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