Background: Anthropogenic factors potentially affect observed biogeographical patterns in genetic variations of populations, but the effects of ancient human activities on the original patterns that were created by natural processes are unknown. Sinotaia quadrata, a widely distributed freshwater snail species in East Asia, was used to investigate this issue. It is unclear if S. quadrata in Japan was introduced from China, and how different human uses and varying geographic patterns affect the genetic structure of contemporary populations between the two regions. Thus, we investigated the population history of S. quadrata and detected its genetic structure in Japan and continental East Asia.

Results: S. quadrata populations first naturally migrated from continental East Asia to Japan, which is associated with the ancient period in Japanese geohistory (about 70,000 years ago). They were then artificially introduced in association with agriculture expansion by human movements in two recent periods (about 8000 and 1200 years ago). Populations in different parts of Japan have their own sources. Natural migration in the ancient period and artificial introduction in the recent period suggest that the population distribution is affected by both the geohistory of East Asia and the history of human expansion. In the background of the historical migration and introduction, contemporary populations in the two regions show different genetic patterns. Population divergence levels were significantly correlated with geographical patterns in Japan, and significantly correlated with human interventions variables in continental East Asia, suggesting that long-term geographical isolation is likely the major factor that shaped the genetic structure of contemporary populations in Japan, while modern human uses are likely the major factor in continental East Asia.

Conclusions: Our preliminary results show a complex population history and unusual genetic patterns in the contemporary populations for a common freshwater snail and are of significance to determine the historical formation and contemporary patterns of biogeography in Japan and continental East Asia.

This data set is used for population genetics analysis for the freshwater snail, Sinotaia quadrata. Genetic data set is genotyped using 12 microsatellite loci, and divided to three structure files of total, Japan, and (East Asia) continent, respectively. The DIYABC input file contains 237 randomly sampled individuals representing for the four groups in the East Asia continent and Japan. It is used for population history analysis in software DIYABC. The variable data are extracted from WorldClim (http://worldclim.org) and NASA’s Earth Observation system Data and Information System (EOSDIS) (https://sedac.ciesin.columbia.edu). Appendix 1 and Appendix 2 are files corresponding to the main text.