We also calculated the amount of differentiation between each population and all other populations, as the fixation index, FST, using the total polymorphism across the Muller elements (Drosophila chromosomes) (Weir and Cockerham 1984). FST appears to be generally low across the genes in theD. innubila genome (Figure 1B, total median = 0.00567), consistent with nuclear gene flow between populations (Weir and Cockerham 1984). In contrast, there is higher FSTbetween mitochondrial genomes (Figure 1C). Both nuclear and mitochondrial results are consistent with the Structure/StairwayPlot results. However, consistent with a more recent population contraction upon migration into PR, FST of the nuclear genome is significantly higher in PR (Figure 2A, GLM t-value = 93.728,p -value = 2.73e-102). Though PR FST is still extremely low genome-wide (PR median = 0.0105), with some outliers on Muller element B like other populations (Supplementary Figure 2). We also calculated the population genetic statistics pairwise diversity and Tajima’s D for each gene using total polymorphism (Tajima 1989). As expected with a recent population contraction in PR (suggesting recent migration and establishment in a new location), pairwise diversity is significantly lower (Figure 2B, GLM t-value = -19.728, p -value = 2.33e-86, Supplementary Table 2) and Tajima’s D is significantly higher than all other populations (Figure 2C, GLM t-value = 4.39, p -value = 1.15e-05, Supplementary Table 2). This suggests that there is also a deficit of polymorphism in general in PR, consistent with a more recent population bottleneck, removing rare alleles from the population (Figure 2C, Supplementary Figure 3). Conversely, the other populations show a genome wide negative Tajima’s D, consistent with a recent demographic expansion (Supplementary Figure 3).
Figure 2: Summary statistics for each population. A.Distribution of FST across genes for each population versus all other populations. B. Distribution of pairwise diversity for each population. C. Distribution of Tajima’s D for each population. D. FST distribution for Antifungal associated genes for each population. E.FST distribution for cuticular proteins for each population. F. FST distribution for all immune genes (excluding antifungal genes). In A, B & C all cases significant differences from CH are marked with an * and outliers are removed for ease of visualization. In D, E & F, significant differences from the genome background in each population are marked with a + and white diamond mark the whole genome average of FST for each population.