Molecular analysis for evaluation of genetic diversity and taxonomic relationships among populations of Japanese newts

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We investigated the phylogenetic relationships and estimated the historical demography of the Japanese fire-bellied newt, Cynops pyrrhogaster, from Japanese mainlands using 1407-bp sequences of the mitochondrial DNA (NADH6, tRNAglu, cyt b) and 1208-bp sequences of nuclear DNA (Rag-1) genes. Phylogenetic trees based on mitochondrial DNA revealed four major clades (NORTHERN, CENTRAL, WESTERN, and SOUTHERN clades) within this species. Nuclear gene presented no obvious patterns of geographic structure except for the NORTHERN clade, suggesting results of incomplete lineage sorting. We developed 15 novel microsatellite markers for C. pyrrhogaster using next generation sequencer. Genetic survey using these markers around a boundary region revealed allele frequencies of CENTRAL clade differ from those of WESTERN clade, suggesting these clades reproductively isolated from each other.