5. Comparison of eDNA- and tissue-based genetic differentiation
Correlations between the metrics calculated by eDNA- and tissue-based
approaches were examined for each statistic of genetic diversity and
differentiation. For genetic differentiation, statistics were calculated
in the three datasets: the entire dataset, the dataset upstream of the
Kanayama dam (upstream dataset), and the dataset only between population
pairs with a waterway distance of <15 km (15-km dataset). The
upstream dataset was used to exclude the effects of a long spatial gap
and a dam, and the 15-km dataset was used to reveal the pattern at the
spatial scale where gene flow is especially dominant (Nakajima et al.
2021). Correlations of genetic differentiations for the entire dataset
and upstream dataset were tested by Mantel tests (9999 permutations and
10000 times bootstrapping to estimate confidence intervals) using the
package ecodist in R, and the statistics for datasets not in matrix
style (genetic differentiation in the 15-km dataset and genetic
diversity) were tested by simple bootstrapping (10000 times) using the
package CarletonStats 2.2 (Chihara and Loy 2023).