• Proceedings of the IEEK Conference
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• 2003.07d
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• pp.1507-1510
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• 2003

We propose UPGMA(Unweighted Pair Group Method using Average distance) as hierarchical clustering to detect abrupt shot changes using multiple features such as pixel-by-pixel difference, global and local histogram difference. Conventional $\kappa$-means algorithm which is a method of the partitional clustering, has to select an efficient initial cluster center adaptively UPGMA that we propose, does not need initial cluster center because of agglomerative algorithm that it starts from each sample for clusters. And UPGMA results in stable performance. Experiment results show that the proposed algorithm works not only well but also stably.

• Archives of Pharmacal Research
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• v.27 no.12
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• pp.1270-1274
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• 2004

Random amplified polymorphic DNA (RAPD) analysis was used to determine the genetic relationships among seventeen species of the Acanthopanax species. The DNA isolated from the leaves of the samples was used as template in polymerase chain reaction (PCR) with twenty random decamer primers in order to distinguish plant subspecies at the level of their genomes. The RAPD patterns were compared by calculating pairwise distances using Dice similarity index, and produced to the genetic similarity dendrogram by unweighted pair-group method arithmetic averaged (UPGMA) analysis, showing three groups; a major cluster(twelve species), minor cluster (4 species) and single-clustering species. The results of RAPD were compatible with the morphological classification, as well as the chemotaxonomic classification of the Acanthopanax species. The Acanthopanax species containing 3,4-seco-lupane type triterpene compounds in their leaves corresponded to the major cluster, another species having oleanane or normal lupane type constituents to minor clusters, and one species not containing triterpenoidal compound to single-cluster.

• Korean Journal of Plant Resources
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• v.26 no.6
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• pp.718-725
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• 2013

Components extracted from 7 species and 18 populations of Chrysosplenium in Korea were compared and analyzed using GC-MS analysis. 57 components (${\geq}80%$ quality) were identified, of which neophytadiene, palmitic acid and phytol were found at all the taxa. Percentage composition of isolated extracts showed a clear difference in components type and GC-MS profile. On the basis of that result, data matrix was made and cluster analysis using UPGMA was conducted. From the result of cluster analysis, two groups were recombined; one with alternate leaves comprised C. japonicum in Ser. Alternifolia and C. flagelliferum in Ser. Flagellifera and the other with opposite leaves gradationally comprised C. psuedofauriei in Ser. Sinica, C. ramosum in Ser. Oppositifolia and C. sphaerospermum, C. valdepilosum, C. flaviflorum in Ser. Pilosa. These chemotaxonomic results agreed in general with those of existing studies on external morphology and molecular. In conclusion, chemical composition can be an useful characters in understanding the relation analysis among interspecific and intraspecific complex with the help of cluster analysis of 7 species and 18 populations of Chrysosplenium in Korea.

• Journal of Korean Society of Forest Science
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• v.103 no.2
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• pp.182-188
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• 2014

Genetic diversity and genetic differentiation in six natural populations of Abies holophylla Max were investigated using ISSR marker system. From 6 ISSR primers, the average percentage of polymorphic loci was 85.6%, and the average expected heterozygosity ($H_e$) was 0.288. From the result of AMOVA, 94.4% of total genetic variation came from the differences among individuals within populations, and 5.6% was caused by those of among-populations. On the basis of Bayesian inference, genetic differentiation (${\theta}^{II}$ and $G_{ST}$) and inbreeding coefficient for all populations were 0.045, 0.038, and 0.509, respectively. The correlation between genetic distance and geographical distance was highly significant at the Mental's test (r = 0.74, P < 0.05). Six populations divided into two groups according to the results of UPGMA and PCA. One group included Namwon, Cheongdo and Mungyeong population. The other was Inje, Hongcheon and Pyeongchang population. Also, in Bayesian clustering analysis, 6 populations were divided into two clusters. But Cheongdo population was assigned into the other cluster unlike those of UPGMA or PCA. Taking the regions based on the results of the cluster analysis into consideration of AMOVA, 3.9% of genetic variation came from the regional difference. The dendrogram from UPGMA could provide the most genetically reasonable explanation for the distribution of Abies holophylla populations in South Korea.

• International Journal of Industrial Entomology and Biomaterials
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• v.41 no.2
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• pp.56-62
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• 2020

Mulberry (Morus spp. family: Moraceae) has prime importance in the sericulture industry, and its foliage is the only natural feed of the silkworm Bombyx mori L. Traditional classification methods using morphological traits were largely unsuccessful in assessing the diversity and relationships among different mulberry species because of environmental influences on the traits of interest. For these reasons, it is difficult to differentiate between the varieties and cultivars of Morus spp. In the present study, inter-simple sequence repeat (ISSR) markers were used to investigate the genetic diversity of 48 mulberry samples genotyped using nine ISSR primers. The ISSR markers exhibited polymorphisms (53.2%) among mulberry genotypes. Furthermore, similarity coefficient estimated for these ISSR markers was found to vary between 0.67 and 0.99 for the combined pooled data. The phenogram drawn using the UPGMA cluster method based on combined pooled data of the ISSR markers divided the 48 mulberry genotypes into seven major groups. No genetic association was found in the collection area, and there was a mixed pattern between the mulberry lines. The hybridization between different mulberry species is highly likely to be homogenized due to natural hybridization.

• Journal of Plant Biotechnology
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• v.42 no.4
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• pp.401-408
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• 2015

Horticultural traits and genetic relationship were evaluated for 83 melon (Cucumis melo L.) cultivars. Survey of a total of 36 characteristics for seedling, leaf, stem, flower, fruit, and seed and subsequent multiple analysis of variance (MANOVA) were conducted. Principal component analysis (PCA) showed that 8 principle components including fruit weight, fruit length, fruit diameter, cotyledon length, seed diameter, and seed length accounted for 76.3% of the total variance. Cluster analysis of the 83 melon cultivars using average linkage method resulted in 5 clusters at coefficient of 0.7. Cluster I consisted of cultivars with high values for fruit-related traits, Cluster II for soluble solid content, and Cluster V for high ripening rate. Genotyping of the 83 cultivars was conducted using 15 expressed-sequence tagged-simple sequence repeat (EST-SSR) from the Cucurbit Genomics Initiative (ICuGI) database. Analysis of genetic relatedness by UPGMA resulted in 6 clusters. Mantel test indicated that correlation between morphological and genetic distance was very low (r = -0.11).

• Korean Journal of Plant Taxonomy
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• v.34 no.3
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• pp.205-220
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• 2004

Numerical analysis based on the 67 morphological characters from 28 populations of 6 species of Korean Rhus sensu lato (Anacardiaceae) was performed for the taxonomic delimitation. Based on the results of PCA with 47 quantitative characters, the sum of contributions for the total variance of three major principal components was 77,9% (PCl 35.2%, PC2 22.5% and PC3 20.2%). The sum of contributions for the total variance of three major principal components were 90,7% (PCl 37.7%, PC2 33.0% and PC3 20.0%) based on the results of PCA with 20 qualitative The characters. Two dimensional plotting from PCA results recognized six distinct species. UPGMA phenogram based on simple matching coefficient method recognized clear taxonomic delimitations among six taxa. On the cluster analysis, qualitative characters were more useful for grouping the species treated. Numerical analysis was very valuable to delimit the Korean taxa of Rhus s.l.

• Journal of Life Science
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• v.13 no.5
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• pp.590-595
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• 2003

The objective of this study was to assess of genetic variation within and between pumpkin species including Cucurbita maxima, C. moschata, C. pepo and C. maxima${\times}$C. moschata using RAPD markers. The 16 primers showed the amplification of 136 scorable fragments ranging from about 100 bp to 2300 bp. A total of 94 DNA fragments were polymorphic with an average 5.9 polymorphic bands per primer. A species $(C. maxima\timesC. moschata)$ has the highest number of polymorphic loci. Based on obtained data, UPGMA cluster analysis was conducted. Twenty pumpkin cultivars were classified into three large categories and identified genetic distance of cluster ranging from 0.38 and 1.00. Clustering was in accordance with the division of Curcurbitaceae into four species, C. maxima, C. moschata, C. pepo and C. $C. maxima\timesC. moschata$. Therefore, RAPD method may be essential tool for enabling discrimination of pumpkin cultivars.

• Korean Journal of Plant Resources
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• v.19 no.6
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• pp.716-720
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• 2006

The genetic diversity among the genus Viola was evaluated using the random amplified polymorphic DNA (RAPD) method. A total of 142 distinct amplification fragments by 18 random primers were scored to perform the cluster analysis with UPGMA. Viola species from the subsection Patellares were clustered into group I to IV. The groups from I to IV were consistent with its morphological taxonomy, series Pinnatae, Chinensis, Variegatae, and Patellares in the subsection Patellares, respectively. Even though V. albida and V. albida var. takahasii were classified in Chinensis, they were assigned into group I. The cluster analysis separated other subsections from Patellares in the section Nomimium. Interestingly, V. verecunda and V. grypoceras in subsections Biobatae and Trigonocarpae, respectively, were clustered into group C with a high similarity coefficient. Therefore, RAPD analysis can be used for providing an alternative classification system to identify genotypes and morphological characters of Viola species.

• Korean Journal of Plant Resources
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• v.11 no.2
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• pp.210-216
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• 1998

Taxonomic studies in external morphology, principal component analysis and cluster analysis were conducted to understand the intraspecific relationship among three habitats (Jirisan, Odaesan and Ulleungdo) of allium voctorialis var. platyphyllum. External morphology such as bulb color, leaf blade length and width, petiole length, total leaf length, peduncle length, perianth lobe length and width, length of anther and filament were useful characters for identification of poplations in three habitats. The results obtained based on the principal component (Pc) analysis of treated 72 OTUs(included outgroup) were divided into three groups by the PC 1 ,2,3 and the sums of contributions for the total variance were 84.1%(PC1 51.0%, PC2 24.9% and PC3 8.2%, respectively). In cluster analysis by the UPGMA and Ward's methods , there was similarities in the compostion of clustered taxa, and only Ulleungdo population was distinctly identified from population of other two habitats.