• Korean Journal of Ichthyology
• /
• v.33 no.4
• /
• pp.205-216
• /
• 2021

Phylogenetic reconstruction based on one locus or a few loci can be misleading due to gene-tree/species-tree discordance. Species delimitation and intraspecific studies also often suffered from low resolution because of insufficient statistic power when few loci were used. Exon capture method is one of the most efficient way to collect genome-scale data, which can significantly augment studies that aimed to investigate patterns and histories of organisms at both intraspecific and high level. Here, I showed the advancement of shifting from single-gene method to genomic approach and the benefit of applying exon capture method comparing to alternative genomic techniques. Then, I explained the principle of exon capture method as well as providing detailed recommendations for applying this method. Finally, I demonstrated exon capture method using two applications and discussed future perspectives of this technology.

• Journal of Ecology and Environment
• /
• v.37 no.4
• /
• pp.395-410
• /
• 2014

The genus Callophyllis is recorded as six separate species with imprecise species delimitation in Korea. To elucidate the species boundaries of Korean Callophyllis, we performed morphological observations and molecular analyses, and included three Japanese Callophyllis species from the type locality. From the results of molecular analyses using plastid rbcL and mitochondrial COI-5P genes, we confirmed ten Callophyllis species, including five cryptic ones: C. adhaerens, C. adnata, C. crispata, and C. japonica from Korea and Japan; C. hayamensis as an unrecorded species from Korea; C. cartilaginea, C. mollitia, C. repens, C. serratifolia, and C. undulata as new species from Korea. There were no Korean specimens that matched C. adnata or C. crispata from Japan, except Korean C. japonica, which formed a genetic group with the Japanese species. We obtained the interspecific divergences among the five cryptic species as 0.6-4.5% in rbcL and 2.8-8.4% in COI-5P. We recognized that the species diversity of Callophyllis has been underestimated from the northwestern Pacific region. The species boundary of Callophyllis from Korea and Japan will be a cornerstone to revealing the phylogenetic affinity of the genus distributed in both hemispheres of the western Pacific.

• ALGAE
• /
• v.27 no.4
• /
• pp.249-258
• /
• 2012

Nongeniculate coralline red algae are a common element of the Brazilian coastal zone, especially associated to coral reefs. During the course of ecological studies at Parque Municipal Marinho do Recife de Fora, two species of non-geniculate Corallinales were the major organisms covering the reef. Analyses of the vegetative and reproductive features of the species were analyzed; indicating that one new species of the genus Lithothamnion is proposed here based on the combination of several features associated with anatomy of the tetrasporangial conceptacles in relation to other species of the genus for which modern accounts are available. This new proposal along with other new species, new combinations and range extension of some species of the genus based in similar features clearly suggest that stability in species delimitation is possible. The second species found Pneophyllum conicum represents a range extension of more than 6,000 km from the Pacific in to the Atlantic Ocean suggesting that some nongeniculate species are widely distributed. The occurrence and abundance of these species supports and emphasizes the need for an extensive taxonomic reassessment of coralline red algae in the context of Brazilian coral reef biodiversity.

• Korean Journal of Plant Taxonomy
• /
• v.50 no.1
• /
• pp.22-26
• /
• 2020

Chrysosplenium aureobracteatum Y. I. Kim & Y. D. Kim (Saxifragaceae) is a recently described endemic species growing in the central part of the Korean peninsula. It requires constant monitoring for conservation due to its limited distributions. There is also a need for molecular markers for proper assessments of the genetic differentiation of C. aureobracteatum from species morphologically similar to it. In this study, we developed microsatellite markers that can be used to evaluate the genetic diversity of this species, representing fundamental data with which to conserve the natural populations of the species. A total of 17 expressed sequence tag-simple sequence repeat (EST-SSR) markers were developed by the Illumina pair-end sequencing of the transcriptomes of C. aureobracteatum. These markers were successfully applied to populations of C. aureobracteatum and to its most closely related species, C. barbatum, revealing high polymorphism in both species. The EST-SSR markers developed in this study were proven to be useful not only to monitor the population genetic structure of C. aureobracteatum for conservation purposes but also to study the genetic delimitation of the species from species closely related to it.

• ALGAE
• /
• v.34 no.4
• /
• pp.253-266
• /
• 2019

Several species classified to the genus Ulva are primarily responsible for causing green tides all over the world. For almost two decades, green tides have been resulted in numerous ecological problems along the eastern coast of Jeju Island, Korea. In order to characterize the species of Ulva responsible for causing the massive blooms on Jeju Island, we conducted DNA barcoding of tufA and rbcL sequences on 183 specimens of Ulva from eight sites on Jeju Island. The concatenated analysis identified five bloom-forming species: U. australis, U. lactuca, U. laetevirens, U. ohnoi and a novel species, U. pseudo-ohnoi sp. nov. Among them, U. australis, U. lactuca, and U. laetevirens caused to the blooms coming mainly from the substratum. U. ohnoi and U. pseudo-ohnoi sp. nov. were causative the free-floating blooms. Four species, except U. australis, are characterized by marginal teeth. A novel species, U. pseudo-ohnoi sp. nov., is clearly diverged from the U. lactuca, U. laetevirens, and U. ohnoi clade in the concatenated maximum likelihood analysis. Accurate species delimitation will contribute to a management of massive Ulva blooms based on this more comprehensive knowledge.

• Proceedings of the Plant Resources Society of Korea Conference
• /
• 2020.08a
• /
• pp.36-36
• /
• 2020

Symplocos Jacq. including about 350 species is the sole isolated genus of the family Symplocaceae. Despite poorly documented species delimitation and unresolved taxonomic nomenclature four species of Symplocos (S. coreana, S purnifolia, S sawafutagi, and S. tanakana) have been described in Korea. In this study, we carried the comparative wood anatomy of all the four species of Korean Symplocos to understand the wood anatomical variations within these four species. The result of this study indicated that Korean Symplocos are comparatively indistinguishable in terms of their qualitative wood features except for exclusively uniseriate rays present in S. purnifolia instead of uni- to- multiseriate in other three species. However, discrepancies are observed in quantitative wood variables such as vessel density, vessel size, and ray density. The vessel density of S. purnifolia (highest among the four species) is more than two times higher than the S. sawafutagi (lowest among the four species) and S. tanakana. On the other hand, vessel size is likewise reverse to the vessel number relationships i. e. vessel circumference and diameter in both planes of S. sawafutagi and S. tanakana is almost twice a larger than S. purnifolia. Interestingly, S. coreana remains in between of these two groups in terms of vessel features and closer to S. purnifolia in terms of ray density. The cluster analysis based on the paired group (UPGMA) algorithm using the Euclidean similarity index clearly differentiates S. purnifolia from the rest of the taxa representing the first isolated clade of the tree.

• Animal Systematics, Evolution and Diversity
• /
• v.28 no.4
• /
• pp.269-278
• /
• 2012

Gobiids are hyperdiverse compared with other teleost groups, with about 2,000 species occurring in marine, freshwater, and blackish habitats, and they show a remarkable variety of morphologies and ecology. Testing the effectiveness of DNA barcodes on species that have emerged as a result of radiation remains a major challenge in evolutionary biology. Here, we used the cytochrome c oxidase subunit 1 (COI) sequences from 144 species of gobies and related species to evaluate the performance of distance-based DNA barcoding and to conduct a phylogenetic analysis. The average intra-genus genetic distance was considerably higher than that obtained in previous studies. Additionally, the interspecific divergence at higher taxonomic levels was not significantly different from that at the intragenus level, suggesting that congeneric gobies possess substantial interspecific sequence divergence in their COI gene. However, levels of intragenus divergence varied greatly among genera, and we do not provide sufficient evidence for using COI for cryptic species delimitation. Significantly more nucleotide changes were observed at the third codon position than that at the first and the second codons, revealing that extensive variation in COI reflects synonymous changes and little protein level variation. Despite clear signatures in several genera, the COI sequences did resolve genealogical relationships in the phylogenetic analysis well. Our results support the validity of COI barcoding for gobiid species identification, but the utilization of more gene regions will assist to offer a more robust gobiid species phylogeny.

• Korean Journal of Plant Taxonomy
• /
• v.45 no.4
• /
• pp.306-317
• /
• 2015

This study was conducted to address the taxonomic status of the Korean endemic species Saxifraga octopetala, which is sometimes considered conspecific to Micranthes manchuriensis. Extensive molecular phylogenetic analysis using nrITS sequences as well as morphological examination of type specimens of the two species were undertaken to ascertain the phylogenetic position and species delimitation of S. octopetala. In the resulting nrITS trees, a total of 65 accessions representing S. octopetala grouped together and nested within the Micranthes clade, exhibiting a close relationship with M. nelsoniana and M. manchuriensis. Multiple accessions of M. manchuriensis collected from China and Russia also formed a clade, showing a sister group relationship with M. nelsoniana var. pacifica and M. fusca. The ambiguous species entity of S. octopetala is thought to have originated from Nakai's misinterpretation of Wilford's collection (type specimens of M. manchuriensis), which is a complex collection including an inflorescence of M. nelsoniana. In spite of apparent morphological similarity between S. octopetala and M. manchuriensis, they differ in the presence and absence of underground stolons. The distinct position of S. octopetala within the Micranthes clade on the nrITS tree suggests that it should retain species status in Micranthes. Thus a new combination (Micranthes octopetala) is proposed.

• Journal of Ecology and Environment
• /
• v.36 no.4
• /
• pp.449-463
• /
• 2013

DNA barcoding is becoming a widely applied tool to accurately discriminate red algae. We tested the effectiveness of DNA barcoding for identification and discovery of Champia species in Korea and clarified the phylogenetic relationships using the plastid rbcL gene. As results, we described four species of Champia such as C. inkyua sp. nov., C. recta Noda, C. bifida Okamura, and C. expansa Yendo. A new species, C. inkyua, is characterized by entangled thallus, terete and irregular branches, hooked apices, and longitudinal filaments running throughout the frond periphery only. Longitudinal filaments were composed of a complete cell with two half cells between diaphragms in the cavity. C. recta and C. bifida were reinstated with previously used names of C. parvula and C. compressa, respectively. C. recta is the first recorded species from Korea and is characterized by an erect thallus, terete and irregular branches, and straight apices. C. bifida is characterized by compressed thallus, pinnate or alternate branches, and bifid apices. C. expansa is characterized by flabellate thallus and dichotomous branches. Molecular analyses of COI and rbcL genes revealed sufficient sequence divergence to warrant species recognition in the genus Champia.