Thirty-five clusters of C. hainanense were formed, which resulted in four independent clusters. Among these clusters, 13 samples from Jianfengling (JFL_1-JFL_5) and BWL (BWL_1-BWL_8) populations with similar genetic backgrounds, gathered to form cluster 1 (Figure 5). Six samples of C. hainanense from Huishan (HS_1-HS_6) and Wuzhishan (WZS_3) populations, with similar genetic backgrounds, clustered together to form cluster 2. Thirteen samples of C. hainanensefrom Diaoluoshan (DLS_1-DLS_10) and Baishaling (BSL_1-BSL_3) populations, with similar genetic backgrounds, clustered together to form cluster 3. The C. hainanense from the Wuzhishan (WZS_1-WZS_2) population was distant from the other three clusters, showing relatively long genetic distances, and so formed a separate cluster 4.

Figure 5 PCA analysis diagram of C. hainanense

We calculated the relatedness between pairs of all samples based on the SNPs (Figure 6). Kinship analysis reveals the genetic distance between samples, aiding evolutionary analysis. In the kinship heatmap, redder colors indicate closer kinship between individuals on the horizontal and vertical axes. In contrast, a red heatmap among multiple individuals suggests they may belong to a closely related family group. Conversely, bluer colors indicate more distant kinship between individuals. In the correlation heat map, the correlation coefficients of BSL_1 and BSL_2 were more outstanding than 0.4, indicating that the two samples of Bawangling were very closely related to each other. The correlation coefficients of Bawangling (BWL_1 and BWL_4), Hangluo Mountain (DLS_6 and DLS_9; DLS_7 and DLS_9; DLS_8 and DLS_10), and Huishan (HS_1-HS_6) are just between 0.2 and 0.3, indicating that some genetic exchange still exists between clusters in the case of geographical isolation (Figure 6).