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Ozaki K, Tominaga A, Matsui M, Hara S, Nishikawa K. Geographic Variation in Skull Morphology of the Japanese Crocodile Newt, Echinotriton andersoni (Amphibia: Urodela: Salamandridae), Inferred from Geometric Morphometrics. CURRENT HERPETOLOGY 2023. [DOI: 10.5358/hsj.42.9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Affiliation(s)
- Kotaro Ozaki
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo, Kyoto 606–8501, JAPAN
| | - Atsushi Tominaga
- Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903–0213, JAPAN
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo, Kyoto 606–8501, JAPAN
| | - Sotaro Hara
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo, Kyoto 606–8501, JAPAN
| | - Kanto Nishikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida Nihonmatsu-cho, Sakyo, Kyoto 606–8501, JAPAN
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Tominaga A, Yoshikawa N, Matsui M, Nagata N, Sato Y. The emergence of a cryptic lineage and cytonuclear discordance through past hybridization in the Japanese fire-bellied newt, Cynops pyrrhogaster (Amphibia: Urodela). Biol J Linn Soc Lond 2022. [DOI: 10.1093/biolinnean/blac120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Discrepancies in geographic variation patterns between nuclear DNA and mitochondrial DNA (mtDNA) are the result of the complicated differentiation processes in organisms and are the key to understanding their true evolutionary processes. The genetic differentiation of the northern and Southern-Izu lineages of the Japanese newt, Cynops pyrrhogaster, was investigated through their single nucleotide polymorphism variations obtained via multiplexed ISSR genotyping by sequencing (MIG-seq). We found three genetic groups (Tohoku, N-Kanto and S-Kanto), that were not detected by mtDNA variations, in the northern lineage. N-Kanto has intermediate genetic characteristics between Tohoku and S-Kanto. The genetic groups are now moderately isolated from each other and have unique genetic characteristics. An estimation of the evolutionary history using the approximate Bayesian computation (ABC) approach suggested that Tohoku diverged from the common ancestor of S-Kanto and S-Izu. Then, S-Kanto and S-Izu split, and the recent hybridization between Tohoku and S-Kanto gave rise to N-Kanto. The origin of N-Kanto through the hybridization is relatively young and seems to be related to changes in the distributions of Tohoku and S-Kanto as a result of climatic oscillation in the Pleistocene. We conclude that the mitochondrial genome of S-Kanto was captured in Tohoku and that the original mitochondrial genome of Tohoku was entirely removed through hybridization.
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Affiliation(s)
- Atsushi Tominaga
- Faculty of Education, University of the Ryukyus , Senbaru 1, Nishihara, Okinawa 903-0213 , Japan
| | - Natsuhiko Yoshikawa
- National Museum of Nature and Science , 4-1-1 Amakubo, Tsukuba, Ibaraki 305 - 0005 , Japan
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University , Yoshida Nihonmatsu-cho, Sakyo, Kyoto 606 - 8501 , Japan
| | - Nobuaki Nagata
- National Museum of Nature and Science , 4-1-1 Amakubo, Tsukuba, Ibaraki 305 - 0005 , Japan
| | - Yukuto Sato
- Faculty of Medicine, University of the Ryukyus , Uehara 207, Nishihara, Okinawa 903 - 0215 , Japan
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Senzaki M, Sano S, Takemoto A, Miura I, Ogata M. Phylogenetic Origins of a Newly Found Japanese Red-Bellied Newt Population in Yokohama City and Other Populations in Kanagawa Prefecture. CURRENT HERPETOLOGY 2022. [DOI: 10.5358/hsj.41.132] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Masaru Senzaki
- Kanazawa Zoological Gardens, Kamariya-higashi 5–15–1, Kanazawa, Yokohama, Kanagawa 236–0042, JAPAN
| | - Shingo Sano
- Kannonzaki Nature Museum, Kamoi 4–1120, Yokosuka, Kanagawa 239–0813, JAPAN
| | - Atsushi Takemoto
- Sagamigawa Fureai Science Museum, Suigo-tana 1–5–1, Chuo, Sagamihara, Kanagawa 252–0246, JAPAN
| | - Ikuo Miura
- Amphibian Research Center, Hiroshima University, Kagamiyama 1–3–1, Higashi-Hiroshima, Hiroshima 739–8526, JAPAN
| | - Mitsuaki Ogata
- Preservation and Research Center, city of Yokohama, Kawaijyuku155–1, Asahi, Yokohama, Kanagawa 241–0804, JAPAN
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Distribution and Genetic Diversity of the Amphibian Chytrid in Japan. J Fungi (Basel) 2021; 7:jof7070522. [PMID: 34210103 PMCID: PMC8307550 DOI: 10.3390/jof7070522] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/25/2021] [Accepted: 06/27/2021] [Indexed: 11/28/2022] Open
Abstract
While research on frog chytrid fungus Batrachochytrium dendrobatidis (Bd), an infectious disease that threatens amphibian diversity, continues to advance worldwide, little progress has been made in Japan since around 2010. The reason for this is, which we pointed out in 2009, that the origin of frog chytrid fungus may be in the East Asian region, including Japan based on the Bd ITS-DNA variation, and as few cases of mass mortality caused by this fungus have been observed in wild amphibian populations in Japan, the interest of the Japanese government and the general public in Bd has waned. However, we believe that organizing the data obtained so far in Japan and distributing the status of frog chytrid fungus in Japan to the world will provide useful insight for future risk management of this pathogen. We collected more than 5500 swab samples from wild amphibians throughout Japan from 2009 to 2010. Then, we investigated the infection status using the Nested-PCR method. We sequenced the obtained DNA samples and constructed a maximum-parsimony (MP) tree to clarify the phylogenetic diversity of Bd. We detected Bd infection in 11 (nine native and two alien) amphibian species in Japan and obtained 44 haplotypes of Bd ITS-DNA. The MP tree showed a high diversity of Bd strains in Japan, suggesting that some strains belong to Bd-GPL and Bd-Brazil. Except for local populations of the Japanese giant salamanders Andrias japonicus in Honshu Island and the sword tail newts Cynops ensicauda in Okinawa Island, the Bd infection prevalence in native amphibian species was very low. The alien bullfrog Aquarana catesbeiana had high Bd infection rates in all areas where they were sampled. No Bd infection was detected in other native amphibians in the areas where giant salamanders, sword tail newts, and bullfrogs were collected, suggesting that many native amphibians are resistant to Bd infection. The sword tail newt of Okinawa Island had both the highest infectious incidence and greatest number of haplotypes. The giant salamanders also showed relatively high infection prevalence, but the infected strains were limited to those specific to this species. These two Caudata species are endemic to a limited area of Japan, and it was thought that they may have been refugia for Bd, which had been distributed in Japan Islands for a long time.
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Kuraishi N, Matsui M, Ota H, Eto K. Unique Evolution of Hyla hallowellii Among Amphibians of the Central Ryukyus, Japan (Anura: Hylidae). Zoolog Sci 2021; 38:112-121. [PMID: 33812351 DOI: 10.2108/zs200105] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 09/21/2020] [Indexed: 11/17/2022]
Abstract
Fauna of the Central Ryukyus includes a high percentage of endemic species, and Hallowell's tree frog Hyla hallowellii Thompson, 1912 is one of such elements, occurring in a total of eight islands in the Amami and Okinawa Island groups. Using samples representing all of these eight island populations, we studied variations in morphology, karyotype, allozyme, and mtDNA, to clarify the pattern of geographic differentiation of H. hallowellii and consider factors for its formation. We could not clearly discriminate one population from another in morphology, nor could we find any interpopulation difference in karyotype. From genetic analyses, using allozymes and cyt b, we found low overall differentiations among populations. However, the southern populations from Okinawajima and Yoronjima were genetically nearly identical with the northern Amamioshima population. From that group the geographically intermediate Tokunoshima and Kakeromajima populations showed prominent differentiations. These patterns of geographical differentiation greatly differ from those known in other amphibian species of the Central Ryukyus, and suggest that H. hallowellii has evolutionary history unique to the species.
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Affiliation(s)
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies, Kyoto University, Sakyo-ku, Kyoto 606-8501, Japan,
| | - Hidetoshi Ota
- Institute of Natural and Environmental Sciences, University of Hyogo, Museum of Nature and Human Activities, Sanda, Hyogo 669-1546, Japan
| | - Koshiro Eto
- Kitakyushu Museum of Natural History & Human History, Yahatahigashi, Kitakyushu, Fukuoka 805-0071, Japan
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Tominaga A, Matsui M, Matsui M. Structure and movement of the hybrid zone between two divergent lineages of the Japanese newt
Cynops pyrrhogaster
(Amphibia: Urodela) in central Japan. J ZOOL SYST EVOL RES 2021. [DOI: 10.1111/jzs.12467] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | - Masafumi Matsui
- Graduate School of Human and Environmental Studies Kyoto University Kyoto Japan
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Origin and intraspecific diversification of the scincid lizard Ateuchosaurus pellopleurus with implications for historical island biogeography of the Central Ryukyus of Japan. ZOOL ANZ 2020. [DOI: 10.1016/j.jcz.2020.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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8
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Igawa T, Sugawara H, Honda M, Tominaga A, Oumi S, Katsuren S, Ota H, Matsui M, Sumida M. Detecting inter- and intra-island genetic diversity: population structure of the endangered crocodile newt, Echinotriton andersoni, in the Ryukyus. CONSERV GENET 2019. [DOI: 10.1007/s10592-019-01219-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Sato Y, Mizuyama M, Sato M, Minamoto T, Kimura R, Toma C. Environmental DNA metabarcoding to detect pathogenic Leptospira and associated organisms in leptospirosis-endemic areas of Japan. Sci Rep 2019; 9:6575. [PMID: 31024059 PMCID: PMC6484013 DOI: 10.1038/s41598-019-42978-1] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/11/2019] [Indexed: 02/06/2023] Open
Abstract
Leptospires, which cause the zoonotic disease leptospirosis, persist in soil and aqueous environments. Several factors, including rainfall, the presence of reservoir animals, and various abiotic and biotic components interact to influence leptospiral survival, persistence, and pathogenicity in the environment. However, how these factors modulate the risk of infection is poorly understood. Here we developed an approach using environmental DNA (eDNA) metabarcoding for detecting the microbiome, vertebrates, and pathogenic Leptospira in aquatic samples. Specifically, we combined 4 sets of primers to generate PCR products for high-throughput sequencing of multiple amplicons through next-generation sequencing. Using our method to analyze the eDNA of leptospirosis-endemic areas in northern Okinawa, Japan, we found that the microbiota in each river shifted over time. Operating taxonomic units corresponding to pathogenic L. alstonii, L. kmetyi, and L. interrogans were detected in association with 12 nonpathogenic bacterial species. In addition, the frequencies of 11 of these species correlated with the amount of rainfall. Furthermore, 10 vertebrate species, including Sus scrofa, Pteropus dasymallus, and Cynops ensicauda, showed high correlation with leptospiral eDNA detection. Our eDNA metabarcoding method is a powerful tool for understanding the environmental phase of Leptospira and predicting human infection risk.
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Affiliation(s)
- Yukuto Sato
- Center for Strategic Research Project, Organization for Research Promotion, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan.
| | - Masaru Mizuyama
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.,Graduate School of Engineering and Science, University of the Ryukyus, 1 Senbaru, Nishihara, Okinawa, 903-0213, Japan
| | - Megumi Sato
- Graduate School of Health Sciences, Niigata University, 2-746 Asahimachi-dori, Chuo-ku, Niigata, 951-8122, Japan
| | - Toshifumi Minamoto
- Graduate School of Human Development and Environment, Kobe University, 3-11 Tsurukabuto, Nada-ku, Kobe, 657-8501, Japan
| | - Ryosuke Kimura
- Department of Human Biology and Anatomy, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan
| | - Claudia Toma
- Department of Bacteriology, Graduate School of Medicine, University of the Ryukyus, 207 Uehara, Nishihara, Okinawa, 903-0215, Japan.
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Kurita T, Honda M, Toda M. Species delimitation and biogeography of the Ryukyu ground geckos, Goniurosaurus kuroiwaessp. (Squamata: Eublepharidae), by use of mitochondrial and nuclear DNA analyses. J ZOOL SYST EVOL RES 2018. [DOI: 10.1111/jzs.12198] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Takaki Kurita
- Graduate School of Engineering and Science; University of the Ryukyus; Nishihara Okinawa Japan
| | - Masanao Honda
- Faculty of Life and Environmental Sciences; University of Tsukuba; Tsukuba Ibaraki Japan
| | - Mamoru Toda
- Tropical Biosphere Research Center; University of the Ryukyus; Nishihara Okinawa Japan
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Kaito T, Ota H, Toda M. The evolutionary history and taxonomic reevaluation of the Japanese coral snake, Sinomicrurus japonicus(Serpentes, Elapidae), endemic to the Ryukyu Archipelago, Japan, by use of molecular and morphological analyses. J ZOOL SYST EVOL RES 2017. [DOI: 10.1111/jzs.12162] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Takuma Kaito
- Graduate School of Engineering and Science; University of the Ryukyus; Nishihara Okinawa Japan
| | - Hidetoshi Ota
- Institute of Natural and Environmental Science; University of Hyogo, and Museum of Nature and Human Activities; Sanda Hyogo Japan
| | - Mamoru Toda
- Tropical Biosphere Research Center; University of the Ryukyus; Nishihara Okinawa Japan
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Shibata H, Chijiwa T, Hattori S, Terada K, Ohno M, Fukumaki Y. The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands. Mol Phylogenet Evol 2016; 101:91-100. [PMID: 27132943 DOI: 10.1016/j.ympev.2016.04.027] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2015] [Revised: 03/15/2016] [Accepted: 04/20/2016] [Indexed: 11/26/2022]
Abstract
There are four Habu species currently recognized in Japan: Protobothrops flavoviridis from the Amami Islands and the Okinawa Islands, P. tokarensis from the Tokara Islands, P. elegans from the Yaeyama Islands and Ovophis okinabvensis from the Amami Islands and the Okinawa Islands. To clarify their taxonomic positions, we determined the complete mitochondria genome sequence (approx. 17kb) from two specimens from two different islands each for P. flavoviridis, P. tokarensis and P. elegans as well as one specimen of O. okinavensis and reconstructed the molecular phylogeny of Protobothrops using the published sequences of related species. The maximum likelihood tree showed four major species groups within Protbothrops: Group I consisting of P. cornutus, P. dabieshanensis, P. jerdonii and P. xiangchengensis; Group II consisting of P. flavoviridis and P. tokarensis; Group III consisting of P. maolensis, P. mucrosquamatus and P. elegans; Group IV consisting of P. himalayanus and P. kaubacki. Since we observed an unexpected divergence and the paraphyly of the two samples of P. flavoviridis collected from different islands, Amami-Oshima and Okinawajima within the Group II, we expanded the analysis by increasing the number of P. flavoviridis and P. tokarensis collected from 10 islands: Amami-Oshima (5 specimens), Kakeromajima (4) and Tokunoshima (4) from the Amami Islands, Okinawajima (4), Iheyajima (4), Iejima (4), Tokashikijima (4) and Kumejima (4) from the Okinawa Islands, Kodakarajima (P. tokarensis) (4) and Takarajima (P. tokarensis) (4) from the Tokara Islands. The maximum likelihood tree of the 44 samples replicated the significant divergence of P. flavoviridis between the Amami Clade including Amami-Oshima, Kakeromajima and Tokunoshima and the Okinawa Clade including Okinawajima, Iheyajima, Iejima, Tokashikijima and Kumejima. The Amami Clade also include all specimens from the Tokara Islands currently known as an independent species, P. tokarensis, suggesting the paraphyly of the taxon, P. flavoviridis. In contrast, we observed a distinct lineage of the two specimens from the Yaeyama Islands, supporting the validity of the taxon, P. elegans as an independent species. By MCMC method, we estimated the divergence time between the Amami Clade and the Okinawa Clade to be 6.51MYA, suggesting that the vicariance of the two clades preceded the geological separation of the Amami Islands and the Okinawa Islands (∼1.5MYA). As expected from the limited mobility of terrestrial reptiles including snakes, we observed high genetic divergence in Habu mtDNA among Japanese subtropical island populations.
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Affiliation(s)
- Hiroki Shibata
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
| | - Takahito Chijiwa
- Department of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto, Japan
| | - Shosaku Hattori
- Institute of Medical Science, The University of Tokyo, Oshima-gun, Kagoshima, Japan
| | - Koki Terada
- Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan
| | - Motonori Ohno
- Department of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto, Japan
| | - Yasuyuki Fukumaki
- Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan
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Kaito T, Toda M. The biogeographical history of Asian keelback snakes of the genusHebius(Squamata: Colubridae: Natricinae) in the Ryukyu Archipelago, Japan. Biol J Linn Soc Lond 2016. [DOI: 10.1111/bij.12726] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Takuma Kaito
- Graduate School of Engineering and Science; University of the Ryukyus; Senbaru 1 Nishihara Okinawa 903-0213 Japan
| | - Mamoru Toda
- Tropical Biosphere Research Center; University of the Ryukyus; Senbaru 1 Nishihara Okinawa 903-0213 Japan
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Tominaga A, Matsui M, Eto K, Ota H. Phylogeny and Differentiation of Wide-Ranging Ryukyu Kajika FrogBuergeria japonica(Amphibia: Rhacophoridae): Geographic Genetic Pattern Not Simply Explained by Vicariance Through Strait Formation. Zoolog Sci 2015; 32:240-7. [DOI: 10.2108/zs140227] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Fujii R, Ota H, Toda M. Genetic and Morphological Assessments of Hybridization Between Two Non-Native Geoemydid Turtles,Mauremys reevesiiandMauremys mutica,in Northcentral Japan. CHELONIAN CONSERVATION AND BIOLOGY 2014. [DOI: 10.2744/ccb-1067.1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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Honda M, Kurita T, Toda M, Ota H. Phylogenetic Relationships, Genetic Divergence, Historical Biogeography and Conservation of an Endangered Gecko,Goniurosaurus kuroiwae(Squamata: Eublepharidae), from the Central Ryukyus, Japan. Zoolog Sci 2014; 31:309-20. [DOI: 10.2108/zs130201] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Tominaga A, Matsui M, Nakata K. Genetic Diversity and Differentiation of the Ryukyu Endemic FrogBabina holstias Revealed by Mitochondrial DNA. Zoolog Sci 2014; 31:64-70. [DOI: 10.2108/zsj.31.64] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Suzuki T, Kitano T, Tojo K. Contrasting genetic structure of closely related giant water bugs: phylogeography of Appasus japonicus and Appasus major (Insecta: Heteroptera, Belostomatidae). Mol Phylogenet Evol 2014; 72:7-16. [PMID: 24398367 DOI: 10.1016/j.ympev.2013.12.008] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2013] [Revised: 12/11/2013] [Accepted: 12/24/2013] [Indexed: 11/26/2022]
Abstract
Appasus japonicus and A. major, two belostomatid species of the giant water bug found in parts of East Asia, have very similar morphological characteristics and ecological niches, and also overlapping habitats. However, the results of our previous published study utilizing molecular phylogenetic analyses of mitochondrial and nuclear DNA revealed extensive genetic differences, which indicated that the possibility of inter-specific hybridization was extremely unlikely. We collected A. japonicus and A. major from the Japanese Archipelago, Korean Peninsula, and Russian Far East, and conducted molecular analyses of mitochondrial DNA COI and 16S rRNA to compare phylogenetic relationships between these species. Three major clades were recognized within A. japonicus. Specimens from the Korean population constituted a monophyletic clade, and were a sister group of the western region of the Japanese Archipelago. The Eastern Japanese clade was clearly differentiated. Four major clades were recognized within A. major. Specimens from the Japanese and Korean populations revealed two distinct monophyletic clades. Significant differentiation was clearly observed between their genetic structures. Furthermore, the results of mismatch distribution and Bayesian skyline plot analyses suggested the possibility of a bottleneck effect or founder effect in two of the A. major clades. Collectively, these results demonstrated both similarities and differences in these two species even though their distribution widely overlaps in East Asia, with their morphological characteristics and ecological niches being very similar. These differences in genetic structures are considered to be due to their evolutionary history.
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Affiliation(s)
- Tomoya Suzuki
- Division of Mountain and Environmental Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan
| | - Tadashi Kitano
- Department of Human Development, Tokai University, Kitakaname 4-1-1, Hiratsuka, Kanagawa 259-1292, Japan
| | - Koji Tojo
- Department of Biology, Faculty of Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan; Institute of Mountain Science, Shinshu University, Asahi 3-1-1, Matsumoto, Nagano 390-8621, Japan.
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Mochida K, Inoue E, Kurita K, Hayano A, Inoue-Murayama M. Development of Microsatellite Markers forCynops ensicauda(Amphibia: Caudata) by Using Next-Generation Sequencing Technology. CURRENT HERPETOLOGY 2012. [DOI: 10.5358/hsj.31.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Tominaga A, Matsui M, Yoshikawa N, Nishikawa K, Hayashi T, Misawa Y, Tanabe S, Ota H. Phylogeny and historical demography of Cynops pyrrhogaster (Amphibia: Urodela): taxonomic relationships and distributional changes associated with climatic oscillations. Mol Phylogenet Evol 2012; 66:654-67. [PMID: 23103571 DOI: 10.1016/j.ympev.2012.10.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Revised: 10/13/2012] [Accepted: 10/15/2012] [Indexed: 10/27/2022]
Abstract
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 haplotype clades (NORTHERN, CENTRAL, WESTERN, and SOUTHERN clades) within this species. Degree of genetic differentiation among major haplotype clades was very large for intraspecific variation, suggesting this species to be composed of four species lineages that replace each other geographically. Nuclear genetic variation presented no obvious patterns of geographic structure except for the distinctness of populations diagnosed by NORTHERN clade of mitochondrial haplotypes, suggesting results of incomplete lineage sorting. Current distribution and estimated divergence times for the genus Cynops suggest that the common ancestor of two Japanese species (C. pyrrhogaster and C. ensicauda from the Ryukyu Islands) had diverged at the edge of the continent corresponding to the present East China Sea and Central Ryukyus. Subsequent range expansion to Japanese mainland seems to have occurred in the middle Miocene. Population-genetic analyses indicated that all species lineages, except for the SOUTHERN one, experienced geographic population reductions and expansions associated with glacial and postglacial climatic oscillations.
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Affiliation(s)
- Atsushi Tominaga
- Department of Natural Sciences, Faculty of Education, University of the Ryukyus, Senbaru 1, Nishihara, Okinawa 903-0213, Japan
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Kurabayashi A, Nishitani T, Katsuren S, Oumi S, Sumida M. 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. Genes Genet Syst 2012; 87:39-51. [PMID: 22531793 DOI: 10.1266/ggs.87.39] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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 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.
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Affiliation(s)
- Atsushi Kurabayashi
- Institute for Amphibian Biology, Graduate School of Science, Hiroshima University, Hiroshima, Japan
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Honda M, Matsui M, Tominaga A, Ota H, Tanaka S. Phylogeny and biogeography of the Anderson's crocodile newt, Echinotriton andersoni (Amphibia: Caudata), as revealed by mitochondrial DNA sequences. Mol Phylogenet Evol 2012; 65:642-53. [PMID: 22846685 DOI: 10.1016/j.ympev.2012.07.019] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 07/19/2012] [Accepted: 07/20/2012] [Indexed: 11/16/2022]
Abstract
The Anderson's crocodile newt, Echinotriton andersoni, is considered a relic and endangered species distributed in the Central Ryukyus. To elucidate phylogenetic relationships and detailed genetic structures among populations, we analyzed variation in the mitochondrial cytochrome b gene. Results strongly support a primary dichotomy between populations from the Amami and Okinawa Island Groups with substantial genetic divergence, favoring a primary divergence between the two island groups. Within the latter, populations from the southern part of Okinawajima Island are shown to be more closely related to those from Tokashikijima Island than to those from the northern and central parts of Okinawajima. The prominent genetic divergence between the two island groups of the Central Ryukyus seems to have initiated in the Miocene, i.e., prior to formation of the strait that has consistently separated these island groups since the Pleistocene. The ancestor of the southern Okinawajima-Tokashikijima is estimated to have migrated from the northern and central parts of Okinawajima into southern Okinawajima at the Pleistocene, and dispersed into Tokashikijima subsequently.
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Affiliation(s)
- Masanao Honda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
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MATSUI M. On the Brown Frogs from the Ryukyu Archipelago, Japan, with Descriptions of Two New Species (Amphibia, Anura). CURRENT HERPETOLOGY 2011. [DOI: 10.5358/hsj.30.111] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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