Idealised population

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In population genetics an idealised population is one that can be described using a number of simplifying assumptions. Models of idealised populations are either used to make a general point, or they are fit to data on real populations for which the assumptions may not hold true. For example, coalescent theory is used to fit data to models of idealised populations. [1] The most common idealized population in population genetics is described in the Wright-Fisher model after Sewall Wright and Ronald Fisher (1922, 1930) and (1931). Wright-Fisher populations have constant size, and their members can mate and reproduce with any other member. Another example is a Moran model, which has overlapping generations, rather than the non-overlapping generations of the Fisher-Wright model. The complexities of real populations can cause their behavior to match an idealised population with an effective population size that is very different from the census population size of the real population. For sexual diploids, idealized populations will have genotype frequencies related to the allele frequencies according to Hardy-Weinberg equilibrium.

Population genetics Study of genetic differences within and between populations including the study of adaptation, speciation, and population structure

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.

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. 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.

Sewall Wright American geneticist

Sewall Green Wright 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.

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Hardy-Weinberg

In 1908, G. H. Hardy and Wilhelm Weinberg modeled an idealised population to demonstrate that in the absence of selection, migration, random genetic drift, allele frequencies stay constant over time, and that in the presence of random mating, genotype frequencies are related to allele frequencies according to a binomial square principle called the Hardy-Weinberg law. [2]

Usage in population dynamics

A good example of usage idealised population model, in tracking natural population conditions, could be found in a research of Joe Roman and Stephen R. Palumbi (2003). Using genetic diversity data, they questioned: have populations of North Atlantic great whales recovered enough for commercial whaling? To calculate genetic diversity the authors multiply long term effective population size of the females by two, assuming sex ratio 1:1, and then multiply by mitochondrial genes substitution rate, per generation. Making several assumptions according to the sex ratio and number of juveniles, they were able to calculate that in contrast to historical records, modern whale populations are far from harvestable range. [3]

For other people with similar names, see the disambiguation page Jose Roman (disambiguation)

Genetic diversity The total number of genetic characteristics in the genetic makeup of a species

Genetic diversity is the total number of genetic characteristics in the genetic makeup of a species. It is distinguished from genetic variability, which describes the tendency of genetic characteristics to vary.

Sex ratio ratio of males to females in a population

The sex ratio is the ratio of males to females in a population. In most sexually reproducing species, the ratio tends to be 1:1. This tendency is explained by Fisher's principle. For various reasons, however, many species deviate from anything like an even sex ratio, either periodically or permanently. Examples include parthenogenic species, periodically mating organisms such as aphids, some eusocial wasps such as Polistes fuscatus and Polistes exclamans, bees, ants, and termites.

Application to population history

Idealised population models could not only provide us with information about present populations conditions but are useful in revealing natural history and population dynamics in the past as well. Using an idealised population model, Anders Eriksson and Andrea Manica (2012) tested the hypothesis of the archaic human admixture with modern humans. The authors compare genome sequences of two human populations, Neanderthals and chimpanzee. Eriksson and Manica created a stepping stone model under which Africa and Eurasia are represented as a string of equal size populations. They concluded that under the stepping stone model, in which Europeans can exchange genetic information with Asians and not with Africans, similarities between Neanderthal genome and Eurasian could be explained by ancient populations structure. [4]

Computer simulations

Usage of models, also allows to perform simulations, including in silica ones, to hypothesize evolutionary outcomes. As an example, PopG is a free computer program that is capable of simulating simultaneous evolution of populations based on Fisher-Wright model. Idealised population model also, could be used in several simple simulations designed for education. So, Charles Darwin: Can you survive? Simulation is designed to introduce general public to the concept of natural selection. Another example is Genetic Drift simulator (Requires an updated Java version), which is designed to visualize influence of genetic drift on natural populations.

A simulation is an approximate imitation of the operation of a process or system; that represents its operation over time.

Computer program Instructions to be executed by a computer

A computer program is a collection of instructions that performs a specific task when executed by a computer. Most computer devices require programs to function properly.

Related Research Articles

An allele is a variant form of a given gene. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation. A notable example of this trait of color variation is Gregor Mendel's discovery that the white and purple flower colors in pea plants were the result of "pure line" traits which could be used as a control for future experiments. However, most alleles result in little or no observable phenotypic variation.

Dominance (genetics) relationship between alleles of a gene, in which the phenotypic effect of one allele masks the phenotypic effect (phenotype) of another allele at the same locus

Dominance, in genetics, is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and the second recessive. This state of having two different variants of the same gene on each chromosome is originally caused by a mutation in one of the genes, either new or inherited. The terms autosomal dominant or autosomal recessive are used to describe gene variants on non-sex chromosomes (autosomes) and their associated traits, while those on sex chromosomes (allosomes) are termed X-linked dominant, X-linked recessive or Y-linked, and these show a very different inheritance and presentation pattern to autosomal traits which depends on the sex of the individual. Additionally, there are other forms of dominance such as incomplete dominance, in which a gene variant has a partial effect compared to when it is present on both chromosomes, and co-dominance, in which different variants on each chromosome both show their associated traits.

Genetic drift The change in the frequency of an existing gene variant in a population

Genetic drift is the change in the frequency of an existing gene variant (allele) in a population due to random sampling of organisms. The alleles in the offspring are a sample of those in the parents, and chance has a role in determining whether a given individual survives and reproduces. A population's allele frequency is the fraction of the copies of one gene that share a particular form. Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. It can also cause initially rare alleles to become much more frequent and even fixed.

Fitness (biology) The average contribution to the gene pool of the next generation made by individuals of the specified genotype or phenotype

Fitness 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.

Hardy–Weinberg principle principle within genetics

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.

Allele frequency, or gene frequency, is the relative frequency of an allele at a particular locus in a population, expressed as a fraction or percentage. Specifically, it is the fraction of all chromosomes in the population that carry that allele. Microevolution is the change in allele frequencies that occurs over time within a population.

Quantitative genetics The study of the inheritance of continuously variable traits

Quantitative genetics is a branch of population genetics that deals with phenotypes that vary continuously —as opposed to discretely identifiable phenotypes and gene-products.

Index of evolutionary biology articles Wikimedia list article

This is a list of topics in evolutionary biology.

Balancing selection refers to a number of selective processes by which multiple alleles are actively maintained in the gene pool of a population at frequencies larger than expected from genetic drift alone. This can happen by various mechanisms, in particular, when the heterozygotes for the alleles under consideration have a higher fitness than the homozygote. In this way genetic polymorphism is conserved.

The effective population size is the number of individuals that an idealised population would need to have in order for some specified quantity of interest to be the same in the idealised population as in the real population. Idealised populations are based on unrealistic but convenient simplifications such as random mating, simultaneous birth of each new generation, constant population size, and equal numbers of children per parent. In some simple scenarios, the effective population size is the number of breeding individuals in the population. However, for most quantities of interest and most real populations, the census population size N of a real population is usually larger than the effective population size Ne. The same population may have multiple effective population sizes, for different properties of interest, including for different genetic loci.

In population genetics, the Wahlund effect refers to reduction of heterozygosity in a population caused by subpopulation structure. Namely, if two or more subpopulations have different allele frequencies then the overall heterozygosity is reduced, even if the subpopulations themselves are in a Hardy-Weinberg equilibrium. The underlying causes of this population subdivision could be geographic barriers to gene flow followed by genetic drift in the subpopulations.

Genetic variation in populations can be analyzed and quantified by the frequency of alleles. Two fundamental calculations are central to population genetics: allele frequencies and genotype frequencies. Genotype frequency in a population is the number of individuals with a given genotype divided by the total number of individuals in the population. In population genetics, the genotype frequency is the frequency or proportion of genotypes in a population.

In population genetics and population ecology, population size is the number of individual organisms in a population. Population size is directly associated with amount of genetic drift, and is the underlying cause of effects like population bottlenecks and the founder effect. Genetic drift is the major source of decrease of genetic diversity within populations which drives fixation and can potentially lead to speciation events.

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 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.

Genetic equilibrium describes the condition of an allele or genotype in a gene pool where the frequency does not change from generation to generation. Genetic equilibrium describes a theoretical state that is the basis for determining whether and in what ways populations may deviate from it. Hardy-Weinberg equilibrium is one theoretical framework for studying genetic equilibrium. It is commonly studied using models that take as their assumptions those of Hardy-Weinberg, meaning:

In population genetics, fixation is the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) in a given population to a situation where only one of the alleles remains. In the absence of mutation or heterozygote advantage, any allele must eventually be lost completely from the population or fixed. Whether a gene will ultimately be lost or fixed is dependent on selection coefficients and chance fluctuations in allelic proportions. Fixation can refer to a gene in general or particular nucleotide position in the DNA chain (locus).

Population stratification is the presence of a systematic difference in allele frequencies between subpopulations in a population, possibly due to different ancestry, especially in the context of association studies.

Fixed allele

A fixed allele is an allele that is the only variant that exists for that gene in all the population. A fixed allele is homozygous for all members of the population. The term allele normally refers to one variant gene out of several possible for a particular locus in the DNA. When all but one allele go extinct and only one remains, that allele is said to be fixed.

References

  1. ↑ . Nielsen, Rasmus, and Montgomery Slatkin. An Introduction to Population Genetics: Theory and Applications. Sunderland, MA: Sinauer Associates, 2013. Print.
  2. ↑ .Crow, James F. "Population genetics history: a personal view." Annual Review of Genetics 21, no. 1 (1987): 1-22.
  3. ↑ Roman, Joe; Palumbi, Stephen R. (2003). "Whales before whaling in the North Atlantic" (PDF). Science . 301 (5632): 508–510. CiteSeerX   10.1.1.1025.5800 . doi:10.1126/science.1084524. PMID   12881568.
  4. ↑ Eriksson, Anders, and Andrea Manica. "Effect of ancient population structure on the degree of polymorphism shared between modern human populations and ancient hominins." Proceedings of the National Academy of Sciences 109, no. 35 (2012): 13956-13960.
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