Mitochondrial genomes and divergence times of crocodile newts: Inter-islands distribution of Echinotriton andersoni and the origin of a unique repetitive sequence found in Tylototriton mt genomes

Crocodile newts, which constitute the genera Echinotriton and Tylototriton, are known as living fossils, and these genera comprise many endangered species. To id entify mitochondrial (mt) genes suitable for future population genetic analyses for endangered taxa, we determined the complete nucleotide sequences of the mt genomes of the Japanese crocodile newt Echinotriton andersoni and Himalayan crocodile newt Tylototriton verrucosus. Although the control region (CR) is known as the most variable mtDNA region in many animal taxa, the CRs of crocodile newts are highly conservative. Rather, the genes of NADH dehydrogenase subunits and ATPase subunit 6 were found to have high sequence divergences and to be usable for population genetics studies. To estimate the inter-population divergence ages of E. andersoni ende mic to the Ryukyu Islands, we performed molecular dating analysis using whole and partial mt genomic data. The estimated di vergence ages of the inter-island individuals are older than the paleogeographic segmentation ages of the islands, suggesting that the lineage splits of E. andersoni populations were not caused by vicariant events. Our phylogenetic analysis with pa rtial mt sequence data also suggests the existence of at least two more undescribed species in the genus Ty lototriton. We also found unusual repeat s equences containing the 3′ region of cytochrome apoenzyme b gene, whole tRNAThr gene, and a noncoding region (the T-P noncoding region characteristic in caudate mtDNAs) from T. v errucosus mtDNA. Similar repeat sequences were found in t wo other Tylototriton species. The Ty lototriton taxa with the repeats become a monophyletic group, indicating a single origin of the repeat sequences. The intraa nd inter-specific comparisons of the repeat sequences suggest the occurrences of homologous recombination-based concerted evolution among the repeat sequences.