Population divergence and demography
The admixture analyses of the population genomics data revealed that the
isolates of S. lacrymans were divided into geographically
structured groups and sub-groups (Figure 1). When enforcing a two-group
structure (K = 2), isolates from Europe and New Zealand were clearly
separated from Japanese isolates (the cross-validation error was clearly
lowest for K = 2; Supplementary Figure S1). The Principal Component
Analysis (PCA, Figure 2a) likewise divided the isolates into the same
two main groups (Europe/New Zealand vs Japan) along the first axis,
explaining 49.8% of the variation. FST and
DXY estimates confirmed that the Japanese and European
populations were strongly differentiated, both based on average
FST of 0.572, DXY of 0.524 and the
genome-wide plots (Figure 3).
When the number of groups in the admixture analysis was raised to four
(K = 4), both the Japanese population and the European/New Zealand group
split into two (Figure 1d). Four French individuals were separated from
the rest of the European/New Zealand isolates and five Japanese isolates
were separated from the rest of the Japanese isolates. One individual
from New Zealand (ICMP18202) was separated from the European samples
along axis 1 in the PCA plot and from the European population in the
admixture analyses at K = 7 (Figure 1d).
Admixture and PCA analyses performed on the European and
Japanese populations separately revealed further geographic
sub-structuring within both populations (Figure 1 and 2). For K = 4, the
European population was divided into a northern European group, two
groups in eastern France, and a southern French group, also visible in
the PCA plot (Figure 2). When splitting the Japanese population into K =
7, a distinct northern group was identified, three additional admixed
groups and three southern groups. These groups were also partially
recognized in the PCA (Figure 2). Demographic analyses based on a
mutation rate of 10-7, indicated that the historic
population that gave rise to the current European population split from
the Japanese population around 3,000 generations ago (confidence
interval 2012-6157; Figure 4). The estimated divergence time (i.e.
generations) was highly sensitive to the selected mutation rate, which
increased to 18,770 generations with a mutation rate of
10-8. The modelled demographic scenario where both the
European and the Japanese population experienced a change in population
size was more likely than the scenario with only a population size
change in Europe (the difference in likelihood between the two models,
ΔAIC = 58,899). The European population went through a strong bottleneck
about 250 generations ago (confidence interval 198-650), and
Fastsimcoal2 analyses indicated that only six haplotypes were
involved (confidence interval: 4.18-19.40). This could be a slight
underestimate, since some of the European isolates were sampled at
earlier time points (i.e. from 1935 to 2014; Table 1), which may affect
the models. Nevertheless, based on our model, the Japanese population
experienced a reduction in population size considerably earlier and in
the same time period as the ancestral population diverged (around 3,500
generations). The reduction in the ancestral Japanese population was
less severe, with an estimated effective population size of 1,337. The
current effective population sizes were estimated to 1,273 individuals
in Europe and 12,500 individuals in Japan (Figure 4).