• Proceedings of the Plant Resources Society of Korea Conference
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• 2012.05a
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• pp.19-19
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• 2012

The Colchicaceae comprising 250 species and 15-19 genera of rhizomatous or cormous perennials, the moderate sized family in Liliales, distributes widely through the temperate and tropical areas of Africa, Asia and North America. The division of two subfamilies in Colchicaceae is still unclear because of different results in previous studies. Moreover, sister taxa of this family has not been determined. In genus level, it was uncertain that whether expand circumscription of three genera of Colchicum, Gloriosa, and Wurmbea which are include Androcymbium, Littonia and Onixotis, respectively, is reasonable or not. In this study, three coding genes of atpB, matK and rbcL were analyzed to reconstruct phylogenetic relationship of Colchicaceae and both of maximum parsimony (MP) and Bayesian analysis were conducted. Among three genes, matK region was most variable and provided more parsimony-informative sites, whereas the atpB and rbcL regions were similar in the variation and number of informative characters. Monophyly of Colchicaceae was strongly supported and it was divided into two subfamilies (Wurmbeoideae and Uvulariodeae). Uvularia-Disporum clade, comprises the subfamily Uvularioideae, is a sister of the rest Colchicaceae and subsequently differentiated Burchardia was a sister within subfamily Wurmbeoideae. Burchadia was used to be supposed to be a sister of the family in the previous studies. It was clear the monophyly and phylogenetic relationship among six tribes sensu Vinnersten and Manning (2007) within the family. In addition, the expanded circumscription of three genera was also strongly supported; Colchicum-Androcymbium (BP99), Wurmbea-Onixotis (BP100), and Littonia-Gloriosa (BP100). Here, we propose a re-circumscription among taxa of Colchicaceae.

• Journal of Life Science
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• v.18 no.6
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• pp.759-763
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• 2008

Halophila ovalis (R. Br.) Hook. fil. was first collected from the Ando, Yeosu, Korea in 2007. H. ovalis is Widely distributed from sub-tropical to even tropical areas and produces the seeds using bisexual reproduction. Its leaf shape was oblong to ovate. Its leaf blades were rigid in texture, with a strong support to the leaf. Erect shoots arose at irregular intervals along the rhizome. The distance between the intramarginal vein and leaves margin was small. Nucleotides in ITS 1 and ITS 2 regions between the Korean and Japanese H. ovalis were found to be 100% similar, whereas Korean H. ovalis was found to have four nucleotides in the positions of 202 bp to 206 bp for 5.8S. In the analysis of the phylogenetic relationship using NJ method, Korean H. ovalis had a monophyletic genetic tree with Japanese H. ovalis, but no phylogenetic relationship with types from the Philippines, Australia, Malaysia, and Vietnam. The first occurrence of H. ovalisin Korea was associated with a strong migration of gene flow from Japan and high water temperature caused by the variations in climate.

• Asian-Australasian Journal of Animal Sciences
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• v.32 no.2
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• pp.176-182
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• 2019

Objective: This study was conducted to investigate basic information on genetic structure and characteristics of Limousin population in Hungary. Obtained results will be taken into consideration when adopting the new breeding strategy by the Association of Hungarian Limousin and Blonde d'Aquitaine Breeders (AHLBB). Methods: Genetic diversity and phylogenetic relationship of 3,443 Limousin cattle from 16 different herds were investigated by performing genotyping using 18 microsatellite markers. Amplified DNA was genotyped using an automated genetic analyzer. Results: Mean of effective alleles ($n_e$) of the populations was 3.77. Population C had the lowest number of effective alleles (3.01) and the lowest inbreeding coefficient ($F_{IS}$) value (-0.15). Principal component analysis of estimated genetic distance ($F_{ST}$) values (p<0.000) revealed two herds (C and E) distinct from the majority of other Limousin herds. The pairwise $F_{ST}$ values of population C compared to the others (0.066 to 0.120) fell into the range of moderate genetic distance: 0.050 to 0.150, while population E displayed also moderate genetic distance ($F_{ST}$ values in range 0.052 to 0.064) but only to six populations (G, H, J, L, N, and P). $F_{ST(C-E)}$ was 0.148, all other pairs -excluding C and E herds- displayed low genetic distance ($F_{ST}$<0.049). Population D, F, I, J, K, L, N, O, and P carried private alleles, which alleles belonged to 1.1% of the individuals. Most probable number of clusters (K) were 2 and 7 determined by Structure and BAPS software. Conclusion: This study showed useful genetic diversity and phylogenetic relationship data that can be utilized for the development of a new breeding strategy by AHLBB. The results presented could also contribute to the proper selection of animals for further whole genome scan studies of Limousins.

• The Korean Journal of Malacology
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• v.27 no.4
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• pp.395-400
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• 2011

Phylogenetic analyses on the Phylum Mollusks has so far been conducted by many researchers in the world. However, there was no report on taxonomic analysis on Acila divaricata vigila which is belonging to Class Bivalvia, Subclass Protobranchia. In this study, we performed molecular phylogenetic analysis on Acila divaricata vigila using 16S rRNA sequence through maximum likelihood method. As a result, it is clearly divided into the legion of mollusk classification unit (when you zoom in order) and represented to support the current classification in the Phylum Mollusca belong to Class Bivalvia, Subclass Protobranchia, Subclass Pteriomorphia, Subclass Paleoheterodonta, Subclass Heterodonta and Subclass Anomalodesmacea. To our knowledge, this is the first report of molecular phylogenetic analysis on Acila divaricata vigila using 16S rRNA gene and these data suggests that 16S rRNA gene will be useful for analyzing the phylogenetic relationship of Subclass Protobranchia.

• Journal of fish pathology
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• v.22 no.3
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• pp.211-218
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• 2009

In this study, we have compared the genome of marine birnavirus (MABV) detected from starry flounder Platichthys stellatus and olive flounder Paralichthys olivaceus. A molecular analysis based on the nucleotide sequence (433 bases) of VP2-NS-VP3 region revealed that MABV (08-KU) from starry flounder showed 98% similarity with MABV Y6 isolated from Yellowtail Seriola quinqueradita in Japan (Accession no: AY283781) and with other aquabirnaviruses identify more than 76%. Comparison with MABV strains (06-KP, 08-KC) from olive flounder and MABV Y6 strain showed 97-98% sequence identities. Phylogenetic analysis was performed in order to examine the relationship among previously determined aquatic birnaviruses isolates showed that MABV and IPNV strains were classified into seven clusters. Three isolates from starry flounder and olive flounder in this study, belong to the genogroup VII including MABV Y6 strain and other aquabirnaviruses isolated from marine fish and molluscan shellfish in Japan. This report is the first description of a MABV from starry flounder in Korea.

• Journal of Life Science
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• v.21 no.7
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• pp.939-946
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• 2011

Sequence data of Cytochrome Oxidase Subunit I (COI) gene of mitochondria were used to elucidate the taxonomy and phylogenetic relationships of the terrestrial planarian taxa in Korea. Published COI gene sequences from Family Bipaliidae in GenBank were also included in the phylogenetic analysis. The aligned data sets for Terricola ranged from 387 to 444 nucleotides (bp) as a result of differences in insert nucleotides. The phylogeny based on COI analysis was not congruenced with the morphological traits. Bipalium nobile included the remainder taxa (Bipalium adventitium, Bipalium venosum, Bipalium kewense, and Bipalium multilineatum). Internal nodes were strongly supported (>91%). The phylogenetic tree on COI analysis showed that most identified species were well separated from each other. The main phylogenetic analysis formed monophyletic groups. COI gene of mitochondria could have the resolving power for taxonomy information for the terrestrial planarian taxa in Korea.

• Korean Journal of Oriental Medicine
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• v.14 no.1
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• pp.129-135
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• 2008

Phylogenetic relationship and DNA polymorphism among local populations of the Asparagus cochinchinensis have been investigated based on nuclear ribosomal DNA ITS sequences and RAPD analysis in Korea. In result, two genetically distinct groups of local populations except Geoje were recognized by the phylogenetic tree both in rDNA-ITS and RAPD. One was called 'western coast group' that includes the Buan 1, 2 and Taean and the other was 'southern coast group' that includes Haenam, Yeosu and Namhae. Thus, the geographical relationship of Asparagus cochinchinensis was two well-typified clades. These results suggest that the geographical genetic variation of Asparagus cochinchinensis is closely connected with the slow and long period of propagation via the coast in Korean Peninsula.

• Asian-Australasian Journal of Animal Sciences
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• v.20 no.12
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• pp.1783-1790
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• 2007

The genetic diversity of domestic quail and two wild quail species, Japanese （Coturnix coturnix）and Common quail (Coturnix japonica), found in China was studied using microsatellite DNA markers. According to a comparison of the corresponding genetic indices in the three quail populations, such as Polymorphism Information Content (PIC), Mean Heterozygosity ($\bar{H}$) and Fixation Index, wild Common quail possessed rich genetic diversity with 4.67 alleles per site. Its values for PIC and $\bar{H}$ were the highest, 0.5732 and 0.6621, respectively. Domestic quail had the lowest values, 0.5467 and 0.5933, respectively. Wild Japanese quail had little difference in genetic diversity from domestic quail. In addition, from analyses of the fuzzy cluster based on standard genetic distance, the similarity relationship matrix coefficient between wild Japanese quail and domestic quail was 0.937, and that between wild Common quail and domestic quail was 0.783. All of these results showed that the wild Japanese quail were closer to the domestic quail for phylogenetic relationship than wild Common quail. These results at the molecular level provide useful data about quail's genetic background and further supported the hypothesis that the domestic quail originated from the wild Japanese quail.

• Journal of Forest and Environmental Science
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• v.32 no.3
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• pp.291-301
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• 2016

One of the most concerned topics in ecology is the relationship between biodiversity and ecosystem functioning. However, there are few field studies, carried out in forests, although many studies have been done in controlled experiments in grasslands. In this paper, we describe the relationship pattern between three facets of diversity and productivity at Ratargul Fresh Water Swamp Forest (RFWSF) in Bangladesh, which is the only remaining fresh water swamp forest of the country. Sixty sample plots were selected from RFWSF and included six functional traits including leaf area (LA), specific leaf area (SLA), leaf dry matter content (LDMC), tree height, bark thickness and wood density. In analyzing TD, we used Shannon diversity and richness indices, functional diversity was measured by Rao's quadratic entropy (Rao 1982) and Faith's (1992) index was used for phylogenetic diversity (PD). It was found that, TD, FD and PD were positively related with productivity (basal area) due to resource use complementarity but surprisingly the best predictor of tree productivity was FD. The results contribute to the understanding the effects of biodiversity loss and it is essential for conservation decision-making and policy-making of Ratargul Fresh Water Swamp Forest.

• Korean Journal of Ichthyology
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• v.18 no.4
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• pp.293-299
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• 2006

Copper,zinc superoxide dismutase (Cu,Zn-SOD) plays a key role to the first antioxidant defense system against oxidative stress in diverse aerobic organisms. Due to the housekeeping action of Cu,Zn-SOD, it was reported that the structure and function have been conserved during evolution. In this study Cu,Zn-SOD from cloudy catshark Scyliorhinus torazame was subjected to phylogenetic analyses to know its evolutionary relationship in the vertebrate lineage. Molecular phylogenetic trees inferred by NJ, MP, ML and/or Bayesian analyses showed two shark species, Prionace glauca and S. torazame grouped together with high statistical supports. In general, they placed at the separated position from bony vertebrates. Thereafter, bony vertebrates composed of teleosts and birds/mammals (amniotes) formed a monophyletic group. Each teleost and amniote clade was also supported by relatively high statistical values. These phylogenetic relationships are well congruent with the phylogenetic hypothesis of the ancestral position of cartilaginous fishes to bony vertebrates.