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. 2018 Jan 31;13(1):e0191329.
doi: 10.1371/journal.pone.0191329. eCollection 2018.

Mitochondrial DNA Reveals Secondary Contact in Japanese Harbour Seals, the Southernmost Population in the Western Pacific

Free PMC article

Mitochondrial DNA Reveals Secondary Contact in Japanese Harbour Seals, the Southernmost Population in the Western Pacific

Mariko Mizuno et al. PLoS One. .
Free PMC article


In this study, we used relatively large number of samples (n = 178) and control region of mtDNA (454bp) to clearify the divergence history of Japanese harbour seals (Phoca vitulina stejnegeri) and phylogenetic relationship between the seals in Japan and other countries. Our results suggested that Japanese harbour seals possibly consisted of more than two lineages and secondary contact of populations after a long isolation. Furthermore, one of the lineage was made only by Japanese harbour seals (Group P1). The proportion of Group P1 was the highest at the South West and gradually decreased towards the North East of Hokkaido, Japan. On the other hand, the haplotypes do not belonged to Group P1 showed close relationship to the seals in the North Pacific. Based on the fossil record of harbour seal in Japan and the range of sea ice during the Last Glacial Maximum (LGM), Group P1 might have entered Japan before the LGM and became isolated due to the geographical boundary, and gradually extended its range from the South West towards the North East of Hokkaido after the disappearance of the sea ice, while the seals which are not in Group P1 immigrated into Japan from the North Pacific.

Conflict of interest statement

Competing Interests: The authors have declared that no competing interests exist.


Fig 1
Fig 1. Distribution range of harbour seals (shaded) and sampled localities (squares).
Sampling locations of published sequences outside Hokkaido, Japan, used in phylogenetic analysis are indicated with stars (Accession numbers U36342–U36371 [3]). Samples of Japanese harbour seals (Phoca vitulina stejnegeri) were taken from four administrative districts (Erimo, Akkeshi, Hamanaka, and Nemuro) in Hokkaido, Japan. Each district contains several haul-out sites where the seals breed.
Fig 2
Fig 2. Phylogenetic tree of harbour seals based on the mtDNA control region.
The bootstrap values of branches of the maximum-likelihood (left) and neighbour-joining method (right). 454 bp of the control region was used to compare the phylogenetic relationships of seals. Data outside Japan were obtained from GenBank (Accession numbers U36342–U36371 [3]).
Fig 3
Fig 3. Median-joining network based on the mtDNA control region of harbour seals.
The node colours and sizes of circles represent the different sites, area, and sample size. The length of the node is proportional to the number of substitutions. Groupings of the nodes are based on the division of the phylogenetic tree in Fig 2.
Fig 4
Fig 4. Proportions of haplogroups among the four districts.
The haplogroups (Group P, A, P1 and P2) were defined in the phylogenetic tree and the median-joining network. The numbers in the bar indicate the number of samples.
Fig 5
Fig 5. Mismatch distribution of mtDNA haplotypes for Japanese harbour seals.
The bar charts indicate the observed number of pairwise differences and the dashed line represents the expected distribution under a spatial expansion model (SSD: p = 0.07; Hrag: p = 0.41).

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Grant support

MK received Grant No:4-1301 from The Environment Research and Technology Development Fund (ERTDF), MM received Grant No:2014 from The Inui Memorial Trust for Research on Animal Science, Japan, The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.