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

## TL;DR

This study finds that Chinese crocodile lizard populations in nearby streams have distinct genetics and reduced diversity, with immune-related genes showing different selection patterns.

## Contribution

The study reveals contrasting genetic patterns in neutral and immune-related markers among adjacent lizard populations, emphasizing the need for integrated genetic monitoring in conservation.

## Key findings

- Clear genetic differentiation was found between DaChai and the ChiShui-YuSan lizard populations.
- Both subpopulations showed reduced genome-wide diversity and signs of inbreeding.
- The MHC gene region showed higher diversity in DaChai and signs of recent selection in ChiShui-YuSan.

## Abstract

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 (Shinisaurus crocodilurus) 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.

•Fine-scale genetic differentiation was detected among adjacent S. crocodilurus streams•Both subpopulations show reduced genome-wide diversity and inbreeding•MHC loci reveal contrasting selection patterns between subpopulations•Integrating neutral and functional markers is essential for conservation management

Fine-scale genetic differentiation was detected among adjacent S. crocodilurus streams

Both subpopulations show reduced genome-wide diversity and inbreeding

MHC loci reveal contrasting selection patterns between subpopulations

Integrating neutral and functional markers is essential for conservation management

Evolutionary biology; Genomics; Zoology