Single nucleotide variations (SNVs) in the nuclear genome have been used widely to analyze phylogenetic and population genomic structure. Cost-effective genotyping can be achieved by sequencing PCR amplicons using short 3-10 base sequences as primers to arbitrarily amplify thousands of sites in the genome using only a few primers. While previous methods have produced an insufficient number of SNVs to perform population genomic analyses, we designed a new primer set to improve the sequencing efficiency. To demonstrate the effectiveness of our method, we examined the population genetic structure of the small freshwater fish, medaka (Oryzias latipes). Specifically, we attempted to reconstruct the genetic admixture of the orange mutant strain, Himedaka. Although the strain is widely kept as an ornamental fish and for experimental purposes, the genetic background of the nuclear genome of commercial stock is less clear. We obtained 2987 informative SNVs with no missing genotype calls for 67 individuals from 15 wild populations and three artificial strains using the HiSeq X platform. The estimated phylogenic and population genetic structures of the wild populations were consistent with previous studies, corroborating the accuracy of our genotyping method. Admixture analysis focusing on Himedaka showed that at least two wild populations contributed SNVs to the nuclear genome of this mutant strain. Population genomics analyses based on nuclear SNVs data are indispensable to identify admixture events, including natural hybridization and anthropogenic introductions. The method developed in this study will be useful for future population genomics studies on medaka and on other organisms.

Batesian mimicry is a striking example of Darwinian evolution, in which a mimetic species resembles toxic or unpalatable model species, thereby, receiving protection from predators. In some species exhibiting Batesian mimicry, non-mimetic individuals coexist in the same population despite the benefits of mimicry, and the relative abundance of mimetic individuals in the population varies among localities. In a previous study, we found that the mimic ratios (MRs), which varied among the Islands, were likely to be explained by the model abundance of each habitat, rather than isolation-by-distance or phylogenetic constraint in the swallowtail butterfly, Papilio polytes, on the Ryukyu Islands in Japan. Because the previous study, however, was based on the mitochondrial DNA (mtDNA) that may sometimes mislead conclusion stemming from the inherent genetic properties, this possibility was reexamined based on hundreds of nuclear single-nucleotide polymorphisms (SNPs) of 95 P. polytes individuals from five Islands of the Ryukyus. We found that the population genetic and phylogenetic structures of P. polytes largely corresponded to the geographic arrangement of the habitat Islands, and the genetic distances among island populations significantly correlated with the geographic distances, which was not evident by the mtDNA-based analysis. The revised SNP-based genetic distances with a partial correlation approach revealed that the MRs of P. polytes were strongly correlated with the model abundance of each island, implying that negative frequency-dependent selection shaped and maintained the mimetic polymorphism. Taken together, we suggest that predation pressure, not neutral factors, is major driving force to determine the relative abundance of Batesian mimicry in P. polytes from the Ryukyus.