Population structure and gene flow
The three geographic populations classified a priori according to our assumptions demonstrated moderate genetic differentiation from pairwise F ST, with all comparisons being significant (p < 0.05; Table S7), but being highest between Northern and Southern (F ST = 0.12) and lowest between Central and Northern (F ST = 0.06) populations. All populations displayed comparable expected heterozygosity, ranging from 0.53-0.54, and a lowF IS value of less than 0.1. The summary statistics for each population are provided in Table S8.
The STRUCTURE analysis indicated a best K of 2 (Fig. S2), which roughly separated the Northern group from the other two populations, and samples with admixed genetic composition were found in all populations (Fig. 5). Based on K = 3, the Central and Southern populations were further differentiated by different genetic components with a certain level of admixture. The results of our DAPC support a similar pattern to that revealed by STRUCTURE, indicating an overall North-South differentiation and mixing in the Central region (Fig. 5).
Accounting for these spatial relationships, we tested for the presence of autocorrelation using Morans’ I and various spatial structures (i.e., global and local). We generated statistically significant results for Morans’ I (p < 0.05) and global structure (p < 0.05), indicating the presence of positive spatial autocorrelation. The lagged principal scores from axis 1, which had the highest eigenvalue, also support a North-South division of genetic structure (Fig. S3), in accordance with our STRUCTURE and DAPC findings.
Significant migration among populations was inferred using BayesAss, with 2 to 6% of individuals immigrating from each population per generation, even between the Northern and Southern populations (Table S9), implying that the longest dispersal distances (>50 km) are much greater than the average home ranges (5.0 km2) of leopard cats in Taiwan (Chen et al., 2016). From the Estimated Effective Migration Surfaces (EEMS) plot, we observed two noticeable barriers with reduced gene flow, corresponding to highways and mountainous areas (Fig. 6). The first barrier, reflecting north-south highways and mountain ridges, separates the Northern and Central populations. The second barrier, represented by a highway and unfenced main roads extending from the west coast to mountains in the (south)east, separates the Southern population from the other populations. One obvious diversity hotspot encompassing the Central population was revealed by EEMS, which harbors a larger proportion of samples with admixed genetic composition (based on STRUCTURE analysis) compared to other regions. Two diversity coldspots are located at the northernmost and southernmost borders of the current distribution of the leopard cat in Taiwan.