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

Abstract

Crocodile newts, which constitute the genera Echinotriton and Tylototriton, are known as living fossils, and these genera comprise many endangered species. To identify 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 endemic to the Ryukyu Islands, we performed molecular dating analysis using whole and partial mt genomic data. The estimated divergence 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 partial mt sequence data also suggests the existence of at least two more undescribed species in the genus Tylototriton. We also found unusual repeat sequences 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. verrucosus mtDNA. Similar repeat sequences were found in two other Tylototriton species. The Tylototriton taxa with the repeats become a monophyletic group, indicating a single origin of the repeat sequences. The intraand inter-specific comparisons of the repeat sequences suggest the occurrences of homologous recombination-based concerted evolution among the repeat sequences.

Mitochondrial genomes of Japanese <i>Babina</i> frogs (Ranidae, Anura): unique gene arrangements and the phylogenetic position of genus <i>Babina</i>

“…For example, cox1, cox3, and cob have low divergence in the ranid taxa examined here (~17.4-19.7%), but these genes have high nucleotide substitution rates in plethodontid salamanders and their related taxa (Mueller, . Furthermore, the CR shows low divergence in salamanders and newts (Mueller, 2006;Kurabayashi et al, 2012), yet the CR is the third-most variable region in Odorrana . These findings emphasize that performing a preliminary survey of fastevolving genes and the CR is important for determining phylogenetic and/or population genetic markers for closely related amphibian taxa.…”

Phylogeny and Differentiation of Wide-Ranging Ryukyu Kajika FrogBuergeria japonica(Amphibia: Rhacophoridae): Geographic Genetic Pattern Not Simply Explained by Vicariance Through Strait Formation

“…Divergence time between the AM/TK and the ON subclades is estimated as 6.07 (3.81-7.75) MYA in the Calibration I and 3.21 (1.77-4.97) MYA in the Calibration II. The estimated times of divergence between the Amami and Okinawa populations in several amphibians falls within the range from the late Miocene to the early Pleistocene (1.7 [1.1-2.4] MYA for two species of the Odorrana narina complex [Matsui et al, 2005b]; 2.3 [1.5-3.2] MYA for two species of the O. ishikawae species group [Matsui et al, 2005b]; 2.4-8.3 MYA for two species of Babina [Tominaga et al, 2014]; 3.3-6.8 MYA for Cynops ensicauda [Tominaga et al, 2010[Tominaga et al, , 2013; and 3.1-18.0 MYA for Echinotriton andersoni [Honda et al, 2012;Kurabayashi et al, 2012]). Most of these estimations are much older than the formations of straits in the Pleistocene (0.12-1.3 MYA; Kizaki and Oshiro, 1980;Ota, 1998;Kimura, 2003), which have separated the Amami and the Okinawa Groups, and should have induced divergence of the terrestrial animals of the Central Ryukyus into two island group elements.…”

Afrobatrachian mitochondrial genomes: genome reorganization, gene rearrangement mechanisms, and evolutionary trends of duplicated and rearranged genes

“…However, observational evidence to validate these models is still insufficient because of the rarity of mt genomes having intermediate conditions in the gene rearrangement process (but see [4,13,26,28,29]). Furthermore, different nucleotide substitution trends, such as the relaxation of purifying pressure and accompanying substitution rate acceleration, have been suspected for (nuclear) duplicated genes (e.g., [30,31]).…”