Genome-wide diversity in the California condor tracks its prehistoric abundance and decline.

Summary Due to their small population sizes, threatened and endangered species frequently suffer from a lack of genetic diversity, potentially leading to inbreeding depression and reduced adaptability. 1 During the latter half of the twentieth century, North America’s largest soaring bird, 2 the California condor (Gymnogyps californianus; Critically Endangered 3 ), briefly went extinct in the wild. Though condors once ranged throughout North America, by 1982 only 22 individuals remained. Following decades of captive breeding and release efforts, there are now >300 free-flying wild condors and ∼200 in captivity. The condor’s recent near-extinction from lead poisoning, poaching, and loss of habitat is well documented, 4 but much about its history remains obscure. To fill this gap and aid future management of the species, we produced a high-quality chromosome-length genome assembly for the California condor and analyzed its genome-wide diversity. For comparison, we also examined the genomes of two close relatives: the Andean condor (Vultur gryphus; Vulnerable 3 ) and the turkey vulture (Cathartes aura; Least Concern 3 ). The genomes of all three species show evidence of historic population declines. Interestingly, the California condor genome retains a high degree of variation, which our analyses reveal is a legacy of its historically high abundance. Correlations between genome-wide diversity and recombination rate further suggest a history of purifying selection against linked deleterious alleles, boding well for future restoration. We show how both long-term evolutionary forces and recent inbreeding have shaped the genome of the California condor, and provide crucial genomic resources to enable future research and conservation.