• 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.

• International Journal of Industrial Entomology and Biomaterials
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• v.9 no.2
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• pp.155-165
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• 2004

In Korean Peninsula including neighboring islands and Japanese Islands identical firefly species or the species belonging to same genera occur together in both territories. These geographic firefly species, nonetheless, have never been subject to taxonomic consideration together until recently, lacking clear species status and phylogenetic relationships. A recent serial study of these fireflies using luciferase gene and/or portions of mitochondrial DNA sequences provided some insight into these populations in terms of validity of species name, phylogenetic relationships, and speciation event. In this article, thus, we have reviewed the recent progress on phylogenetic and/or population genetic aspects of these species, i.e., Hotaria-group fireflies, Luciola lateralis, and Pyrocoelia rufa to better understand the firefly species in these regions.

• Proceedings of the Korean Society of Applied Entomolohy Conference
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• 2002.11a
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• pp.43-43
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• 2002

• Korean Journal of Plant Resources
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• v.27 no.6
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• pp.671-679
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• 2014

Molecular phylogenetic analyses of Korean Elaeagnus L. were conducted using seven species, one variety, one forma and four outgroups to evaluate their relationships and phylogeny. The sequences of internal transcribed spacer regions in nuclear ribosomal DNA were employed to construct phylogenetic relationships using maximum parsimony (MP) and Bayesian analysis. Molecular phylogenetic analysis revealed that Korean Elaeagnus was a polyphyly. E. umbellata var. coreana formed a subclade with E. umbellata. Additionally, the genetic difference between E. submacrophylla and E. macrophylla was very low. Moreover, E. submacrophylla formed a branch from E. macrophylla, indicating that E. submacrophylla can be regarded as a variety. However, several populations of this species were not clustered as a single clade; therefore, further study should be conducted using other molecular markers. Although E. glabra f. oxyphylla was distinct in morphological characters of leaf shape with E. glabra. But E. glabra f. oxyphylla was formed one clade by molecular phylogenetic with E. glabra. Additionally, this study clearly demonstrated that E. pungens occurs in Korea, although it was previously reported near South Korea in Japan and China. According to the results of ITS regions analyses, it showed a resolution and to verify the relationship between interspecies of Korean Elaeagnus.

• Korean Journal of Plant Taxonomy
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• v.52 no.3
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• pp.127-143
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• 2022

This study was conducted to clarify the phylogenetic position and relationships of Korean Poaceae taxa. A total of 438 taxa including 155 accessions of Korean Poaceae (representing 92% and 72% of Korean Poaceous genera and species, respectively) were employed for phylogeny reconstruction. Sequence data of eight chloroplast DNA markers were used for molecular phylogenetic analyses. The resulted phylogeny was mostly concordant with previous phylogenetic hypotheses, especially in terms of subfamilial and tribal relationships. Several taxa-specific indels were detected in the molecular phylogeny, including a 45 bp deletion in rps3 (PACMAD [Panicoideae, Arundinoideae, Chloridoideae, Micrairoideae, Aristidoideae, Danthonioideae] clade), a 15 bp deletion in ndhF (Oryzeae + Phyllorachideae), a 6 bp deletion in trnLF (Poeae s.l.), and two (17 bp and 378 bp) deletions in atpF-H (Pooideae). The Korean Poaceae members were classified into 23 tribes, representing eight subfamilies. The subfamilial and tribal classifications of the Korean taxa were generally congruent with a recently published system, whereas some subtribes and genera were found to be non-monophyletic. The taxa included in the PACMAD clade (especially Andropogoneae) showed very weak and uncertain phylogenetic relationships, presumably to be due to evolutionary radiation and polyploidization. The reconstructed phylogeny can be utilized to update the taxonomic positions of the newly examined grass accessions.

• Proceedings of the Plant Resources Society of Korea Conference
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• 2022.09a
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• pp.69-69
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• 2022

Commelinaceae (Commelinales), consist of three subfamiles and 40 genera, are distributed in the Old and New world, except Europe. This family is commonly known as dayflower and spiderwort due to their short bloom time and a viscous stem secretion. Although, several morphological and molecular analysis were conducted, the relationships among the genera are still ambiguous. The rapid advances in next-generation sequencing (NGS) enable us to do genomic research widely. Here, we assembled 12 new plastomes of Commelinaceae including Cartonematoideae and compared with previously published data. We identified pseudogened accD and rpoA in Commelinoideae taxa. Phylogenetic analysis inferred from 78 protein-coding genes showed that Rhopalephora scaberrima was nested within Aneilema. Also, there is a need to revise the subtribal relationships in Tradescantieae. This study will contribute to define the genome structures, phylogenetic and biogeographic studies of Commelinaceae.

• Korean Journal of Fisheries and Aquatic Sciences
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• v.37 no.5
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• pp.414-422
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• 2004

To infer phylogenetic relationships among Epinephelus species inhabiting coastal regions of Korean peninsula, mitochondrial cytochrome b genes from 9 species belonging to the subfamily Epinephelinae were PCR-amplified, cloned and sequenced. Aligned cytochrome b sequences of 10 species containing one additional sequence from GenBank were 1,140 base pairs in length, including 439 variable and 330 parsimony informative sites. The cytochrome b genes of 10 species, as other vertebrates studied to date, exhibit unequal base compositions: an entirely low G content ($15.2{\pm}0.3{\%}$on average) and almost equal T, C and A contents ($29.3{\pm}0.8{\%},\;30.7{\pm}1.0{\%},\;and\;24.8{\pm}0.5{\%}$ on average, respectively).In third codon positions, transitional substitutions especially between Epinephelus species and outgroup species are almost certainly saturated or near saturation. Phylogenetic analyses were performed with sequence data from 8 Epinephelus species and 2 outgroup species (Cephalopholis urodela and Vaviola louti) by using distance-based (neighbor-joining and minimum evolution) and parsimony-based (maximum parsimony) methods. The results showed that the monophyly of the genus Epinephelus was supported by relatively high bootstrap values. However, phylogenetic relationships among E. areolatus, E. moara, E. septemfasciatus, and Epinephelus sp were poorly resolved. Within the genus Epinephelus, three resolved monophyletic groups were found: clade 1 included E. akaara and E. awoara;, clade 2 included E. fasciatus and E. merra; and clade 3 included E. akaara, E. awoara, E. fasciatus, E. merra, E. areolatus, E. moara, E. septemfasciatus and Epinephelus Sp.

• Korean Journal of Plant Resources
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• v.25 no.6
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• pp.753-761
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• 2012

We performed phylogenetic analyses of a total of 21 acessions covering 5 species in the Korean Trigonotis and one outgroup species using nuclear ribosomal ITS and chloroplast rbcL, matK, ndhF sequences. Outgroup were chosen from the closely related genus Lithospermum zollingeri. Both parsimony and Bayesian Inference methods were used to reconstruct the evolutionary history of the group. The evidence collected indicated that phylogenetic relationships among Korean Trigonotis species are unresolved based on nuclear marker (ITS), as the same as based on separated chloroplast sequences. While the phylogenetic relationships of Korean Trigonotis species almost clearly were resolved in combined chloroplast sequences. Thus, the members of Trigonotis coreana can be distinguished to the members of Trigonotis peduncularis in combined cpDNA sequences and Trigonotis nakaii was treated as a synonymed to Trigonotis radicans var. sericea. In addition, the MP and BI analysis showed Trigonotis icumae as sister of the remained Korean Trigonotis species based on combined molecular markers (BI: PP = 1).

• ALGAE
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• v.22 no.2
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• pp.57-67
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• 2007

We analyzed the nuclear-encoded large subunit ribosomal RNA gene (LSU rDNA) sequences of 19 dinoflagellates occurring in costal waters off Korea and reconstructed a phylogenetic tree containing 74 representative species from 37 distinct genera. Of these, the LSU rDNA sequences of Amylax triacantha (Jörgensen) Sournia, Gonyaulax verior Sournia (= Amylax diacantha Meunier), Gyrodinium fissum (Levander) Kofoid et Swezy, Katodinium glaucum (Lebour) Lebour III, Noctiluca scintillans (Macartney) Kofoid et Swezy, Oxyphysis oxytoxoides Kofoid, and Pyrophacus steinii (Schiller) Wall et Dale are reported for the first time. Our LSU rDNA tree consistently placed Oxyrrhis marina Dujardin and N. scintillans at the most primitive positions, giving rise to a strongly supported monophyletic group of typical dinoflagellate species belonging to the Dinophyceae. The phylogenetic relationships among the typical dinoflagellates, however, were not resolved in the higher taxonomic levels in general. Only genera at terminal branches were usually supported with high confidence. The Dinophysiales, represented by Dinophysis species and O. oxytoxoides, formed a strongly supported monophyletic assemblage. The Gymnodiniales and Peridiniales were recovered as polyphyletic groupings. Members of the Gonyaulacales were consistently grouped together, but lacked statistical support. Within this order, the Ceratiaceae and Goniodomataceae each formed a monophyletic group, but the Gonyaulacaceae was polyphyletic. The phylogenetic relationships of the Gonyaulacaceae were generally congruent with differences in the combinations of the apical pore complex, hypothecal organization and thecal formula.

• Animal cells and systems
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• v.6 no.2
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• pp.145-151
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• 2002

Phylogenetic signal present in the mitochondrial 16S ribosomal RNA gene (16S rDNA) and the nuclear large subunit ribosomal RNA gene (28S rDNA) was explored to assess their utility in resolving family level relationships of the superfamily Tephritoidea. These two genes were chosen because they appear to evolve at different rates, and might contribute to resolve both shallow and deeper phylogenetic branches within a highly diversified group. For the 16S rDNA data set, the number of aligned sites was 1,258 bp, but 1,204 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1,204 sites, 662 sites were variable and 450 sites were informative for parsimony analysis. For the 28S rDNA data set, the number of aligned sites was 1,102 bp, but 1,000 bp were used for analysis after excluding sites of ambiguous alignment. Among these 1000 sites, 235 sites were variable and 95 sites were informative for parsimony analysis. Our analyses suggest that: (1) while 16S rDNA is useful for resolving more recent phylogenetic divergences, 28S rDNA can be used to define much deeper phylogenetic branches; (2) the combined analysis of the 16S and 28S rDNAs enhances the overall resolution without losing phylogenetic signal from either single gene analysis; and (3) additional genes that evolve at intermediate rates between the 16S and 28S rDNAs are needed to further resolve relationships among the tephritoid families.