Spatial demography and population expansion
To examine the process of regional demography and the potential
occurrence of genetic bottlenecks, we performed a mismatch distribution
analysis using the spatial expansion model in Arlequin ver. 3.5.2.2
(27 , 28 ). Within each group except Group 1, the models did
not reject the expected spatial expansion scenario with multimodal
distributions of pairwise haplotypic differences (fig. S6 and table S3).
In Group 1, the mismatch distribution exhibited a dominant frequency
peak at one pairwise difference, indicating that the populations in this
group had experienced a genetic bottleneck. The τ value, indicating the
relative time span since a population spatially expanded through a
region, was high in Group 2 (Clade-A) and also in Group 4 (Clade-B).
The southwestern part of Hokkaido, in which Group 1 is distributed with
low genetic variation, had unique geological characteristics. For
instance, the Ishikari Lowland (Fig. 3b) was submerged in seawater
during the Mindel–Riss
(0.18–0.23 Mya) and Riss–Würm
(0.07–0.13 Mya) Interglacial periods (14 ). Moreover, results of
the MiFish metabarcoding (fig. S1) also suggested the existence of many
rivers in the west of the Ishikari Lowland where B. toni could
not be detected using eDNA. This finding is consistent with the
conventional view that the Ishikari Lowland prevented the southward
dispersal of primary freshwater fishes from Siberia (13 ). In
addition, the Shikotsu–Toya volcanic field have many active volcanoes,
where large caldera-forming eruptions have occurred since approx. 0.10
Mya (15 ). Repeated seawater transgressions and large eruptions in
this region have probably isolated the B. toni populations in
southwestern Hokkaido, causing their genetic bottleneck. Several
previous studies, mainly on terrestrial animals, have reported similar
phylogeographies in this region. For example, the phylogeographic
vicariance of the brown bear Ursus arctos , red fox Vulpes
vulpes , and ezo salamander Hynobius retardatus in the Ishikari
Lowland (29 –31 ) and low genetic variability among the
southwestern populations of the dark red-backed vole Myodes rex(32 ) support the hypothesis that geological events affected the
historical expansion and demography of terrestrial and freshwater
organisms in southwestern Hokkaido.
Several rivers in our study were found to co-host populations of
different lineages. In the Tokoro River system (No. 17 in Fig. 3b),
phylogenetically distant genetic groups have seemingly and uniquely
experienced secondary contact. The presence of genetically distinct
individuals in this river was further confirmed through Sanger
sequencing of DNA from captured individual fish samples (fig. S5).
Examination of the evolutionary mechanism of this coexistence, such as
reproductive isolation of the lineages, might reveal cryptic diversity
in B. toni . Co-occurrences of phylogenetically distant groups
were also found in other rivers, but whether such coexistence results
from natural distribution or artificial translocations cannot be
discerned. Although B. toni is not a target for aquaculture,
human transmission through Hokkaido is possible through mixing with
other fish resources such as salmon.