• Animal Systematics, Evolution and Diversity
• /
• v.36 no.4
• /
• pp.336-346
• /
• 2020

Mitochondrial genome is an important molecule for systematic and evolutionary studies in metazoans. The development of next-generation sequencing (NGS) technique has rapidly increased the number of mitogenome sequences. The process of generating mitochondrial genome based on NGS includes different steps, from DNA preparation, sequencing, assembly, and annotation. Despite the effort to improve sequencing, assembly, and annotation methods of mitogenome, the low quality and/or quantity sequence in the final map can still be generated through the work. Therefore, it is necessary to check and curate mitochondrial genome sequence after annotation for proofreading and feedback. In this study, we introduce the pipeline for sequencing and curation for mitogenome based on NGS. For this purpose, two mitogenome sequences of Dermatobranchus otome were sequenced by Illumina Miseq system with different amount of raw read data. Generated reads were targeted for assembly and annotation with commonly used programs. As abnormal repeat regions present in the mitogenomes after annotation, primers covering these regions were designed and conventional PCR followed by Sanger sequencing were performed to curate the mitogenome sequences. The obtained sequences were used to replace the abnormal region. Following the replacement, each mitochondrial genome was compared with the other as well as the sequences of close species available on the Genbank for confirmation. After curation, two mitogenomes of D. otome showed a typically circular molecule with 14,559 bp in size and contained 13 protein-coding genes, 22 tRNA genes, two rRNA genes. The phylogenetic tree revealed a close relationship between D. otome and Tritonia diomea. The finding of this study indicated the importance of caution and curation for the generation of mitogenome from NGS.

• Animal Systematics, Evolution and Diversity
• /
• v.38 no.4
• /
• pp.226-237
• /
• 2022

Arcuospathidium is a haptorian ciliate genus composed of 18 species, and only one species has been reported in Korea. Here, we identify two unrecorded Arcuospathidium subspecies by morphological observation of both living and protargol-impregnated specimens with the small subunit ribosomal RNA (18S rRNA) gene sequence. These subspecies, Arcuospathidium cultriforme cultriforme (Penard, 1922) Foissner, 1984 and A. cultriforme scalpriforme (Kahl, 1930) Foissner, 2003, were isolated from various terrestrial habitats in July and August 2013, respectivley. Arcuospathidium cultriforme cultriforme is similar to A. cultriforme scalpriforme by a knife-shaped body, a twisted-shaped macronucleus, number of dorsal brushes, position of dorsal brushes, and shape of macronucleus but former mainly differs from the body length to oral bulge length ratio (27-38% vs. 41-53%), extrusome (one types vs. three types), cyst shape (roughly faceted wall vs. smooth surface and thin wall) and number of somatic kinety rows(18-30 vs. 30-44). Additionally, we analyzed the 18S rRNA gene sequences of two A. cultriforme subspecies and compared them with the sequences from GenBank to confirm their identification at the molecular level. As the results of genetic analysis, the 18S rRNA gene sequence of the Korean A. cultriforme cultriforme population is most similar to that of Austrian population. Also, the sequence of the Korean A. cultriforme scalpriforme population is most similar to that of another population with some nucleotide differences.

• 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.

• Animal Systematics, Evolution and Diversity
• /
• v.5 no.1
• /
• pp.77-88
• /
• 1989

Genetic and morphometric comparison between two species of the genus Agkistrodon were performed to estimate the degree of genic variation and to clarify the taxonomic status of Cheju population, a suspected hybrid form between A. blomhoffii brevicaudus and A u ussuriensis. A sum of 147 specimens representing six populations of A.b. brevicaudus and two populations of A ussuriensis was used in this study. Out of the 21 loci examined, 5 loci (Adh, Ldh-2, Mdh-2, Mpi, Pgi) were monomorphic with identical mobility in both species. O Other Sioci (Aco, Gp, Fum, [po and Xdh in A b. brevicaudus; Est, Got-l, Gp, Mdh-l and 6Pgd in A ussuriensis) were highly poplymorphic. The degree of genic variation of Ab. b brevicaudus and A ussuriensis was A=1.SS, P=42.1%, HD=0.096, HG=O.l1S, and A= 1.4S, P = 31.6%, HD=0.117, HG =0.121, repectively. These values are twofold higher t than those of other reptilian species reported (Selander, 1976) including Korean species of Rhabdophis tigrina and Elaphe dione (Paik and Yang, 1986, 1987). The average values of t the genetic similarities among six populations of A b. brevicaudus and two populations of A ussuriensis were S=0.919 and S=0.962, respectively, whereas the value between species was S = 0.662. Presumed divergent time estimate (Nei, 1975) of these two species was about 1 1.8 million years ago. The analysis of the geographic variations of various morphological c characters was based on Gloyd’s criteria (Gloyd, 1972). Coloration of tongue and tail tip, t the number of ventral scales, and the number of subcaudal scales are good diagnostic c characters to identify these two species. The pattern of cross band is, however, highly variable within and between populations of both species. No hybrid was detected and the s suspected hybrid form of Cheju population falls within the range of A. ussuriensis in the g genetic and morphometric analyses.

• Animal Systematics, Evolution and Diversity
• /
• v.5 no.2
• /
• pp.107-119
• /
• 1989

Three species of Korean sticklebacks family Gasterosteidae were reviewed based on the specimens of several populations for the study of their morphological variations and taxonomical positions. All specimens of Gasterosteus aculeatus observed have a complte row of lateral plates ranging from thirty-two to thirty-five in number. The low-plate morph regarded as landlocked type is virtually absent. And no difference was recognized among six populations of G. aculeatus in the meristic chracters, i.e. number of vertebrae, gill rakers and finrays. The Pungitius sinensis and P.kaibarae ssp. shown local variations have scutes ranging from 31 to 35, but not clinal in the morphometric characters. But P.sinensis was statistically different from P.kaibarae ssp. in some characters such as the number of dorsal spine rays and vertebrae, and body depth, although their ranges overlapped. No significant taxonomic difference was detected between white from and black from in dorsal spinous membrane of P.kailbarae ssp. Although these three species of Korean sticklebacks have the same diploid chromosome number (2N=42), G. aculeatus is obviously different from the two species of genus Pungitius in their karyotype ; G. aculeatus consists of six metacentrics, six submetacentrics, and thiry subtelo-acrocentrics, and both P.sinensis and P.kaibarae ssp. have four metacentrics, six submetacentrics, and thirty-four subtelo-acrocentrics.

• Animal Systematics, Evolution and Diversity
• /
• v.19 no.2
• /
• pp.167-176
• /
• 2003

This study sought to observe systematic relationships through taximetrical analyses by morphological characters among the 10 species, on three species in the virilis section (D. virilis, D. tsigana and D. lacertosa) and seven species in the quinaria section (D. angularis, D. brachvnephros, D. curvispina, D. kuntzei, D. nigromaculata, D. takadai and D. unispina) of the subgenus Drosophila. In the cluster and the cladistic analysis among the members of subgenus Drosophila, 10 species was divided into the 1st group of D. virilis, D. tsigana, and D. lacertosa and the 2nd group of D. angularis, D. brachynephros, D. curvispina, D. kuntzei, D. nigromaculata, D. takadai, and D. unispina. In cluster analysis, the 2nd group had three sister groups; one sister group that clustered D. angularis and D. brachynephros then D. unispina was clustered to them, another sister group clustered D, curvispina and D. takadai then D. kuntzei was clustered to them and the other sister group of D. nigromaculata. In the 10 species, D. virilis and D. lacertosa were the first to be divided and then D. tsigana. Although 1st group which D. virilis was belonged can be determined as more primitive than the 2nd group, it seemed that this group was not the direct ancestor of the 2nd group, rather there should be another ancestor. Among the quinaria species group, D. nigromaculata was the first to be divided and D. kuntzei was the most recent species to be divided.

• Animal Systematics, Evolution and Diversity
• /
• v.16 no.1
• /
• pp.125-131
• /
• 2000

This paper deals with the morphology and taxonomy of the first reported species of echinostome belonging to the genus Himasthla Dietz, 1909, found from dunlins (Calidris alpina sakhalina) in Korea. Birds were captured with mist-nets at the tidal flat of Yeochari, Kanghwa-gun, Kyunggi-do, Korea. The worms were removed from avian intestines in physiological saline, fixed, acetocarmine stained and observed. Himasthla kusasigi Yamaguti, which was found in 1939, was characterized morphologically by a long and slender body (5.27 mm in length), besetting with spines and reniform head collar (0.27 mm) in a form of a single and uninterrupted row of 31 spines. The oral sucker (0.057$\times$0.0684 mm) is smaller than the ventral sucker (0.35$\times$0.29 mm). The ventral sucker was close to the anterior extremity of the body. The worm had two elliptical testes (anterior 0.47$\times$0.30 mm, posterior 0.59$\times$0.27 mm). The testes were close to the posterior end of the body. The uterus was very long, winding and extending through at least two thirds of the body length. The ovary (0.13$\times$0.14mm) was round and small. Below the ovary, a round and small seminal receptacle was found.

• Animal Systematics, Evolution and Diversity
• /
• v.28 no.1
• /
• pp.48-53
• /
• 2012

The tiger population that once inhabited the Korean peninsula was initially considered a unique subspecies (Panthera tigris coreensis), distinct from the Amur tiger of the Russian Far East (P. t. altaica). However, in the following decades, the population of P. t. coreensis was classified as P. t. altaica and hence forth the two populations have been considered the same subspecies. From an ecological point of view, the classification of the Korean tiger population as P. t. altaica is a plausible conclusion. Historically, there were no major dispersal barriers between the Korean peninsula and the habitat of Amur tigers in Far Eastern Russia and northeastern China that might prevent gene flow, especially for a large carnivore with long-distance dispersal abilities. However, there has yet to be a genetic study to confirm the subspecific status of the Korean tiger. Bone samples from four tigers originally caught in the Korean peninsula were collected from two museums in Japan and the United States. Eight mitochondrial gene fragments were sequenced and compared to previously published tiger subspecies' mtDNA sequences to assess the phylogenetic relationship of the Korean tiger. Three individuals shared an identical haplotype with the Amur tigers. One specimen grouped with Malayan tigers, perhaps due to misidentification or mislabeling of the sample. Our results support the conclusion that the Korean tiger should be classified as P. t. altaica, which has important implications for the conservation and reintroduction of Korean tigers.

• Animal Systematics, Evolution and Diversity
• /
• v.21 no.1
• /
• pp.45-56
• /
• 2005

Three species of Gastrostyla ciliates collected from the sewage treatment plant and a puddle in the valley from Korea were identified as Gastrostyla minima Hemberger, 1985, G. steinii Engelmann, 1862 and G. setifera (Engelmann, 1862). The description was based on the observation of living specimens, protargol impregnated specimens and biometric analysis. The morphological variations among the populations of these species were investigated with morphometry. These species have not been reported in Korea and their diagnostic characteristics are as follows: G. minima normally has two oval macronuclei (Ma) with one spherical micronucleus (Mi) respectively, continuous ventral cirral row (VCR) with additional one postoral ventral cirrus (poVC), five transverse cirri (TC), six dorsal kineties (DK) with broken 4th kinety, and cortical granules. G. steinii has four oval Ma with three to five Mi, discontinuous VCR with additional one poVC, four TCs, six DKs, and no cortical granules. G. setifera has two oval Ma with one spherical Mi respectively, five TCs which distinctly separate in two groups, six DKs, discontinuous VCR with additional two poVCs, and no cortical granules.

• Animal Systematics, Evolution and Diversity
• /
• v.21 no.2
• /
• pp.233-241
• /
• 2005

Two new marine sponges of family Tedaniidae, Tedania (Tedon iu) songakensis n. sp. and Tedania (Tedonia) sasuensis n. sp. were collected from Jeju Island and Chuja Island, Korea between 2004 and 2005. T. (T.) songakensis n. sp. is similar to T (T.) purpurescen Bergquist and Fromont, 1988 based on its type of spicules, but is distinguished from growth form and size of small onychaetes. The growth form of this species is massive, and is compared with thin encrusting of Tedania (T.) purpurescen. The onychaetes of the new species is twice as long as that of T. (T.) purpurescen. T. (T.) sasuensis n. sp. is closely related to T. (T.) connectens (Bronsted, 1924) in type of spicules. However, it is different in size of onychaetes and growth form. The large onychaetes of new species is larger than that of T (T.) connectens. The small onychaetes of new species is smaller than that of T. (T.) connectens. The growth form is massive in new species, but thick encrustins in T.(T.) connectens. And T. (T.) songakensis n. sp. is similar to T. (T.) sasuensis n. sp. in growth form. However, the former is widely different from the latter in shape, color and size of all spicules.