Multi-source captive breeding maintains nuclear genetic diversity in Alpine musk deer (Moschus chrysogaster) despite severe mitochondrial erosion

The Alpine musk deer ( Moschus chrysogaster ) is endemic to China and designated as a first-class nationally protected animal due to its critically endangered status, with wild populations sharply declining from poaching and habitat loss. Since 1990, a captive-breeding program in Xinglong Mountain, Gansu Province, has maintained the only population for musk production and potential reintroduction. However, the genetic consequences of three decades of closed, multi-source breeding remain unclear, limiting assessments of long-term survival and rewilding potential. We assessed nuclear genetic diversity in this captive population using 12 polymorphic microsatellite loci genotyped in 340 individuals. Diversity metrics (allelic richness, heterozygosity, inbreeding coefficient, and PIC) were compared to published data from wild and related musk deer. Our analyses revealed that the captive population includes at least three distinct ancestral lineages and retains nuclear genetic diversity comparable to or higher than wild populations. This contrasts with earlier findings of severely reduced mitochondrial diversity, indicating maternal genetic erosion. The disparity between high nuclear and low mitochondrial variation underscores the benefits of a multi-source founding strategy. While the limited number of founding females constrained mitochondrial lineages, the mixing of several source populations preserved nuclear diversity through combined contributions. We conclude that effective captive management should focus on maintaining multiple lineages, particularly regarding maternal diversity, given the severe mitochondrial erosion, there should be a regular priority to introduce genetically validated females from distinct wild sources to mitigate genetic drift. Overall, this study demonstrates that a diversified captive-breeding strategy can sustain high nuclear genetic diversity in Alpine musk deer.