Distinct seasonal migration patterns of Japanese native and non‐native genotypes of common carp estimated by environmental DNA

Understanding behavioral differences between intraspecific genotypes of aquatic animals is challenging because we cannot directly observe the animals underwater or visually distinguish morphologically similar counterparts. Here, we tested a new monitoring tool that uses environmental DNA (eDNA), an assemblage of DNA in environmental water, to specifically detect Japanese native and introduced non‐native genotypes of common carp (Cyprinus carpio) in Lake Biwa, Japan, and estimated differences between the two genotypes in the use of inland habitats. We monitored the ratios of native and non‐native single nucleotide polymorphism alleles of a mitochondrial locus of common carp in a lagoon connected to Lake Biwa for 3 years using eDNA. We observed seasonal dynamics in the allele frequency showing that the native genotype frequency peaked every spring, suggesting that native individuals migrated to the lagoon for spawning and then returned to the main lake, whereas non‐native individuals tended to stay in the lagoon. The estimated migration patterns corresponded with the estimates of a previous study, which were based on commercial fish catch data. Our findings suggest that eDNA‐based monitoring can be useful tool for addressing intraspecific behavioral differences underwater.