Reduced representation sequencing reveals genetic diversity and adaptive genetic divergence in Calamus rhabdocladus

Small, isolated populations are more susceptible to natural disturbances and declines in genetic diversity. Calamus rhabdocladus has a scattered and fragmented natural distribution across South China, where only a few relict populations still exist. However, no population genetic studies have been conducted to date, and conservation management plans are lacking. In this study, we examined the genetic diversity, genetic differentiation, and environmental adaptability of all sampled individuals of C. rhabdocladus using reduced representation sequencing technology. We observed a moderate level of genetic diversity, with the values of unbiased observed heterozygosity (Ho), unbiased expected heterozygosity (He), Nei's gene diversity (Nei's), and Shannon's information index (I) being 0.180, 0.282, 0.279, and 0.436, respectively. Additionally, the Guangzhou (GZ), Heyuan (HY), and Foshan (FS) sites exhibited higher genetic diversity than other sites. Large genetic differentiation was detected in C. rhabdocladus. Structure analysis, phylogenetic tree, and principal component analysis all clustered the samples into three distinct genetic groups, shaped by geographical barriers, heterogeneous environments, and germplasm reproduction characteristics. Redundancy analysis (RDA) identified the driest month (bio14) and the mean temperature of the wettest quarter (bio8) as the two most important environmental factors driving adaptive genetic variation. The Latent Factor Mixed Model (LFMM) identified 955 loci significantly associated with environmental adaptation and successfully aligned 469 genes from related species, which were enriched in functional categories involving cell structure, carbohydrate metabolism, and protein degradation. Overall, this study represents the first investigation into the genetic diversity and structure of C. rhabdocladus. Our findings will aid in the conservation and utilization of the species, providing a theoretical basis for future ecological and evolutionary research.