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New California Condor Genome Assembly Reveals High Genetic Diversity

NEW YORK – Researchers from California, Texas, and West Virginia have assembled the first completed genome of the California condor, or Gymnogyps californianus, which shows that the species has a high degree of genetic diversity that could help it survive long term.

In a paper published on Thursday in the journal Current Biology, the researchers noted that threatened and endangered species like the California condor, which is listed as critically endangered, can suffer from a lack of genetic diversity because of their small population sizes. This leads to inbreeding and reduced adaptability. The California condor briefly went extinct in the wild — by 1982, only 22 individual condors remained in North America. But after decades of captive breeding and release efforts, there are now more than 300 free-flying wild condors and about 200 in captivity.

In order to learn more about the species' history and aid in future conservation efforts, the researchers produced a high-quality, chromosome-length genome assembly and analyzed its genome-wide diversity. They also examined the genomes of the Andean condor, or Vultur gryphus, and the turkey vulture, or Cathartes aura, for comparison. They found that the genomes of all three species showed evidence of historic population declines, but that the California condor genome unexpectedly retained a high degree of variation as a legacy of its historically high abundance.

"You need genetic diversity in order to adapt, and the more genetic diversity they have, hopefully, the more chance they have to adapt and persist," first author Jacqueline Robinson, a University of California, San Francisco postdoctoral fellow, said in a statement. "Our study is the first to begin quantifying diversity across the entire California condor genome, which provides us a lot of baseline information and will inform future research and conservation. I think there is a chance that, with genetic information, we could manage the population going into the future to really maintain the genetic diversity that they do have now and not have any further losses."

Co-author Cynthia Steiner, associate director in conservation genetics for the San Diego Zoo Wildlife Alliance, also noted that the genomic information could help conservationists refine their breeding strategies in order to weed out genetic diseases and deleterious phenotypic traits, such as a lethal form of dwarfism called chondrodystrophy or a syndrome that causes an increase in the number of tail feathers to 14 from the usual 12.

For their study, the researchers used a combination of long reads and chromatin interaction mapping to assemble a genome 1.24 Gb in length. The assembly was highly contiguous, and repetitive sequences accounted for 20.3 percent of the California condor genome, compared to 18.0 percent in the turkey vulture genome and 21.2 percent in the chicken genome. Whole-genome alignment with the chicken suggested that the largest scaffolds in the California condor assembly represented whole chromosomes. The California condor genome is thought to contain about 40 pairs of chromosomes, including one pair of sex chromosomes (Z/W), 10 pairs of autosomal macrochromosomes, and about 30 pairs of microchromosomes.

When they aligned short-read sequences from two California condors, one Andean condor, and one turkey vulture to the California condor genome assembly, the researchers observed distinct patterns of genome-wide diversity in each of the three species. Overall, mean genome-wide heterozygosity was highest in the turkey vulture and lowest in the Andean condor, and heterozygosity in the California condor was most similar to the turkey vulture. Unlike the turkey vulture, however, California condor genomes contained long runs of homozygosity, suggesting a history of inbreeding.

Notably, the researchers found significantly elevated heterozygosity on smaller chromosomes and in the distal regions of larger chromosomes. Similar patterns have been observed in other bird species, and may be due to varying recombination rates across the genome, they said. One possible explanation is that background selection against linked deleterious alleles caused more pronounced reductions of diversity in regions with lower recombination rates. When they investigated further, they found that nucleotide composition, sequence diversity, and recombination rates were all associated with each other in the California condor genome, though they weren't able to determine causal relationships.

Overall, the researchers said, the results suggested that California condors were more abundant than either Andean condors or turkey vultures for much of the Pleistocene era. California condors have low diversity relative to species with shorter lifespans and higher reproductive rates, such as passerines, but similar diversity compared to long-lived species, such as the white-tailed eagles (Haliaeetus albicilla), barn owls (Tyto alba), and American crows (Corvus brachyrhynchos), all of which are relatively abundant. Further, they said, genome-wide diversity in California condors is higher than in bald eagles (Haliaeetus leucocephalus), which also came very close to extinction in the 20th century but have since rebounded.

Importantly, genome-wide diversity in the California condor is more consistent with factors such as its large body size, long lifespan, and low fecundity than with its status as a critically endangered species, suggesting that it retains a high degree of ancestral variation and could have the potential for future adaptation.

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