Long-term and extensive population decline drives elevated expression of genetic load in a critically endangered seabird

Abstract Endangered species serve as valuable models to understand the genetic legacy of historical demographic bottlenecks. Genomic erosion compromises the efficiency of purifying selection on deleterious mutations, thus reducing species’ adaptive potential. Untangling demographic history and its genetic legacy remains a significant challenge for endangered species. Comparing genomic characteristics between a critically endangered seabird, the Chinese crested tern and its abundant sister species, the Great crested tern, we show that the current small population size (< 150 individuals) of the Chinese crested tern is due to massive reduction of effective population size by 98.8% through the Last Glacial Maximum. We found evidence of inbreeding depression in the Chinese crested tern because of elevated expression of deleterious mutations, and more pathogenic variants of disease-related genes, likely leading to fitness loss. These findings highlight the power of conservation genomics between species with different conservation status to understand genomic erosion and inform future conservation management.