Genetic evidence for a high diversity and wide distribution of endemic strains of the pathogenic chytrid fungus Batrachochytrium dendrobatidis in wild Asian amphibians.

Population declines and extinctions of amphibians have been attributed to the chytrid fungus Batrachochytrium dendrobatidis (Bd), especially one globally emerging recombinant lineage ('Bd-GPL'). We used PCR assays that target the ribosomal internal transcribed spacer region (ITS) of Bd to determine the prevalence and genetic diversity of Bd in South Korea, where Bd is widely distributed but is not known to cause morbidity or mortality in wild populations. We isolated Korean Bd strains from native amphibians with low infection loads and compared them to known worldwide Bd strains using 19 polymorphic SNP and microsatellite loci. Bd prevalence ranged between 12.5 and 48.0%, in 11 of 17 native Korean species, and 24.7% in the introduced bullfrog Lithobates catesbeianus. Based on ITS sequence variation, 47 of the 50 identified Korean haplotypes formed a group closely associated with a native Brazilian Bd lineage, separated from the Bd-GPL lineage. However, multilocus genotyping of three Korean Bd isolates revealed strong divergence from both Bd-GPL and the native Brazilian Bd lineages. Thus, the ITS region resolves genotypes that diverge from Bd-GPL but otherwise generates ambiguous phylogenies. Our results point to the presence of highly diversified endemic strains of Bd across Asian amphibian species. The rarity of Bd-GPL-associated haplotypes suggests that either this lineage was introduced into Korea only recently or Bd-GPL has been outcompeted by native Bd strains. Our results highlight the need to consider possible complex interactions among native Bd lineages, Bd-GPL and their associated amphibian hosts when assessing the spread and impact of Bd-GPL on worldwide amphibian populations.

The complete mitochondrial genome of the Amur soft-shelled turtle (Pelodiscus maackii Brandt, 1858), from South Korea.

In this study, we use a specimen from wild-caught individual to determine the complete mitochondrial genome of the Amur soft-shelled turtle (Pelodiscus maackii). The complete mitogenome of P. maackii has 16,258 bp in length and consists of 13 protein-coding genes (PCGs), 22 tRNAs, two rRNAs, and one control region. The arrangement of genes of P. maackii is identical with previously reported mitogenomes in the family Trionychoidea. According to our result, the ML tree for the phylogenetic reconstruction revealed that the individuals used in present study is closely related with the previously reported sequences of P. sinensis (AY962573 and MG431983) in p-distance 0.7% and 2.5%.

Characteristic of complete mitochondrial genome and phylogenetic status of a muskrat, Ondatra zibethicus (Rodentia: Cricetidae) in South Korea.

The complete mitochondrial genome of Muskrat, Ondatra zibethicus (Rodentia: Cricetidae) in Korea was sequenced for the first time using the next-generation sequencing method to understand its evolutionary relationship and to be helpful to establish a management plan. This mitogenome was 16,350 base pairs in length, containing 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and one control region. Its overall A, C, G, and T contents were 32.0%, 26.9%, 12.6%, and 28.5%, respectively. A + T content (63.7%) was higher than G + C content (36.3%). We made the phylogenetic tree of muskrat and other 12 species of order Rodentia distributed in Korea.

Genetic and phylogenetic structure of Hynobius quelpaertensis, an endangered endemic salamander species on the Korean Peninsula.

BACKGROUND: The Korean Peninsula is a small but unique area showing great endemic Hynobius diversity with H. quelpaertensis, H. yangi, H. unisacculus and three species candidates (HC1, HC3 and HC4). H. quelpaertensis is distributed in the southern part and in Jeju Island, while the remaining species have extremely narrow distributions. OBJECTIVES: To examine the genetic structure of H. quelpaertensis and the phylogenetic placement in Hynobius. METHODS: Three mitochondrial and six microsatellite loci were genotyped for 204 Hynobius quelpaertensis, three H. leechii, three H. yangi, three HC1, two H. unisacculus, three HC3, three HC4 and ten Japanses H. lichenatus. RESULTS: A high level of mitochondrial diversity was found in H. quelpaertensis. Our mitochondrial data showed evidence of a historical link between inland and Jeju Island despite the signature of founder effect likely experienced by the early island populations. However, our microsatellite analysis showed the fairly clear signature of isolation history between in- and island populations. Upon phylogenetic analysis, H. quelpaertensis, H. unisacculus and HC1 formed a cluster, whereas H. yangi belonged to a separate cluster. HC3 and HC4 were clustered with either H. quelpaertensis or H. yangi depending on the locus used. CONCLUSION: Our results show at least partially the historical imprints engraved by dispersal of Korean endemic Hynobius during Pleistocene, potentially providing a fundamental basis in determining the conservation units and finding management strategies for these species.

A new species of salamander of the genus Hynobius (Amphibia, Caudata, Hynobiidae) from South Korea.

We describe a new species of lentic-breeding Hynobius salamander from the Naro Islands, near the village of Bongrae-myeon, Goheung-gun, Jeollanam-do, South Korea, on the basis of results of morphological, ecological and genetic analyses. Hynobius unisacculus sp. nov. is distinguished from its congeners by a combination of the following morphological attributes: (1) comparatively small size (adult SVL up to 61 mm; range 38.3-60.3 mm in males and 37.5-59.9 mm in females); (2) relatively slender short limbs; tips of fore- and hindlimbs adpressed on body never meeting, but separated by a large gap (gap of -3.0 to -1.5 costal folds in males and -3.5 to -1.5 in females); (3) comparatively short tail (TL/SVL ratio in adult males varying from 0.54-0.98, in adult females from 0.55 to 0.89), tail flattened and with a low dorsal fin extending to the posterior one-third of tail length; (4) usually 11 (occasionally 12) costal grooves; (5) in adults, dark brown dorsum with indistinct bronze or dark copper spots, lighter greyish-white or pinkish belly; (6) well developed fifth toe; (7) comparatively shallow vomerine tooth series with 13-23 vomerine teeth; (8) small, pigmented ova, located in one, occasionally two, strings in a small, curved egg sac with folded envelope, lacking distinct mucous stalks or whiptail-like structures on both ends. The molecular differentiation among Korean Hynobius is high; Hynobius unisacculus sp. nov. is genetically highly divergent from the morphologically similar H. leechii, H. yangi and H. quelpaertensis: pairwise distances are 9.7%, 9.1% and 8.0% of sequence divergence at the COI mtDNA gene respectively, and 10.9%, 10.9% and 9.4% of sequence divergence at the cyt b mtDNA gene, respectively. At present, the new species is known from coastal areas and offshore islands in southeastern part of Jeollanam-do in South Korea. We suggest the species should be considered as Vulnerable (Vu2a) in accordance with IUCN's Red List categories. Our study supports the presence of undiagnosed taxonomic diversity among Korean Hynobius.

Mitochondrial DNA data unveil highly divergent populations within the genus Hynobius (Caudata: Hynobiidae) in South Korea.

Korean salamanders of the genus Hynobius are currently classified into 3 species, H. leechii, H. quelpaertensis, and H. yangi. To investigate the phylogenetic relationship of these species, we analyzed the partial sequence of mitochondrial cytochrome b gene (907 bp) of 197 specimens from 43 regions in South Korea. Of these specimens, 93 were additionally examined with 12S rRNA (799 bp). Based on the partial sequence of the mitochondrial cytochrome b gene and 12S rRNA, 89 and 36 haplotypes were defined, respectively, consisting of six subclades (H. leechii, H. quelpaertensis, H. yangi, HC1, HC2, and HC3). Among these subclades, the three subclades (HC1, HC2, and HC3) were clearly separated from the 3 previously reported species in the genus Hynobius. Pairwise sequence divergence between the six subclades ranged from 6.3 to 11.2% in cytochrome b gene and 2.0 to 4.3% in 12S rRNA. These results indicate there may be more divergent populations than the three currently described. Moreover, the estimation of divergence time revealed that the Hynobius species in South Korea diverged during the Miocene epoch, approximately 9 - 5 MYA. In addition, we confirmed the distribution of the three known species (H. leechii, H. quelpaertensis, and H. yangi) and determined the distributions of new, distinct groups (or subclades; HC1, HC1, and HC3). To more accurately establish the taxonomic status and population structure, further genetic, morphological, and ecological studies will be needed.