• Molecules and Cells
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• v.19 no.2
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• pp.283-288
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• 2005

Complete 18S rDNA sequences were determined for 10 vetigastropods in order to investigate the phylogeny of Vetigastropoda, which is controversial. These sequences were analyzed together with published sequences for nine other vetigastropods and two nerites. With the two nerites as outgroups, the phylogeny was inferred by three analytical methods, neighbor-joining, maximum likelihood, and maximum parsimony. The 18S rDNA sequence data support the monophyly of four vetigastropod superfamilies, the Pleurotomarioidea, the Fissurelloidea, the Haliotoidea, and the Trochoidea. The present results yield the new branching order: (Pleurotomarioidea (Fissurelloidea ((Scissurelloidea, Lepetodriloidea) (Haliotoidea, Trochoidea)))) within the vetigastropod clade.

• Molecules and Cells
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• v.23 no.1
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• pp.64-71
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• 2007

To investigate the phylogeny of Patellogastropoda, the complete 18S rDNA sequences of nine patellogastropod limpets Cymbula canescens (Gmelin, 1791), Helcion dunkeri (Krauss, 1848), Patella rustica Linnaeus, 1758, Cellana toreuma (Reeve, 1855), Cellana nigrolineata (Reeve, 1854), Nacella magellanica Gmelin, 1791, Nipponacmea concinna (Lischke, 1870), Niveotectura pallida (Gould, 1859), and Lottia dorsuosa Gould, 1859 were determined. These sequences were then analyzed along with the published 18S rDNA sequences of 35 gastropods, one bivalve, and one chiton species. Phylogenetic trees were constructed by maximum parsimony, maximum likelihood, and Bayesian inference. The results of our 18S rDNA sequence analysis strongly support the monophyly of Patellogastropoda and the existence of three subgroups. Of these, two subgroups, the Patelloidea and Acmaeoidea, are closely related, with branching patterns that can be summarized as [(Cymbula + Helcion) + Patella] and [(Nipponacmea + Lottia) + Niveotectura]. The remaining subgroup, Nacelloidea, emerges as basal and paraphyletic, while its genus Cellana is monophyletic. Our analysis also indicates that the Patellogastropoda have a sister relationship with the order Cocculiniformia within the Gastropoda.

• Proceedings of the Korean Society for Applied Microbiology Conference
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• 2000.04a
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• pp.128-134
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• 2000

In the course of flora analysis of soil Archaea, we found very strange 16S rDNA clones, which could possibly constitute a sister clade from known two archael, Crenarchaeota and Euryarchaeota, lineages. Overall signature sequences showed that the clones were closely related to domains Archaea and Eucarya. However, at least nine nucleotides distinguished the novel clones from domains Archaea and Eucarya. Phylogenetic trees drawn by maximum parsimony, neighbor joining and maximum likelihood methods also showed unique phylogenetic position of the clones. A very specific primer set was synthesized to detect the presence of the novel group of organisms in terrestrial environments. A specific DNA fragment was amplified from all of paddy soil DNAs, and this fact suggests that the novel organisms inhabit paddy soils.

• Korean Journal of Ichthyology
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• v.21 no.sup1
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• pp.75-75
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• 2009

The previous morphology-based taxonomic frameworks within the family Sygnathidae had emphasized the significance of the male brood pouch and reproductive biology in defining the group. However, several different hypotheses had been proposed by different investigators. This study have beencarried out to determine the phylogenetic relationships among 19 species belonging to the order Syngnathiformes with three Gasterosteiformes species as outgroup taxa by using the mitochondrial cytochrome b and Rag2 nuclear DNA sequences. Phylogenetic analyses based on neighbor-joining distance, maximum parsimony, minimum evolution and maximum likelihood method strongly supported that the family Syngnathidae, the suborder Syngnathoidei and the order Syngnathiformes were all monophyletic group. Much of previous morphological analyses were supported by our molecular data, but some deep relationships were not clearly resolved with regard to members of the suborder Aulostomoidei.

• BMB Reports
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• v.39 no.5
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• pp.522-529
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• 2006

Silk moths are the best studied silk secreting insects and belong to the families Bombycidae and Saturniidae. The phylogenetic relationship between eleven silk producing insects was analyzed using the complete DNA sequence of the internal transcribed spacer DNA 1 locus. The PCR amplification and sequence analysis showed variation in length ranging from 138 bp (Antheraea polyphemus) to 911 bp (Hyalopora cecropia). Microsatellite sequences were found and was be used to distinguish Saturniidae and Bombycidae members. The nucleotide sequences were aligned manually and used for construction of phylogenetic trees based on Maximum parsimony and Maximum likelihood methods. The topology in both the approaches yielded a similar tree that supports the ancestral position of the Antheraea assama.

• Korean Journal of Plant Taxonomy
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• v.48 no.1
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• pp.1-8
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• 2018

Mankyua chejuense is the only member of the monotypic genus Mankyua (Ophioglossaceae) and is endemic to Jejudo Island, Korea. To determine the precise phylogenetic position of M. chejuense, two cpDNA regions of 42 accessions representing major members of lycophytes are obtained from GenBank and analyzed using three phylogenetic analyses (maximum parsimony, maximum likelihood, and Bayesian inference). In addition, the divergence time is estimated based on a relaxed molecular clock using four fossil calibration points. The phylogenetic position of Mankyua still appears to be uncertain, representing either the earliest diverged lineage within Ophioglossaceae or a sister to the clade containing Ophioglossum and Helminthostachys. The most recent common ancestor of Ophioglossaceae and its sister lineage, Psilotum, was estimated to be 256 Ma, while the earliest divergence of Mankyua was estimated to be 195 Ma in the early Jurassic.

• Korean Journal of Plant Taxonomy
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• v.34 no.2
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• pp.173-183
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• 2004

한국산 미나리아재비속 미나리아재비(Acris Schur)절에 속하는 미나리아재비(Ranunculus japonicus)와 근연종인 산미나리아재비(R. acris var. nipponicus) 및 바위미나리아재비(R. crucilobus)의 실체와 분류학적 한계를 파악하기위해 속, 종간 규명에 많이 이용하고 있는 핵리보좀(ribosomal) DNA의 internal transcribed spacer 구간의 염기서열을 분석하였다. 본 연구는 6개의 군외군을 포함하여 총 18개의 DNA 재료(accessions)의 정열된 염기서열들을 바탕으로 bootsrap을 포함한 maximum parsimony와 maximum likelihood 분석법에 의한 계통수로 평가하였다. 연구 결과 Acris절에 속하는 미나리아재비, 산미나리아재비 및 바위미나리아재비는 단계통군으로 나타났으며 특히 미나리아재비(R. japonicus)와 산미나리아재비(R. acris var. nipponicus)는 같은 분계조를 형성하였다. 이와 달리 바위미나리아재비는 미나리아재비와 산미나리아재비에서 분지된 결과를 보여, 한라산 해발 1500m이상의 높은 지역에 분포하는 바위미나리아재비는 미나리아재비의 아종(R. japonicus Thunb. subsp. chrysotrichus (Nakai) Y. N. Lee, comb. nud.)으로 처리하기보다는, 독립된 고유종인 R. crucilobus H. L$\acute{e}$v.으로의 처리를 지지하였다.

• Animal cells and systems
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• v.4 no.3
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• pp.257-261
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• 2000

To elucidate phylogenetic relationships among poecilostome families 18S rDNA sequence data were generated for seven poecilostome and one cyclopoid copopods by PCR cloning and sequencing techmiques. Phylogenetic trees were constructed by maximum parsimony, neighbor joining, and maximum likelihood methods using cyclopoid sequence as an outgroup. The results from three different analyses showed that the seven poecilostome families were eiridel into two groups: Clausidiidae-Myicolidae-Synaptiphillidae-bomolochidae and Lichomologidae-Chondracanthidae-Ergasilidae. The molecular phylogenies were consistent with those from the morphological characters. Therefore, these analyses porvide further evidence for the utility of 18S rDNA sequences in addressing phylogenetic relationships among poecilostome families.

• Korean Journal of Plant Taxonomy
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• v.34 no.4
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• pp.335-358
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• 2004

To investigate molecular phylogenetic relationships and to test hypothesis of hybrid origin of Ranunculus cantoniensis (Ranunculaceae), the sequences of nrDNA and chloroplast DNA were analyzed for 8 taxa and 25 accessions including 5 accessions of outgroup. In the phylogenetic trees by analyses of maximum parsimony and maximum likelihood for ITS nrDNA sequences and combined data of psbA-trnH, rps16 and trnL sequences of cpDNA, R. cantoniensis was most closely related to R. chinensis, and then to R. taciroi and R. silerifolius. The molecular phylogenetic relationships were not congruent with the previous report that R. cantoniensis was most closely related to R. silerifolius. In the sequence analysis of ITS and psbA-trnH, rps16, trnL for R. cantoniensis and the related taxa, R. cantoniensis showed polymorphism. It supported that the polymorphism also was reported in chromosome number and karyotype of R. cantoniensis. Ranunculus cantoniensis shared the marker gene of R. chinensis and R. silerifolius in ITS, and one of R. silerifolius in cpDNA. These results supported the hypothesis that R. cantoniensis was caused by hybridization between R. chinensis and R. silerifolius based on chromosome number and karyotype, and also estimated that R. silerifolius might be of maternal origin and R. chinensis be paternal.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2012.05a
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• pp.19-19
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• 2012

The Colchicaceae comprising 250 species and 15-19 genera of rhizomatous or cormous perennials, the moderate sized family in Liliales, distributes widely through the temperate and tropical areas of Africa, Asia and North America. The division of two subfamilies in Colchicaceae is still unclear because of different results in previous studies. Moreover, sister taxa of this family has not been determined. In genus level, it was uncertain that whether expand circumscription of three genera of Colchicum, Gloriosa, and Wurmbea which are include Androcymbium, Littonia and Onixotis, respectively, is reasonable or not. In this study, three coding genes of atpB, matK and rbcL were analyzed to reconstruct phylogenetic relationship of Colchicaceae and both of maximum parsimony (MP) and Bayesian analysis were conducted. Among three genes, matK region was most variable and provided more parsimony-informative sites, whereas the atpB and rbcL regions were similar in the variation and number of informative characters. Monophyly of Colchicaceae was strongly supported and it was divided into two subfamilies (Wurmbeoideae and Uvulariodeae). Uvularia-Disporum clade, comprises the subfamily Uvularioideae, is a sister of the rest Colchicaceae and subsequently differentiated Burchardia was a sister within subfamily Wurmbeoideae. Burchadia was used to be supposed to be a sister of the family in the previous studies. It was clear the monophyly and phylogenetic relationship among six tribes sensu Vinnersten and Manning (2007) within the family. In addition, the expanded circumscription of three genera was also strongly supported; Colchicum-Androcymbium (BP99), Wurmbea-Onixotis (BP100), and Littonia-Gloriosa (BP100). Here, we propose a re-circumscription among taxa of Colchicaceae.