Additional file 2: of Extensive deep vein thrombosis treatment using fondaparinux and edoxaban: a case report

Ultrasonography (Noblus, Hitachi Aloka Medical) images of the left lower extremity after 3 months of treatment. (JPG 53 kb

Additional file 3: of Extensive deep vein thrombosis treatment using fondaparinux and edoxaban: a case report

Ultrasonography (Aplio XG, Toshiba) images of the left lower extremity after 6 months of treatment. (JPG 38 kb

Mitochondrial DNA reveals secondary contact in Japanese harbour seals, the southernmost population in the western Pacific

<div><p>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 (<i>Phoca vitulina stejnegeri</i>) 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.</p></div

Proportions of haplogroups among the four districts.

<p>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.</p

Phylogenetic tree of harbour seals based on the mtDNA control region.

<p>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 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0191329#pone.0191329.ref003" target="_blank">3</a>]).</p

Mismatch distribution of mtDNA haplotypes for Japanese harbour seals.

<p>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).</p

Median-joining network based on the mtDNA control region of harbour seals.

<p>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 <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0191329#pone.0191329.g002" target="_blank">Fig 2</a>.</p

Distribution range of harbour seals (shaded) and sampled localities (squares).

<p>Sampling locations of published sequences outside Hokkaido, Japan, used in phylogenetic analysis are indicated with stars (Accession numbers U36342–U36371 [<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0191329#pone.0191329.ref003" target="_blank">3</a>]). Samples of Japanese harbour seals (<i>Phoca vitulina stejnegeri</i>) 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.</p

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

<div><p>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 <i>Lutra lutra</i>. 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 (<i>L</i>. <i>lutra</i>). 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 <i>ND5</i> (692 bp) and cytochrome <i>b</i> (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 <i>Lutra</i> 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 <i>L</i>. <i>lutra</i>; JO2 represented the old Japanese otter lineage, which may be a distinct new species or subspecies of <i>Lutra</i>. 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.</p></div

Phylogenetic tree of Eurasian and Japanese otters based on the mtGenome.

<p>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 <i>E</i>. <i>lutris</i> and <i>L</i>. <i>lutra</i> (South Korea) were reported previously NC_009692 and FJ236015, respectively.</p