Genetic Diversity and Population Structure of tufted deer (<em>Elaphodus cephalophus</em>) in Chongqing, China

Effective conservation and management of the endangered tufted deer (Elaphodus cephalophus) necessitate genetic diversity research. This study systematically assessed the genetic diversity, population structure, gene flow, and demographic history of three representative tufted deer populations in Chongqing, China (Jinfo Mountain, Simian Mountain, Northeastern Mountainous area) using combined mitochondrial Cytochrome b (Cyt b) gene and D-loop region analysis. Our findings reveal the D-loop region demonstrates significantly higher genetic variability and a faster mutation rate than Cyt b. The Simian Mountain population consistently displayed the highest haplotype diversity, suggesting its role as a genetic diversity hotspot and crucial hub for regional gene flow. Haplotype network analysis showed frequent gene exchange between Simian Mountain and Northeastern Mountainous populations, while the Jinfo Mountain population exhibits significant genetic isolation, likely due to unique topographical features. Historical demographic analyses suggest a likely slow expansion, with evidence for recent population expansion despite concurrent regional genetic isolation. This study underscores the critical importance of multi-scale genetic markers for deciphering species’ evolutionary histories and provides essential groundwork for tufted deer conservation. We recommend prioritizing Simian Mountain conservation, enhancing Jinfo Mountain genetic management, and maintaining regional population connectivity through ecological corridors and continuous monitoring.