3.5. Major Archipelagos-segregating SNPs
Finally, we explored environmental and geographic variables driving outlier distribution. PERMANOVA analyses indicated that Major Archipelago (Menorca and Mallorca/Cabrera, Table 1) was the only explanatory variable for all three datasets (p<0.001, 1000 permutations), with all individual outliers, except one, significantly contributing to geographic between these two major phylogenetic lineages (Figure 6) (binomial test p<0.01). PCA based on outlier genotype matrix clearly evidenced this major clustering (85.5% of variance explained for the COMBINED dataset, Figure 7C, see also Figure S4 for individual outlier genotype clustering). Only one SNP departed from this trend (SNP Chr2_24907248), recovering a clustering of South Mallorca with a subset of the Menorcan islands (Figure 7C and Figure S4). The SNP falls within the sidekick2 protein (Table S4).
A high percentage of outliers had allelic variants that perfectly segregated between major archipelagos, i.e., had null frequency in one archipelago while being present in the other (n total = 154; 11% for COMBINED, 42% for GBS and 31% for RADSeq) (Table S5). These fixed allelic differences can be considered as specific markers of the two major phylogenetic clades (Figure 6).
Discussion