Environmental DNA phylogeography: successful reconstruction of phylogeographic patterns of multiple fish species from a cup of water

Phylogeography is an integrative field of science linking micro- and macro-evolutionary processes and contributes to the inference of vicariance, dispersal, speciation, and other population-level processes. The phylogeographic surveys usually require considerable effort and time to obtain many samples from many geographical sites covering the distribution range of target species, such costs for sampling often being a bottleneck in the research. Recently, environmental DNA (eDNA) analysis has been shown to be highly useful not only for detecting species but also for assessing genetic diversity, and hence there has been growing interest in its application to phylogeography. As the first step of eDNA-based phylogeography, we examined (1) data screening procedures suitable for phylogeography and (2) whether the results of the eDNA analysis accurately reflect the known phylogeographic patterns. For these purposes, we targeted five freshwater fish species belonging to two taxonomic groups and used a total of 94 water samples collected from western Japan for quantitative eDNA metabarcoding using group-specific primer sets.