Population Genomic Analysis Provides Insights Into the Evolution and Conservation of Two Critically Endangered Musk Deer Species.

Musk deer (), the sole genus in the family Moschidae, are critically endangered and face an uncertain future due to the limited understanding of their taxonomy, evolutionary history, genetic load, and adaptive evolution. These knowledge gaps hinder conservation efforts at crucial stages. Here, we conducted a comprehensive conservation genomic analysis by sequencing eight genomes and integrating public data from 15  individuals. Phylogenomic and population genomic analyses confirmed that is a distinct phylogenetic species that diverged approximately 260 thousand years ago (kya). Both species experienced severe population bottlenecks, subsequently exhibiting marked genetic divergence. Over the past 200 kya, has undergone multiple admixture events and bottlenecks, whereas has steadily declined and maintained a small, stable population. Anthropogenic activities have intensified these pressures, leading to sharp declines in both species. Notably, has accumulated homozygous deleterious mutations, thereby heightening its extinction risk. Moreover, selective sweep analysis revealed 32 positively selected genes, including olfactory receptor genes ( and ), which are essential for foraging, reproduction, and social interactions; the proliferation-related gene (), which responds to environmental changes and injury; and the thermoregulation gene (), which helps maintain body temperature stability in extreme conditions. These findings shed light on the speciation and evolutionary history of musk deer, offering crucial insights into their local adaptations and vulnerabilities. This work provides a foundation for targeted conservation efforts to avert extinction and safeguard biodiversity.