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Evaluating the Phylogenetic Status of the Extinct Japanese Otter on the Basis of Mitochondrial Genome Analysis
- Source :
- PLoS ONE, PLoS ONE, Vol 11, Iss 3, p e0149341 (2016)
- Publication Year :
- 2016
- Publisher :
- Public Library of Science, 2016.
-
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.
- Subjects :
- 0301 basic medicine
Male
Lineage (evolution)
Carnivora
lcsh:Medicine
Artificial Gene Amplification and Extension
Subspecies
Polymerase Chain Reaction
Biochemistry
Geographical Locations
Monophyly
Japan
Japanese otter
lcsh:Science
Energy-Producing Organelles
Phylogeny
Data Management
Mammals
education.field_of_study
Multidisciplinary
Phylogenetic tree
Phylogenetic Analysis
Cytochromes b
Mitochondria
Phylogenetics
Europe
Phylogeography
Vertebrates
Female
Lutra
Cellular Structures and Organelles
Sequence Analysis
Research Article
Computer and Information Sciences
Asia
Genetic Speciation
Population
Zoology
Biology
Bioenergetics
Research and Analysis Methods
Extinction, Biological
Otter
03 medical and health sciences
biology.animal
parasitic diseases
Animals
Evolutionary Systematics
education
Molecular Biology Techniques
Sequencing Techniques
Molecular Biology
Taxonomy
Molecular Biology Assays and Analysis Techniques
Evolutionary Biology
lcsh:R
Organisms
Biology and Life Sciences
Genetic Variation
Cell Biology
biology.organism_classification
030104 developmental biology
People and Places
Genome, Mitochondrial
lcsh:Q
Animal Migration
Otters
Subjects
Details
- Language :
- English
- ISSN :
- 19326203
- Volume :
- 11
- Issue :
- 3
- Database :
- OpenAIRE
- Journal :
- PLoS ONE
- Accession number :
- edsair.doi.dedup.....c3e701644ca213a0fabbe39bd9a453ad