Population structure and gene flow
The three geographic populations classified a priori according to our assumptions demonstrated moderate genetic differentiation (pairwise FST, Fig.2c), with all pairwise differentiation being statistically significant (p < 0.05; Fig 2c). The highest value was observed between Northern and Southern (FST = 0.12) and the lowest between Central and Northern (FST = 0.06) populations. All populations displayed comparable expected heterozygosity (He), ranging from 0.53-0.54, and a low FIS value of less than 0.1. The genetic statistics for each population are provided in Table S4.
The two independent STRUCTURE analyses suggested similar results, indicating a best K of 2 (Fig. S4a) based on ΔK, which roughly separated the Northern group from the other two populations, and samples with admixed genetic composition were found in all populations (Fig. 2a). Based on K = 3, the Central and Southern populations were further differentiated with a certain level of admixture. The results of the DAPC supported a similar pattern with STRUCTURE, indicating an overall North-South differentiation and mixing in the Central region (Fig. 2a). Results of other numbers of K of STRUCTURE and clustering numbers of DAPC are provided in Fig. S5.
Regarding these spatial relationships, the statistically significant Morans' I (p < 0.05) and global structure (p < 0.05) indicated positive spatial autocorrelation. The lagged principal scores from axis 1 also support a North-South division of genetic structure (Fig. 2b; Fig. S6), following our STRUCTURE and DAPC findings.
BayesAss indicated significant population migration, with 2 to 6% of individuals emigrating per generation, even between the Northern and Southern populations (Table S5). From the EEMS plot, we observed two noticeable barriers with reduced gene flow, corresponding to highways and mountainous areas (Fig. 3). 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 genetic diversity hotspot encompassing the Central population was revealed by EEMS, which harboured a highly proportional admixed genetic composition (based on STRUCTURE analysis) compared to other regions (Fig. 3). Last, two genetic diversity coldspots were located at the northernmost and southernmost borders of the current distribution of the leopard cat in Taiwan (Fig. 3).