Some population genetics parameters of the present Hungarian Hucul Horse population

We examined the Hungarian population of the Hucul horse breed, under genetic protection, based on population genetic indicators until the year 2014 included. The evaluation was performed using the Endog programme based on the following indicators: inbreeding coefficient, average relatedness, the maximum number of generations, the number of full generations traced and offspring number. Our findings were as follows: the average inbreeding coefficient of the total population was 5.99%, average relatedness was 11.82%, the maximum number of generations was, on the average, 16.04%, and the number of full generations traced with reference to the whole population was 4.15% on the average. 40% of the whole population (723 individuals) did not have any offspring; 42% (759 individuals) attained an offspring of 1 or 2, while 3.4% (88 individuals) had a surviving offspring of 3. The highest offspring number according to the national database (92) was attained by one stallion.

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Genetic analysis of the Hungarian population of endangered Hucul horses

Czech Journal of Animal Science ◽

10.17221/54/2017-cjas ◽

2018 ◽

Vol 63 (No. 6) ◽

pp. 237-246 ◽

Cited By ~ 2

Author(s):

E. Somogyvári ◽

J. Posta ◽

S. Mihók

Keyword(s):

Population Genetic ◽

Inbreeding Coefficient ◽

Genome Equivalent ◽

Effective Number ◽

Effective Population ◽

Horse Population ◽

Inbreeding Coefficients ◽

Hungarian Population ◽

Loss Of Genetic Diversity ◽

Reference Stock

The population genetic evaluation of the Hungarian Hucul horse population was performed based on pedigree records. Herd book data of registered Hucul horses available up to 2016 were analysed using ENDOG (Gutierrez and Goyache 2005) and POPREP (Groeneveld et al. 2009) on the whole population (WP) as well as on the reference stock (RS) (breeding stock registered in 2016). Inbreeding coefficients were 5.57% (WP) and 7.18% (RS). Average relatedness was 10.39% in WP and higher in RS (12.67%). Effective population size was 52.32. Generation interval was 13.01 years for WP and 10.99 years for RS. The values for equivalent complete generations were 6.07 and 8.75, for the maximum number of generations 14.11 and 19.16, and for the number of full generations traced 3.77 and 5.50 for WP and RS, respectively. The effective number of founders (fe) was 23 both for WP and RS. The effective number of ancestors (fa) was 20 in WP and lower in RS (16). The fa/fe ratio was 0.869 in WP and 0.696 in RS. Founder genome equivalent (fg) was 9.618 in WP and 5.790 in RS. The fg/fe ratio was 0.481 in WP and 0.361 in RS. The study revealed that both the inbreeding coefficient and the average relatedness were high. The above mentioned ratios indicated loss of genetic diversity in the Hungarian Hucul population.

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Conservation of Forest Biodiversity: how sample size affects the estimation of genetic parameters

Anais da Academia Brasileira de Ciências ◽

10.1590/0001-3765201520140064 ◽

2015 ◽

Vol 87 (2) ◽

pp. 1095-1100 ◽

Cited By ~ 4

Author(s):

Leonardo S. da Costa ◽

Nathana S. Corneleo ◽

Valdir M. Stefenon

Keyword(s):

Population Genetic ◽

Genetic Parameters ◽

Total Population ◽

Allelic Richness ◽

Inbreeding Coefficient ◽

Forest Biodiversity ◽

Forest Species ◽

Genetic Studies ◽

Minimal Sample ◽

Estimation Of Genetic Parameters

Efficient designs are crucial for population genetic studies on forest species. In this study we employed individual based simulations aiming to evaluate what fraction of a population should be sampled to obtain confident estimations of allelic richness and of inbreeding coefficient in population genetic surveys. The simulations suggest that at least 10% of the total population has to be sampled to ensure reliable estimations of allelic richness and inbreeding coefficient. This approach will allow the confidence of the genetic parameters estimations of a larger number of populations, based on a minimal sample within each one.

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Allozyme variation and an estimate of the inbreeding coefficient in the coffee berry borer, Hypothenemus hampei (Coleoptera: Scolytidae)

Bulletin of Entomological Research ◽

10.1017/s000748530005197x ◽

1995 ◽

Vol 85 (1) ◽

pp. 21-28 ◽

Cited By ~ 9

Author(s):

Philippe Borsa ◽

D. Pierre Gingerich

Keyword(s):

Genetic Diversity ◽

Population Structure ◽

Population Genetic ◽

New Caledonia ◽

Allozyme Variation ◽

Inbreeding Coefficient ◽

Hypothenemus Hampei ◽

Coffee Berry ◽

Biological Features ◽

High Degree

AbstractSeven presumed Mendelian enzyme loci (Est-2, Est-3, Gpi, Idh-l, Idh-2, Mdh-2 and Mpi) were characterized and tested for polymorphism in coffee berry borers, Hypothenemus hampei (Ferrari), sampled in Côte d′Ivoire, Mexico and New Caledonia. The average genetic diversity was H = 0.080. Two loci, Mdh-2 and Mpi were polymorphic, and thus usable as genetic markers. The population structure of H. hampei was analysed using Weir & Cockerham's estimators of Wright's F-statistics. A high degree of inbreeding (f = 0.298) characterized the elementary geographic sampling unit, the coffee field. The estimate of gene flow between fields within a country was Nm = 10.6 and that between countries was Nm = 2. The population genetic structure in H. hampei could be related to its known population biological features and history.

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Epidemiologic Study of the Discoid Meniscus: Investigating Demographic-Based Predictors in Large-Scale Claims Database

Orthopaedic Journal of Sports Medicine ◽

10.1177/2325967121s00086 ◽

2021 ◽

Vol 9 (7_suppl3) ◽

pp. 2325967121S0008

Author(s):

Sahej S Randhawa ◽

Emily P Tran ◽

Nicole A Segovia ◽

Theodore J Ganley ◽

Marc Tompkins ◽

...

Keyword(s):

Logistic Regression ◽

Total Population ◽

Clinical Care ◽

Epidemiologic Study ◽

Case Series ◽

Incidence Rates ◽

National Database ◽

Discoid Meniscus ◽

Racial Categories ◽

Claims Database

Background: Discoid meniscus epidemiology remains poorly defined for race and sex, in part, due to limitations of retrospective studies and small case series. A better understanding of epidemiology may improve clinical care and diagnostic precision. Purpose: Our purpose is to better define the epidemiology of discoid meniscus by analyzing a large, national database for incidence rates by sex and race. Methods: Analysis was conducted on the national-scale Clinformatics Data Mart Database by Optum. Proportions of the database’s racial categories (Asian, Black, Hispanic, White, and Unknown) in the total population of diagnosed discoid meniscus cases (n = 1,006) were calculated and compared via chi-squared tests to the total database population (n = 65,759,970). This analysis was repeated for the population of patients who received knee arthroscopies (81,205). Incidence rates were calculated from these populations as well. Finally, a multivariable logistic regression analysis based on the population of arthroscopy-receiving patients was performed to control for age, reported gender, and income. Results: Proportions of Asian, Black, Hispanic, and White racial categories in the discoid meniscus group were 5.7%, 7.3%, 20.6%, 66.4%, respectively; the proportions of each racial category in the total population were 5.2%, 10.3%, 13.5%, 71.0%, respectively. Incidence rates (per 10,000) for these groups in the arthroscopy population were 72.9, 25.6, 49.2, 25.6, respectively. Our logistic regression model indicated that race was not a statistically significant predictor for our dataset after income adjusting. Adjusting for other covariates, the odds of a discoid meniscus diagnosis decreased by 6% for each increase in age (p < 0.001) and were 41% lower for males compared to females (p < 0.001). Conclusion: Prior studies have suggested that race (Asian and Hispanic, is a predictor of higher incidence of discoid meniscus – this study did not show a difference in incidence based upon race. Patient sex and age was identified as significant predictors for discoid meniscus, and increasing age showed a decreasing incidence of this condition. This study’s analysis of a large, national claims database allows for a comprehensive epidemiological study on this topic, offering proportions and incidence rates by race appropriate for application to the US population. Its conclusions promote patient sex and age as significant predictors and question the beliefs on race-associated incidence often based on comparing results from the corpus of single-site cohort studies. Tables/Figures: [Table: see text]

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The patterns of the dropout of doctoral students

The Hungarian Educational Research Journal ◽

10.1556/063.9.2019.1.25 ◽

2019 ◽

Vol 9 (2) ◽

pp. 288-302

Author(s):

Fruzsina Szigeti

Keyword(s):

Social Sciences ◽

Doctoral Students ◽

Doctoral Education ◽

National Database ◽

The Past ◽

The Arts ◽

Human And Social Sciences ◽

Hungarian Population ◽

Higher Educational ◽

Informational System

Compared to the trends of the OECD countries, the proportion of graduated higher educational students is low in Hungary, especially in the doctoral education; however, the need for doctoral education has been increased due to the expansion in the past two and half decades. According to the report of the European Committee, the ratio of those having a PhD degree is 0.8 per mille among the 25- to 34-year-old Hungarian population that is not advantageous. As a causal factor, the dropout can be detected. The aim of my investigation is to detect the pattern of the dropout of the doctoral students. Who are those who quit their studies before finishing it? In which field is the ratio of graduation the lowest? I hypothesize that approximately one fifth of the students enrolled for a doctoral course quit their studies during the education. According to the educational fields, the dropout ratio is the lowest in the natural, medical, and agricultural sciences, whereas it is the highest in the arts, human, and social sciences. The basis of the current research is provided by a huge national database entitled Higher Educational Informational System, containing the data of doctoral students enrolled in the autumn semester of the school years 2010/2011 and 2014/2015.

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Why most Principal Component Analyses (PCA) in population genetic studies are wrong

10.1101/2021.04.11.439381 ◽

2021 ◽

Author(s):

Eran Elhaik

Keyword(s):

Population Genetics ◽

Population Genetic ◽

Genetic Model ◽

Principal Component ◽

Population Data ◽

Test Cases ◽

Validity Of Results ◽

Genetic Studies ◽

Minimal Loss ◽

Admixture Population

Principal Component Analysis (PCA) is a multivariate analysis that allows reduction of the complexity of datasets while preserving data's covariance and visualizing the information on colorful scatterplots, ideally with only a minimal loss of information. PCA applications are extensively used as the foremost analyses in population genetics and related fields (e.g., animal and plant or medical genetics), implemented in well-cited packages like EIGENSOFT and PLINK. PCA outcomes are used to shape study design, identify and characterize individuals and populations, and draw historical and ethnobiological conclusions on origins, evolution, whereabouts, and relatedness. The replicability crisis in science has prompted us to evaluate whether PCA results are reliable, robust, and replicable. We employed an intuitive color-based model alongside human population data for eleven common test cases. We demonstrate that PCA results are artifacts of the data and that they can be easily manipulated to generate desired outcomes. PCA results may not be reliable, robust, or replicable as the field assumes. Our findings raise concerns on the validity of results reported in the literature of population genetics and related fields that place a disproportionate reliance upon PCA outcomes and the insights derived from them. We conclude that PCA may have a biasing role in genetic investigations. An alternative mixed-admixture population genetic model is discussed.

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Case studies in molecular population genetics

A Primer of Molecular Population Genetics ◽

10.1093/oso/9780198838944.003.0009 ◽

2019 ◽

pp. 195-216

Author(s):

Asher D. Cutter

Keyword(s):

Population Genetics ◽

Case Studies ◽

Real World ◽

Population Genetic ◽

Genome Wide Association Study ◽

Molecular Genetic ◽

Raw Material ◽

Genetic Analyses ◽

Molecular Population Genetics ◽

Population Genetic Analyses

Collections of DNA from nature for many individuals and loci give us the raw material for studying evolution at the molecular level. Chapter 9, “Case studies in molecular population genetics: genotype to phenotype to selection,” dives into several case studies of exciting real-world organisms that demonstrate the application from A to Z of the concepts developed throughout the book. It includes summaries of the natural context for each organism, ranging from armoring in fish (Eda, Pitx1) and color crypsis in mice (Mc1r) to butterfly flight ability (Pgi) and toxin metabolism in Drosophila fruit flies (Cyp6g1, Adh), then walks through the molecular data, their visualization, and their analysis. Complications and caveats to real-world analysis are discussed for how to identify demographic and selective effects in empirical datasets. The approaches include both candidate gene studies and genome scans, and show how different molecular population genetic analyses work in concert with one another. These population genetic analyses also can dovetail with functional molecular genetic experiments and with genetic mapping using crosses or genome-wide association study analysis. Chapter 9 ends by introducing a summary of several advanced topics in molecular population genetics, including concepts and tests for selection on standing variation, the genomic scale of data computation and evolutionary modelling, and connections to human evolution.

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Coalescence theory for a general class of structured populations with fast migration

Advances in Applied Probability ◽

10.1017/s0001867800005280 ◽

2011 ◽

Vol 43 (04) ◽

pp. 1027-1047 ◽

Cited By ~ 4

Author(s):

O. Hössjer

Keyword(s):

Population Size ◽

General Class ◽

Population Genetic ◽

Total Population ◽

Structured Populations ◽

Effective Population ◽

Constant Change ◽

Skorokhod Topology ◽

Age Structured ◽

Dependency Structures

In this paper we study a general class of population genetic models where the total population is divided into a number of subpopulations or types. Migration between subpopulations is fast. Extending the results of Nordborg and Krone (2002) and Sagitov and Jagers (2005), we prove, as the total population sizeNtends to ∞, weak convergence of the joint ancestry of a given sample of haploid individuals in the Skorokhod topology towards Kingman's coalescent with a constant change of time scalec. Our framework includes age-structured models, geographically structured models, and combinations thereof. We also allow each individual to have offspring in several subpopulations, with general dependency structures between the number of offspring of various types. As a byproduct, explicit expressions for the coalescent effective population sizeN/care obtained.

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Multiple Linear Regression Model of Meningococcal Disease in Ukraine: 1992–2015

Computational and Mathematical Methods in Medicine ◽

10.1155/2020/5105120 ◽

2020 ◽

Vol 2020 ◽

pp. 1-7

Author(s):

Hennadii Mokhort

Keyword(s):

Linear Regression ◽

Multiple Linear Regression ◽

Meningococcal Disease ◽

Total Population ◽

Linear Models ◽

National Level ◽

Multiple Linear Regression Model ◽

National Database ◽

Linear Regression Models ◽

Susceptible Population

Estimating the rates of invasive meningococcal disease (IMD) from epidemiologic data remains critical for making public health decisions. In Ukraine, such estimations have not been performed. We used epidemiological data to develop a national database. These data were used to estimate the population susceptible to IMD and identify the prevalence of asymptomatic carriers of N. meningitidis using simple epidemiological models of meningococcal disease that may be used by the national policy makers. The goal was to create simple, easily understood analysis of patterns of the infection within Ukraine that would capture the major features of the infection dynamics. Studies used nationally reported data during 1992–2015. A logic model identified the prevalence of carriage and the proportion of the population susceptible to IMD as key drivers of IMD incidence. Multiple linear regression models for all ages (total population) and for children ≤14 years old were fit to national-level data. Linear models with the incidence of IMD as an outcome were highly associated with carriage and estimated susceptible population in both total population and children (R2 = 0.994 and R2 = 0.978, respectively). The susceptibility rate to IMD in the study total population averaged 0.0034 ± 0.0009% annually. At the national level, IMD can be characterized by the simple interaction between the prevalence of asymptomatic carriage and the proportion of the susceptible population. IMD association with prevalence rates of carriage and the proportion of susceptible population is sufficiently strong for national-level planning of intervention strategies for IMD.

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