• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.183-192
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• 2003

With the availability of complete whole-genomes such as the human, mouse, fugu and chimpanzee chromosome 22, comparative analysis of large genomes from cross-species at varying evolutionary distances is considered one of a powerful approach for identifying coding and functional non-coding sequences. Here we describe a fast and efficient global alignment method especially for large genomic regions over mega bases pair. We used an approach for identifying all similarity regions by HSP (Highest Segment Pair) regions using local alignments and then large syntenic genome based on the both extension of anchors at HSP regions in two species and global conservation map. Using this alignment approach, we examined rearrangement loci in human chromosome 21 and chimpanzee chromosome 22. Finally, we extracted syntenic genome 30 Mb of human chromosome 21 with chimpanzee chromosome 22, and then identified genomic rearrangements (deletions and insertions ranging h size from 0.3 to 200 kb). Our experiment shows that all jnsertion/deletion (indel) events in excess of 300 bp within chimpanzee chromosome 22 and human chromosome 21 alignments in order to identify new insertions that had occurred over the last 7 million years of evolution. Finally we also discussed evolutionary features throughout comparative analyses of Ka/ks (non-synonymous / synonymous substitutions) rate in orthologous 119 genes of chromosome 21 and 53 genes of MHC-I class in human and chimpanzee genome.

• Korean Journal of Agricultural Science
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• v.41 no.4
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• pp.405-413
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• 2014

The evolutionary history of cattle and buffalo has always been a topic of great interest to the evolutionary biologists. The phylogenetic studies of bovin species has been carried out at various levels, varying from the study of domestication and migration of populations to major cladogenesis. Along with the archeological studies there are studies from molecular biology and more recently from genomics. The phylogenetic perspective of the bovins and their evolutionary history, are reviewed in terms of what has been done, what needs to be done and potential challenges in doing it.

• BMB Reports
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• v.40 no.2
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• pp.172-179
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• 2007

PCR-mediated recombination describes the process of in vitro chimera formation from related template sequences present in a single PCR amplification. The high levels of genetic redundancy in eukaryotic genomes should make recombination artifacts occur readily. However, few evolutionary biologists adequately consider this phenomenon when studying gene lineages. The cytosolic glyceraldehyde-3-phosphate dehydrogenase gene (GapC), which encodes a NADP-dependent nonphosphorylating glyceraldehyde-3-phosphate dehydrogenase in the cytosol, is a classical lowcopy nuclear gene marker and is commonly used in molecular evolutionary studies. Here, we report on the occurrence of PCR-mediated recombination in the GapC gene family of Hibiscus tiliaceus. The study suggests that recombinant areas appear to be correlated with DNA template secondary structures. Our observations highlight that recombination artifacts should be considered when studying specific and allelic phylogenies. The authors suggest that nested PCR be used to suppress PCRmediated recombination.

• Molecules and Cells
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• v.40 no.10
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• pp.796-804
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• 2017

Endogenous retroviruses (ERVs) have been integrated into vertebrate genomes and have momentously affected host organisms. Horses (Equus caballus) have been domesticated and selected for elite racing ability over centuries. ERVs played an important role in the evolutionary diversification of the horse genome. In the present study, we identified six equine ERV families (EqERVs-E1, I1, M2, P1, S1, and Y4), their full-length viral open reading frames (ORFs), and elucidated their phylogenetic relationships. The divergence time of EqERV families assuming an evolutionary rate of 0.2%/Myr indicated that EqERV-S3 (75.4 million years ago; mya) on chromosome 10 is an old EqERV family and EqERV-P5 (1.2 Mya) on chromosome 12 is a young member. During the evolutionary diversification of horses, the EqERV-I family diverged 1.7 Mya to 38.7 Mya. Reverse transcription quantitative real-time PCR (RT-qPCR) amplification of EqERV pol genes showed greater expression in the cerebellum of the Jeju horse than the Thoroughbred horse. These results could contribute further dynamic studies for horse genome in relation to EqERV gene function.

• The Korean Journal of Zoology
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• v.22 no.3
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• pp.115-124
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• 1979

Two homotetrameric lactate dehydrogenase isozymes from Fluta alba and one from Ophicephalus argus were purified by combination of gel filtration and DEAE-cellulose chromatogrphy. The final preparations were isozymically pure and used to elicit antibodies in rabbits. The immunochemical reactivities demonstrated that the amino acids of active site is not to be included in the antigenic determinants, that antibodies or unknown component of immunized rabbit serum might be responsible for the electrophoretic abnormality and that two subunits share common antigenic determinants, reflecting that these polypeptides have a common evolutionary origin.

• Animal cells and systems
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• v.9 no.4
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• pp.211-213
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• 2005

In bird species that suffer brood parasitism, the question about which sex is responsible for egg rejection has important implications for determining the coevolutionary relationship between brood parasites and their hosts. In order to determine which sex rejects a parasitic egg in vinous-throated parrotbills (Paradoxornis webbianus) which have egg color dimorphism, we conducted model egg experiments and video-recorded the behavior of the focal pair. Both sexes showed rejection behavior to the parasitic eggs. It indicates that the vinous-throated parrotbill may have a high rejection rate and faster spread of any rejection alleles through out populations. However, further studies are still needed to confirm the egg recognition mechanism in this species, which will expand our knowledge of the evolutionary relationship between host and parasite.

• The Korean Journal of Ecology
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• v.28 no.6
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• pp.405-415
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• 2005

This paper considers the advantage of Machine Learning (ML) implemented to freshwater ecosystem research. Currently, many studies have been carried out to find the patterns of environmental impact on dynamics of communities in aquatic ecosystems. Ecological models popularly adapted by many researchers have been a means of information processing in dealing with dynamics in various ecosystems. The up-to-date trend in ecological modelling partially turns to the application of ML to explain specific ecological events in complex ecosystems and to overcome the necessity of complicated data manipulation. This paper briefly introduces ML techniques applied to freshwater ecosystems in Korea. The manuscript provides promising information for the ecologists who utilize ML for elucidating complex ecological patterns and undertaking modelling of spatial and temporal dynamics of communities.

• Development and Reproduction
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• v.22 no.2
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• pp.119-132
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• 2018

GnRH (gonadotropin-releasing hormone) is a supreme hormone regulating reproductive activity in most animals. The sequences of amino acid and nucleic acid of GnRH reported up to now are examined from the evolutionary framework of Chordata. All identified GnRH are classified into GnRH1, GnRH2, or GnRH3. In all three forms of GnRH both N-terminal and C-terminal are conserved, which allows for effective binding to their receptors. The three amino acids in the middle of GnRH1 sequence have altered diversely from the primitive Chordata, which is indicative of the adaptation process to the ambient environment. GnRH2 and GnRH3 sequences are well conserved. There are more diverse modifications in the nucleic acids than in amino acid sequence of GnRH1. These variations can result from meiosis, mutation, or epigenetics and indicate that GnRH is the product of natural selection.

• Parasites, Hosts and Diseases
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• v.37 no.4
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• pp.197-213
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• 1999

Phylogeny is the evolutionary history of a group or the lineage of organisms and is reconstructed based on morphological, molecular and other characteristics. The genealogical relationship of a group of taxa is often expressed as a phylogenetic tree. The difficulty in categorizing the phylogeny is mainly due to the existence of frequent homoplasies that deceive observers. At the present time, cladistic analysis is believed to be one of the most effective methods of reconstructing a phylogenetic tree. Excellent computer program software for phylogenetic analysis is available. As an example, cladistic analysis was applied for nematode genera of the family Acuariidae, and the phylogenetic tree formed was compared with the system used currently. Nematodes in the genera Nippostrongylus and Heligmonoides were also analyzed, and the validity of the reconstructed phylogenetic trees was observed from a zoogeographical point of view. Some of the theories of parasite evolution were briefly reviewed as well. Coevolution of parasites and humans was discussed with special reference to the evolutionary relationship between Enterobius and primates.

• ALGAE
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• v.33 no.3
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• pp.243-267
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• 2018

A taxonomic study was recently carried out on species of the tribe Ceramieae (Ceramiaceae, Rhodophyta), following an evaluation of previously published records and on the basis of field and laboratory investigations. In Morocco, the tribe is represented by 5 genera: Ceramium (21 taxa at specific and infraspecific levels), Gayliella (3 species), and by one species each of Centroceras, Corallophila and Microcladia. Among these, there are five new records for Morocco: Centroceras gasparrinii, Ceramium botryocarpum, Ceramium cingulatum, Ceramium echionotum var. mediterraneum, and Gayliella taylorii. The report of C. echionotum var. mediterraneum from the Atlantic coast of Morocco is one of the rare records from outside the Mediterranean. Ceramium ciliatum var. robustum and Ceramium codii are recorded for the first time from the Atlantic coast of Morocco. Centroceras clavulatum is excluded from Moroccan flora having been misidentified for C. gasparrinii. This paper summarizes the taxonomic characters of these species with images and presents a key for their identification. This report is the first detailed record of the species of the tribe Ceramieae for Morocco. As a result, the total number of taxa at both specific and infraspecific levels accepted in the tribe Ceramieae for Morocco, under current taxonomy and nomenclature, is 27.