Genetic structure of Ayu inferred by eDNA. Plecoglossus altivelis altivelis

Ayu, Plecoglossus altivelis, is primarily an annual, freshwater amphidromous fish, but a landlocked population inhabits Lake Biwa, the largest lake of Japan. The landlocked population includes two migrant groups which differ in run timing to inlet rivers from the lake, i.e. spring migrants and autumn migrants. In this study, we attempted to clarify the genetic structure of this landlocked Ayu population with different migration patterns in Lake Biwa by using environmental DNA (eDNA) analysis, which is suggested to be more sensitive and cost-effective than capture surveys. We conducted water sampling in spring and autumn for two successive years in 11 inlet rivers, and quantitatively detected a total of 265 haplotypes of the mitochondrial D-loop region. The pairwise fixation index (FST) and haplotype diversity suggested that there were genetic differences between the two migrant groups in respective rivers, and the FST values were negatively related to latitude and the presence of artificial fish release. Additionally, the isolation by distance within each 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 the 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 presence/absence applications.