Phylogenetic analysis of Neottia japonica (Orchidaceae) based on ITS and matK regions

소지현,이남숙 한국식물분류학회 2020 식물 분류학회지 Vol.50 No.4

To elucidate the molecular phylogeny of Neottia japonica, which is a terrestrial orchid distributed in East Asia, the internal transcribed spacer (ITS) of nuclear DNA and the matK of chloroplast DNA were used. A total 22 species of 69 accessions for ITS and 21 species of 114 accessions for matK phylogeny were analyzed with the maximum parsimony and Bayesian methods. In addition, we sought to establish a correlation between the distribution, morphology of the auricles and genetic association of N. japonica with phylogenetic data. The phylogenetic results suggest that N. japonica is monophyletic and sister to N. suzukii in ITS phylogeny, while it is paraphyletic with N. suzukii in matK phylogeny. Neottia japonica and N. suzukii show similar morphologies of the lip and column. They both flower in April, and are distributed sympatrically in Taiwan. Therefore, it appears to be clear that N. japonica and N. suzukii are close taxa within Neottia, although there is incongruence between the nrDNA and cpDNA phylogenies of N. japonica. The incongruence between the two datasets may have various causes, meaning that further studies are needed to confirm the evolutionary process of N. japonica. The phylogenetic status of N. kiusiana, which was not included in previous studies, was as a sister to N. nidus-avis. Meanwhile, the ITS and matK phylogenies are unsuitable for identifying genetic associations with the characteristic of auricles. The phylogenetic topologies of Korean, Taiwanese and mainland Chinese individuals suggest that the populations of N. japonica in Korea originated from China’s mainland and island areas. The characterization of regional gene differences could provide useful preliminary data for future studies.

Molecular Phylogeny of the Genus Hypericum (Hypericaceae) from Korea and Japan: Evidence from Nuclear rDNA ITS Sequence Data

( Seon Joo Park ),( Ki Joong Kim ) 한국식물학회 2004 Journal of Plant Biology Vol.47 No.4

As part of our ongoing phylogenetic study of genus Hypericum, nuclear ribosomal DNA internal transcribed spacer sequences were analyzed for 36 species of Hypericum as ingroup and two species of Thornea as outgroup. This sampling included most of the previously described species from both Korea and Japan. The ITS phylogeny suggested that the surveyed Hypericum species belong to a monophyletic section, Trigynobrathys, and a polyphyletic section, Hypericum. In addition, two monotypic sections, Sampsonia and Roscyna, were identified. Members of section Hypericum occur in four different lineages worldwide, which imply at least four independent origins. The Korean and Japanese species of section Hypericum form a monophyletic group, except for H. vulcanicum. Instead, that particular species belongs to a distinct monophyletic group with H. scoreri and H. formosa from other geographic areas, and is a sister to section Trigynobrathys. The Korean and Japanese species of section Trigynobrathys show a monophyletic origin. H. sampsonii is now recognized as a distinct section rather than being a member of sections Hypericum or Drosocarpium, as had been indicated previously. Our results differ somewhat from those of recent morphological and cytological studies. The phylogenetic relationships among Korean and Japanese species have now been mostly resolved via ITS phylogeny.

Bayesian Inference in Phylogeny via Sequential Stochastic Approximation Monte Carlo

전수영,김효성 한국자료분석학회 2009 Journal of the Korean Data Analysis Society Vol.11 No.3

The Sequential Stochastic approximation Monte Carlo(SSAMC) algorithm has recently been proposed by Cheon and Liang(2008) as a new phylogenetic tree construction method. SSAMC is an efficient algorithm to alleviate local trap problems and the curse of dimensionality in simulations simultaneously by making use of the sequential structure of phylogenetic trees in conjunction with stochastic approximation Monte Carlo(SAMC) simulations. In this paper, we discuss the application of SSAMC to the Bayesian inference in phylogeny. Two real datasets are used for SSAMC to show the capability of a phylogeny tree reconstruction and existing Bayesian methods, BAMBE and MrBayes, are applied for comparison. Numerical results indicate that SSAMC is a useful algorithm for phylogeny inference in terms of quality of the resulting phylogenetic trees.

A mitochondrial genome phylogeny of Mytilidae (Bivalvia: Mytilida)

Lee, Yucheol,Kwak, Haena,Shin, Jinkyung,Kim, Seung-Chul,Kim, Taeho,Park, Joong-Ki Academic Press 2019 Molecular phylogenetics and evolution Vol.139 No.-

<P><B>Abstract</B></P> <P>The family Mytilidae is a family of bivalve mussels that are distributed worldwide in diverse marine habitats. Within the family, classification systems and phylogenetic relationships among subfamilies remain not yet fully resolved. In this study, we newly determined 9 mitochondrial genome sequences from 7 subfamilies: <I>Bathymodiolus thermophilus</I> (Bathymodiolinae), <I>Modiolus nipponicus</I> (Modiolinae), <I>Lithophaga curta</I> (the first representative of Lithophaginae), <I>Brachidontes mutabilis</I> (Brachidontinae), <I>Mytilisepta virgata</I> (Brachidontinae), <I>Mytilisepta keenae</I> (Brachidontinae), <I>Crenomytilus grayanus</I> (Mytilinae), <I>Gregariella coralliophaga</I> (Crenellinae), and <I>Septifer bilocularis</I> (the first representative of Septiferinae). Phylogenetic trees using maximum likelihood and Bayesian inference methods for 28 mitochondrial genomes (including 19 previously published sequences) showed two major clades with high support values: Clade 1 ((Bathymodiolinae + Modiolinae) + (Lithophaginae + Limnoperninae)) and Clade 2 (((Mytilinae + Crenellinae) + Septiferinae) + Brachidontinae). The position of the genus <I>Lithophaga</I> (representing Lithophaginae) differed from a previously published molecular phylogeny. Divergence time analysis with a molecular clock indicated that lineage splitting among the major subfamilies of Mytilidae (including the habitat transition from marine to freshwater environments by ancestral Limnoperninae) occurred in the Mesozoic period, coinciding with high diversification rates of marine fauna during that time. This is the first mitochondrial genome-based phylogenetic study of the Mytilidae that covers nearly all subfamily members, excluding the subfamily Dacrydiinae.</P> <P><B>Highlights</B></P> <P> <UL> <LI> The phylogenetic relationships among subfamilies of the Mytilidae are uncertain. </LI> <LI> A mitochondrial genome phylogeny was reconstructed for 27 mytilid species. </LI> <LI> The phylogeny shows two major clades that have diverged in the Devonian. </LI> <LI> The splitting time among the major subfamilies occurred in the Mesozoic period. </LI> </UL> </P> <P><B>Graphical abstract</B></P> <P>[DISPLAY OMISSION]</P>

Complete Mitochondrial Genomes of the Caddisflies (Trichoptera): an Implication for Lepidopteran Phylogeny

Min Jee Kim,Iksoo Kim 한국응용곤충학회 2014 한국응용곤충학회 학술대회논문집 Vol.2014 No.10

The sister relationship between Trichoptera and Lepidoptera has often been supported in a diverse study, but mitochondrial genomes (mitogenomes) based lepidopteran phylogenetic studies have never utilized Trichoptera as outgroup mainly due to unavailability. Therefore, the effect of alternatives that were previously used (e.g., Diptera, Hymenoptera, and Orthoptera) or Trichoptera as outgroups on the lepidopteran phylogeny remained unknown. In this study, we sequenced three complete mitogenomes of Trichoptera belonging to two suborders and characterized the genomic features of Trichoptera and tested the outgroup effect for lepidopteran phylogeny. The 15,208 ~ 15,285-bp long caddisfly mitogenomes harbor gene content typical of the animal mitogenomes. The orientation and gene order of the three species belonging to the suborder Integripalpia was identical to that of the most common type that has been hypothesized as ancestral for insects, but Cheumatopsyche brevilineata belonging to another suborder Annulipalpia has rearranged QIM, all encoded in forward direction between the A+T-rich region and ND2, instead of the ancestral IQM, with Q inverted. Further, the annulipalpian species had a typical start codon ATG, instead of CGA that are commonly found in other trichopteran species and majority of Lepidoptera. Phylogenetic analysis with different outgroups (Diptera, Hymenoptera, and Orthoptera, Coleoptera, and Trichoptera) and 115 lepidopteran mitogenomes has shown insensitivity either with Trichoptera, Diptera, or Coleoptera, but artificial grouping and lowered nodal support were found with Hymenoptera. The Trichoptera-based consensus topology were: (((((((Bombycoidea + Noctuoidea) + Pyraloidea) + Papilionoidea) + Cossoidea) + Tortricoidea) + Yponomeutoidea) + Hepialoidea).

UACG: Up-to-Date Archaeal Core Genes and Software for Phylogenomic Tree Reconstruction

Na Seong-In,Bailey Michael James,Chalita Mauricio,Cho Jae Hyoung,Chun Jongsik 한국미생물학회 2023 The journal of microbiology Vol.61 No.7

In the post-genomic era, phylogenomics is a powerful and routinely-used tool to discover evolutionary relationships between microorganisms. Inferring phylogenomic trees by concatenating core gene sequences into a supermatrix is the standard method. The previously released up-to-date bacterial core gene (UBCG) tool provides a pipeline to infer phylogenomic trees using single-copy core genes for the Bacteria domain. In this study, we established up-to-date archaeal core gene (UACG), comprising 128 genes suitable for inferring archaeal phylogenomic trees. To test the gene set, we selected the Haloarcula genus and scrutinized its phylogeny. The phylogeny inferred using the UACG tool was consistent with the orthoANIu dendrogram, whereas the 16S rRNA gene phylogeny showed high intragenomic heterogeneity resulting in phylogenetic discrepancies. The software tool using the UACG set is available at https:// www. ezbio cloud. net/ tools/ uacg.

최대가능도와 베이즈 붓스트랩 방법을 이용한 생물계통수 추정

김명숙,이정형 한국자료분석학회 2010 Journal of the Korean Data Analysis Society Vol.12 No.4

It is very important to evaluate a reliability of phylogenetic relationships among diverse taxa in the estimation of phylogeny. Bootstrapping(BT) is a method for certainty of phylogeny which is retested within existing data matrix in random sampling by repetition from DNA sequence data. In this paper, to confirm monophyletic clade in phylogeny using bootstrap, we examine an efficiency of bootstrap method used maximum likelihood(ML) and Bayesian analysis for estimation and hypothesis testing. The materials of rbcL DNA sequences are produced from 45 species of red algal genus Gracilaria and selected GTR+I+GAMMA as a molecular evolutionary model for ML and Bayesian BT. As a result, Gracilaria textorii, Gracilaria pavispora, Gracilaria vermiculophylla and Gracilariopsis chorda are supported a monophyletic clade with 100 credibility of BT. In addition, Gracilaria chorda has to be changed the genus to Gracilariopsis chorda. 다양한 분류군들의 계통학적 유연관계를 보여주는 생물계통수의 추정에 있어서 신뢰도를 평가하는 것은 매우 중요하다. 비교 분류군의 수에 따라서 증가하는 수 많은 계통수의 확실성을 평가하는 한 가지 방법으로 붓스트랩이 있다. 붓스트랩은 DNA 자료를 무작위로 반복 추출하여 원래의 자료행렬을 재분석하는 방법이다. 본 논문은 붓스트래핑이 생물계통수의 특정 절 또는 분지에서 단계통성을 어느 정도로 나타내는지 알아보기 위하여, 최대가능도(maximum likelihood: ML)와 Bayes 분석법에서 생물계통의 추정과 가설검정을 위해 사용되었던 BT 방법의 효율성에 대해 살펴보았다. 구체적인 대상 분류군은 홍조류 Gracilaria 45종의 rbcL 염기서열 자료를 이용하였고, ML과 Bayes BT 계통수 추정을 위한 분자진화 모형은 GTR+I+GAMMA이 선택되었다. 홍조류 Gracilaria 속의 생물계통수를 추정한 결과 G. pavispora와 G. textorii의 분지형태가 다른 점을 제외한 나머지 Gracilaria textorii, Gracilaria vermiculophylla, Gracilariopsis chorda 등은 BT 신뢰도 100의 단계통군으로 나타나 기존의 연구 결과와 일치하며, 또한 Gracilaria chorda가 Gracilariopsis chorda로 재분류되어짐을 확인할 수 있었다.

Small-subunit Ribosomal DNA of an Ectomycorrhizal Fungus Tricholoma matsutake : Sequence, Structure, and Phylogenetic Analysis

Hwang, Seon-Kap,Kim, Jong-Guk Korean Society of Molecular Biology 1998 Molecules and cells Vol.8 No.3

Phylogeny and systematics of Crossosomatales as inferred from chloroplast atpB, matK, and rbcL sequences

오상훈 한국식물분류학회 2010 식물 분류학회지 Vol.40 No.4

Crossosomatales is a recently recognized order in the rosid II clade with about 64 species in eight morphologically distinct families that have been previously classified in as many as 15 other orders. Phylogenetic relationships among the families and genera within Crossosomatales were investigated using chloroplast atpB, matK, and rbcL sequences employing maximum parsimony, maximum likelihood, and Bayesian methods. The phylogenetic framework was used to examine the patterns of morphological evolution and synapomorphies for subclades within Crossosomatales. The combined data with representative species from all genera in the order strongly supported monophyly of Crossosomatales. Strong support was found for the families in the Southern Hemisphere, in which Aphloiaceae is sister to the clade of (Geissolomataceae, (Ixerbaceae + Strasburgeriaceae)). The sister relationship between the Southern Hemisphere clade and families distributed primarily in the Northern Hemisphere was also supported. As in the previous studies, following relationships were found within the Northern Hemisphere clade: Staphyleaceae is sister to a clade of (Guamatelaceae, (Stachyuraceae + Crossosomataceae)). The pattern analysis indicates that evolutionary pattern of morphological characters is complex, requiring multiple changes within Crossosomatales. Several reproductive traits, such as inflorescence, aril, stigma, and conspicuous protrusion from pollen aperture, corroborate the molecular phylogeny.

UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction

나성인,김영욱,윤석환,하성민,백인우,천종식 한국미생물학회 2018 The journal of microbiology Vol.56 No.4

Genome-based phylogeny plays a central role in the future taxonomy and phylogenetics of Bacteria and Archaea by replacing 16S rRNA gene phylogeny. The concatenated core gene alignments are frequently used for such a purpose. The bacterial core genes are defined as single-copy, homologous genes that are present in most of the known bacterial species. There have been several studies describing such a gene set, but the number of species considered was rather small. Here we present the up-to-date bacterial core gene set, named UBCG, and software suites to accommodate necessary steps to generate and evaluate phylogenetic trees. The method was successfully used to infer phylogenomic relationship of Escherichia and related taxa and can be used for the set of genomes at any taxonomic ranks of Bacteria. The UBCG pipeline and file viewer are freely available at https://www.ezbiocloud.net/ tools/ubcg and https://www.ezbiocloud.net/tools/ubcg_viewer, respectively.