3.2. Population genetic differentiation and structure
Pairwise Fst values (Weir & Cockerham, 1984) estimated for the combined dataset (2876 SNPs after LD pruning, Table 2) indicated that all populations were significantly differentiated (p<0.01 for all pair-wises) (Figure 4). Global levels of differentiation among islet populations were generally high, with a mean Fst = 0.247 (ranging between 0.030 and 0.473). These values were highly comparable to those estimated on individual datasets, indicating that this reduced SNP dataset is also representative of the genetic differentiation among the studied populations.
The most discriminated population was the small islet of en Curt (Mallorca), showing an average Fst of 0.338 with respect to all other islands (minimum value with Moltona, Fst =0.24, Figure 4). The least differentiated populations were Aire and Colom (0.047, Menorca), Na Guardis and Na Moltona (0.064, Mallorca), and the two Cabrera localities (0.030). In this latter case, Fst value <0.05 supports the existence of a unique panmictic population within the major Cabrera Island.
Within major archipelagos, no significant correlation was found between genetic (Fst) and geographic distances (p>0.1), excluding a scenario of isolation-by-distance.
Population genetic clustering with DAPC (Figure 5A) was consistent with Fst-based distances (Figure 4) and the geographic distribution of these populations (Figure 1). Membership probabilities according to the retained discriminant function (64 PCs) correctly assigned all individuals to their source population/islet, excluding recent translocations or mislabeling. According to the first Discriminant Function (DF) (35% of variance), three major genetic clusters were identified (Figure 5A): I) the group of Menorca islands, highly homogeneous and with poor internal discrimination, II) the group of Cabrera and Mallorca islands, characterized by a stronger genetic differentiation among populations, and III) the islet of en Curt, forming an independent lineage. DAPC on the subset of Menorcan populations only (30 PCs retained) slightly increased the population resolution, highlighting a clear divergence of the islet of Porros (Figure 5A, top left panel).
ADMIXTURE analyses were used to further explore population structure, as well as shared ancestry (Figure 5B). Genetic clustering clearly evidenced a major discrimination between Menorca and Cabrera/Mallorca populations (K=2), followed by progressive substructuring within Cabrera/Mallorca (from K=3), and ultimately within Menorca (from K=5). The best-supported number of present genetic clusters is 9 (CV=0.386), corresponding to four genetic clusters in Menorca and five in Mallorca/Cabrera, in line with the major structure recovered by DAPC analysis (Figure 5A). The proportion of shared ancestry among populations varies from zero (independent lineages of the islets of en Curt, Porros, Foradada and Esclatasang) up to 40% (the highly admixed population of Colom). Cabrera island and distant islands from North-West of Mallorca (Dragonera and Colomer) formed a unique genetic cluster, with a small proportion of shared ancestries also with the small islets of Foradada and Esclatasang (North and South of Cabrera, respectively) (see map in Figure 1). According to the optimal current grouping (K=9), no shared ancestry was detected between the two major archipelagos of Menorca and Mallorca/Cabrera, indicating a strong genetic differentiation. However, lower substructuring, from K=2 to K=9 retrieved a clear signature of shared ancestry between the Northern Mallorca populations of Dragonera and Colomer with the Menorcan populations of Colom, Rei and Aire.