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Mammalian, Bird Sequencing Projects Highlight Genetic Diversity, Extinction Risk

NEW YORK – Two sequencing studies — one of mammals and one of birds — that aim to better understand genetic diversity within those classes have presented results they hope will inform conservation and other efforts.

The Zoonomia Project has built off the 29 Mammals Project, which began in 2006 with the goal of comparing conserved sites within mammalian genomes. It expanded into the 200 Mammals Project with a similar objective, before being renamed the Zoonomia Project. The Bird 10,000 Genomes Project, meanwhile, grew out of the Avian Phylogenomics Consortium, with the goal of sequencing the genomes of all approximately 10,500 living bird species.

In two papers appearing in Nature on Wednesday, the researchers reported their progress on these fronts. The Zoonomia researchers have sequenced representatives from more than 80 percent of mammalian families and the B10K researchers have sequenced genomes from more than 92 percent of bird families.

The Zoonomia researchers noted that such projects can help identify species that may benefit from conservation efforts and inform studies of human disease, and they further call for data like theirs to be released publicly. "We hope that our extensive data set, which is available to all scientists in the world, will be used for understanding disease genetics and the protection of biodiversity," co-senior author Kerstin Lindblad-Toh from Uppsala University and the Broad Institute said in a statement.

For Zoonomia, the researchers generated genome assemblies for 131 species using the DISCOVAR approach. For this, they sought to analyze one species from each mammalian eutherian family and included a number of species that are the only member of their family in existence as well as others from critically endangered species. They folded in other previously assembled genomes to analyze a set of 240 mammals in total.

Not only could this dataset help pinpoint what genes are highly conserved among mammals to home in on changes that could contribute to human disease, the researchers found it could also suggest ways animals have adapted to their environments.

In addition, the researchers found that a reference genome from just a single member of a species could shed light on that species' genetic diversity. They found that an individual's fraction of heterozygous sites and segments of homozygosity were correlated and that both these measures of genomic diversity varied by the species' International Union for Conservation of Nature category. Heterozygosity, they noted, decreases with increasing level of conservation concern. 

According to the Zoonomia team, their findings suggests that sequencing even one individual from a species could help determine whether a population is at increased risk of extinction and may benefit from conservation efforts.

The B10K researchers, meanwhile, generated genomic data for 267 birds, including 68 species of concern on the IUCN list, and analyzed them in combination with the genomes of previously sequenced birds, for a total of 363 bird genomes. Using the reference-free aligner Cactus, they further developed a whole-genome alignment of the bird genomes to examine their evolutionary relationships and changes.

From this, they confirmed, for instance, that the growth hormone gene had been duplicated in Passeriformes — which encompasses perching or songbirds — and identified the ancestral and derived copies. They additionally uncovered 154 Passeriformes-specific genes.

Their dense alignment further enabled the researchers to identify patterns of weak selection within the birds' genomes, including within non-coding regions. This suggested to the B10K team that though functional non-coding regions are more variable and less strongly conserved than coding regions, they are under a higher degree of constraint than previously appreciated through analyses of smaller sample sizes.

Based on this, the researchers said their dataset would enable the study of species-specific traits and conservation efforts, but also wider studies of bird evolution and genomic diversity. "Our results demonstrate that increasing the diversity of genomes used in comparative studies can reveal more shared and lineage-specific variation, and improve the investigation of genomic characteristics," senior author Guojie Zhang from BGI-Shenzhen and his colleagues wrote in their paper.

The Zoonomia researchers also argued that datasets like theirs and other large-scale genome sequencing efforts should be shared as quickly as possible. "One of the most exciting things about the Zoonomia Project is that many of our core questions are accessible to people both within and outside of science," first author Diane Genereux from the Broad said in a statement. "By designing scientific projects that are accessible to all, we can ensure benefits for public, human, and environmental health."