Genomic islands of differentiation and selective sweeps
BayeScan analyses were used to detect genetic loci with
signatures of selection. When comparing the European and Japanese
populations using a false discovery rate of α < 0.05, two loci
were detected (Supplementary Figure S2; S. lacrymans S7.3 v. 2:
scaffold 27, position 4,748 and S. lacrymans S7.3 v. 2: scaffold
8, position 2,440,344). Both loci had significantly lower
FST than expected from the BayeScan analyses,
with FST of 0.45 and 0.36 for the loci at scaffold 27
and 8, respectively, indicating purifying or balancing selection (See
Supplementary Figure S3 for FST and
DXY along these scaffolds).
The locus at scaffold 8 is in a predicted gene (protein ID 139103) with
a SNF1 protein kinase subunit beta-2/beta-3 Interpro domain (Table 3).
The DXY of a 10 kb genomic window surrounding
this locus was intermediate (0.525). The European population had low π
(0.00025) and negative Tajima’s D (-2.388), and the opposite was
recorded for the Japanese population (π = 0.00560 and Tajima’s D =
2.042) (Table 2, see Supplementary Figure S3 and S4 for detailed plots
of DXY, FST, π and Tajima’s D
along scaffold 8). The locus at scaffold 27, was located in a predicted
gene (protein ID 79357/190659) with an oxysterol-binding Interpro domain
(Table 3). As opposed to the locus at scaffold 8, the locus at scaffold
27 had a less than average DXY (0.450).
Further, the π for the European population was high compared to the
average for this population (0.00184), while the Japanese population had
an average π = 0.00245. Tajima’s D estimate for the Japanese populations
was negative (-0.648) and opposite of what was described for the
European population (0.829) (Table 2, Supplementary Figure S3 and S5).
Extended haplotype homozygosity (EHH) indicates selective sweeps, and
more recent selection than the FST outliers detected by
BayeScan (Gautier & Vitalis 2012; Vitti et al. 2013).
EHH identified two selective sweeps in the European population, located
in a gene in scaffold 8 (protein ID 79617) and a gene in scaffold 13
(protein ID 77115; Supplementary Table 1), annotated with DNA helicase
Pif1-like and a GDP-fucose protein O-fucosyltransferase Interpro
domains, respectively (Table 3). For the Japanese population, the EEH
analyses detected a selective sweep in a locus between predicted genes
on scaffold 32. Within a 10 kb window surrounding this sweep there are
three predicted genes, one with a Cytochrome P450 Interpro domain
(protein ID 79618), one with a WW Interpro domain (protein ID 79617),
and one without any conserved domains.