• Title/Summary/Keyword: phylogenetic

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Authentication of Cervus Species by Phylogenetic analysis (Cervus 종의 Phylogenetic analysis에 의한 판별)

  • Seo, Jung-Chul;Kim, Min-Jung;Lee, Chan;Kim, Myung-Gyou;Lee, Jeong-Soo;Choi, Kang-Duk;Leem, Kang-Hyun
    • The Korea Journal of Herbology
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    • v.21 no.3
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    • pp.91-95
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    • 2006
  • Objectives : This study was performed to determine if an antler could be identified as one of the Cervus species by phylogenetic analysis, which was used to assess genetic authentication. Methods : The DNAs of an antler were extracted, amplified by PCR, and sequenced. The DNAs of an antler were identified by Phylogenetic analysis. Phylogenetic analysis was made using MEGA software (Molecular Evolutionary Genetics Analysis, 3.1) Results : By phylogenetic analysis an antler was identified as Cervus elaphus nelsoni not as Cervus elaphus sibericus. This work showed that authentication can efficiently be performed by phylogenetic analysis. Conclusion : These results suggest that phylogenetic analysis might be able to provide the authentication of Cervus species.

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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.

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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Phylogeny, host-parasite relationship and zoogeography

  • Hasegawa, Hideo
    • 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.

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Co-Occurrence of Two Phylogenetic Clades of Pseudoperonospora cubensis, the Causal Agent of Downy Mildew Disease, on Oriental Pickling Melon

  • Lee, Dong Jae;Lee, Jae Sung;Choi, Young-Joon
    • Mycobiology
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    • v.49 no.2
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    • pp.188-195
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    • 2021
  • The genus Pseudoperonospora, an obligate biotrophic group of Oomycota, causes the most destructive foliar downy mildew disease on many economically important crops and wild plants. A previously unreported disease by Pseudoperonospora was found on oriental pickling melon (Cucumis melo var. conomon) in Korea, which is a minor crop cultivated in the temperate climate zone of East Asia, including China, Korea, and Japan. Based on molecular phylogenetic and morphological analyses, the causal agent was identified as Pseudoperonospora cubensis, and its pathogenicity has been proven. Importantly, two phylogenetic clades of P. cubensis, harboring probably two distinct species, were detected within the same plots, suggesting simultaneous coexistence of the two clades. This is the first report of P. cubensis causing downy mildew on oriental pickling melon in Korea, and the confirmation of presence of two phylogenetic clades of this pathogen in Korea. Given the high incidence of P. cubensis and high susceptibility of oriental pickling melon to this disease, phytosanitary measures, including rapid diagnosis and effective control management, are urgently required.

Phylogenetic Characteristics of Fasciola hepatica Isolated from a Korean Patient

  • Jeong, Mi Jin;Park, Jae Kyun;Yu, Hak Sun
    • Parasites, Hosts and Diseases
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    • v.60 no.5
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    • pp.367-370
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    • 2022
  • Fascioliasis is a parasitic infection caused by liver flukes. Although several cases have been reported in Korea, phylogenetic analysis of isolates is lacking. In this study, a 66-year-old woman with right upper quadrant (RUQ) abdominal pain was diagnosed as fascioliasis involving abdominal muscle by imaging study. She received praziquantel treatment, but symptoms were not improved. Lateral movement of the abscess lesion was followed. Trematode parasite was surgically removed from the patient's rectus abdominis muscle. The fluke was identified as Fasciola hepatica based on sequence analysis of 18S rDNA. To determine the phylogenetic position of this Fasciola strain (named Korean Fasciola 1; KF1), the cox1 gene (273 bp) was analyzed and compared with the genes of 17 F. hepatica strains isolated from cows, sheep, goats, and humans from various countries. Phylogenetic analysis showed that KF1 was closely related with the isolates from China goat.

General properties and phylogenetic utilities of nuclear ribosomal DNA and mitochondrial DNA commonly used in molecular systematics

  • Hwang, Ui-Wook;Kim, Won
    • Parasites, Hosts and Diseases
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    • v.37 no.4
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    • pp.215-228
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    • 1999
  • To choose one or more appropriate molecular markers or gene regions for resolving a particular systematic question among the organisms at a certain categorical level is still a very difficult process. The primary goal of this review, therefore, is to provide a theoretical information in choosing one or more molecular markers or gene regions by illustrating general properties and phylogenetic utilities of nuclear ribosomal DNA (rDNA) and mitochondrial DNA (mtDNA) that have been most commonly used for phylogenetic researches. The highly conserved molecular markers and/or gene regions are useful for investigating phylogenetic relationships at higher categorical levels (deep branches of evolutionary history). On the other hand, the hypervariable molecular markers and/or gene regions are useful for elucidating phylogenetic relationships at lower categorical levels (recently diverged branches). In summary, different selective forces have led to the evolution of various molecular markers or gene regions with varying degrees of sequence conservation. Thus, appropriate molecular markers or gene regions should be chosen with even greater caution to deduce true phylogenetic relationships over a broad taxonomic spectrum.

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A Review of the Phylogenetic Studies on the Kentish & Snowy Plovers

  • Woo-Yuel Kim;Dong-Yun Lee;Gun-hwa Kang;Ha-Cheol Sung
    • Proceedings of the National Institute of Ecology of the Republic of Korea
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    • v.4 no.2
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    • pp.63-68
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    • 2023
  • The Kentish Plover (Charadrius alexandrinus ; family Charadriidae; genus Charadrius) is a small bird that moves from continent to continent depending on the season. On the Kentish Plovers, phylogenetic studies have been widely conducted to classify different species or subspecies and to determine the time of speciation. However, the perspectives on the interspecific or intraspecific relationships in the phylogenetic analysis of Kentish Plovers remain debatable. Here, we reviewed the differences between the Kentish and Snowy Plovers (C. nivosus ) in terms of their morphology, ecology, and genetic information. Particularly, their differences in genetic information can be well demonstrated; however, the intraspecies differences in the populations that live in different environments can relatively be poorly explained. We suggest that not only genetic features but also morphological, ecological, and behavioral traits are important when comparing the Kentish Plovers with other species, such as the Snowy Plovers, in phylogenetic studies. Furthermore, we suggest that phylogenetic studies on the subspecies of the Kentish and Snowy Plovers should be conducted for their better identification.

Monophyly of the Family Desmoscolecidae (Nematoda, Demoscolecida) and Its Phylogenetic Position Inferred from 18S rDNA Sequences

  • Hwang, Ui Wook;Choi, Eun Hwa;Kim, Dong Sung;Decraemer, Wilfrida;Chang, Cheon Young
    • Molecules and Cells
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    • v.27 no.5
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    • pp.515-523
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    • 2009
  • To infer the monophyletic origin and phylogenetic relationships of the order Desmoscolecida, a unique and puzzling group of mainly free-living marine nematodes, we newly determined nearly complete 18S rDNA sequences for six marine desmoscolecid nematodes belonging to four genera (Desmoscolex, Greeffiella, Tricoma and Paratricoma). Based on the present data and those of 72 nematode species previously reported, the first molecular phylogenetic analysis focusing on Desmoscolecida was done by using neighbor joining (NJ), maximum parsimony (MP), maximum likelihood (ML) and Bayesian inference (BI) methods. All four resultant trees consistently and strongly supported that the family Desmoscolecidae forms a monophyletic group with very high node confidence values. The monophyletic clade of desmocolecid nematodes was placed as a sister group of the clade including some members of Monhysterida and Araeolaimida, Cyartonema elegans (Cyartonematidae) and Terschellingia Iongicaudata (Linhomoeidae) in all the analyses. However, the present phylogenetic trees do not show any direct attraction between the families Desmoscolecidae and Cyartonematidae. Within the monophyletic clade of the family Desmoscolecidae in all of the present phylogenetic trees, there were consistently observed two distinct subgroups which correspond to the subfamilies Desmoscolecinae [Greeffiella sp. + Desmoscolex sp.] and Tricominae [Paratricoma sp. + Tricoma sp].

Comparative Analysis of Chloroplast Genome of Dysphania ambrosioides (L.) Mosyakin & Clemants Understanding Phylogenetic Relationship in Genus Dysphania R. Br.

  • Kim, Yongsung;Park, Jongsun;Chung, Youngjae
    • Korean Journal of Plant Resources
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    • v.32 no.6
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    • pp.644-668
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    • 2019
  • Dysphania ambrosioides (L.) Mosyakin & Clemants which belongs to Chenopodiaceae/Amaranthaceae sensu in APG system has been known as a useful plant in various fields as well as an invasive species spreading all over the world. To understand its phylogenetic relationship with neighbour species, we completed chloroplast genome of D. ambrosioides collected in Korea. Its length is 151,689 bp consisting of four sub-regions: 83,421 bp of large single copy (LSC) and 18,062 bp of small single copy (SSC) regions are separated by 25,103 bp of inverted repeat (IR) regions. 128 genes (84 protein-coding genes, eight rRNAs, and 36 tRNAs) were annotated. The overall GC content of the chloroplast genome is 36.9% and those in the LSC, SSC and IR regions are 34.9%, 30.3%, and 42.7%, respectively. Distribution of simple sequence repeats are similar to those of the other two Dysphania chloroplasts; however, different features can be utilized for population genetics. Nucleotide diversity of Dysphania chloroplast genomes 18 genes including two ribosomal RNAs contains high nucleotide diversity peaks, which may be genus or species-specific manner. Phylogenetic tree presents that D. ambrosioides occupied a basal position in genus Dysphania and phylogenetic relation of tribe level is presented clearly with complete chloroplast genomes.