Differences in the genetic structure between and within two landlocked Ayu groups with different migration patterns in Lake Biwa revealed by environmental DNA analysis

Ayu ( Plecoglossus altivelis ) is largely an annual amphidromous fish, although a landlocked population lives in Lake Biwa, the largest lake in Japan. The landlocked population comprises two migrant groups, spring migrants and autumn migrants, which run to inlet rivers from the lake at different seasons. We used environmental DNA (eDNA) analysis, which is reported to be more sensitive and cost‐effective than capture surveys, to clarify the genetic structure of this landlocked Ayu population with different migration patterns in Lake Biwa. We took water samples in 11 inlet rivers in the spring and autumn for 2 years in a row and quantitatively detected a total of 265 haplotypes of the mitochondrial D‐loop region. The pairwise fixation index ( F ST ) value and haplotype diversity indicated that there were genetic differences between the two migrant groups in their respective rivers, and the F ST values were negatively related to latitude and the presence of artificial fish stocking. Additionally, isolation by distance within spring migrant group was observed when the lake was divided into the east and west sides. These findings show that the landlocked Ayu population in Lake Biwa has genetic structure associated with migration patterns and geographical distance. This study demonstrates that the eDNA approach will be effective for conducting a large‐scale investigation of genetic structure beyond simple presence/absence tests.