Genetic structure of Ayu inferred by eDNA

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.

香鱼（Plecoglossus altivelis）多为一年生淡水洄游鱼类，但日本最大湖泊琵琶湖中存在陆封种群。该陆封种群包含两个洄游类群，二者从湖泊向入河的洄游时间存在差异，即春季洄游型与秋季洄游型。本研究借助环境DNA（environmental DNA, eDNA）分析，尝试阐明琵琶湖中具有不同洄游模式的陆封香鱼种群的遗传结构；现有研究表明，该方法相较捕捞调查具备更高的灵敏度与成本效益。研究团队于连续两年的春、秋两季，在11条入河开展水体采样，最终定量检测出线粒体D-loop区域共计265个单倍型。成对固定指数（FST）与单倍型多样性分析结果显示，两个洄游类群在对应河流中存在遗传分化，且FST值与纬度以及人工鱼类放流行为呈负相关。此外，当将琵琶湖划分为东西两侧区域时，各洄游类群内部均呈现距离隔离效应。上述研究结果表明，琵琶湖陆封香鱼种群的遗传结构与洄游模式及地理距离密切相关。本研究证实，环境DNA技术可有效用于遗传结构的大规模调查，其应用场景不限于物种存在/缺失检测。