Fig 1.
Map showing the locations of Japanese and Eurasian otters.
(A) Map of East Asia. (B) Map of Shikoku Island. The capture locations of the individual Japanese otters used in this study are indicated by filled circles (JO1, JO2, and JO3). The capture location of the individual Japanese otter used by Suzuki et al. [10] is indicated by an open circle. EO indicates the locations from where Eurasian otter samples were obtained (EO3, EO5). Reprinted from PLOS ONE under a CC BY license, with permission from Environmental Systems Research Institute, Inc. (Esri), original copyright 2015.
Table 1.
Origins of the Eurasian and Japanese otters used in this study.
Fig 2.
Diagnostic nucleotides in the ND5 and cytb genes compared with those used in previous studies.
(A) Partial ND5 gene (692 bp). (B) Complete cytb gene (1,140 bp). Nucleotide positions that are identical to those in the Aonyx capensis sequence are denoted by a period (.). The nucleotide position numbers are based on a Eurasian otter from China (EO4). Letters highlighted in black indicate two Japanese otters (JO1 and JO2) shared diagnostic nucleotides with the Eurasian otter. The sites highlighted in gray indicate the diagnostic nucleotides shared by JO1 (Kanagawa) and the Eurasian otter.
Fig 3.
Phylogenetic tree for Lutrinae based on the partial mtDNA together with the L. nippon (Ehime).
This ML tree was based on the partial ND5 gene (692 bp) and complete cytb gene (1,134 bp) dataset, which included the L. nippon (Ehime) sequence (224 bp) [10]. This tree was estimated using the GTR+Γ+I model. Numbered boxes denote nodes. The nodal number indicates the BP value. BP was estimated on the basis of 1,000 bootstrap replicates. The evolutionary constraints on the nucleotide substitutions must differ between the first, second, and third codon positions; therefore, we specified partitions for each region. OTUs without localities are previously reported data (Koepfli and Wayne [1]; Koepfli et al. [12]). Data for L. lutra (South Korea) is FJ236015.
Fig 4.
Phylogenetic tree of Eurasian and Japanese otters based on the mtGenome.
The ML tree based on the mtGenome comprised 14,740 bp (tRNAs = 1,488 bp, rRNAs = 2,532 bp, and protein-coding genes = 10,720 bp). This tree was estimated using the GTR+Γ+I model. Numbered boxes denote nodes. The nodal number indicates the BP value. BP was estimated on the basis of 1,000 bootstrap replicates. The evolutionary constraints on nucleotide substitutions must differ between the first, second, and third codon positions as well as between tRNA and rRNA. Therefore, we specified partitions for each region. Data for the E. lutris and L. lutra (South Korea) were reported previously NC_009692 and FJ236015, respectively.