• Animal Systematics, Evolution and Diversity
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• 제27권1호
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• pp.1-17
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• 2011

Thais Roding, 1798, commonly known as rock-shell, is among the most frequently found gastropod genera worldwide on intertidal rocky shores including those of Japan, China, Taiwan and Korea. This group contains important species in many marine environmental studies but species-level taxonomy of the group is quite complicated due to the morphological variations in shell characters. This study examined the genetic variations and relationships among three Korean Thais species based on the partial nucleotide sequences of mitochondrial cox1 gene fragments. Phylogenetic trees from different analytic methods (maximum parsimony, neighbor-joining, and maximum likelihood) showed that T. bronni and T. luteostoma are closely related, indicating the most recent common ancestry. The low sequence divergence found between T. luteostoma and T. bronni, ranging from 1.53% to 3.19%, also corroborates this idea. Further molecular survey using different molecular marker is required to fully understand a detailed picture of the origin for their low level of interspecific sequence divergence. Sequence comparisons among conspecific individuals revealed extensive sequence variations within the three species with maximum values of 2.43% in T. clavigera and 1.37% in both T. bronni and T. luteostoma. In addition, there is an unexpectedly high level of mitochondrial genotypic diversity within each of the three Korean Thais species. The high genetic diversity revealed in Korean Thais species is likely to reflect genetic diversity introduced from potential source populations with diverse geographic origins, such as Taiwan, Hong Kong, and a variety of different coastal regions in South China and Japan. Additional sequence analysis with comprehensive taxon sampling from unstudied potential source populations will be also needed to address the origin and key factors for the high level of genetic diversity discovered within the three Korean Thais species studied.

• Asian-Australasian Journal of Animal Sciences
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• 제25권7호
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• pp.935-944
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• 2012

Amur grayling, Thymallus grubii, is an important economic cold freshwater fish originally found in the Amur basin. Currently, suffering from loss of habitat and shrinking population size, T. grubii is restricted to the mountain river branches of the Amur basin. In order to assess the genetic diversity, population genetic structure and infer the evolutionary history within the species, we analysised the whole mitochondrial DNA control region (CR) of 95 individuals from 10 rivers in China, as well as 12 individuals from Ingoda/Onon and Bureya River throughout its distribution area. A total of 64 variable sites were observed and 45 haplotypes were identified excluding sites with gaps/missing data. Phylogenetic analysis was able to confidently predict two subclade topologies well supported by maximum-parsimony and Bayesian methods. However, basal branching patterns cannot be unambiguously estimated. Haplotypes from the mitochondrial clades displayed local homogeneity, implying a strong population structure within T. grubii. Analysis of molecular variance detected significant differences among the different geographical rivers, suggesting that T. grubii in each river should be managed and conserved separately.

• Asian-Australasian Journal of Animal Sciences
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• 제21권6호
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• pp.789-793
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• 2008

The gayal (Bos frontalis) in China is a very rare semi-wild and semi-domestic bovine species. There still exist remarkable divergences on the gayal's origin and taxonomic status. In the present study, the cytochrome b (Cyt b) gene entire sequences (1,140 bp) of 11 gayals in Yunnan China were analyzed. Combined with other bovine Cyt b sequences cited in GenBank, the phylogenetic trees of genus Bos were reconstructed by neighbor-joining (NJ) and maximum parsimony (MP) methods with Bubalus bubalis as outgroup. Sequence analysis showed that, among 1,140 sites compared for 11 gayals, 95 variable sites (8.33% of all sites) and 6 different haplotypes were observed, showing abundant mitochondrial genetic diversity in gayals. Both NJ and MP trees demonstrated that gayals in this study were markedly divided into three embranchments: one embranchment clustering with Bos gaurus, another clustering with Bos taurus, and the third clustering with Bos indicus. The result of phylogenetic analysis suggested that the gayal might be the domesticated form of the gaur, and a great proportion of the gayal bloodline in China was invaded by other bovine species.

• 한국자원식물학회지
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• 제27권6호
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• pp.671-679
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• 2014

Molecular phylogenetic analyses of Korean Elaeagnus L. were conducted using seven species, one variety, one forma and four outgroups to evaluate their relationships and phylogeny. The sequences of internal transcribed spacer regions in nuclear ribosomal DNA were employed to construct phylogenetic relationships using maximum parsimony (MP) and Bayesian analysis. Molecular phylogenetic analysis revealed that Korean Elaeagnus was a polyphyly. E. umbellata var. coreana formed a subclade with E. umbellata. Additionally, the genetic difference between E. submacrophylla and E. macrophylla was very low. Moreover, E. submacrophylla formed a branch from E. macrophylla, indicating that E. submacrophylla can be regarded as a variety. However, several populations of this species were not clustered as a single clade; therefore, further study should be conducted using other molecular markers. Although E. glabra f. oxyphylla was distinct in morphological characters of leaf shape with E. glabra. But E. glabra f. oxyphylla was formed one clade by molecular phylogenetic with E. glabra. Additionally, this study clearly demonstrated that E. pungens occurs in Korea, although it was previously reported near South Korea in Japan and China. According to the results of ITS regions analyses, it showed a resolution and to verify the relationship between interspecies of Korean Elaeagnus.

• Weed & Turfgrass Science
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• 제3권3호
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• pp.183-189
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• 2014

The genus Echinochloa (L.) P. Beauv. comprised of approximately 30-40 species in the tropical and warm temperate regions of the world, including numerous interspecific and intraspecific types which make the genus difficult to identify. As an attempt to identify the species within the genus easier, the taxonomy of the genus Echinochloa, Poaceae in Korea was reviewed on the basis of sequencing data derived from nuclear ribosomal DNA internal transcribed spacer (ITS) and external transcribe spacer and chloroplast DNA trnL intron, trnL-F intergenic spacer and matK regions using a total of 46 accessions representing all the species in Korea. The results of maximum parsimony found separate lineage comprised of E. colona and E. frumentaceae which are not Korean species, but no resolution within Korean Echinochloa species, supporting the suggestion of Yamaguchi group that E. crus-galli, E. oryzoides, and E. esculenta should be considered to belong to the same species. However, the relationship between these three species and the other species, i.e. E. oryzicola should be better understood with more detail studies.

• 식물분류학회지
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• 제48권4호
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• pp.289-300
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• 2018

Coreanomecon is a monotypic and endemic genus in Korea, distributed mainly in the southern regions. Coreanomecon is morphologically similar to Hylomecon by producing red latex, easily distinguished from Chelidonium, which produces yellow latex. Coreanomecon were merged into Hylomecon or Chelidonium depending on the authors. To understand the phylogenetic relationship of Coreanomecon, DNA sequences of chloroplast rbcL and matK and nuclear Internal Transcribed Spacer (ITS) regions were determined from the species of Papaveroideae (Papaveraceae) in Korea and analyzed with the Maximum Parsimony and Bayesian methods. Phylogenetic analyses of Papaveroideae suggest that Coreanomecon is sister to the clade of Chelidonium and Stylophorum in the ITS data and that it is sister to Hylomecon in the chloroplast (cpDNA) data. A constraining analysis using the Shimodaira-Hasegawa test (S-H test) suggested that the ITS data do not reject the sister relationship of Coreanomecon and Hylomecon. The S-H test also suggested that the cpDNA data is compatible with the placement of Coreanomecon as a sister to the clade of Chelidonium and Stylophorum. Although the conflicting phylogenetic results may stem from insufficient phylogenetic signals, they may also be associated with hybridization between Hylomecon and an ancestor of Stylophorum and Chelidonium. The results of this study suggest that Coreanomecon is a distinct lineage as an endemic genus, supporting the morphological data.

• 한국자원식물학회지
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• 제23권4호
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• pp.293-302
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• 2010

한국산 쑥속 분류군의 계통분류학적 연구를 위해 Nuclear ribosome DNA의 ITS 염기서열 분석을 실시하였다. 정렬된 염기의 총 길이는 635~643 bp이며, ITS1과 ITS2 부위의 길이는 각각 251~255 bp와 217~222 bp로 나타났다. 염기서열 변이를 보이는 site는 95개로 확인되었다. 그 중 ITS1이 35개, ITS2가 26개로 총 72개의 site가 계통학적으로 유효한 것으로 나타남으로써 ITS1이 ITS2보다 종 분화의 변이가 다양하게 발생하는 것으로 확인되었다. ITS 염기서열을 기초한 계통학적 분석은 쑥속 내에 5개의 Clade를 형성하였다. 그 결과 자방이 퇴화된 분류군들(사철쑥, 제비쑥, 섬쑥, 갯제비쑥)이 하나의 분계조(Clade 1)를 형성함으로써 아속 수준(Subgen. Dracunculus)으로 취급되는 결과를 뒷받침 하였다. 애기비쑥과 큰비쑥은 거의 동일한 유전적 정보를 보였으며(Boostrap 99%), 한국산 참쑥의 학명은 재고 되어야할 것으로 사료된다. 또한, 강화약쑥(A. sp.)은 황해쑥과 매우 가까운 상동성을 보였다(Boostrap 89%). 따라서, 형태적 형질의 변이가 다소 연속적인 쑥속은 DNA 염기서열에 기초한 분자계통학적 연구가 유용한 방법으로 판단되며, 본 ITS 연구결과는 한국산 쑥속의 계통분류를 이해하는데 유용한 형질로 기여할 것으로 기대된다.

• Animal cells and systems
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• 제13권3호
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• pp.323-329
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• 2009

We analyzed partial sequences of cytochrome b (cyt-b), a mitochondrial DNA (mtDNA) gene, to determine the genetic relationships between six horsehead fish species: Branchiostegus japonicus, Branchiostegus albus, Branchiostegus auratus, Branchiostegus argentatus, Branchiostegus wardi, and an unidentified Branchiostegus species. The specimens were collected in Korea, China, Japan, and Vietnam. We compared their molecular phylogenetic relationships inferred from mtDNA cyt-b sequences with an osteological analysis. The unidentified species, B. sp., was similar to B. albus in terms of the lack of triangular silver-white dot at the posterior region of eyes (vs. large one present in B. japonicus), but was also similar to B. japonicus in terms of the presence of a straight-shaped first hemal spine (vs. a curve-shaped hemal spine in B. albus). Analysis of the mtDNA cyt-b sequences indicated that the smallest estimated sequence divergence was between the B. japonicus and B. sp. (0.70-0.94%), whereas the largest difference was between B. auratus and B. argentatus (23.06-23.36%). Both the maximum parsimony and maximum likelihood trees showed that the B. sp. was closely clustered with B. japonicus, and that B. auratus was most distant from the other species. When comparing the osteological characters, UPGMA tree showed that the B. japonicus and B. sp. were the most closely clustered species, and B. auratus was the most distantly clustered fish relative to the other species. The shape of the nasal, otolith and first hemal spine was informative for distinguishing B. auratus from the other species. These osteological differences were consistent with the differences in mtDNA.

• 한국어류학회지
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• 제18권4호
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• pp.293-299
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• 2006

두툽상어 (Scyliorhinus torazame)부터 분리된 항산화 효소 Cu,Zn-superoxide dismutase (Cu,Zn-SOD 또는 SOD1)의 핵산 염기서열 및 추정 아미노산 서열을 대상으로 분자 계통학적 분석을 실시하였다. 종래 알려져 있는 척추동물의 Cu,Zn-SOD 서열들을 포함하여 neighbor-joining (NJ), maximum parsimony (MP), maximum likelihood (ML) 및 Bayesian 분석 등을 포함한 다양한 계통 분석을 수행하였으며, 이를 통해 연골어류인 본 어종의 척추동물 분류군 내에서의 계통적 위치를 추정하고자 하였다. 다양한 분자 계통수로부터 얻어진 대부분의 consensus tree들에서 분석에 사용한 분류군들은 종래 알려진 분류학적 위치와 비교적 잘 일치하였고, 이중 두툽상어는 같은 연골어류종인 blue shark와 높은 유연관계를 나타내면서 보다 진화한 경골어류들과는 확연히 구분되는 분지를 형성하였다. 특히 핵산 염기서열을 바탕으로 한 neighbor-joining 분석에서 두툽상어는 경골어류와 양막동물에 비해 보다 원시형태의 척추동물 Cu,Zn-SOD 유전자의 한 형태를 보유하고 있는 것으로 나타났다.

• Parasites, Hosts and Diseases
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• 제54권4호
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• pp.455-460
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• 2016

Blastocystis is a common zoonotic enteric protozoan that has been classified into 17 distinct subtypes (STs). A cross-sectional study was conducted to determine the prevalence and subtype distributions of Blastocystis in villagers living along the Chao Phraya River, Ayutthaya Province, Thailand, and to assess the risk of zoonotic infection. In total, 220 stool samples were collected, and DNA was extracted. PCR and sequencing were performed with primers targeting the small-subunit ribosomal RNA (SSU rRNA) genes. Blastocystis was present in 5.9% (13/220) of samples, and ST3 (5.0%; 11/220) was the predominant subtype, followed by ST2 (0.45%; 1/220) and ST6 (0.45%; 1/220). Phylogenetic trees were constructed with the maximum-likelihood method based on the Hasegawa-Kishino-Yano + G + I model, neighbor-joining, and maximum parsimony methods. The percentage of bootstrapped trees in which the associated taxa clustered together was relatively high. All the sequences of the Blastocystis-positive samples (KU051524-KU051536) were closely related to those from animals (pig, cattle, and chicken), indicating a zoonotic risk. Therefore, the villagers require proper health education, especially regarding the prevention of parasitic infection, to improve their personal hygiene and community health. Further studies are required to investigate the Blastocystis STs in the animals living in these villages.