A mitogenomic phylogenetic analysis of the Japanese Plestiodon species (Scincidae, Squamata) clarifies a mito-nuclear discordance caused by a past long distance dispersal.

The whole mitochondrial genomes (mitogenomes) excluding the control region were sequenced for 42 samples of the ten species of scincid lizards of the genus Plestiodon occurring in Japan, and the mitochondrial genealogy of the East Asian Plestiodon was reconstructed on the basis of the mitogenomic dataset. A comparison with a species phylogeny based on five nuclear DNA fragments revealed that P. latiscutatus, a species distributed on the Izu Peninsula of the Japanese Main Islands, was a sister to the clade consisting of P. japonicus and P. finitimus, species occurring in the remaining parts of the Main Island in the species phylogeny, whereas the former species was a sister to the P. capito group occurring in continental China in the mitogenomic phylogeny. A tree reconciliation analysis of the species and the mitochondrial phylogenies revealed horizontal transfer of mitochondria, suggesting that the position of P. latiscutatus was caused by past introgression of mtDNA from the ancestral P. capito group to the ancestral P. latiscutatus. This further suggests a past long-distance dispersal of the skink from the Eurasian continent to the Izu Peninsula and Izu Islands beyond the western part of the Japanese Main Islands in the Miocene.