Environmental DNA reveals nonmigratory individuals of Palaemon paucidens overwintering in Lake Biwa shallow waters

In Lake Biwa, the largest freshwater lake in Japan, the lacustrine shrimp Palaemon paucidens has been reported to undertake seasonal migrations, living in deep waters from autumn to winter and in shallow waters from spring to summer. Some investigators have suggested that some individuals overwinter in shallow waters, but the ecology and life history of such nonmigratory populations are poorly understood. We developed a species-specific environmental DNA (eDNA) marker to detect P. paucidens in water samples and used it to examine the distribution and relative abundance of overwintering individuals in the shallow waters of Lake Biwa. Water samples were collected from 21 shore sites and 32 surrounding freshwater lagoons of Lake Biwa in November 2015 and February 2016. In November, 4 shore and 12 freshwater lagoon sites were positive for P. paucidens eDNA, and in February, 4 shore and 9 freshwater lagoon sites were positive. The relative abundance of eDNA copies was estimated by quantitative real-time polymerase chain reaction (PCR). Simultaneous sampling of P. paucidens and its eDNA, conducted at the inlet and outlet of 5 freshwater lagoons in December 2016, validated our method as a quantitative measure of the relative abundance of P. paucidens local populations. The eDNA approach used here confirmed that some P. paucidens individuals overwinter in the shallow waters, suggesting life-history diversity in Lake Biwa populations.