• Title, Summary, Keyword: phylogenetic tree

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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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SPECTRAL METHOD FOR RECONSTRUCTING PHYLOGENETIC TREE

  • Paeng, Seong-Hun;Park, Chunjae
    • Communications of the Korean Mathematical Society
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    • v.34 no.3
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    • pp.1005-1014
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    • 2019
  • A new simple method is proposed for reconstructing phylogenetic trees, which we call the spectral method. The most common distance based method is the neighbor-joining method which is based on the minimum evolution principle. The spectral method shows similar performance to the neighbor-joining method for simulated data generated by seq-gen. For real data, the spectral method shows much better performance than the neighbor-joining method. Hence it can be a complementary method for reconstructing phylogenetic trees.

Construction of a Phylogenetic Tree from tRNA Sequences (tRNA 염기 순서를 이용한 계통학적 연구)

  • 이병재;이동훈;김영준;강현삼
    • Korean Journal of Microbiology
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    • v.24 no.4
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    • pp.400-405
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    • 1986
  • We have constructed a phylogenetic tree for eleven species by comparing their tRNA sequences. The tree suggests that prokaryotes diverged very early before the emergence of animals. The fact that H. volcano, an archaebacterium, clusters with eukaryotes implied that eukaryotes did not diverge directly from thier common ancestor with eubacteria. The branching order of phage $T_{4}$ and phage $T_{5}$ indicates that they have diverged separately from thier hosts and they might have evolved independently. A correlation between nucleotide substitution in tRNAs and paleontological record was observed. We verified that our phylogenetic tree fits very well with traditional ones very well by imposing the molecular clock on the tree.

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A phylogenetic amino acid substitution matrix from Kogs database (Kogs데이타베이스로부터 얻은 계통학적인 아미노산 치환행렬)

  • An, Hui-Seong;Kim, Sang-Su
    • Bioinformatics and Biosystems
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    • v.2 no.1
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    • pp.7-11
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    • 2007
  • Methods for making scoring matrix based on phylogenetic tree for all possible exchanges of one amino acid with another. PFMT(Phylogenetic focused Mutation Tendency) matrix is different BLOSUM62 and PAM160 which are the most used scoring matrixes. This matrix calculates possibility of substitution from common ancestor to high spices. PFMT matrix scores substitution frequency in COGs databases which contain 152 KOGs's dataset. PFMT matrix usefully is able to compare between query sequence and sequences of more higher species and show detailed substitution relation of 20 amino acids.

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QUARTET CONSISTENCY COUNT METHOD FOR RECONSTRUCTING PHYLOGENETIC TREES

  • Cho, Jin-Hwan;Joe, Do-Sang;Kim, Young-Rock
    • Communications of the Korean Mathematical Society
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    • v.25 no.1
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    • pp.149-160
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    • 2010
  • Among the distance based algorithms in phylogenetic tree reconstruction, the neighbor-joining algorithm has been a widely used and effective method. We propose a new algorithm which counts the number of consistent quartets for cherry picking with tie breaking. We show that the success rate of the new algorithm is almost equal to that of neighbor-joining. This gives an explanation of the qualitative nature of neighbor-joining and that of dissimilarity maps from DNA sequence data. Moreover, the new algorithm always reconstructs correct trees from quartet consistent dissimilarity maps.

Polymorphisms of Blood Proteins In Cheju Native Horses and Tsushima Native Horses (제주 재래마아 쓰시마 재래마의 혈액내 단백질의 다형)

  • 오유성;오문유;김세재;김기옥;고미희;모야박;양영훈
    • The Korean Journal of Zoology
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    • v.38 no.3
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    • pp.324-329
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    • 1995
  • The phylogenetic relationships between Cheju native horses and Tsushima native horses were studied by protein polymorphism analyses in 16 gene loci (Trypsin inhibitor: Ti, Chymotrypsin inhibitor: CTi, Albumin: Al, Esterase: Es, Transferrin: Tf, Hemoglobin: Hb, Catalase: Cat, Esterase D: EsD, Glutamate oxaloacetate transaminase: GOT, Glyoxalase I: GLO I, Acid phosphatase: AcP, Superoxide dismutase: SOD, Lactate dehydrogenase: LDH, Hexokinase: HK, Malate dehydrogenase: MDH, Malic enzyme: ME). All allelic patterns of the protein loci, except 5 loci (SOD, LDH, HK, MDH, ME), were polymorphic in both two populations. Gene frequencies of the polymorphic loci of the population of Cheju native horses were higher than those of Tsushima native horses. Average heterozygosity in Cheju native horses was 0.375, showing higher than that of Tsushima native horses (0.304). The Da distance and gene identity of two populations were 0.108 and 0.868, respectively. The phylogenetic tree constructed by these results and those previously reported in other horse populations, consisted of three clusters. From this phylogenetic tree, it could be suggested that Cheju native horses and Tsushima native horses had diverged from the Mongolian wild horse (Equus prsewolskii).

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Classification of Archaebacteria and Bacteria using a Gene Content Tree Approach (Gene Content Tree를 이용한 Archaebacteria와 Bacteria 분류)

  • 이동근;김수호;이상현;김철민;김상진;이재화
    • KSBB Journal
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    • v.18 no.1
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    • pp.39-44
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    • 2003
  • A Gene content phylogenetic tree and a 16s rRNA based phylogenetic tree were compared for 33 whole-genome sequenced procaryotes, neighbor joining and bootstrap methods (n=1,000). Ratio of conserved COG (clusters of orthologous groups of proteins) to orthologs revealed that they were within the range of 4.60% (Mezorhizobium loti) or 56.57% (Mycopiasma genitalium). This meant that the ratio was diverse among analyzed procaryotes and indicated the possibility of searching for useful genes. Over 20% of orthologs were independent among the same species. The gene content tree and the 16s rDNA tree showed coincidence and discordance in Archaeabacteria, Proteobacteria and Firmicutes. This might have resulted from non-conservative genes in the gene content phylogenetic tree and horizontal gene transfer. The COG based gene content tree could be regarded as a midway phylogeny based on biochemical tests and nucleotide sequences.

Arthonia dokdoensis and Rufoplaca toktoana - Two New Taxa from Dokdo Islands (South Korea)

  • Kondratyuk, Sergij;Lokos, Laszlo;Halda, Josef;Lee, Beeyoung Gun;Jang, Seol-Hwa;Woo, Jeong-Jae;Park, Jung Shin;Oh, Soon-Ok;Han, Sang-Kuk;Hur, Jae-Seoun
    • Mycobiology
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    • v.47 no.4
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    • pp.355-367
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    • 2019
  • Arthonia dokdoensis sp. nov., a lichenicolous fungus from the subcosmopolitan Arthonia molendoi complex growing on crustose thalli of species of the genus Orientophila (subfamily Xanthorioideae, Teloschistaceae), as well as the lichen species Rufoplaca toktoana sp. nov. (subfamily Caloplacoideae, Teloschistaceae) similar to Rufoplaca kaernefeltiana, both from Dokdo Islands, Republic of Korea, are described, illustrated, and compared with closely related taxa. In the phylogenetic tree of the Arthoniaceae based on 12S mtSSU and RPB2 gene sequences, the phylogenetic position of the A. dokdoensis and the relationship with the A. molendoi group are illustrated, while the position of the newly described R. toktoana is confirmed by phylogenetic tree based on ITS nrDNA data.

Genealogical Relationship between Pedigree and Microsatellite Information and Analysis of Genetic Structure of a Highly Inbred Japanese Black Cattle Strain

  • Sasazaki, S.;Honda, T.;Fukushima, M.;Oyama, K.;Mannen, H.;Mukai, F.;Tsuji, S.
    • Asian-Australasian Journal of Animal Sciences
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    • v.17 no.10
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    • pp.1355-1359
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    • 2004
  • Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree nformation. Japanese Black cattle of Hyogo prefecture (Tajima strain) are famous for its ability to produce high-quality meat and have been maintained as a closed system for more than 80 years. In order to assess the usefulness of microsatellite markers in closed cattle populations, and evaluate the genetic structure of the Tajima strain, we analyzed representative dams of the Tajima strain comprised of the substrains Nakadoi and Kinosaki. Genetic variability analyses indicated low genetic diversity in the Tajima strain. In addition, a recent genetic bottleneck, which could be accounted for by the high level of inbreeding, was detected in both substrains. In phylogenetic analyses, relationship coefficients and genetic distances between individuals were calculated using pedigree and microsatellite information. Two phylogenetic trees were constructed from microsatellite and pedigree information using the UPGMA method. Both trees illustrated that most individuals were distinguished clearly on the basis of the two substrains, although in the microsatellite tree some individuals appeared in clusters of different substrains. Comparing the two phylogenetic trees revealed good consistency between the microsatellite analysis tree and the pedigree information. The correlation coefficient between genetic distances derived from microsatellite and pedigree information was 0.686 with a high significance level (p<0.001). These results indicated that microsatellite information may provide data substantially equivalent to pedigree information even in unusually inbred herds of cattle, and suggested that microsatellite markers may be useful in revealing genetic structure without accurate or complete pedigree information.

Identification and Phylogenetic Relationship at Cytochrome Oxidase Subunit I (COI) Gene among Korean Terrestrial Planarian Taxa (한국 내 육지플라나리아 간 치토크롬 산화효소의 동정과 계통유전학적 관계)

  • Moon, Doo-Ho;Lee, Young-Ah;Huh, Man-Kyu
    • Journal of Life Science
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    • v.21 no.7
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    • pp.939-946
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    • 2011
  • Sequence data of Cytochrome Oxidase Subunit I (COI) gene of mitochondria were used to elucidate the taxonomy and phylogenetic relationships of the terrestrial planarian taxa in Korea. Published COI gene sequences from Family Bipaliidae in GenBank were also included in the phylogenetic analysis. The aligned data sets for Terricola ranged from 387 to 444 nucleotides (bp) as a result of differences in insert nucleotides. The phylogeny based on COI analysis was not congruenced with the morphological traits. Bipalium nobile included the remainder taxa (Bipalium adventitium, Bipalium venosum, Bipalium kewense, and Bipalium multilineatum). Internal nodes were strongly supported (>91%). The phylogenetic tree on COI analysis showed that most identified species were well separated from each other. The main phylogenetic analysis formed monophyletic groups. COI gene of mitochondria could have the resolving power for taxonomy information for the terrestrial planarian taxa in Korea.