title: The taxonomic position and the unexpected divergence of the Habu viper, Protobothrops among Japanese subtropical islands.
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.
authors.affiliation: Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan. Electronic address: hshibata@gen.kyushu-u.ac.jp.
authors.forename: Hiroki
authors.initials: H
authors.lastname: Shibata
authors.affiliation: Department of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto, Japan.
authors.forename: Takahito
authors.initials: T
authors.lastname: Chijiwa
authors.affiliation: Institute of Medical Science, The University of Tokyo, Oshima-gun, Kagoshima, Japan.
authors.forename: Shosaku
authors.initials: S
authors.lastname: Hattori
authors.affiliation: Okinawa Prefectural Institute of Health and Environment, Okinawa, Japan.
authors.forename: Koki
authors.initials: K
authors.lastname: Terada
authors.affiliation: Department of Applied Life Science, Faculty of Bioscience and Biotechnology, Sojo University, Kumamoto, Japan.
authors.forename: Motonori
authors.initials: M
authors.lastname: Ohno
authors.affiliation: Medical Institute of Bioregulation, Kyushu University, Fukuoka, Japan.
authors.forename: Yasuyuki
authors.initials: Y
authors.lastname: Fukumaki
mesh_terms: D000818:Animals; D004272:DNA, Mitochondrial / Q000235:genetics; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D005843:Geography; D062312:Islands; D007564:Japan; D016013:Likelihood Functions; D008390:Markov Chains; D009010:Monte Carlo Method; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D013997:Time Factors; D017841:Trimeresurus / Q000145:classification* / Q000235:genetics*; D014329:Tropical Climate
chemical_list: D004272:DNA, Mitochondrial
keywords: Cyt b; Divergence time; Habu snake; Mitochondria genome; Protobothrops