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.