Phylogenetic position of the Japanese river otter Lutra nippon inferred from the nucleotide sequence of 224 bp of the mitochondrial cytochrome b gene

What is the taxonomic status of East Asian otter species based on molecular evidence?: focus on the position of the Japanese otter holotype specimen from museum

The Japanese otter (Lutra nippon), once inhabited in most islands of Japan, is now considered as an extinct species. Although the Japanese otter is regarded as a distinct species from the Eurasian otter (L. lutra), its phylogeny and taxonomic status are based on limited information on morphological and genetic data, and thus further clarification is required. Here, we assessed the phylogenetic relationship among the genus Lutra and taxonomic status of L. nippon by using the complete sequences of cytochrome b gene of its holotype. The present phylogenic trees supported that the genus Lutra specimens largely formed monophyletic group, with L. sumatrana as a basal to other Lutra species. Within Lutra species, L. nippon was distantly related with L. lutra. The European otter population of L. l. lutra were clustered together with its subspecies, L. l. chinensis rather than the same subspecies, Korean otter population. The discrepancy between the genetic data and traditional taxonomy justifies the necessity of reexamination of the current subspecific classification system of Eurasian otters. Level of genetic divergence between the holotype of L. nippon and L. lutra was two to three-fold lower than those among the other sister species of the Lutrinae. Based on the level of divergence between the L. nippon and L. lutra, and insufficient evidence of morphological difference between them, it is suggested that designation of Japanese otter as a separate species from L. lutra will be reconsidered.

Geographic variation of craniodental morphology of the Eurasian otter (Lutra lutra) in East Asia

Craniodental morphology of the Eurasian otter (Lutra lutra) in the Korean Peninsula, Japanese islands and Kinmen Island (Taiwan) was studied using geometric morphometrics to identify the skull variations between the populations. Forty adult skulls were examined (29 specimens from the Korean Peninsula, six from Shikoku, Honshu and Hokkaido of Japan, and five from Kinmen Island). Images of the dorsal and ventral views of the skull and the right lateral view of the mandible were analyzed. Specimens from the Korean Peninsula were larger than those from the Japanese islands and Kinmen Island. However, no correlation was observed between the shape variations in the three populations and the centroid size of the skull. The Mann-Whitney U-test showed that relative warps (RWs) RW1, RW2 and RW4 of the dorsal view and RW2 of the ventral view of the skull differed significantly between the populations. Some craniodental differences between the populations were seen in the dorsal and ventral views of the skull, mostly at the snout and parietal regions. The MANOVA test revealed significant differences between the specimens from the Japanese islands and Korean Peninsula and between the specimens from the Korean Peninsula and Kinmen Island. RWs plots showed an overlap of all three populations. In conclusion, the comparisons of the three examined populations revealed significant differences in their craniodental morphology.

Evaluating the Phylogenetic Status of the Extinct Japanese Otter on the Basis of Mitochondrial Genome Analysis

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.