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.