• 제어로봇시스템학회논문지
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• 제17권12호
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• pp.1210-1218
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• 2011

GA (Genetic Algorithms) are efficient for searching for global optima but may have some problems such as premature convergence, convergence to local extremum and divergence. These phenomena are related to the evolutionary operators. As population diversity converges to low value, the search ability of a GA decreases and premature convergence or converging to local extremum may occur but population diversity converges to high value, then genetic algorithm may diverge. To guarantee that genetic algorithms converge to the global optima, the genetic operators should be chosen properly. In this paper, we analyze the effects of the selection operator, crossover operator, and mutation operator on convergence properties, and propose the sweeping method of mutation probability and elitist propagation rate to maintain the diversity of the GA's population for getting out of the premature convergence. Results of simulation studies verify the feasibility of using these sweeping operators to avoid premature convergence and convergence to local extrema.

• BMB Reports
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• 제46권8호
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• pp.416-421
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• 2013

Genome-wide association studies (GWAS) have become popular as an approach for the identification of large numbers of phenotype-associated variants. However, differences in genetic architecture and environmental factors mean that the effect of variants can vary across populations. Understanding population genetic diversity is valuable for the investigation of possible population specific and independent effects of variants. EvoSNP-DB aims to provide information regarding genetic diversity among East Asian populations, including Chinese, Japanese, and Korean. Non-redundant SNPs (1.6 million) were genotyped in 54 Korean trios (162 samples) and were compared with 4 million SNPs from HapMap phase II populations. EvoSNP-DB provides two user interfaces for data query and visualization, and integrates scores of genetic diversity (Fst and VarLD) at the level of SNPs, genes, and chromosome regions. EvoSNP-DB is a web-based application that allows users to navigate and visualize measurements of population genetic differences in an interactive manner, and is available online at [http://biomi.cdc.go.kr/EvoSNP/].

• Animal Bioscience
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• 제34권5호
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• pp.789-800
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• 2021

Objective: Conservation and genetic improvement of cattle breeds require information about genetic diversity and population structure of the cattle. In this study, we investigated the genetic diversity and population structure of the three cattle breeds in the Korean peninsula. Methods: Jeju Black, Hanwoo, Holstein cattle in Korea, together with six foreign breeds were examined. Genetic diversity within the cattle breeds was analyzed with minor allele frequency (MAF), observed and expected heterozygosity (HO and HE), inbreeding coefficient (FIS) and past effective population size. Molecular variance and population structure between the nine breeds were analyzed using a model-based clustering method. Genetic distances between breeds were evaluated with Nei's genetic distance and Weir and Cockerham's FST. Results: Our results revealed that Jeju Black cattle had lowest level of heterozygosity (HE = 0.21) among the studied taurine breeds, and an average MAF of 0.16. The level of inbreeding was -0.076 for Jeju Black, while -0.018 to -0.118 for the other breeds. Principle component analysis and neighbor-joining tree showed a clear separation of Jeju Black cattle from other local (Hanwoo and Japanese cattle) and taurine/indicine cattle breeds in evolutionary process, and a distinct pattern of admixture of Jeju Black cattle having no clustering with other studied populations. The FST value between Jeju Black cattle and Hanwoo was 0.106, which was lowest across the pair of breeds ranging from 0.161 to 0.274, indicating some degree of genetic closeness of Jeju Black cattle with Hanwoo. The past effective population size of Jeju Black cattle was very small, i.e. 38 in 13 generation ago, whereas 209 for Hanwoo. Conclusion: This study indicates genetic uniqueness of Jeju Black cattle. However, a small effective population size of Jeju Black cattle indicates the requirement for an implementation of a sustainable breeding policy to increase the population for genetic improvement and future conservation.

• The Plant Pathology Journal
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• 제29권4호
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• pp.435-439
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• 2013

Rice blast fungus, Magnaporthe oryzae, inflicts serious damage to global rice production. Due to high variability of this fungal pathogen, resistance of newly-released rice cultivars is easily broken down. To understand the population structure of M. oryzae, we analyzed the genetic diversity of the Korean population using multilocus microsatellite typing. Eleven microsatellite markers were applied to the population of 190 rice isolates which had been collected in Korea for two decades since the 1980's. Average values of gene diversity and allele frequency were 0.412 and 6.5, respectively. Comparative analysis of the digitized allele information revealed that the Korean population exhibited a similar level of allele diversity to the integrated diversity of the world populations, suggesting a particularly high diversity of the Korean population. Therefore, these microsatellite markers and the comprehensive collection of field isolates will be useful genetic resources to identify the genetic diversity of M. oryzae population.

• 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.

• Asian-Australasian Journal of Animal Sciences
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• 제22권1호
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• pp.1-6
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• 2009

Genetic variability is an important component in the ability of populations to adapt in the face of environmental change. Severe human impacts reduced Muzzafarnagri sheep of India from 500,000 in 1972 to 10,989 in 1973-74. Here we report for the first time the effect of this population decline on levels of genetic variability at 13 FAO recommended ovine microsatellite loci and contrast levels of variability to that in a breed from the same geographical region, which differed in numbers, by an order of magnitude (Marwari sheep). Of the 13 loci, 100% were polymorphic in both breeds. A high degree of genetic variation was observed within populations in terms of both allele diversity (number of alleles per locus, >4) and gene diversity (expected heterozygosity, >0.5), which implied that there is still a substantial amount of genetic diversity at the nuclear loci in a declining population. Nevertheless, overall low number of alleles per locus and relatively less abundance of low frequency alleles in Muzzafarnagri sheep suggested that genetic variability has been comparatively reduced in this population. Bottleneck analysis indicated that a genetic bottleneck did not occur during the most recent decline. In addition, we found that the differentiation among populations was moderate ($F_{ST}$= 11.8%). This study on assessment of genetic effects of the population declines in ovines is a step towards identification of genetically impoverished or healthy populations, which could prove to be a useful tool to facilitate conservation planning in this important species of small ruminants.

• Journal of Ecology and Environment
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• 제42권3호
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• pp.111-119
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• 2018

Background: Juniperus chinensis L. populations are distributed locally on several areas including coastal cliffs which are difficult to access in the central eastern Korea. Wild populations inhabit relatively barren environments such as rocky areas and cliffs, which are very sensitive to even minor environmental disturbances including artificial interventions and natural disturbances, and thus demonstrate great fluctuations in the population size and density. This study aims to analyze the genetic diversity, differentiation, and genetic structure of each population in order to provide useful data required to establish a substantial conservation strategy of J. chinensis. Results: The genetic diversity of J. chinensis at the population level (P = 78.7%, h = 0.282, S.I. = 0.420) was somewhat higher compared with those measured in the same genus, Juniperus. The genetic differentiation degree among nine populations established naturally in central eastern Korea was 11.50% and that among sub-populations within the same area was 5.52%. On the other hand, genetic variation of individuals within the populations was 82.93%. But frequency of the main allele was different among loci. In particular, fixation of allele frequency and occurrence of rare allele in the highly isolated population suggest a likelihood that genetic drift would occur in populations of this plant. As the result of analysis on the genetic structure of nine populations, nearby populations and isolated populations tended to form separate clusters from each other as the hypothetical number of clusters (K) increase. Conclusions: This result implies that if the population size of J. chinensis is reduced due to environmental change and artificial and/or natural disturbances in the future, it could affect negatively on the genetic diversity of the plant species. In order to maintain and conserve genetic diversity of J. chinensis, ecological network, which can help genetic exchange among the local populations, should be prepared, and conservation strategies in situ as well as ex situ are also required with continuous monitoring.

• Plant Resources
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• 제8권3호
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• pp.293-299
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• 2005

This study used RAPD markers to assume genetic diversity and variation in selected populations of Hovenia dulcis var. koreana. Ratio of polymorphic RAPD markers were 93.4% in selected populations of Hovenia dulcis Thunb., difference of genetic structure among populations and within populations showed 16.45%, 83.55%, respectively in amount of total genetic variation of 4 populations. Total gene diversity($H_T$) that show genetic diversity appeared 0.313 and coefficient of gene differentiation($G_{ST}$) that compare genetic differentiation of populations appeared 0.1645, analysis of AMOVA for variation among populations and within populations was significantly different (P<0.001). Genetic diversity of whole populations showed that 12.44% difference among population and 87.56% difference within populations. As a result, difference within populations was larger than difference among populations in genetic diversity. Nei's genetic distance and cluster analysis appeared that mean genetic distance among populations was 0.076, thus dividing two main groups and geographic relationship did not show in populations.

• Journal of Ecology and Environment
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• 제35권1호
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• pp.27-34
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• 2012

Typha angustifolia has ecological characteristics of clonal growth similar to Phragmites australis. The plant spreads byclonal growth and seed dispersal. In this study, for the three stands which have different settlement age at the Baksilji wetland in Korea, genetic diversity was estimated by random amplification of polymorphic DNA analysis to evaluate the change in genetic diversity of T. angustifolia during stand development in the same population. Stand (ST) 1 was the oldest and ST 4 was the youngest. ST 5 was in a small ditch out of the Baksilji. Although the ST 1, ST 2, and ST 3 did not differ significantly in vegetational or physical environment, the genetic diversity estimated according to Nei's gene diversity (h) and the Shannon index (i) increased in the order of ST 1 < ST 2 < ST 3 contrary to formative age. The genetic diversity of ST 4 was much higher than that of the other three stands. ST 4 has similar abiotic environmental conditions with slight T. angustifolia dominance, and seems to be in the early establishment stage. ST 5 differed from the other stands in vegetational and soil environments, which can result in stressful cattail conditions. Even though the ST 5 stand was not younger than the ST 4 stand, ST 5 showed the highest genetic diversity. Our results indicate that after early settlement of the T. angustifolia population, genetic diversity within the species decreased over time and that the decreasing pattern of genetic diversity within T. angustifolia stands is not likely to occur under stressful conditions.

• Parasites, Hosts and Diseases
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• 제56권2호
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• pp.175-181
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• 2018

The giant roundworm Ascaris infects pigs and people worldwide and causes serious diseases. The taxonomic relationship between Ascaris suum and Ascaris lumbricoides is still unclear. The purpose of the present study was to investigate the genetic diversity and population genetic structure of 258 Ascaris specimens from humans and pigs from 6 sympatric regions in Ascaris-endemic regions of China using existing simple sequence repeat data. The microsatellite markers showed a high level of allelic richness and genetic diversity in the samples. Each of the populations demonstrated excess homozygosity (Ho0). According to a genetic differentiation index (Fst=0.0593), there was a high-level of gene flow in the Ascaris populations. A hierarchical analysis on molecular variance revealed remarkably high levels of variation within the populations. Moreover, a population structure analysis indicated that Ascaris populations fell into 3 main genetic clusters, interpreted as A. suum, A. lumbricoides, and a hybrid of the species. We speculated that humans can be infected with A. lumbricoides, A. suum, and the hybrid, but pigs were mainly infected with A. suum. This study provided new information on the genetic diversity and population structure of Ascaris from human and pigs in China, which can be used for designing Ascaris control strategies. It can also be beneficial to understand the introgression of host affiliation.