• Title, Summary, Keyword: phylogeny

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Phylogeny, host-parasite relationship and zoogeography

  • Hasegawa, Hideo
    • The Korean Journal of Parasitology
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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.

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New Animal Phylogeny (새로운 동물계통)

  • Kim, Chang-Bae;Kim, Won
    • 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.

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A Phylogenetic Study of Korean Rodents (Muridae, Sciuridae) Based on Mitochondrial and Nuclear DNA

  • Jung, Gi-La;Lee, Seo-Jin;Kim, Chuel-Kyu;Lee, Hang;Kim, Chang-Bae
    • 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.

Phylogeographic Messages Encoded in the rDNA of the Commercial Mushroom Zhenghonggu@ From Fujian, China

  • Chen, Yu H.;Chen, Peng D.;Chen, Liu Y.;Ma, Li Z.
    • 한국균학회소식:학술대회논문집
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    • pp.45-45
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    • 2014
  • Individualities of precious health mushroom called Zhenghonggu@ from respective protections scattered among all main mountains of Fujian China were collected and recognized locally, then compared with Russula griseocarnosa. Their internal transcribed spacer (ITS) region (ITS1, ITS2 and 5.8S rDNA) of the nuclear rDNA were amplified, AMOVA analyzed, nested clade analyzed and then compared with the ITS sequences of relative Russula species from other regions of China to confirm the taxonomic status of Zhenghonggu$^@$ and its population structure. Total 23 haplotypes from different protections of Fujian can be clustered into three clades similar to the three lineages of Dahongjun$^@$ from southeastern China reported by Li et al. The geographic distribution characteristic of these three phylogeny clades may be closely coupled with the vegetation regionalization and/or the differences of coenosium construction of Fagaceae that is the host of Russula griseocarnosa. The correlation of taxonomy, phylogeny and geographical distribution of Russula are discussed.

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Molecular Phylogeny of the Family Tephritidae (Insecta: Diptera): New Insight from Combined Analysis of the Mitochondrial 12S, 16S, and COII Genes

  • Han, Ho-Yeon;Ro, Kyung-Eui
    • 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.

Phylogenetic Contributions of Partial 26S rDNA Sequences to the Tribe Helleboreae (Ranunculaceae)

  • Ro, Kyung-Eui;Han, Ho-Yeon;Lee, Sang-Tae
    • Animal cells and systems
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    • v.3 no.1
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    • pp.9-15
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    • 1999
  • Monophyly and intergeneric relationships of the tribe Helleboreae, sensu Tamura, and related genera were studied using a 1,100-bp segment at the 5'end of the 26S ribosomal RNA gene. Forty-one OTUs, including eight species of the Helleboreae, were either directly sequenced or obtained from previous publications. Data were analyzed using distance and discrete character methods to infer phylogenetic relationships among the included taxa. The inferred phylogeny did not support monophyly of either Helleboreae or Cimicifugeae whose members were intermixed in our inferred phylogeny. This result is congruent with our previous study, which recommended against finely subdividing, suprageneric higher taxa within the R-chromosome group (subfamily Ranuncluloideae, sensu lato) until more molecular data were accumulated. Our data convincingly suggest the presence of the following three monophyletic groups: the Cimicifuga group (the clade of Actaea, Cimicifuga, Souliea, Eranthis, Anemonopsis, and Beesia), the Trollius group (the clade of Trollius, Megaleranthis, Adonis), and a clade including Anemonopsis and Beesia. Our data also suggest that Trollius and Megaleranthis might be congeners and Eranthis a paraphyletic group.

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Haplotype Phylogeny of a 200kb Region in the Human Chromosome X Terminal Band (q28)

  • Kim, Sang-Soo
    • 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.

Diversity of the Lichenized Fungi in King George Island, Antarctica, Revealed by Phylogenetic Analysis of Partial Large Subunit rDNA Sequences

  • Lee, Jin-Sung;Lee, Hong-Kum;Hur, Jae-Seoun;Andreev, Mikhail;Hong, Soon-Gyu
    • Journal of Microbiology and Biotechnology
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    • v.18 no.6
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    • pp.1016-1023
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    • 2008
  • Lichens are predominant and important components of flora in the terrestrial ecosystem of Antarctica. However, relatively few researches on the phylogenetic position of Antarctic lichen-forming fungi have been accomplished. In this study, partial sequences of nuclear large subunit rDNAs from 50 Antarctic specimens were obtained and the phylogeny was reconstructed. Antarctic lichen species were distributed in 4 orders, including the monophyletic order Agyrales, paraphyletic orders Pertusariales and Teloschistales, and polyphyletic order Lecanorales. Species diversity was highest in the order Lecanorales, followed by Teloschistales and Pertusariales. Based on the phylogeny and sequence similarity analyses, it is proposed that the taxonomy of Stereocaulon alpinum, Physcia caesia, Usnea aurantiacoatra, and Cladonia species should be revised by careful examination of their phenotypic and molecular characteristics. Six species known to be endemic to Antarctica, Catillaria corymbosa, Himantormia lugubris, Leptogium puberulum, Pertusaria pertusa, Rhizoplaca aspidophora, and Umbilicaria antarctica, formed unique lineages, implying independent origins in the Antarctic area.

Tempo of Diversification of Global Amphibians: One-Constant Rate, One-Continuous Shift or Multiple-Discrete Shifts?

  • Chen, Youhua
    • 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.

Intraspecific Phylogeny of the Korean Water Deer, Hydropotes inermis argyropus (Artiodactyla, Cervidae)

  • Kim, Hye Ri;Kim, Eui Kyung;Jeon, Mi Gyung;Park, Yung Chul
    • 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.