Figure Legends
Figure 1 Sampling localities. The number on the map indicates
the population ID. Pop 1–13 are located upstream of the Kanayama dam
and can be particularly assumed to be within the local scale. The map
was created using the National Land Numerical Information from the MLIT
of Japan (nlftp.mlit.go.jp/)
Figure 2 Spatial population structure among 21 sites estimated
by three types of markers. (A, B) The haplotype compositions in each
site estimated by the D-loop region using eDNA-based (A) and
tissue-based (B) approaches. Haplotype names correspond to Table S2.
Within each site, boxes separated by black lines indicate different
haplotypes, and the box size reflects haplotype frequency. Only the
haplotypes with high frequency (the sum of \(p_{i}\) ≥ 0.5 in either
eDNA or tissue) are shown in color (except white). Different colors
except white indicate different haplotypes. (C) Population structure
inferred by the STRUCTURE analysis using SNP data obtained by MIG-seq.
Barplots display the proportion of the membership coefficients in the
inferred subpopulations (clusters) at K = 6 for all individuals. The
number indicates the population ID.
Figure 3 Congruence of eDNA- and tissue-based genetic
differentiation. (A) Mantel correlograms showing the spatial
autocorrelation of genetic data. The r values obtained from the three
types of markers are displayed. Filled markers indicate significant
correlations from a null model of spatial structure (p< 0.05). (B, C) Correlation of genetic differentiation
statistics calculated by haplotype frequencies estimated from eDNA- and
tissue-based approaches for statistics D PS (B)
and G ST(C). (D, E) Correlation between genetic differentiation statistics
calculated by eDNA samples and genome-wide SNP data for statisticsD PS (D) and G ST (E).
Filled circles indicate the population pairs less than 15 km apart, and
correlations in this 15-km dataset are also shown.
Figure 4 Relationship of eDNA-based genetic differentiation
with geographic distance and water temperature in the 13 sites upstream
of the Kanayama dam. Scatter plots of D PS versus
waterway distance (A) and summer water temperature differences (B)
between populations are displayed.