Whole-Genome Resequencing Reveals the Genetic Diversity and Adaptive Evolution of Rhabdophis nuchalis.

Snakes are valuable for studying adaptive evolution due to their morphological specialization, wide distribution, and strong adaptability. However, genomic studies on Rhabdophis nuchalis are limited. We resequenced 19 individuals from four regions to assess genetic diversity and adaptation. We obtained 39,226,324 high-quality SNPs and 15,838,348 high-quality INDELs. Genetic structure analysis showed Sichuan and Yunnan populations forming one cluster, and Hubei with Shaanxi another. Yunnan exhibited high nucleotide diversity and observed heterozygosity among the four sampled populations (Sichuan, Shaanxi, Hubei, and Yunnan), indicating substantial genetic diversity. Shaanxi showed low linkage disequilibrium, suggesting a larger effective population size, consistent with historical estimates. GO enrichment revealed differentiated genes related to reproduction and calcium-dependent cell adhesion. KEGG identified only the cell adhesion molecules pathway. BLAST aligned these sequences with protocadherin β and γ subclusters. Overall, clear genetic clustering and differentiation exist among the four populations, with differentiation-related genes involved in reproduction and cell adhesion, providing insights for genetic diversity conservation.