Portal:Population genetics
Portal maintenance status: (October 2018)
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Introduction
Population genetics is a subfield of genetics that deals with genetic differences within and between populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.
Population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis. Its primary founders were Sewall Wright, J. B. S. Haldane and Ronald Fisher, who also laid the foundations for the related discipline of quantitative genetics. Traditionally a highly mathematical discipline, modern population genetics encompasses theoretical, lab, and field work. Population genetic models are used both for statistical inference from DNA sequence data and for proof/disproof of concept.
Selected general articles
A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events (such as famines, earthquakes, floods, fires, disease, or droughts) or human activities (such as genocide). Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring through sexual reproduction. Genetic diversity remains lower, increasing only when gene flow with another population occurs or very slowly increasing with time as random mutations occur. As a consequence of such population size reductions and the loss of genetic variation, the robustness of the population is reduced and its ability to adapt to and survive selecting environmental changes, such as climate change or a shift in available resources, is reduced. Alternatively, if survivors of the bottleneck are the individuals with the greatest genetic fitness, the frequency of the fitter genes within the gene pool is increased, while the pool itself is reduced.
The genetic drift caused by a population bottleneck can change the proportional distribution of alleles by chance and even lead to fixation or loss of alleles. Due to the smaller population size after a bottleneck event, the chances of inbreeding and genetic homogeneity increase, leading to the potential for inbreeding depression to occur. Smaller population size can also cause deleterious mutations to accumulate Read more...- Evolutionary game theory (EGT) is the application of game theory to evolving populations in biology. It defines a framework of contests, strategies, and analytics into which Darwinian competition can be modelled. It originated in 1973 with John Maynard Smith and George R. Price's formalisation of contests, analysed as strategies, and the mathematical criteria that can be used to predict the results of competing strategies.
Evolutionary game theory differs from classical game theory in focusing more on the dynamics of strategy change. This is influenced by the frequency of the competing strategies in the population. Read more... - The coefficient of relationship is a measure of the degree of consanguinity (or biological relationship) between two individuals. The term coefficient of relationship was defined by Sewall Wright in 1922, and was derived from his definition of the coefficient of inbreeding of 1921. The measure is most commonly used in genetics and genealogy. A coefficient of inbreeding can be calculated for an individual, and is typically one-half the coefficient of relationship between the parents.
In general, the higher the level of inbreeding the closer the coefficient of relationship between the parents approaches a value of 1, expressed as a percentage, and approaches a value of 0 for individuals with arbitrarily remote common ancestors. Read more... - In the theory of evolution and natural selection, the Price equation (also known as Price's equation or Price's theorem) describes how a trait or gene changes in frequency over time. The equation uses a covariance between a trait and fitness to give a mathematical description of evolution and natural selection. It provides a way to understand the effects that gene transmission and natural selection have on the proportion of genes within each new generation of a population. The Price equation was derived by George R. Price, working in London to re-derive W.D. Hamilton's work on kin selection. The Price equation also has applications in economics. Examples of the Price equation can be found here: Price equation examples. Read more...
Sexual selection creates colourful differences between sexes (sexual dimorphism) in Goldie's bird-of-paradise. Male above; female below. Painting by John Gerrard Keulemans (d.1912)
Sexual selection is a mode of natural selection where members of one biological sex choose mates of the other sex to mate with (intersexual selection), and compete with members of the same sex for access to members of the opposite sex (intrasexual selection). These two forms of selection mean that some individuals have better reproductive success than others within a population, either from being more attractive or preferring more attractive partners to produce offspring. For instance, in the breeding season, sexual selection in frogs occurs with the males first gathering at the water's edge and making their mating calls: croaking. The females then arrive and choose the males with the deepest croaks and best territories. Generalizing, males benefit from frequent mating and monopolizing access to a group of fertile females. Females have a limited number of offspring they can have and they maximize the return on the energy they invest in reproduction.
The concept was first articulated by Charles Darwin and Alfred Russel Wallace who described it as driving species adaptations and that many organisms had evolved features whose function was deleterious to their individual survival, and then developed by Ronald Fisher in the early 20th century. Sexual selection can, typically, lead males to extreme efforts to demonstrate their fitness to be chosen by females, producing sexual dimorphism in secondary sexual characteristics, such as the ornate plumage of birds such as birds of paradise and peafowl, or the antlers of deer, or the manes of lions, caused by a positive feedback mechanism known as a Fisherian runaway, where the passing-on of the desire for a trait in one sex is as important as having the trait in the other sex in producing the runaway effect. Although the sexy son hypothesis indicates that females would prefer male offspring, Fisher's principle explains why the sex ratio is 1:1 almost without exception. Sexual selection is also found in plants and fungi. Read more...- In population genetics, linkage disequilibrium is the non-random association of alleles at different loci in a given population. Loci are said to be in linkage disequilibrium when the frequency of association of their different alleles is higher or lower than what would be expected if the loci were independent and associated randomly.
Linkage disequilibrium is influenced by many factors, including selection, the rate of genetic recombination, mutation rate, genetic drift, the system of mating, population structure, and genetic linkage. As a result, the pattern of linkage disequilibrium in a genome is a powerful signal of the population genetic processes that are structuring it. Read more... - Coalescent theory is a model of how gene variants sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time (with wide variance). Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles.
The mathematical theory of the coalescent was developed independently by several groups in the early 1980s as a natural extension of classical population genetics theory and models, but can be primarily attributed to John Kingman. Advances in coalescent theory include recombination, selection, overlapping generations and virtually any arbitrarily complex evolutionary or demographic model in population genetic analysis. Read more...
Hardy–Weinberg proportions for two alleles: the horizontal axis shows the two allele frequencies p and q and the vertical axis shows the expected genotype frequencies. Each line shows one of the three possible genotypes.
The Hardy–Weinberg principle, also known as the Hardy–Weinberg equilibrium, model, theorem, or law, states that allele and genotype frequencies in a population will remain constant from generation to generation in the absence of other evolutionary influences. These influences include genetic drift, mate choice, assortative mating, natural selection, sexual selection, mutation, gene flow, meiotic drive, genetic hitchhiking, population bottleneck, founder effect and inbreeding.
In the simplest case of a single locus with two alleles denoted A and a with frequencies {{{1}}} and {{{1}}}, respectively, the expected genotype frequencies under random mating are {{{1}}} for the AA homozygotes, {{{1}}} for the aa homozygotes, and {{{1}}} for the heterozygotes. In the absence of selection, mutation, genetic drift, or other forces, allele frequencies p and q are constant between generations, so equilibrium is reached. Read more...
John Burdon Sanderson Haldane FRS (/ˈhɔːldeɪn/; 5 November 1892 – 1 December 1964) was an English scientist known for his work in the study of physiology, genetics, evolutionary biology, and in mathematics, where he made innovative contributions to the fields of statistics and biostatistics. He was the son of the equally famous John Scott Haldane and was a professed socialist, Marxist, atheist, and humanist whose political dissent led him to leave England in 1956 and live in India, becoming a naturalised Indian citizen in 1961.
His first paper in 1915 demonstrated genetic linkage in mammals while subsequent works helped to create population genetics, thus establishing a unification of Mendelian genetics and Darwinian evolution by natural selection whilst laying the groundwork for modern evolutionary synthesis. His article on abiogenesis in 1929 introduced the "primordial soup theory", and it became the foundation to build physical models for the chemical origin of life.
Haldane established human gene maps for haemophilia and colour blindness on the X chromosome, and codified Haldane's rule on sterility in the heterogametic sex of hybrids in species. He correctly proposed that sickle-cell disease confers some immunity to malaria. He was the first to suggest the central idea of in vitro fertilisation, as well as concepts such as: the hydrogen economy, cis and trans-acting regulation, coupling reaction, molecular repulsion, the darwin (as a unit of evolution) and organismal cloning. In 1957 he articulated Haldane's dilemma, a limit on the speed of beneficial evolution which subsequently proved incorrect. He willed his body for medical studies, as he wanted to remain useful even in death. Read more...- Fitness (often denoted
or ω in population genetics models) is the quantitative representation of natural and sexual selection within evolutionary biology. It can be defined either with respect to a genotype or to a phenotype in a given environment. In either case, it describes individual reproductive success and is equal to the average contribution to the gene pool of the next generation that is made by individuals of the specified genotype or phenotype. The fitness of a genotype is manifested through its phenotype, which is also affected by the developmental environment. The fitness of a given phenotype can also be different in different selective environments.
With asexual reproduction, it is sufficient to assign fitnesses to genotypes. With sexual reproduction, genotypes are scrambled every generation. In this case, fitness values can be assigned to alleles by averaging over possible genetic backgrounds. Natural selection tends to make alleles with higher fitness more common over time, resulting in Darwinian evolution. Read more... - Genetic genealogy is the use of DNA testing in combination with traditional genealogical methods to infer relationships between individuals and find ancestors. Genetic genealogy involves the use of genealogical DNA testing to determine the level and type of the genetic relationship between individuals. This application of genetics became popular with family historians in the 21st century, as tests became affordable. The tests have been promoted by amateur groups, such as surname study groups, or regional genealogical groups, as well as research projects such as the genographic project. As of 2018, 12 million people had been tested. As this field has developed, the aims of practitioners broadened, with many seeking knowledge of their ancestry beyond the recent centuries for which traditional pedigrees can be constructed. Read more...
Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charles Darwin popularised the term "natural selection", contrasting it with artificial selection, which is intentional, whereas natural selection is not.
Variation exists within all populations of organisms. This occurs partly because random mutations arise in the genome of an individual organism, and offspring can inherit such mutations. Throughout the lives of the individuals, their genomes interact with their environments to cause variations in traits. The environment of a genome includes the molecular biology in the cell, other cells, other individuals, populations, species, as well as the abiotic environment. Because individuals with certain variants of the trait tend to survive and reproduce more than individuals with other, less successful variants, the population evolves. Other factors affecting reproductive success include sexual selection (now often included in natural selection) and fecundity selection. Read more...
A Belgian Blue cow. The defect in the breed's myostatin gene is maintained through linebreeding and is responsible for its accelerated lean muscle growth.
Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant males and females will sexually reproduce and have offspring together. Domesticated animals are known as breeds, normally bred by a professional breeder, while domesticated plants are known as varieties, cultigens, or cultivars. Two purebred animals of different breeds produce a crossbreed, and crossbred plants are called hybrids. Flowers, vegetables and fruit-trees may be bred by amateurs and commercial or non-commercial professionals: major crops are usually the provenance of the professionals.
In animal breeding, techniques such as inbreeding, linebreeding, and outcrossing are utilized. In plant breeding, similar methods are used. Charles Darwin discussed how selective breeding had been successful in producing change over time in his 1859 book, On the Origin of Species. Its first chapter discusses selective breeding and domestication of such animals as pigeons, cats, cattle, and dogs. Darwin used artificial selection as a springboard to introduce and support the theory of natural selection. Read more...- Ecological selection (or environmental selection or survival selection or individual selection or asexual selection) refers to natural selection without sexual selection, i.e. strictly ecological processes that operate on a species' inherited traits without reference to mating or secondary sex characteristics. The variant names describe varying circumstances where sexual selection is wholly suppressed as a mating factor.
Ecologists often study ecological selection when examining the abundance of individuals per population across regions, and what governs such abundances. Read more... - Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction. Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together. Markers on different chromosomes are perfectly unlinked.
Genetic linkage is the most prominent exception to Gregor Mendel's Law of Independent Assortment. The first experiment to demonstrate linkage was carried out in 1905. At the time, the reason why certain traits tend to be inherited together was unknown. Later work revealed that genes are physical structures related by physical distance. Read more... - Evolution is change in the heritable characteristics of biological populations over successive generations. These characteristics are the expressions of genes that are passed on from parent to offspring during reproduction. Different characteristics tend to exist within any given population as a result of mutation, genetic recombination and other sources of genetic variation. Evolution occurs when evolutionary processes such as natural selection (including sexual selection) and genetic drift act on this variation, resulting in certain characteristics becoming more common or rare within a population. It is this process of evolution that has given rise to biodiversity at every level of biological organisation, including the levels of species, individual organisms and molecules.
The scientific theory of evolution by natural selection was proposed by Charles Darwin and Alfred Russel Wallace in the mid-19th century and was set out in detail in Darwin's book On the Origin of Species (1859). Evolution by natural selection was first demonstrated by the observation that more offspring are often produced than can possibly survive. This is followed by three observable facts about living organisms: 1) traits vary among individuals with respect to their morphology, physiology and behaviour (phenotypic variation), 2) different traits confer different rates of survival and reproduction (differential fitness) and 3) traits can be passed from generation to generation (heritability of fitness). Thus, in successive generations members of a population are more likely to be replaced by the progenies of parents with favourable characteristics that have enabled them to survive and reproduce in their respective environments. In the early 20th century, other competing ideas of evolution such as mutationism and orthogenesis were refuted as the modern synthesis reconciled Darwinian evolution with classical genetics, which established adaptive evolution as being caused by natural selection acting on Mendelian genetic variation. Read more...
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) (note: the acronym IBD is also used for another concept in population genetics, isolation by distance) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment. Read more...
Fisher's fundamental theorem of natural selection is an idea about genetic variance in population genetics developed by the statistician and evolutionary biologist Ronald Fisher. The proper way of applying the abstract mathematics of the theorem to actual biology has been a matter of some debate.
It states: Read more...
Heritability is a statistic used in the fields of breeding and genetics that estimates the degree of variation in a phenotypic trait in a population that is due to genetic variation between individuals in that population. In other words, the concept of heritability can alternately be expressed in the form of the following question: "What is the proportion of the variation in a given trait within a population that is not explained by the environment or random chance?"
Other causes of measured variation in a trait are characterized as environmental factors, including measurement error. In human studies of heritability these are often apportioned into factors from "shared environment" and "non-shared environment" based on whether they tend to result in persons brought up in the same household being more or less similar to persons who were not. Read more...- In evolutionary biology, fitness landscapes or adaptive landscapes (types of evolutionary landscapes) are used to visualize the relationship between genotypes and reproductive success. It is assumed that every genotype has a well-defined replication rate (often referred to as fitness). This fitness is the "height" of the landscape. Genotypes which are similar are said to be "close" to each other, while those that are very different are "far" from each other. The set of all possible genotypes, their degree of similarity, and their related fitness values is then called a fitness landscape. The idea of a fitness landscape is a metaphor to help explain flawed forms in evolution by natural selection, including exploits and glitches in animals like their reactions to supernormal stimuli.
The idea of studying evolution by visualizing the distribution of fitness values as a kind of landscape was first introduced by Sewall Wright in 1932. Read more... - Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection (natural and artificial), gene flow and genetic drift. This change happens over a relatively short (in evolutionary terms) amount of time compared to the changes termed macroevolution which is where greater differences in the population occur.
Population genetics is the branch of biology that provides the mathematical structure for the study of the process of microevolution. Ecological genetics concerns itself with observing microevolution in the wild. Typically, observable instances of evolution are examples of microevolution; for example, bacterial strains that have antibiotic resistance. Read more...
Sketch of a fitness landscape. The arrows indicate the preferred flow of a population on the landscape. The red ball indicates a population that moves from an adaptive valley to the top of an adaptive peak. Under a strict regime of natural selection (which usually acts to increase fitness in a population), it is not possible for a population at peak A to reach peak B because this requires descending into an adaptive valley. Shifting balance theory aims to explain how this may be possible.
The shifting balance theory is a theory of evolution proposed in 1932 by Sewall Wright, suggesting that adaptive evolution may proceed most quickly when a population divides into subpopulations with restricted gene flow. The name of the theory is borrowed from Wright's metaphor of fitness landscapes (evolutionary landscapes), attempting to explain how a population may move across an adaptive valley to a higher adaptive peak. According to the theory, this movement occurs in three steps:- Genetic drift allows a locally adapted subpopulation to move across an adaptive valley to the base of a higher adaptive peak.
- Natural selection will move the subpopulation up the higher peak.
- This new superiorly adapted subpopulation may then expand its range and outcompete or interbreed with other subpopulations, causing the spread of new adaptations and movement of the global population toward the new fitness peak.
Although shifting balance theory has been influential in evolutionary biology, inspiring the theories of quantum evolution and punctuated equilibrium, little empirical evidence exists to support the shifting balance process as an important factor in evolution. Read more...- Quantitative genetics is a branch of population genetics that deals with phenotypes that vary continuously (in characters such as height or mass)—as opposed to discretely identifiable phenotypes and gene-products (such as eye-colour, or the presence of a particular biochemical).
Both branches use the frequencies of different alleles of a gene in breeding populations (gamodemes), and combine them with concepts from simple Mendelian inheritance to analyze inheritance patterns across generations and descendant lines. While population genetics can focus on particular genes and their subsequent metabolic products, quantitative genetics focuses more on the outward phenotypes, and makes summaries only of the underlying genetics. Read more... - Small populations can behave differently from larger populations. They are often the result of a population bottlenecks from larger populations, leading to loss of heterozygosity and reduced genetic diversity and loss or fixation of alleles and shifts in allele frequencies. A small population is then more susceptible to demographic and genetic stochastic events, which can impact the long-term survival of the population. Therefore, small populations are often considered at risk of endangerment or extinction, and are often of conservation concern. Read more...
In population genetics, the founder effect is the loss of genetic variation that occurs when a new population is established by a very small number of individuals from a larger population. It was first fully outlined by Ernst Mayr in 1942, using existing theoretical work by those such as Sewall Wright. As a result of the loss of genetic variation, the new population may be distinctively different, both genotypically and phenotypically, from the parent population from which it is derived. In extreme cases, the founder effect is thought to lead to the speciation and subsequent evolution of new species.
In the figure shown, the original population has nearly equal numbers of blue and red individuals. The three smaller founder populations show that one or the other color may predominate (founder effect), due to random sampling of the original population. A population bottleneck may also cause a founder effect, though it is not strictly a new population. Read more...- Genetic hitchhiking, also called genetic draft or the hitchhiking effect, is when an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain. When one gene goes through a selective sweep, any other nearby polymorphisms that are in linkage disequilibrium will tend to change their allele frequencies too. Selective sweeps happen when newly appeared (and hence still rare) mutations are advantageous and increase in frequency. Neutral or even slightly deleterious alleles that happen to be close by on the chromosome 'hitchhike' along with the sweep. In contrast, effects on a neutral locus due to linkage disequilibrium with newly appeared deleterious mutations are called background selection. Both genetic hitchhiking and background selection are stochastic (random) evolutionary forces, like genetic drift. Read more...
- Sewall Green Wright (December 21, 1889 – March 3, 1988) was an American geneticist known for his influential work on evolutionary theory and also for his work on path analysis. He was a founder of population genetics alongside Ronald Fisher and J.B.S. Haldane, which was a major step in the development of the modern synthesis combining genetics with evolution. He discovered the inbreeding coefficient and methods of computing it in pedigree animals. He extended this work to populations, computing the amount of inbreeding between members of populations as a result of random genetic drift, and along with Fisher he pioneered methods for computing the distribution of gene frequencies among populations as a result of the interaction of natural selection, mutation, migration and genetic drift. Wright also made major contributions to mammalian and biochemical genetics. Read more...
- The neutral theory of molecular evolution holds that at the molecular level most evolutionary changes and most of the variation within and between species is not caused by natural selection but by genetic drift of mutant alleles that are neutral. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory allows for the possibility that most mutations are deleterious, but holds that because these are rapidly removed by natural selection, they do not make significant contributions to variation within and between species at the molecular level. Mutations that are not deleterious are assumed to be mostly neutral rather than beneficial. In addition to assuming the primacy of neutral mutations, the theory also assumes that the fate of neutral mutations is determined by the sampling processes described by specific models of random genetic drift.
The theory was introduced by the Japanese biologist Motoo Kimura in 1968, and independently by two American biologists Jack Lester King and Thomas Hughes Jukes in 1969, and described in detail by Kimura in his 1983 monograph The Neutral Theory of Molecular Evolution. According to Kimura, the theory applies only for evolution at the molecular level, and phenotypic evolution is controlled by natural selection, as postulated by Charles Darwin. The proposal of the neutral theory was followed by an extensive "neutralist-selectionist" controversy over the interpretation of patterns of molecular divergence and polymorphism, peaking in the 1970s and 1980s. Since then, much evidence has been found for selection at molecular level. Read more...
Sir Ronald Aylmer Fisher FRS (17 February 1890 – 29 July 1962) was a British statistician and geneticist. For his work in statistics, he has been described as "a genius who almost single-handedly created the foundations for modern statistical science" and "the single most important figure in 20th century statistics". In genetics, his work used mathematics to combine Mendelian genetics and natural selection; this contributed to the revival of Darwinism in the early 20th-century revision of the theory of evolution known as the modern synthesis. For his contributions to biology, Fisher has been called "the greatest of Darwin’s successors".
From 1919 onward, he worked at the Rothamsted Experimental Station for 14 years; there, he analysed its immense data from crop experiments since the 1840s, and developed the analysis of variance (ANOVA). He established his reputation there in the following years as a biostatistician. He is known as one of the three principal founders of population genetics. He outlined Fisher's principle, the Fisherian runaway and sexy son hypothesis theories of sexual selection. His contributions to statistics include the maximum likelihood, fiducial inference, the derivation of various sampling distributions, founding principles of the design of experiments, and much more. Read more...
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The logarithm of fitness as a function of the number of deleterious mutations. Synergistic epistasis is represented by the red line - each subsequent deleterious mutation has a larger proportionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line shows the non-epistatic case, where fitness is the product of the contributions from each of its loci.
Gene flow is the transfer of alleles from one population to another population through immigration of individuals. In this example, one of the birds from population A immigrates to population B, which has fewer of the dominant alleles, and through mating incorporates its alleles into the other population.
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