title: Evaluating the Phylogenetic Status of the Extinct Japanese Otter on the Basis of Mitochondrial Genome Analysis.
abstract: The Japanese otter lived throughout four main Japanese islands, but it has not been observed in the wild since 1979 and was declared extinct in 2012. Although recent taxonomic and molecular phylogenetic studies suggest that it should be treated as an independent species, International Union for Conservation of Nature Red List considers it as subspecies of Lutra lutra. Therefore, the taxonomic status of this species needs to be resolved. Here we determined the complete mitochondrial genome of two Japanese otters caught in Kanagawa and Kochi prefectures and five Eurasian otters (L. lutra). We reconstructed a molecular phylogenetic tree to estimate the phylogenetic position of the Japanese otter in Lutrinae using the Japanese otters and the other 11 Lutrinae species on the basis of ND5 (692 bp) and cytochrome b (1,140 bp) sequences. We observed that the two Japanese otters had close relationships with Eurasian otters, forming a monophyletic group (100% bootstrap probability). To elucidate detailed phylogenetic relationships among the Japanese and Eurasian otters, we reconstructed a maximum likelihood tree according to mitochondrial genome sequences (14,740 bp). The Japanese otter (JO1) collected in Kanagawa was deeply nested in the Eurasian otter clade, whereas the Japanese otter (JO2) collected in Kochi formed a distinct independent lineage in the Lutra clade. The estimated molecular divergences time for the ancestral lineages of the Japanese otters was 0.10 Ma (95%: 0.06-0.16 Ma) and 1.27 Ma (95%: 0.98-1.59 Ma) for JO1 and JO2 lineages, respectively. Thus, JO1 was identified as a member of L. lutra; JO2 represented the old Japanese otter lineage, which may be a distinct new species or subspecies of Lutra. We suggest that the ancestral population of the JO2 lineage migrated to Japan via the land bridge that existed between western Japanese islands and Asian continent at 1.27 Ma.
authors.affiliation: Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan.
authors.forename: Daisuke
authors.initials: D
authors.lastname: Waku
authors.affiliation: National Institute of Polar Research, Midori-cho, Tachikawa-shi, Tokyo, Japan.|Transdisciplinary Research Integration Center, Toranomon, Minato-ku, Tokyo, Japan.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Segawa
authors.affiliation: School of Life Sciences, Fudan University, SongHu Rd., Shanghai, China.|School of Advanced Science, The Graduate University for Advanced Studies, Shonan, Hayama-cho, Miura-gun, Kanagawa, Japan.
authors.forename: Takahiro
authors.initials: T
authors.lastname: Yonezawa
authors.affiliation: National Institute of Polar Research, Midori-cho, Tachikawa-shi, Tokyo, Japan.|Transdisciplinary Research Integration Center, Toranomon, Minato-ku, Tokyo, Japan.
authors.forename: Ayumi
authors.initials: A
authors.lastname: Akiyoshi
authors.affiliation: NODAI Genome Research Center, Nodai Research Institute, Tokyo University of Agriculture, Sakuragaoka, Setagaya-ku, Tokyo, Japan.
authors.forename: Taichiro
authors.initials: T
authors.lastname: Ishige
authors.affiliation: Yokohama Zoological Gardens, Kamishirane-cho, Asahi-ku, Yokohama-shi, Kanagawa, Japan.
authors.forename: Miya
authors.initials: M
authors.lastname: Ueda
authors.affiliation: Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Ogawa
authors.affiliation: Department of Contemporary Social Studies, Chikushi Jogakuen University, Ishizaka, Dazaifu, Fukuoka, Japan.
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Sasaki
authors.affiliation: Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan.
authors.forename: Motokazu
authors.initials: M
authors.lastname: Ando
authors.affiliation: Department of Geology and Paleontology, National Museum of Nature and Science, Tokyo, Amakubo, Tsukuba, Ibaraki, Japan.|Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennoudai, Tsukuba, Ibaraki, Japan.
authors.forename: Naoki
authors.initials: N
authors.lastname: Kohno
authors.affiliation: Graduate School of Human and Animal-Plant Relationships, Tokyo University of Agriculture, Funako, Atsugi, Kanagawa, Japan.
authors.forename: Takeshi
authors.initials: T
authors.lastname: Sasaki
mesh_terms: D025041:Animal Migration; D000818:Animals; D045303:Cytochromes b / Q000235:genetics*; D005060:Europe; D053476:Extinction, Biological; D005260:Female; D049810:Genetic Speciation; D014644:Genetic Variation; D054629:Genome, Mitochondrial; D007564:Japan; D008297:Male; D010041:Otters / Q000145:classification / Q000235:genetics*; D010802:Phylogeny; D058974:Phylogeography
chemical_list: D045303:Cytochromes b