• Proceedings of the Zoological Society Korea Conference
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• 2003.08a
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• pp.49-49
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• 2003

No Abstract, See Full Text

• Journal of Life Science
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• v.11 no.5
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• pp.400-404
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• 2001

A new human endogenous retroviral family (HERV-S) has recently been identified from human X chromosome. It is 6.7 kb in length and has a typical retroviral structure with LTR-gag-pol-env-LTR. Using the PCR and sequencing approach, we investigated LTR elements of the HERV-S family from a human genomic DNA. Four LTR elements (HSL-1, HSL-5, HSL-10, HSL-11) were identified and have a high degree of sequence similarity(96-99%) with that of the HERV-S. Phylogenetic analysis from the HERV-S family indicated that the LTR elements were mainly divided into 2- groups through evolutionary divergence in the primate evolution. Further investigation of the HERV-S LTR elements in primates may cast light on the integration timing into the primate genome and understanding of human evolution.

• Journal of Life Science
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• v.14 no.4
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• pp.716-725
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• 2004

Sox protein family, a transcription factor, has been found in whole animal kingdom, and contains a sequence-specific DNA binding domain called high mobility group domain (HMG). The Sox protein family based on the amino acid sequence of HMG domain was classified into 10 groups. Each group of Sox family shows significant conservation from nematode to human. The HMG domain affect to various developmental cell differentiation through binding to enhancer and regulating other transcription factors. Recently, many molecular biologists focus their research on the illustration of Sox-related disease, evolution and phylogeny. Especially, stem cell research with Sox gene family is indispensable field for understanding of their biological functions. The understanding of Sox genes may contribute to understand their role in human genetic disease and whole animal evolution.

• International Journal of Control, Automation, and Systems
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• v.6 no.6
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• pp.809-817
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• 2008

Program plagiarism is widespread due to intelligent software and the global Internet environment. Consequently the detection of plagiarized source code and software is becoming important especially in academic field. Though numerous studies have been reported for detecting plagiarized pairs of codes, we cannot find any profound work on understanding the underlying mechanisms of plagiarism. In this paper, we study the evolutionary process of source codes regarding that the plagiarism procedure can be considered as evolutionary steps of source codes. The final goal of our paper is to reconstruct a tree depicting the evolution process in the source code. To this end, we extend the well-known bioinformatics approach, a local alignment approach, to detect a region of similar code with an adaptive scoring matrix. The asymmetric code similarity based on the local alignment can be considered as one of the main contribution of this paper. The phylogenetic tree or evolution tree of source codes can be reconstructed using this asymmetric measure. To show the effectiveness and efficiency of the phylogeny construction algorithm, we conducted experiments with more than 100 real source codes which were obtained from East-Asia ICPC(International Collegiate Programming Contest). Our experiments showed that the proposed algorithm is quite successful in reconstructing the evolutionary direction, which enables us to identify plagiarized codes more accurately and reliably. Also, the phylogeny construction algorithm is successfully implemented on top of the plagiarism detection system of an automatic program evaluation system.

• Molecules and Cells
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• v.27 no.1
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• pp.55-66
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• 2009

The phylogeny of the family Tephritidae (Diptera: Tephritidae) was reconstructed from mitochondrial 12S, 16S, and COII gene fragments using 87 species, including 79 tephritid and 8 outgroup species. Minimum evolution and Bayesian trees suggested the following phylogenetic relationships: (1) A sister group relationship between Ortalotrypeta and Tachinisca, and their basal phylogenetic position within Tephritidae; (2) a sister group relationship between the tribe Acanthonevrini and Phytalmiini; (3) monophyly of Plioreocepta, Taomyia and an undescribed new genus, and their sister group relationship with the subfamily Tephritinae; (4) a possible sister group relationship of Cephalophysa and Adramini; and (5) reconfirmation of monophyly for Trypetini, Carpomyini, Tephritinae, and Dacinae. The combination of 12S, 16S, and COII data enabled resolution of phylogenetic relationships among the higher taxa of Tephritidae.

• Animal Systematics, Evolution and Diversity
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• v.31 no.2
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• pp.118-121
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• 2015

The water deer, Hydropotes inermis (Cervidae), is native to China and Korea and has two subspecies of the Chinese water deer (Hydropotes inermis inermis) and Korean water deer (Hydropotes inermis argyropus). To date, only the Korean water deer has been reported in South Korea. In this study, however, an intraspecific phylogeny and haplotype analysis based on mitochondrial cytochrome oxidase I indicated that both Korean and Chinese water deer are found in South Korea. The populations of the two Korean genetic lineages did not show distinct geographic distributions. Further morphological studies on the Korean water deer will be required to confirm its taxonomic status.

• Genomics & Informatics
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• v.6 no.3
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• pp.130-135
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• 2008

The haplotypes of a 200 kb region in the human chromosome X terminal band (q28) were analyzed using the International HapMap Project Phasell data, which had been collected for three analysis panels (YRI, CEU, and CHB＋JPT). When multiple linkage disequilibrium blocks were encountered for a panel, the neighboring haplotypes that had crossover rate of 5% or more in the panel were combined to generate 'haploid' configurations. This resulted in 8, 7, and 5 'haploid' configurations for the panels of YRI, CEU, and CHB＋JPT, respectively. The multiple sequence alignment of these 'haploids' was used for the calculation of allele-sharing distances and the subsequent principal coordinate analysis. Two 'haploids' in CEU and CHB＋JPT were hypothesized as 'parental' in light of the observations that the successive recombinants of these haploids can model two other haploids in CEU and CHB＋JPT, and that their configurations were consistent with those in YRI. This study demonstrates the utility of haplotype phylogeny in understanding population evolution.

• Animal Systematics, Evolution and Diversity
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• v.30 no.1
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• pp.39-43
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• 2014

In this brief report, alternative time-varying diversification rate models were fitted onto the phylogeny of global amphibians by considering one-constant-rate (OCR), one-continuous-shift (OCS) and multiple-discrete- shifts (MDS) situations. The OCS diversification model was rejected by ${\gamma}$ statistic (${\gamma}=-5.556$, p<0.001), implying the existence of shifting diversification rates for global amphibian phylogeny. Through model selection, MDS diversification model outperformed OCS and OCR models using "laser" package under R environment. Moreover, MDS models, implemented using another R package "MEDUSA", indicated that there were sixteen shifts over the internal nodes for amphibian phylogeny. Conclusively, both OCS and MDS models are recommended to compare so as to better quantify rate-shifting trends of species diversification. MDS diversification models should be preferential for large phylogenies using "MEDUSA" package in which any arbitrary numbers of shifts are allowed to model.

• Animal Systematics, Evolution and Diversity
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• v.26 no.2
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• pp.99-104
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• 2010

The subfamily Murinae is a very controversial group concerning their phylogenetic relationship. Previous studies could not resolve phylogeny among four genera Apodemus, Micromys, Mus and Rattus of the Muridae. In the present study, eight rodent species resident in South Korea were collected and phylogenetically analyzed based on sequence data of five mitochondrial and nuclear DNA regions: 12S rRNA, cytochrome b gene (cyt b), cytochrome oxidase II (COII), control region of mitochondrial DNA, and a thyroglobulin (Tg) of nuclear DNA. According to the phylogeny of the concatenated data, M. musculus separated early in Murinae (ML 100%; BA 1.00 pp) and the genus Rattus grouped with the harvest mouse, M. minutes; these were separated from the genus Apodemus with relatively strong support (ML 74%; BA 0.76 pp). The Siberian chipmunk population was also examined using the five genes to obtain better resolution. The phylogeny for Korean rodents determined using the 12S rRNA, cyt b, COII and control regions discriminated the Siberian chipmunk populations from Korea, Russia, and China.

• Animal Systematics, Evolution and Diversity
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• v.17 no.2
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• pp.263-275
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• 2001

Animal phyla in the traditional animal phylogeny were organized into an order of increasing body plan complexity, which was based on the similarities in early embryonic stages. Molecular phylogeny mainly by 18S rRNA data provides recently re-evaluation of the traditional evolutionary scenario. The current molecular-based view of animal relationships strongly suggest the burst of two groups regraded as intermediate grades of body complexity in the traditional concept and displacement of them into higher positions in the tree. The new animal tree provides a framework within new picture of bilaterian ancestor could be drawn, and comparative developmental and genomic data to be interpreted.