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

Abstract

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 (FST) value and haplotype diversity indicated that there were genetic differences between the two migrant groups in their respective rivers, and the FST 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.

Beyond species detection—leveraging environmental DNA and environmental RNA to push beyond presence/absence applications

“…Two research articles use vastly different approaches to demonstrate how population genetic data can be extracted from eDNA samples. Tsuji et al (2023) investigate haplotypic variation between two migratory groups of the Ayu ( Plecoglossus altivelis ), a commercially important fisheries resource, identifying genetic structure associated with migration patterns and geographical distance. The authors provide a prime illustration of how population genetic data obtained from eDNA samples increase our understanding of large‐scale genetic structure and thus also improve fisheries management.…”

“…Two research articles use vastly different approaches to demonstrate how population genetic data can be extracted from eDNA samples Tsuji et al (2023). investigate haplotypic variation between two migratory groups of the Ayu (Plecoglossus altivelis), a commercially important fisheries resource, identifying genetic structure associated with migration patterns and geographical distance.…”

Bacterial cold-water disease in ayu (Plecoglossus altivelis altivelis) inhabiting rivers in Japan

“…There is a concern that some methods, especially tomozuri angling, may skew the catch toward healthy rather than diseased ayu because diseased fish exhibit lower physiological activity than healthy fish. Environmental DNA (eDNA) analysis enables year-round monitoring of ayu in rivers and Lake Biwa (Kono et al, 2017;Inui et al, 2018;Inui et al, 2019;Haga et al, 2020;Inui et al, 2020;Inui et al, 2021;Tsuji et al, 2022). Recently, the combined use of ayu and F. psychrophilum in eDNA analysis has attracted attention owing to its potential utility for predicting the occurrence of BCWD in rivers (Tenma et al, 2021).…”