Captive Breeding of the Chinese Alligator Reduces Inbreeding but Increases Genetic Load

Inbreeding depression is a major threat to the long-term viability of small populations. Although captive breeding and genetic rescue are the main alternative in conservation, their genomic impacts are largely unknown, and the unintended effects of these approaches may intensify the depression by introducing new deleterious mutations. Based on whole-genome sequencing data from 247 critically endangered Chinese alligators, we constructed a high-resolution genetic variation map and identified three distinct genetic populations, clarifying their demographic history and further supporting the independent origin of the American population. Comparisons between captive and semi-wild populations revealed that captive management outperforms semi-wild management in reducing inbreeding and increasing genetic diversity, while simultaneously elevating the accumulation of deleterious mutations, which may result from relaxed purifying selection. Although the inbreeding coefficient in this species is notably higher than in other endangered species, purging has likely played a significant role in reducing the amount of recessive deleterious mutations. Forward-in-time simulations indicated that mixing populations can mitigate the risk of demographic decline, yet current populations still remain vulnerable to future environmental changes. These findings provide valuable genomic evidence to guide balanced and effective conservation strategies for the Chinese alligator.