2.7 | Population genetics statistics
Genetic differentiation between all populations was estimated with SNP markers using pairwise FST(Weir & Cockerham, 1984). With pool-sequencing data, we ran the function computePairwiseFSTmatrix implemented in “Poolfstat” (Hivert et al., 2018). FST were computed between each population pair, with all the SNP markers along the genome, or only with the SNPs found in all the candidate genomic regions identified with genome scan analyses, and neighbor joining dendrograms were computed using the R-function hclust. In the candidate regions, the differentiation between each population pair sampled in the same location and for each region was estimated and compared to an empirical null FST-distribution, as described in Carlier et al. 2021b.
Tajima’s D, nucleotide diversity (π), and Watterson’s Theta (θ) were estimated with Pool-Seq data on 1Kb non-overlapping windows distributed across the genome for each population sampled in 2011 and 2013 using PoPoolation software (Kofler et al., 2011). These three indexes were also estimated on 1Kb non-overlapping windows using the 63 isolates individually sequenced with the library Egglib v.3.0.0 (De Mita & Siol, 2012). For each population, we computed the median for the three statistics based on the distribution of each 1 kb window distributed across the genome as described in Carlier et al. 2021b. We then compared Tajima’s D distributions computed with SNPs found in the candidate genomic regions to the whole genome distribution using a Wilcoxon-Mann-Whitney test.
Linkage disequilibrium (LD) was estimated from the 63 isolates of P. fijiensis sequenced individually using the option hap-r2 implemented in vcftools v.0.1.14 (Danecek et al., 2011). In the present study, LD was estimated for all pairs of loci, for each scaffold forming the core genome and for the two populations separately (CU1S2 and CU1R2). The pattern of LD decay was estimated by calculating the mean Pearson’s correlation coefficient (r2) for intervals of 1 Kb grouping pairs of loci separated by the same distance.