birds, the largest extant order of bird species, possessed genomic features that differed from other bird groups. Passerine 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 Guojie Zhang, a principal investigator on the B10K and head of the Villum Centre for Biodiversity Genomics at Department of Biology, University of Copenhagen. “These genomes allow us to explore the genomic variations among different bird groups and help to understand their diversification processes”.

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. This allowed them to sequence genomes from rare and endangered birds, which will be important resources for conservation actions.

Gary Graves, curator of birds at the Smithsonian National Museum of Natural History in Washington D.C. emphasizes the central role of scientific collections for genomic studies. “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. The relevance of museums to studies of genomic evolution and the diversification of life on Earth has never been greater.” 

Carsten Rahbek, co-organizer of the B10K project and a former bird curator at the Natural History Museum of Denmark, now the director of the Villum Center for Global Mountain Biodiversity, University of Copenhagen recalls how it all started: “This paper is also a testimony of how science advance with time in unpredictable ways, i.e., when we in the 1980s started to collect avian tissue on field-expeditions in the Andes for genetic analyses of small DNA fragments, we could not foresee the arisen of genomic analyses or big data analyses.

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”.

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.

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 world-wide 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. 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”, said Tom Gilbert at Copenhagen’s GLOBE Institute who is leading the push to expand the consortium. “Sequencing the genomic DNA at scale has been a big challenge, but obtaining high-quality blood or tissue samples from which we isolate the DNA is even a bigger one. We need all the help we can get.”, said Erich Jarvis, co-principal investigator on the B10K project, and professor at the Rockefeller University and Howard Hughes Medical Institute. “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”.