Population genetics
We estimated the pairwise of nucleotide diversity, π
and the proportion of segregant
sites, θw using the R package PopGenome (Pfeifer et al.,
2014). Values of F ST were calculated with StAMPP
1.5.1 Weir and Cockerham’s unbiased estimator to obtain 95% confidence
intervals by performing 5,000 bootstraps (Pembleton et al., 2013; Weir
and Cockerham, 1984). The IBD (Isolation by Distance) was performed
using the twelve locations from Chile. The significance of correlations
between distance matrices in the Mantel test was evaluated using 10,000
permutations. The geographic distances were calculated using
latitude/longitude of all relevant sampling points using the function of
GenAlEx v 6.5 (Peakall and Smouse, 2012). Population pairwiseF ST values were used to build the genetic
distance matrices for this test. We predict the number of generations
since the most recent common ancestor of any pair of lineages using the
mutation parameter (θw = 2N θµ) as
previously described (Ruderfer et al., 2006). We used the mutation rate
(µ) previously reported from laboratory estimates on S.
cerevisiae (Lynch et al., 2008).