Population Genetics

A. Amorim , in Brenner's Encyclopedia of Genetics (Second Edition), 2013

Definition and Scope

Population genetics can be broadly and simply defined as the branch of genetics dealing with the description of observed or inferred heritable features in populations through space and time. This definition albeit comprehensive conceals a very deep formal heterogeneity. In fact, population genetics theory and models are quite different according to the type of reproduction of the organism under study: in the case of exclusively asexual reproduction mode, the study of the population heritable properties is obviously simpler and the number of parameters required for description and prediction are a subset of those needed for the analysis of sexually reproducing organisms. Furthermore, population genetics can be dealt with in purely theoretical terms or in a wide range of applications, such as in forensics or in wildlife management. Finally, population genetics approaches can be split into two according to the type of variation studied: Mendelian (limited to traits showing a discontinuous distribution in the population, such as blood groups) or quantitative, in which it is impossible to classify the individuals in discrete classes, as in measurable characteristics (height, weight, etc.).

Here, we will limit ourselves to the theoretical framework of population genetics under the Mendelian approach and, unless otherwise stated explicitly, to the diploid model of sexual reproduction.

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Population Genetics

Conrad J. Burden , in Encyclopedia of Bioinformatics and Computational Biology, 2019

Abstract

Population genetics is concerned with genetic differences within and across populations, and the dynamics of how populations evolve as a result of the propagation of genetic mutations occurring within the germlines of individuals. This article provides a mathematical approach to the most commonly used population genetics models, including Wright-Fisher and related models, and also the less-commonly encountered Bienaymé-Galton-Watson branching model. Topics include fixation times, mutations and their relationship to substitution rates in neutral evolution, selection, multiple alleles, the diffusion limit via the forward Kolmogorov equation, multiple alleles, coalescent theory, and parameter estimation.

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Population Genetics

A.G. Clark , in Encyclopedia of Genetics, 2001

Scope of Population Genetics

Population genetics seeks to understand how and why the frequencies of alleles and genotypes change over time within and between populations. It is the branch of biology that provides the deepest and clearest understanding of how evolutionary change occurs. Population genetics is particularly relevant today in the expanding quest to understand the basis for genetic variation in susceptibility to complex diseases. Many of the factors that affect allelic frequency and associations among alleles of linked genes have been first characterized in Drosophila and other model organisms, but the same principles apply to virtually all organisms.

Shortly after the rediscovery of Mendel's laws in 1900, a raging controversy developed over the relevance of the kind of variation and transmission that Mendel characterized to the smooth, continuous variation that biologists had noted and measured in virtually all organisms. Could the continuous variation in stature, for example, be explained by underlying genes of the sort Mendel described? One of the arguments against Mendel's genes was that recessive alleles would soon be lost from a population by virtue of its recessiveness. Godfrey Hardy and Wilhelm Weinberg independently demonstrated the folly of this argument, and showed instead that randomly mating populations would be expected to retain the allelic variation by simple Mendelian principles unless some other force acted on the variation. But this did not fully resolve the question of why parents and offspring have correlated phenotypes for continuously varying traits.

It was the theoretical population geneticist Ronald Fisher who developed the mathematics to show exactly how many genes acting together could produce the precise quantitative degrees of familial resemblance that are observed. This was one of many instances in the history of population genetics in which a formal mathematical model of the problem paved the way to understanding what empirical data needed to be gathered to test the new conceptualization. Fisher went on to develop, along with Sewall Wright and J. B. S. Haldane, much of the theory for allelic frequency change under simple models of natural selection. Wright and Fisher developed the theoretical machinery needed to understand the complex process of recurrent sampling that we now call random genetic drift. By 1940 much of the theory for the 'modern synthesis' of Darwinian evolution and Mendelian transmission genetics had been developed.

Before considering the development of the empirical aspects of population genetics, the basic mechanisms that underlie the modern synthesis are briefly reviewed below.

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Population Genetics

H. Richard Johnston , ... Stephanie L. Sherman , in Emery and Rimoin's Principles and Practice of Medical Genetics and Genomics (Seventh Edition), 2019

Abstract

Population genetics is the study of genetic variation within and among populations and the evolutionary factors that explain this variation. Its foundation is the Hardy - Weinberg law, which is maintained as long as population size is large, mating is at random, and mutation, selection and migration are negligible. If not, allele frequencies and genotype frequencies may change from one generation to the next. Ethnic variation in allele frequencies is found throughout the genome, and by examining this genetic diversity, evolutionary patterns can be inferred, and variants contributing to the cause of common diseases can be identified. As a result of major international initiatives, extensive databases containing millions of genetic variants are available. Together with automated technology for genotyping, sequencing and bioinformatic analysis, these datasets provide the population geneticist with a huge set of densely mapped polymorphisms for reconciling genome variation with population histories of bottlenecks, admixture, and migration, for revealing evidence of natural selection, and for advancing understanding of many diseases.

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Population Genetics

B.J.B Keats , S.L. Sherman , in Reference Module in Biomedical Sciences, 2014

Abstract

The principles of population genetics attempt to explain the genetic diversity in present populations and the changes in allele and genotype frequencies over time. Population genetic studies facilitate the identification of alleles associated with disease risk and provide insight into the effect of medical intervention on the population frequency of a disease. Allele and genotype frequencies depend on factors such as mating patterns, population size and distribution, mutation, migration, and selection. By making specific assumptions about these factors, the Hardy–Weinberg law, a fundamental principle of population genetics, provides a model for calculating genotype frequencies from allele frequencies for a random mating population in equilibrium.

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Population Genetics

Brian Charlesworth , in Encyclopedia of Biodiversity (Second Edition), 2013

The Island Model

Although the previously mentioned measures of population differentiation are useful as descriptive tools, they can also be used to estimate the evolutionary parameters that determine the extent of population differentiation. This requires the development of models of the joint effects of genetic drift, mutation, and migration, one of the most complex problems in theoretical population genetics. The simplest and most widely used model is the island model, which assumes that the species is divided into d distinct subpopulations or "demes," which each behaves according to the Wright–Fisher model with population size N. After reproduction has occured within each deme, a fraction m of each deme's genes are replaced with genes drawn randomly from the other d–1 demes. Coalescent theory can be used to determine the mean coalescence times of pairs of alleles sampled from the same population (t 0) or from different populations (t 1); it is found that t 0=2Nd and t 1=2Nd(l+[d–1]/[4Ndnm]) (Wakeley, 2008; Charlesworth and Charlesworth, 2010). In the infinite sites model, the mean fraction of nucleotides that differ between a pair of alleles is equal to the product of the mutation rate per site and twice their coalescence time (see The Coalescent Process) so that the expected number of nucleotide site differences between alleles can be derived directly from the corresponding coalescence times.

An important and somewhat counterintuitive conclusion is that the within-population nucleotide site diversity, π S , is equal to 4Ndu, that is, it depends on the total number of individuals in the set of populations in the same way as the diversity in a panmictic population under the infinite sites model, and it is independent of the migration rate (with the proviso that m>0). As expected, the other diversity measures depend inversely on Nm, with large between-population divergence being possible only when Nm<1; for large d, K ST is approximately equal to 1/(1+4Nm). Values of these statistics that are close to zero are generally taken to indicate relatively little population differentiation, whereas values close to one imply considerable differences among local populations relative to the within-population variability.

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Microbial Forensics: Educating the Workforce and the Community

Steven E. Schutzer , ... Paul S. Keim , in Microbial Forensics (Second Edition), 2011

Population Genetics

Population genetics is essential for understanding the rarity of a genetic (and sometimes protein) profile derived from an evidence sample. Molecular epidemiology is increasingly applying the principles of evolutionary and population genetics to pathogens. It is important to understand what constitutes a sample population as opposed to a sample collection, the mode of inheritance related to a genetic marker, what significance or weight to apply to a genetic marker, what the mutation rate of a marker is, and how to combine the weight of multiple markers. Training of the student in this discipline will require basic genetics courses and more advanced courses in phylogenetic analyses. Such educational material will be found in population genetics and systematic and evolutionary biology programs. The population genetics of pathogens and its importance for microbial forensics are covered elsewhere in this book.

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Genetics and Population Analysis

Fotis Tsetsos , ... Peristera Paschou , in Encyclopedia of Bioinformatics and Computational Biology, 2019

Abstract

Population genetics, the systematic study of patterns of genetic variation, has been undergoing an unprecedented, revolutionary phase in the recent years. The advances of modern technology have enabled the rapid and accurate mass-scale output of modern and ancient genetic data. In this article, we delve into the state-of-the-art methods utilized for computational genetic analysis, the knowledge base required for crafting analytical protocols to avoid biased data, along with important considerations for the proper assessment and interpretation of the data, the methods and their output. We also present illustrative examples of population genetics in the exploration of the human past, as well as its applications in disease mapping and association studies.

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Population genetics of Triatominae

L. Stevens , P.L. Dorn , in American Trypanosomiasis Chagas Disease (Second Edition), 2017

Why study the population genetics of insect disease vectors?

Population genetics can provide insight into ecological and evolutionary processes (i.e., mutation, genetic drift, natural selection, and migration) relevant to vector-borne disease transmission by examining spatial and temporal patterns of genetic variation in insect vectors ( Fig. 8.1). How much migration and interbreeding occur among nearby populations? What barriers limit gene flow (e.g., deforestation, mountain ranges, biogeographical limits)? When insects reappear following insecticide treatment, do they represent recrudescent domestic populations, sylvatic colonizers, or migrants from nearby houses or villages? Do genetically different subpopulations also differ in vectorial competence or capacity? How fast might insecticide-resistance alleles spread throughout a population? The answers to these population genetics questions are of fundamental importance to the epidemiology and control of vector-borne diseases.

Figure 8.1. Examples of (A) random population genetic structure and (B) distinct subpopulations with different amounts of gene flow (migration) among them.

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Human Population Genetics/Genomics and Society

Alan R. Templeton , in Human Population Genetics and Genomics, 2019

Abstract

Population genetics/genomics has implications for societal issues. One issue is race: does it exist? Race exists as a cultural construct, but population genetics clearly shows that race does not exist using the criteria for race (subspecies) used for nonhuman species, including our sister species, the common chimpanzee. Race is an example of typological thinking, and human population trees are an example of typological thinking that divides humanity into distinct branches. Such trees are strongly falsified whenever tested, so scientists should avoid the use of population trees. A second issue is medicine. Population genetics/genomics is used for detecting genetic diseases and genetic risk factors for multifactorial disease, understanding diseases using insights obtained from genetic risk factors, and treating diseases using these insights. Population genetics also underlies the field of evolutionary medicine—understanding and treating some of our present diseases in terms of the environments under which they evolved. A final issue is whether or not humans are no longer evolving because cultural evolution has replaced biological evolution. Quite the contrary, cultural evolution induces strong selective forces, so humans have undergone rapid adaptive evolution over the past 10,000  years. Human population structure is also rapidly changing; with dispersal and outbreeding becoming much more common coupled with major demographic transitions and population growth. These changes affect both adaptive and neutral evolution. One possibility for human evolutionary change is eugenics, the deliberate modification of human reproduction or specific genes to change our gene pool. Eugenic proposals are most often based on genetic determinism that ignores the fact that phenotypes emerge from interactions between genotypes and environments. Eugenic proposals also tend to ignore the role of epistasis and pleiotropy, which together seriously undermine the eugenic agenda. Humans have great potential to continue to evolve both biologically and culturally in our rapidly changing environment.

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