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.