Figure legends
Figure 1: Geographic map of the 16 localities (15 islands)
under study, sampled in the archipelagos of Mallorca, Cabrera, and
Menorca.
Figure 2: Chromosome distribution of raw and filtered SNP data
for each of the three datasets (COMBINED, GBS and RADSeq).
Figure 3: Genetic diversity estimates per population (Pi:
nucleotide diversity, Ho: Observed heterozygosity, and Fis: inbreeding
coefficient) with corresponding error bars, based on 5523 SNPs (COMBINED
dataset).
Figure 4: Heatmap of pairwise genetic differentiation (Fst)
between the 16 populations of P. lilfordi (COMBINED
dataset, 2876 SNPs). All Fst estimates were significant
(p< 0.01 after permutations).
Figure 5: Population genetic structure based on 2876 SNPs
(COMBINED dataset, after LD). A) DAPC retaining the first 64 PCs (65%
of the explained variance). B) Unsupervised clustering by ADMIXTURE
depicting K =2 to K=9 (best value) clusters.
Figure 6: Midpoint-rooted ML tree based on consensus sequences
per population after SNP concatenation (2876 SNPs, only variable sites,
model GTR+ASC, 10,000 bootstrap replicates). Node numbers indicate
bootstrap support. The asterisk indicates the most probable ancestral
population according to IQ-TREE 2 root analysis.
Figure 7: Candidate SNP outliers identified for GBS (n= 222),
RADSeq (n=190), and COMBINED (n=18). A) Outliers chromosome distribution
(barplot) and proportion per gene category (coding, CDS and non-coding
regions) (pie chart). B) Proteins with outliers detected by multiple
datasets and corresponding number of outliers. The asterisk indicates
proteins with shared SNP outliers among datasets. C) Distance biplot
of a Principal Component Analysis (PCA) based on the outlier genotype
distance matrix for the COMBINED dataset (18 SNPs). Circles are
specimens plot to optimally reproduce their Euclidean distances; arrows
are unscaled SNPs scores showing their contribution to each principal
component.