Population structure and genie diversity in tamarack, Larixlaricina (Du Roi) K. Koch

1988 ◽  
Vol 18 (10) ◽  
pp. 1318-1324 ◽  
Author(s):  
W. M. Cheliak ◽  
J. Wang ◽  
J. A. Pitel
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Population Distribution ◽  
Great Lakes Basin ◽  
Woody Perennials ◽  
Last Glaciation ◽  
Natural Range ◽  
Genic Variation ◽  
Genotypic Structure ◽  
Weinberg Expectation

Levels of electrophoretically detectable variation at 19 loci were estimated in 36 populations representing the natural range of Larixlaricina (Du Roi) K. Koch. Results of this survey indicated that the species has levels of genic variation comparable with those of other species of woody perennials with extensive transcontinental ranges. There was no evidence of significant departures from Hardy–Weinberg expectation. However, on average, populations of this species were more differentiated and more genetically divergent from one another compared with many randomly mating tree species. A discriminant analysis of the genotypic structure of the populations analyzed indicated a general east versus west pattern, with populations in the Great Lakes basin being further differentiated. Present-day population distribution, population density, and reinvasion routes after the last glaciation could account for the observed patterns of genic variation.

Genome-Wide Single Nucleotide Polymorphisms are Robust in Resolving Fine-Scale Population Genetic Structure of the Small Brown Planthopper, Laodelphax striatellus (Fallén) (Hemiptera: Delphacidae)

2019 ◽  
Vol 112 (5) ◽  
pp. 2362-2368
Author(s):  
Yan Liu ◽  
Lei Chen ◽  
Xing-Zhi Duan ◽  
Dian-Shu Zhao ◽  
Jing-Tao Sun ◽  
...  
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Structure ◽  
Population Genetic ◽  
Brown Planthopper ◽  
Fine Scale ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Small Brown Planthopper ◽  
Scale Population

Abstract Deciphering genetic structure and inferring migration routes of insects with high migratory ability have been challenging, due to weak genetic differentiation and limited resolution offered by traditional genotyping methods. Here, we tested the ability of double digest restriction-site associated DNA sequencing (ddRADseq)-based single nucleotide polymorphisms (SNPs) in revealing the population structure relative to 13 microsatellite markers by using four small brown planthopper populations as subjects. Using ddRADseq, we identified 230,000 RAD loci and 5,535 SNP sites, which were present in at least 80% of individuals across the four populations with a minimum sequencing depth of 10. Our results show that this large SNP panel is more powerful than traditional microsatellite markers in revealing fine-scale population structure among the small brown planthopper populations. In contrast to the mixed population structure suggested by microsatellites, discriminant analysis of principal components (DAPC) of the SNP dataset clearly separated the individuals into four geographic populations. Our results also suggest the DAPC analysis is more powerful than the principal component analysis (PCA) in resolving population genetic structure of high migratory taxa, probably due to the advantages of DAPC in using more genetic variation and the discriminant analysis function. Together, these results point to ddRADseq being a promising approach for population genetic and migration studies of small brown planthopper.

scholarly journals Non-Inverse J - shaped population distribution: Peculiarity of Red Sanders forests

2018 ◽  
Vol 10 (2) ◽  
pp. 11356
Author(s):  
S. Suresh Ramanan ◽  
T. K. Kunhamu
Keyword(s):  
Population Structure ◽  
Andhra Pradesh ◽  
Population Distribution ◽  
Natural Habitat ◽  
Wildlife Sanctuary ◽  
Pterocarpus Santalinus ◽  
Red Sanders ◽  
Density Population

Response to the published article "A study on the density, population structure and regeneration of Red Sanders (Pterocarpus santalinus) (Fabales: Fabaceae) in a protected natural habitat of Sri Lankamalleswara Wildlife Sanctuary, Andhra Pradesh, India" by Ankalaiah et al. 2017. 

Mitochondrial DNA Variation in Great Lakes Walleye (Stizostedion vitreum) Populations

1988 ◽  
Vol 45 (4) ◽  
pp. 643-654 ◽  
Author(s):  
Neil Billington ◽  
Paul D. N. Hebert
Keyword(s):  
Mitochondrial Dna ◽  
Reproductive Success ◽  
Great Lakes ◽  
Stizostedion Vitreum ◽  
Great Lakes Basin ◽  
The West ◽  
Dna Variation ◽  
Sequence Recognition ◽  
Last Glaciation

Mitochondrial DNA variation was examined in 141 walleye (Stizostedion vitreum) from 10 populations in the Great Lakes basin. Twenty-two hexanucleotide sequence recognition endonucleases were used, of which six (Ava I, Bst EII, Cla I, Dra I, Nco I, and Sca I) revealed polymorphisms between fish. Nine mitochondrial clones were resolved which fell into two major groups that differed in their Nco I and Sca I fragment patterns. The "A" group predominates in the eastern Great Lakes, while the "B" group predominates in the west. The geographical distribution of these two groups suggests that Great Lakes walleye persisted in at least two refugia during the last glaciation. The study revealed several rare mitochondrial genotypes which may prove useful in creating genetically marked brood stocks. Since mtDNA is maternally inherited, such markers would provide information on both the survival and long-term reproductive success of stocked fish.

scholarly journals Genetic Diversity Assessed by Genotyping by Sequencing (GBS) in Watermelon Germplasm

Genes ◽  
2019 ◽  
Vol 10 (10) ◽  
pp. 822 ◽  
Author(s):  
Kyung Jun Lee ◽  
Jung-Ro Lee ◽  
Raveendar Sebastin ◽  
Myoung-Jae Shin ◽  
Seong-Hoon Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Single Nucleotide Polymorphisms ◽  
Genetic Differentiation ◽  
Principal Components ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs

Watermelon is an economically important vegetable fruit worldwide. The objective of this study was to conduct a genetic diversity of 68 watermelon accessions using single nucleotide polymorphisms (SNPs). Genotyping by sequencing (GBS) was used to discover SNPs and assess genetic diversity and population structure using STRUCTURE and discriminant analysis of principal components (DAPC) in watermelon accessions. Two groups of watermelons were used: 1) highly utilized 41 watermelon accessions at the National Agrobiodiversity Center (NAC) at the Rural Development Administration in South Korea; and 2) 27 Korean commercial watermelons. Results revealed the presence of four clusters within the populations differentiated principally based on seed companies. In addition, there was higher genetic differentiation among commercial watermelons of each company. It is hypothesized that the results obtained from this study would contribute towards the expansion of this crop as well as providing data about genetic diversity, which would be useful for the preservation of genetic resources or for future breeding programs.

scholarly journals Migration and Selection Enforced Multiple Phenotypic and Genotypic Changes in the Population of Phytophthora infestans in Israel during the Last 36-Year Period

2020 ◽  
Author(s):  
Yigal Cohen ◽  
Avia E. Rubin ◽  
Mariana Galperin ◽  
Esti Shamaba ◽  
Uri Zig ◽  
...  
Keyword(s):  
Population Structure ◽  
Late Blight ◽  
Phytophthora Infestans ◽  
Phenylamide Fungicides ◽  
Selection Processes ◽  
Heterogeneous Nature ◽  
Oomycete Pathogen ◽  
Single Field ◽  
One Year ◽  
Genotypic Structure

Late blight caused by the oomycete pathogen Phytophthora infestans is a devastating disease of potato and tomato worldwide, including Israel. The population structure of this pathogen was monitored in potato and tomato fields in Israel during a 36-year period of 1983-2019. Isolates of the pathogen were tested for sensitivity to phenylamide fungicides, mating type, race structure, and genotype. The phenotypic and genotypic structure of the population from potato have changed greatly from one year to another, from one season to the next, within a season and within a single field. Major changes also occurred in the population collected from tomato crops. The mechanisms driving these multiple changes and the heterogeneous nature of the population in Israel are shown to derive from multiple migration events of the pathogen via seed tubers from Europe and from fitness-driven selection processes.

scholarly journals Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC) significantly improves the accuracy of predicting geographic origin of individuals

2021 ◽  
Author(s):  
Xinghu Qin ◽  
Charleston W.K. Chiang ◽  
Oscar Eduardo Gaggiotti
Keyword(s):  
Population Structure ◽  
Discriminant Analysis ◽  
Principal Components ◽  
Geographic Origin ◽  
Real Data ◽  
Fisher Discriminant Analysis ◽  
Linear Discriminant ◽  
Fisher Discriminant ◽  
Geographic Patterns ◽  
Local Fisher Discriminant Analysis

Geographic patterns of human genetic variation provide important insights into human evolution and disease. A commonly used tool to detect geographic patterns from genetic data is principal components analysis (PCA) or a hybrid linear discriminant analysis of principal components (DAPC). However, genetic features produced from both approaches are only linear combinations of genotypes, which ineluctably miss nonlinear patterns hidden in the genetic variations and could fail to characterize the correct population structure for more complex cases. In this study, we introduce Kernel Local Fisher Discriminant Analysis of Principal Components (KLFDAPC), a nonlinear approach for inferring individual geographic genetic structure that could rectify the limitations of these linear approaches by preserving the nonlinear information and the multimodal space of samples. We tested the power of KLFDAPC to infer population structure and to predict individual geographic origin using simulations and real data sets. Simulation results showed that KLFDAPC significantly improved the population separability compared with PCA and DAPC. The application to POPRES and CONVERGE datasets indicated that the first two reduced features of KLFDAPC correctly recapitulated the geography of individuals and significantly improved the accuracy of predicting individual geographic origin when compared to PCA and DAPC. Therefore, KLFDAPC can be useful for geographic ancestry inference, design of genome scans and correction for spatial stratification in GWAS that link genes to adaptation or disease susceptibility.

scholarly journals Study on the Labor Population Structure and Human Capital Accumulation Characteristics of Different Industries in China

2020 ◽  
Vol 15 (4) ◽  
pp. 210
Author(s):  
Wen Hua
Keyword(s):  
Human Capital ◽  
Population Structure ◽  
Capital Accumulation ◽  
Population Distribution ◽  
Labour Force ◽  
Training System ◽  
Security System ◽  
Human Capital Accumulation ◽  
Demographic Dividend ◽  
Structural Differentiation

Based on the data of China Labor Statistical Yearbook, this paper analyzes the characteristics of the labor population structure and human capital accumulation by industry, and finds that the labor population structure presents the following characteristics: (1) the Labour force is concentrated in service industry; (2) the proportion of labor force in emerging and high skilled industries is small; (3) there is age structure differentiation among industries. The accumulation of human capital is characterized by: (1) a shortage of human capital accumulation in productive industries; (2) a large gap in human capital accumulation in different industries. Therefore, no matter from the perspective of labor population structure or human capital accumulation, there are some structural differentiation problems among different industries, which is directly related to the enjoyment of second demographic dividend. Therefore, we must pay attention to the structural differentiation of labor population distribution and human capital accumulation among industries, and improve the education and training system, employment security system, labor mobility system as well as social security system, so as to eliminate the second demographic dividend barrier caused by structural differentiation.

Study on the dynamic impact of population characteristics on health costs – Empirical study based on the panel smooth transformation model

2021 ◽  
pp. 002072092199823
Author(s):  
Liqing Li ◽  
Mengqi Guan ◽  
Zixuan Liu
Keyword(s):  
Population Structure ◽  
Population Distribution ◽  
Education And Training ◽  
Population Characteristics ◽  
Transformation Model ◽  
Health Costs ◽  
Population Number ◽  
Per Capita ◽  
And Training ◽  
Smooth Transformation

In order to study the dynamic influence mechanism of population characteristics on health expenses, the panel data of 31 provinces, autonomous regions and municipalities directly under the Central Government (excluding Hong Kong, Macao and Taiwan) from 2009 to 2016 were used to construct panel smooth transformation model with population characteristics as heterogeneous variables for empirical analysis. The results show that the population number, population structure and population distribution have significant nonlinear effects on per capita health expenses, and the threshold values of population number, population structure and population distribution are 24.6686 million people, 6.9928%, 40.707%. When the threshold is crossed, The effect of population size on per capita health costs is reduced smoothly, The effect of population structure and population distribution on per capita health cost changed from inhibition to promotion.Therefore, according to the relationship between current population characteristics and health expenses, all regions should optimize the structure of health expenses expenditure, improve the level of health services, especially expand the scale of education and training of targeted rural medical students, strengthen the education and training of rural doctors, in order to narrow the difference between urban and rural diagnosis and treatment level.

scholarly journals Discriminant Canonical Analysis of the Contribution of Spanish and Arabian Purebred Horses to the Genetic Diversity and Population Structure of Hispano-Arabian Horses

Animals ◽  
2021 ◽  
Vol 11 (2) ◽  
pp. 269
Author(s):  
Carmen Marín Navas ◽  
Juan Vicente Delgado Bermejo ◽  
Amy Katherine McLean ◽  
José Manuel León Jurado ◽  
Antonio Rodriguez de la Borbolla y Ruiberriz de Torres ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Discriminant Analysis ◽  
Genetic Parameters ◽  
Canonical Discriminant Analysis ◽  
Canonical Analysis ◽  
Pedigree Information ◽  
Effective Solution ◽  
Negative Effects ◽  
Generation Interval

Genetic diversity and population structure were analyzed using the historical and current pedigree information of the Arabian (PRá), Spanish Purebred (PRE), and Hispano-Arabian (Há) horse breeds. Genetic diversity parameters were computed and a canonical discriminant analysis was used to determine the contributions of ancestor breeds to the genetic diversity of the Há horse. Pedigree records were available for 207,100 animals born between 1884 and 2019. Nei’s distances and the equivalent subpopulations number indicated the existence of a highly structured, integrated population for the Há breed, which is more closely genetically related to PRá than PRE horses. An increase in the length of the generation interval might be an effective solution to reduce the increase in inbreeding found in the studied breeds (8.44%, 8.50%, and 2.89%, for PRá, PRE, and Há, respectively). Wright’s fixation statistics indicated slight interherd inbreeding. Pedigree completeness suggested genetic parameters were highly reliable. High GCI levels found for number of founders and non-founders and their relationship to the evolution of inbreeding permit controlling potential deleterious negative effects from excessively frequent mating between interrelated individuals. For instance, the use of individuals presenting high GCI may balance founders’ gene contributions and consequently preserve genetic diversity levels (current genetic diversity loss in PRá, PRE, and Há is 6%, 7%, and 4%, respectively).

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