3.2.2. FST outliers
High genomic divergence between the demes was found all across the
genome (Figure 4). The POWSIM results showed that the distributions of
the observed and simulated (expected) F ST values
differed from each other (Kolmogorov-Smirnov, p<0.05). The
observed distribution showed a higher frequency of largeF ST values than the expected distribution (Figure
5). The highest value of the expected distribution wasF ST=0.864, and we found 194 SNPs (out of
12,177,462) with a larger F ST in the observed
distribution, of which 19 had F ST=1. Of these 194
outliers, one was associated with a gene significantly enriched
(p<0.05) by two GO terms connected with the growth process
(GO:0048590): ‘extracellular matrix and structure organization’ (Table
S4).
A total of 60,887 SNPs out of 12,177,462 occurred above the
99.5th percentile of the F STdistribution (F ST ≥ 0.53). 698 of these outlier
SNPs were within genes and 432 genes were identified as feasible for
topGO analysis. Results showed that these 432 genes were significantly
(p≤0.01) enriched with 69 GO terms: 21 genes were significantly linked
with GO terms associated to ‘glycosaminoglycan biosynthesis’ (Table S4).
Seven genes were associated to ‘gonad morphogenesis’ while two were
involved in binding of sperm with eggs. The five top GO term
superclusters (the ones associated with the smallest p-values) were:
‘chondroitin sulfate metabolism’ (i.e. glycosaminoglycan biosynthesis),
‘response to ozone’ (linked with animals’ response to stimulus/stress,
GO:0050896), ‘cell-cell adhesion involved in gastrulation’ (linked with
embryonic morphogenesis, GO:0048598), ‘fatty acid derivative metabolism’
(energy storage), and ‘reactive oxygen species metabolism’ (linked with
phagocytosis and signal transduction; Figure S5).
For 5 kb windows, 8,508 out of 340,297 windows were considered as
outliers with F ST-values above the
97.5th percentile (F ST ≥ 0.35).
2,148 outlier windows were within genes. TopGO identified 1,494 feasible
genes, associated to 113 significant GO terms (p≤0.01). Seven genes were
significantly enriched with the GO terms ‘glucose catabolic process to
pyruvate’ and ‘canonical glycolysis’ (Table S4).
Four genes were enriched with the
GO term ‘NADH oxidation’. Furthermore, six genes were significantly
enriched with the GO term ‘sperm capacitation’. Top five GO term
superclusters identified by REVIGO were: ‘phagocytosis’,
‘thrombin-activated receptor signaling pathway’, ‘ciliary body
morphogenesis’, ‘peptidyl-glutamic acid modification’, and ‘fatty acid
derivative biosynthesis’. These GO terms are mainly linked with
metabolic (GO.0008152) or immunological (GO:0006910) processes (Figure
S6).