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).