Fine-scale genetic structure and genetic diversity in the Chinese crocodile lizard

Population fragmentation and restricted dispersal in endangered species can sharply reduce genetic diversity and adaptive potential, making genetic monitoring vital for conservation. However, whether neutral genetic markers alone can adequately assess adaptive potential remains debated. We examined the fine-scale genetic structure and diversity of the endangered Chinese crocodile lizard (<i>Shinisaurus crocodilurus</i>) in three closely located streams: DaChai (DC), YuSan (YS), and ChiShui (CS). Despite their proximity, we found clear genetic differentiation, with DC especially distinct from the CS-YS group. Both subpopulations showed reduced genome-wide diversity and signs of inbreeding. Interestingly, the MHC gene region showed a different pattern. DC individuals had higher MHC diversity, while CS-YS showed signatures of recent selection. These results suggest different evolutionary pressures at immune-related loci in the two subpopulations and highlight the importance of integrating both neutral and functional genetic markers in conservation, as neutral markers alone may overlook key adaptive capacities.