• International Journal of Fuzzy Logic and Intelligent Systems
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• 제11권3호
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• pp.135-142
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• 2011

Unlike using the sequence-based representation for a chromosome in previous genetic algorithms for Bayesian structure learning, we proposed a matrix representation-based genetic algorithm. Since a good chromosome representation helps us to develop efficient genetic operators that maintain a functional link between parents and their offspring, we represent a chromosome as a matrix that is a general and intuitive data structure for a directed acyclic graph(DAG), Bayesian network structure. This matrix-based genetic algorithm enables us to develop genetic operators more efficient for structuring Bayesian network: a probability matrix and a transpose-based mutation operator to inherit a structure with the correct edge direction and enhance the diversity of the offspring. To show the outstanding performance of the proposed method, we analyzed the performance between two well-known genetic algorithms and the proposed method using two Bayesian network scoring measures.

• Animal Systematics, Evolution and Diversity
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• 제29권1호
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• pp.18-22
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• 2013

A recent study on the mitochondrial genetic variation of the Carassius auratus population in South Korea suggested that there are 3 distinct mitochondrial lineages in the country, and that they are geographically separated between westward rivers and southward rivers, respectively. In this study, the population genetic structure of amplified fragment length polymorphism (AFLP) of Carassius auratus was investigated. The results of analysis of molecular variance (AMOVA) supported the geographic distinction between westward and southward river populations, but only 3.66% of total genetic variance lies among these populations. The panmicticity of the AFLP genetic variation is backed up by the results of the neighbor-joining dendrogram drawn from a linearized pairwise $F_{ST}$ matrix and Bayesian clustering analysis. The discordance of genetic structure between mitochondrial and AFLP genetic variation may come from difference in effective population size between these markers and/or gene flow between westward and southward river populations through river capture events.

• Journal of Species Research
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• 제7권4호
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• pp.354-362
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• 2018

Population genetic assessment is essential for the conservation and management of endangered and rare plants. Neofinetia falcata is endangered epiphyte orchid and protected by law in Korea. In Korea, this species is only found on islands in the South Sea of Korea (including Jeju-do) and the southern coast of the Korean Peninsula. We developed nine microsatellite makers to assess the genetic diversity and population genetic structure of three populations of N. falcata. The genetic diversity at the species level was low, which can be attributed to inbreeding or fragmentation into small, isolated populations. A recent bottleneck was detected in one population, likely due to overcollection. N. falcata exhibited moderated levels of differentiation among populations, with the three populations were divided into two clusters based on genetic structure. The genetic diversity and structure of N. falcata are affected by restricted gene flow by pollen or seeds due to isolation and geographic distance. Strategies for in situ and ex situ conservation of this species are been proposed based on the results of our study.

• Journal of Ecology and Environment
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• 제43권4호
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• pp.454-461
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• 2019

Background: Ikonnikov's whiskered bat (Myotis ikonnikovi) is found throughout the Korean Peninsula, as well as in Kazakhstan, Russia, Mongolia, China, and Japan. It is small-sized and primarily inhabits old-growth forests. The decrease and fragmentation of habitats due to increased human activity may influence the genetic structure of bat populations. This study was designed to elucidate the population genetic structure of M. ikonnikovi using mitochondrial genes (cytochrome oxidase I and cytochrome b). Results: The results showed that M. ikonnikovi populations from Korea have high genetic diversity. Although genetic differentiation was not detected for the COI gene, strong genetic differentiation of the Cytb gene between Mt. Jeombong and Mt. Jiri populations was observed. Moreover, the results indicated that the gene flow of the maternal lineage may be limited. Conclusions: This study is the first to identify the genetic population structure of M. ikonnikovi. We suggest that conservation of local populations is important for sustaining the genetic diversity of the bat, and comprehensive studies on factors causing habitat fragmentation are required.

• Journal of Ecology and Environment
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• 제45권3호
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• pp.97-104
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• 2021

Background: Asarum sieboldii Miq., a species of forest understory vegetation, is an herbaceous perennial belonging to the family Aristolochiaceae. The metapopulation of A. sieboldii is distributed sparsely and has a short seed dispersal distance by ants as their seed distributor. It is known that many flowers of A. sieboldii depend on self-fertilization. Because these characteristics can affect negatively in genetic structure, investigating habitat structure and assessment of genetic structure is needed. A total of 27 individuals in a valley were sampled for measuring genetic diversity, genetic distance, and genetic differentiation by RAPDPCR. Results: The habitat areas of A. sieboldii metapopulation were relatively small (3.78~33.60 m²) and population density was very low (five to seven individuals in 20×20 m quadrat). The habitat of A. sieboldii was a very shady (relative light intensity = 0.9%) and mature forest with a high evenness value (J = 0.81~0.99) and a low dominance value (D = 0.19~0.28). The total genetic diversity of A. sieboldii was quite high (h = 0.338, I = 0.506). A total of 33 band loci were observed in five selected primers, and 31 band loci (94%) were polymorphic. However, genetic differentiation along the valley was highly progressed (G_st = 0.548, N_m = 0.412). The average genetic distance between subpopulations was 0.387. The results of AMOVA showed 52.77% of variance occurs among populations, which is evidence of population structuring. Conclusions: It is expected that a small-scale founder effect had occurred, an individual spread far from the original subpopulation formed a new subpopulation. However, geographical distance between individuals would have been far and genetic flow occurred only within each subpopulation because of the low density of population. This made significant genetic distance between the original and new population by distance. Although genetic diversity of A. sieboldii metapopulation is not as low as concerned, the subpopulation of A. sieboldii can disappear by stochastic events due to small subpopulation size and low density of population. To prevent genetic isolation and to enhance the stable population size, conservative efforts such as increasing the size of each subpopulation or the connection between subpopulations are needed.

• 한국산림과학회지
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• 제97권2호
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• pp.144-151
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• 2008

Using 8 isozyme polymorphic loci as gene markers, we studied the spatial distribution of genotypes in a naturally regenerated uneven-aged Eastern Siberian Fir (Abies nephrolepis Max.) stand (1ha, $100{\times}100m$) on Mt. Ohdae in northeastern South Korea. Gregorius' distograms and Moran's I correlograms revealed no evidence of significant genetic structure at three spatial classes of 5 m, 10 m, and 20 m. Extensive gene flow, due to the long distance dispersal of pollen and seeds in A. nephrolepis, may account for the lack of fine-scale spatial structure. Alternatives would be overlapping seed shadows caused by high densities of A. nephrolepis adult trees (160 trees/ha) and/or intraspecific competition resulting in extensive thinning within maternal half-sib groups.

• Proceedings of the National Institute of Ecology of the Republic of Korea
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• 제2권2호
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• pp.120-128
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• 2021

The objective of this study was to analyze the genotype of black-spotted pond frog (Pelophylax nigromaculatus) using seven microsatellite loci to quantify its genetic diversity and population structure throughout the spatial scale of basins of Han, Geum, Yeongsan, and Nakdong Rivers in South Korea. Genetic diversities in these four areas were compared using diversity index and inbreeding coefficient obtained from the number and frequency of alleles as well as heterozygosity. Additionally, the population structure was confirmed with population differentiation, Nei's genetic distance, multivariate analysis, and Bayesian clustering analysis. Interestingly, a negative genetic diversity pattern was observed in the Han River basin, indicating possible recent habitat disturbances or population declines. In contrast, a positive genetic diversity pattern was found for the population in the Nakdong River basin that had remained the most stable. Results of population structure suggested that populations of black-spotted pond frogs distributed in these four river basins were genetically independent. In particular, the population of the Nakdong River basin had the greatest genetic distance, indicating that it might have originated from an independent population. These results support the use of genetics in addition to designations strictly based on geographic stream areas to define the spatial scale of populations for management and conservation practices.

• 한국공간구조학회논문집
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• 제3권4호
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• pp.59-67
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• 2003

Genetic algorithm is one of the best ways to solve a discrete variable optimization problem. Genetic algorithm tends to thrive in an environment in which the search space is uneven and has many hills and valleys. In this study, genetic algorithm is used for solving the design problem of gable structure. The design problem of frame structure has some special features(complicate design space, many nonlinear constrants, integer design variables, termination conditions, special information for frame members, etc.), and these features must be considered in the formulation of optimization problem and the application of genetic algorithm. So, 'FRAME operator', a new genetic operator for solving the frame optimization problem effectively, is developed and applied to the design problem of gable structure. This example shows that the new opreator has the possibility to be an effective frame design operator and genetic algorithm is suitable for the frame optimization problem.

• Journal of Electrical Engineering and Technology
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• 제9권2호
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• pp.749-754
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• 2014

In this paper, we suggest tree-structure-aware GP (Genetic Programming) operators that heed tree distributions in structure space and their possible structural difficulties. The main idea of the proposed GP operators is to place the generated offspring of crossover and/or mutation in a specified region of tree structure space insofar as possible by biasing the tree structures of the altered subtrees, taking into account the observation that most solutions are found in that region. To demonstrate the effectiveness of the proposed approach, experiments on the binomial-3 regression, multiplexor and even parity problems are performed. The results show that the results using the proposed tree-structure-aware operators are superior to the results of standard GP for all three test problems in both success rate and number of evaluations.

• 제어로봇시스템학회:학술대회논문집
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• 제어로봇시스템학회 2001년도 ICCAS
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• pp.71.2-71
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• 2001

This paper deals with nonlinear system modelling using neural network and genetic algorithm. Application of neural network to control and identification is actively studied because of their approximating ability of nonlinear function. It is important to design the neural network with optimal structure for minimum error and fast response time. Genetic algorithm is getting more popular nowadays because of their simplicity and robustness. In this paper, We optimize neural network structure using genetic algorithm. The genetic algorithm uses binary coding for neural network structure and search for optimal neural network structure of minimum error and response time. Through extensive simulation, Optimal neural network structure is shown to be effective for ...