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Dryad

The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela)

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Abstract

 Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and the key to understanding their true evolutionary process. The genetic differentiation of the northern and southern Izu lineages of the Japanese newt Cynops pyrrhogaster was investigated through their single nucleotide polymorphism variations by multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto, and S-Kanto) those not detected by mtDNA in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The western populations of N-Kanto are close to S-Kanto, whereas the eastern populations of N-Kanto are close to Tohoku. Tohoku, N-Kanto, and S-Kanto are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history by the Approximate Bayesian Computation approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of the climatic oscillation in the Pleistocene. We concluded that the mitochondrial genome of S-Kanto was captured into Tohoku and the past original mitochondrial genome of Tohoku was entirely swept out from Tohoku through the hybridization.