Biogeography and genetic variation of freshwater organisms are influenced not only by current freshwater connections but also by past drainage networks. The Seto Inland Sea is a shallow enclosed sea in Japan, but geological evidence showed that a large freshwater drainage had intermittently appeared in this area between the late Pliocene and Pleistocene. Here we demonstrated that this paleodrainage greatly affected the genetic variation of the East Asian freshwater snails, Semisulcospira spp. We found that the mtDNA haplotypes originated in the Lake Biwa endemic Semisulcospira species at the upstream side of the paleodrainage were frequently observed in the riverine Semisulcospira species at its downstream side. The genome-wide DNA and morphological analyses consistently showed that there was no clear evidence of nuclear introgression between the Lake Biwa endemics and riverine species. These results suggest that the large paleodrainage had facilitated mitochondrial introgression and had broadly spread the introgressed mtDNA haplotypes to its downstream region around the Seto Inland Sea. Our study highlights the role of paleodrainages in shaping the genetic variation of freshwater organisms.

There are two phylogenies: One is based on the mtDNA sequences, and the other is based on the genome DNA sequences. The mtDNA phylogeny was constructed by Maximum likelihood algorithms (with HKY + G + I model) using MEGA 7.0.18. The genome phylogeny was constructed by Maximum likelihood algorithms (with GTR + G model) using RAxML 8.0.20.

The phylogenetic tree and sequence alignment were integrated into a single nexus file using Mesquite 3.61 for each analysis (mtDNA and genome DNA). It may be necessary to use Mesquite to open the file correctly. Please check Appendix 1 and 2 in the paper for the sample IDs and their geographical origins.