Museomics Deciphers the Phylogeographic Differentiation and Conservation Status of a Montane Pheasant

Anthropogenic habitat fragmentation and climate change have significantly reduced the genetic diversity and adaptive potential of local populations in numerous species. However, the lack of comprehensive genomic data from local populations has hindered the accurate assessment of their threatened status, hindering the designation of effective conservation units. Museum specimens offer a valuable source of historical DNA, enabling insights into population structure and uncovering hidden genetic diversity. The Koklass Pheasant, a montane species distributed across Central and Southwestern China, is increasingly threatened by habitat loss and climate change. Here, we utilized whole-genome sequencing data of museum samples to decipher the population structure and assess genetic diversity of this species. We identified six distinct populations, five of which corresponded to known subspecies in China, while a newly discovered Sichuan population exhibited clear genetic differentiation. Historical demographic analyses revealed a shared historical trajectory, characterized by expansion following the Last Glacial Maximum and a decline starting around 10 Kya. Genetic diversity and mutational load were unevenly distributed across populations. Notably, the Anhui population, which inhabits a restricted and isolated range, exhibited the lowest genetic diversity and highest mutational load, rendering it particularly vulnerable. Furthermore, ecological niche modeling predicted that climate change will lead to the near-complete loss of suitable habitat for populations in Anhui and Southern China. These findings underscore the importance of incorporating genomic data from museum samples into conservation strategies and highlight the necessity of establishing conservation units based on genetic diversity and evolutionary significance to safeguard the future of threatened species.