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.