We investigated the existence of selection signatures using three complementary methods: (i) detection of selective sweeps for the cultivated individuals using the likelihood-ratio test of SweeD 3.3.2 (18), (ii) calculation of π ratio as πwildcultivated, and (iii) calculation of Weir and Cockerham’s (44) FST between wild and cultivated populations. For composite-likelihood ratio (CLR) computation, we adapted the grid of each chromosome to calculate a CLR peak every 100 bp. We considered CLR within 100-kb windows as potentially resulting from similar selection events. We thus grouped them into common windows of 50 kb on each side of the most extreme peak. We calculated π ratio and FST using sliding windows of 50 kb every 10 kb with VCFtools (36). For the three methods, we reported genome annotations of the 1% most extreme values using BEDTools 2.2 (44) (windowBed command, default parameters) based on D. rotundata genome annotations (34). We only considered genes with a meaningful annotation. We associated GO terms with loci using a customized R script. We performed enrichment tests for GO biological processes, cellular components, and molecular function terms using the Fisher exact test implemented in the R package topGO (45).

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