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Hardy-Weinberg principle
In population genetics, the Hardy–Weinberg principle is a relationship between the frequencies of alleles and the genotype of a population. The occurrence of a genotype, perhaps one associated with a disease, stays constant unless matings are non-random or inappropriate, or mutations accumulate. Therefore, the frequency of genotypes and the frequency of alleles are said to be at "genetic equilibrium". Genetic equilibrium is a basic principle of population genetics. The Hardy-Weinberg principle is like a Punnett square for populations, instead of individuals. A Punnett square can predict the probability of offspring's genotype based on parents' genotype or the offsprings' genotype can be used to reveal the parents' genotype. Likewise, the Hardy-Weinberg principle can be used to calculate the frequency of particular alleles based on frequency of, say, an autosomal recessive disease. In the simplest case of a single locus with two alleles: the dominant allele is denoted A and the recessive a. Their frequencies are p and q; freq(A)=p and freq(a)=q. Based on the fact that the probabilities of all genotypes must sum to unity, we can determine useful, difficult-to-measure facts about a population. For example, a patient's child is a carrier of a recessive mutation that causes cystic fibrosis in homozygous recessive children. The parent wants to know the probability of her grandchildren inheriting the disease. In order to answer this question, the genetic counselor must know the chance that the child will marry a carrier of the recessive mutation. This fact may not be known, but disease frequency is known. We know that the disease is caused by the homozygous recessive genotype; we can use the Hardy-Weinberg principle to work backward from disease occurrence to the frequency of heterozygous recessive individuals. This concept is also known by a variety of names: HWP, Hardy–Weinberg equilibrium, HWE, or Hardy–Weinberg law. It was named after G. H. Hardy and Wilhelm Weinberg. Additional recommended knowledge
DerivationA better, but equivalent, probabilistic description for the HWP is that the alleles for the next generation for any given individual are chosen randomly and independent of each other. Consider two alleles, A and a, with frequencies p and q, respectively, in the population. The different ways to form new genotypes can be derived using a Punnett square, where the fraction in each is equal to the product of the row and column probabilities.
The final three possible genotypic frequencies in the offspring become: These frequencies are called Hardy-Weinberg frequencies (or Hardy-Weinberg proportions). This is achieved in one generation, and only requires the assumption of random mating with an infinite population size. Sometimes, a population is created by bringing together males and females with different allele frequencies. In this case, the assumption of a single population is violated until after the first generation, so the first generation will not have Hardy-Weinberg equilibrium. Successive generations will have Hardy-Weinberg equilibrium. Deviations from Hardy-Weinberg equilibriumViolations of the Hardy–Weinberg assumptions can cause deviations from expectation. How this affects the population depends on the assumptions that are violated. Generally, deviation from the Hardy-Weinberg equilibrium denotes the evolution of a species.
The remaining assumptions affect the allele frequencies, but do not, in themselves, affect random mating. If a population violates one of these, the population will continue to have Hardy-Weinberg proportions each generation, but the allele frequencies will change with that force.
How these violations affect formal statistical tests for HWE is discussed later. Unfortunately, violations of assumptions in the Hardy-Weinberg principle does not mean the population will violate HWE. For example, balancing selection leads to an equilibrium population with Hardy-Weinberg proportions. This property with selection vs. mutation is the basis for many estimates of mutation rate (call mutation-selection balance). Sex linkageWhere the A gene is sex-linked, the heterogametic sex (e.g., mammalian males; avian females) have only one copy of the gene (and are termed hemizygous), while the homogametic sex (e.g., human females) have two copies. The genotype frequencies at equilibrium are p and q for the heterogametic sex but p^{2}, 2pq and q^{2} for the homogametic sex. For example, in humans red-green colorblindness is an X-linked recessive trait. In western European males, the trait affects about 1 in 12, (q = 0.083) whereas it affects about 1 in 200 females (0.005, compared to q^{2} = 0.0070), very close to Hardy-Weinberg proportions. If a population is brought together with males and females with different allele frequencies, the allele frequency of the male population follows that of the female population because each receives its X chromosome from its mother. The population converges on equilibrium very quickly. GeneralizationsThe simple derivation above can be generalized for more than two alleles and polyploidy. Generalization for more than two allelesConsider an extra allele frequency, r. The two-allele case is the binomial expansion of (p + q)^{2}, and thus the three-allele case is the trinomial expansion of (p + q + r)^{2}.
More generally, consider the alleles A_{1}, ... A_{i} given by the allele frequencies p_{1} to p_{i}; giving for all homozygotes: and for all heterozygotes:
Generalization for polyploidyThe Hardy–Weinberg principle may also be generalized to polyploid systems, that is, for organisms that have more than two copies of each chromosome. Consider again only two alleles. The diploid case is the binomial expansion of:
and therefore the polyploid case is the binomial expansion of:
where c is the ploidy, for example with tetraploid (c = 4):
Depending on whether the organism is a 'true' tetraploid or an amphidiploid will determine how long it will take for the population to reach Hardy-Weinberg equilibrium. Complete generalizationThe completely generalized formula is the multinomial expansion of : ApplicationsThe Hardy–Weinberg principle may be applied in two ways, either a population is assumed to be in Hardy–Weinberg proportions, in which the genotype frequencies can be calculated, or if the genotype frequencies of all three genotypes are known, they can be tested for deviations that are statistically significant. Application to cases of complete dominanceSuppose that the phenotypes of AA and Aa are indistinguishable, i.e., there is complete dominance. Assuming that the Hardy–Weinberg principle applies to the population, then q can still be calculated from f(aa): and p can be calculated from q. And thus an estimate of f(AA) and f(Aa) derived from p^{2} and 2pq respectively. Note however, such a population cannot be tested for equilibrium using the significance tests below because it is assumed a priori. Significance tests for deviationTesting deviation from the HWP is generally performed using Pearson's chi-squared test, using the observed genotype frequencies obtained from the data and the expected genotype frequencies obtained using the HWP. For systems where there are large numbers of alleles, this may result in data with many empty possible genotypes and low genotype counts, because there are often not enough individuals present in the sample to adequately represent all genotype classes. If this is the case, then the asymptotic assumption of the chi-square distribution, will no longer hold, and it may be necessary to use a form of Fisher's exact test, which requires a computer to solve. More recently a number of MCMC methods of testing for deviations from HWP have been proposed (Guo & Thompson, 1992; Wigginton et al 2005) Example χ^{2} test for deviationThese data are from E.B. Ford (1971) on the Scarlet tiger moth, for which the phenotypes of a sample of the population were recorded. Genotype-phenotype distinction is assumed to be negligibly small. The null hypothesis is that the population is in Hardy–Weinberg proportions, and the alternative hypothesis is that the population is not in Hardy–Weinberg proportions.
From which allele frequencies can be calculated:
and
So the Hardy–Weinberg expectation is: Pearson's chi-square test states:
There is 1 degree of freedom (degrees of freedom for test for Hardy-Weinberg proportions are # phenotypes - # alleles). The 5% significance level for 1 degree of freedom is 3.84, and since the χ² value is less than this, the null hypothesis that the population is in Hardy–Weinberg frequencies is not rejected. Fisher's exact test (probability test)Fisher's exact test can be applied to testing for Hardy-Weinberg proportions. Because the test is conditional on the allele frequencies, p and q, the problem can be viewed as testing for the proper number of heterozygotes. In this way, the hypothesis of Hardy-Weinberg proportions is rejected if the number of heterozygotes are too large or too small. The conditional probabilities for the heterozygote, given the allele frequencies are given in Emigh (1980) as where n_{11}, n_{12}, n_{22} are the observed numbers of the three genotypes, AA, Aa, and aa, respectively, and n_{1} is the number of A alleles, where n_{1} = 2n_{11} + n_{12}. An Example Using one of the examples from Emigh (1980), we can consider the case where n = 100, and p = 0.34. The possible observed heterozygotes and their exact significance level is given in Table 4.
Using this table, you look up the significance level of the test based on the observed number of heterozygotes. For example, if you observed 20 heterozygotes, the significance level for the test is 0.007. As is typical for Fisher's exact test for small samples, the gradation of significance levels is quite coarse. Unfortunately, you have to create a table like this for every experiment, since the tables are dependent on both n and p. Analysis Software
Inbreeding coefficientThe inbreeding coefficient, F (see also F-statistics), is one minus the observed frequency of heterozygotes over that expected from Hardy–Weinberg equilibrium. where the expected value from Hardy–Weinberg equilibrium is given by For example, for Ford's data above; For two alleles, the chi square goodness of fit test for Hardy-Weinberg proportions is equivalent to the test for inbreeding, F = 0. HistoryMendelian genetics were rediscovered in 1900. However, it remained somewhat controversial for several years as it was not then known how it could cause continuous characteristics. Udny Yule (1902) argued against Mendelism because he thought that dominant alleles would increase in the population. The American William E. Castle (1903) showed that without selection, the genotype frequencies would remain stable. Karl Pearson (1903) found one equilibrium position with values of p = q = 0.5. Reginald Punnett, unable to counter Yule's point, introduced the problem to G. H. Hardy, a British mathematician, with whom he played cricket. Hardy was a pure mathematician and held applied mathematics in some contempt; his view of biologists' use of mathematics comes across in his 1908 paper where he describes this as "very simple".
The principle was thus known as Hardy's law in the English-speaking world until Curt Stern (1943) pointed out that it had first been formulated independently in 1908 by the German physician Wilhelm Weinberg (see Crow 1999). Others have tried to associate Castle's name with the Law because of his work in 1903, but it is only rarely seen as the Hardy-Weinberg-Castle Law.
Graphical representationIt is possible to represent the distribution of genotype frequencies for a bi-allelic locus within a population graphically using a de Finetti diagram. This uses a triangular plot (also known as trilinear, triaxial or ternary plot) to represent the distribution of the three genotype frequencies in relation to each other. Although it differs from many other such plots in that the direction of one of the axes has been reversed.
The curved line in the above diagram is the Hardy-Weinberg parabola and represents the state where alleles are in Hardy-Weinberg equilibrium. It is possible to represent the effects of Natural Selection and its effect on allele frequency on such graphs (e.g. Ineichen & Batschelet 1975) The De Finetti diagram has been developed and used extensively by A.W.F. Edwards in his book Foundations of Mathematical Genetics. References and notesReferences
Notes
Categories: Population genetics | Classical genetics |
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This article is licensed under the GNU Free Documentation License. It uses material from the Wikipedia article "Hardy-Weinberg_principle". A list of authors is available in Wikipedia. |