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Kurabayashi A.,Hiroshima University | Nishitani T.,Hiroshima University | Katsuren S.,Okinawa Prefectural Institute of Health and Environment | Oumi S.,Section of Agriculture and Forest | Sumida M.,Hiroshima University
Genes and Genetic Systems | Year: 2012

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 tRNA-Thr 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 intra-and inter-specific comparisons of the repeat sequences suggest the occurrences of homologous recombination-based concerted evolution among the repeat sequences.


Komaki S.,Hiroshima University | Igawa T.,Hiroshima University | Nozawa M.,National Institute of Genetics | Lin S.-M.,National Taiwan Normal University | And 2 more authors.
Genes and Genetic Systems | Year: 2014

Buergeria japonica is a common frog species distributed throughout almost all islands in Ryukyu Archipelago. Because of their exceptionally wide distribution and higher physiological tolerance comparing to the other anurans, their demographic history and formation of distribution are intrinsic topics in the herpetological fauna of Ryukyu. Microsatellite marker is ideal genetic marker for such studies at inter- and intra-population level. We therefore developed microsatellite markers of B. japonica utilizing Ion PGM™ sequencing. As a result of the screening, we developed a total of 14 polymorphic markers. To test availabilities of these markers, we genotyped four island populations. The total number of alleles and expected hetelozygosities per locus ranged from 4 to 21 and 0.00 to 0.864, respectively. The phylogenetic relationship among the four populations based on the genetic distances of these markers was congruent with general divergence pattern of amphibians and reptiles in Ryukyu area. These markers developed in this study are considered to be useful for future studies about phylogeography and demography of this species.


Igawa T.,Hiroshima University | Okuda M.,Hiroshima University | Oumi S.,Section of Agriculture and Forest | Katsuren S.,Okinawa Prefectural Institute of Health and Environment | And 3 more authors.
Conservation Genetics Resources | Year: 2011

Due to an originally small distribution range and over-exploitation of primary forest, Ishikawa's frog (Odorrana ishikawae) has been steadily declining in number. For effective conservation of this species, a greater amount of genetic information of this species is needed. Here, we isolated and characterized 12 microsatellite loci of O. ishikawae using two different methods. Loci were screened from two populations on the Amami (N = 44) and Okinawa (N = 9) Islands. The total number of alleles per locus ranged from 2 to 30, and the observed heterozygosity ranged from 0 to 0.922. Notably, high F ST values for all examined loci were observed between the two populations. Taken together, our findings suggest that these novel loci will be applicable for conservation genetic studies across varying scales. © Springer Science+Business Media B.V. 2010.


Sugawara H.,Hiroshima University | Igawa T.,Hiroshima University | Yokogawa M.,Kyoto University | Okuda M.,Hiroshima University | And 6 more authors.
Conservation Genetics Resources | Year: 2012

Due to an originally small distribution range and recent habitat loss, Anderson's crocodile newt (Echinotriton andersoni) has been steadily declining in number. For effective conservation of this species, a greater amount of genetic information is needed. Here, we isolated ten microsatellite loci of E. andersoni using three different methods, and polymorphism of these 10 loci were evaluated for 27 individuals collected from three islands. The total number of alleles per locus ranged from 3 to 22, and the expected heterozygosity ranged from 0 to 0.876. Taken together, our findings suggest that these novel loci will be applicable for conservation genetic studies across varying scales. © 2012 Springer Science+Business Media B.V.


Igawa T.,Hiroshima University | Oumi S.,Section of Agriculture and Forest | Katsuren S.,Okinawa Prefectural Institute of Health and Environment | Sumida M.,Hiroshima University
Heredity | Year: 2013

Isolation by distance and landscape connectivity are fundamental factors underlying speciation and evolution. To understand how landscapes affect gene flow and shape population structures, island species provide intrinsic study objects. We investigated the effects of landscapes on the population structure of the endangered frog species, Odorrana ishikawae and O. splendida, which each inhabit an island in southwest Japan. This was done by examining population structure, gene flow and demographic history of each species by analyzing 12 microsatellite loci and exploring causal environmental factors through ecological niche modeling (ENM) and the cost-distance approach. Our results revealed that the limited gene flow and multiple-population structure in O. splendida and the single-population structure in O. ishikawae were maintained after divergence of the species through ancient vicariance between islands. We found that genetic distance correlated with geographic distance between populations of both species. Our landscape genetic analysis revealed that the connectivity of suitable habitats influences gene flow and leads to the formation of specific population structures. In particular, different degrees of topographical complexity between islands are the major determining factor for shaping contrasting population structures of two species. In conclusion, our results illustrate the diversification mechanism of organisms through the interaction with space and environment. Our results also present an ENM approach for identifying the key factors affecting demographic history and population structures of target species, especially endangered species. © 2013 Macmillan Publishers Limited All rights reserved.

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