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.