2.8 Scanning for putative signatures of selection
Regions in the genome showing signatures of selective sweeps were detected by comparing the invasive and source populations using two different approaches. The first method estimated the Fixation index (F ST) values between populations by using the R package PopGenome (Pfeifer et al., 2014). Loci under selection should exhibit large F ST values. The second method calculated the absolute XP-EHH (Cross Population Extended Haplotype Homozygosity) scores to detect selective sweeps in which the selected allele has approached or achieved fixation in one population but remains polymorphic across both populations (Sabeti et al., 2007). Phasing of each individual’s genotype data was inferred using WhatsHap (Patterson et al., 2015) and Shapeit4 (Delaneau et al., 2019) and XP-EHH scores were calculated with the R package rehh (Gautier & Vitalis, 2012). A sliding window of 10 kb was applied for both of the methods, and windows with values above the 99th percentile of the empirical distribution and with more than 10 SNPs were retained for further analyses (Pujolar et al., 2022). Overlapping windows between the two methods were considered as potential regions under selection. The candidate genes were obtained by the SNP annotation within the candidate regions using the ANNOVAR software (Wang et al., 2010). Gene Ontology (GO) enrichment analysis of these genes were performed using the hypergeometric Fisher exact test in an online tool (OmicShare, www.omicshare.com/tools).