Hardy-Weinberg Principle

Hardy–Weinberg Equilibrium (HWE) is a cipher model of the relationship between allele and genotype frequencies, both inside and between generations, under assumptions of no mutation, no migration, no selection, random mating, and infinite population size.

From: American Trypanosomiasis Chagas Disease (Second Edition) , 2017

Genetic Variation in Populations

Robert 50. Nussbaum MD, FACP, FACMG , in Thompson & Thompson Genetics in Medicine , 2016

The Hardy-Weinberg Police

The Hardy-Weinberg law rests on these assumptions:

The population under study is big, and matings are random with respect to the locus in question.

Allele frequencies remain constant over fourth dimension considering of the following:

In that location is no observable rate of new mutation.

Individuals with all genotypes are every bit capable of mating and passing on their genes; that is, there is no choice confronting any item genotype.

There has been no significant immigration of individuals from a population with allele frequencies very different from the endogenous population.

A population that reasonably appears to see these assumptions is considered to be inHardy-Weinberg equilibrium.

Hardy–Weinberg Equilibrium and Random Mating

J. Lachance , in Encyclopedia of Evolutionary Biology, 2016

The Hardy–Weinberg Principle

The Hardy Weinberg principle relates allele frequencies to genotype frequencies in a randomly mating population. Imagine that you lot have a population with two alleles (A and B) that segregate at a single locus. The frequency of allele A is denoted past p and the frequency of allele B is denoted past q. The Hardy–Weinberg principle states that after one generation of random mating genotype frequencies will be p ii, 2pq, and q 2. In the absence of other evolutionary forces (such as natural selection), genotype frequencies are expected to remain constant and the population is said to be at Hardy–Weinberg equilibrium. The Hardy–Weinberg principle relies on a number of assumptions: (1) random mating (i.due east, population construction is absent-minded and matings occur in proportion to genotype frequencies), (2) the absenteeism of natural selection, (iii) a very large population size (i.e., genetic drift is negligible), (4) no cistron flow or migration, (five) no mutation, and (6) the locus is autosomal. When these assumptions are violated, departures from Hardy–Weinberg proportions can result.

One useful way to recall almost the Hardy–Weinberg principle is to use the metaphor of a gene pool (Crow, 2001). Here, individuals contribute alleles to an infinitely large pool of gametes. In a randomly mating population without natural selection, offspring genotypes are found by randomly sampling two alleles from this gene pool (one from their mother and one from their male parent). Because the allele that an individual receives from their mother is independent of the allele they receive from their father, the probability of observing a item genotype is found past multiplying maternal and paternal allele frequencies. Mathematically this involves the binomial expansion: (p + q)2 = p 2 + 2pq + q two (see the modified Punnett Foursquare in Effigy 1 for a graphical representation). Note that there are two ways that an individual tin exist an AB heterozygote: they can either inherit an A allele from their mother and a B allele from their father or they tin can inherit a B allele from their mother and an A allele from their begetter.

Effigy 1. Graphical representation of the Hardy–Weinberg principle. The frequency of A alleles is denoted by p and the proportion of B alleles by q. AA homozygotes are represented by white, AB heterozygotes by greyness, and BB homozygotes by gilded. Shaded areas are proportional to the probability of observing each genotype.

Additional insight can exist found by because an empirical example (Effigy two). Consider a population that initially contains eighteen AA homozygotes, four AB heterozygotes, and 3 BB homozygotes. The alleles in the cistron puddle, eighty% are A and xx% are B. After a single generation of random mating we notice Hardy–Weinberg proportions: 16 AA homozygotes, 8 AB heterozygotes, and 1 BB homozygote. Note that allele frequencies remain unchanged.

Effigy ii. Hardy–Weinberg example. AA homozygotes (black circles), AB heterozygotes (black and gold circles), and BB homozygotes (gold circles) contribute to the gene pool. A alleles are shown as blackness half-circles and B alleles are shown equally gold half-circles. Later a single generation of random mating Hardy–Weinberg proportions are obtained.

At that place are a number of evolutionary implications of the Hardy–Weinberg principle. Near chiefly, genetic variation is conserved in large, randomly mating populations. A second implication is that the Hardy–Weinberg principle allows one to determine the proportion of individuals that are carriers for a recessive allele. 3rd, information technology is important to note that ascendant alleles are non e'er the most common alleles in a population. Some other implication of the Hardy–Weinberg principle is that rare alleles are more likely to be establish in heterozygous individuals than in homozygous individuals. This occurs because q ii is much smaller than 2pq when q is shut to zero.

The Hardy–Weinberg principle tin can be generalized to include polyploid organisms and genes that accept more than two segregating alleles. Equilibrium genotype frequencies are plant by expanding the multinomial (p 1 ++ p chiliad ) n , where n is the number of sets of chromosomes in a cell and k is the number of segregating alleles. For example, tetraploid organisms (n = four) with 2 segregating alleles (k = 2) are expected to accept genotype frequencies of: p 1 four (AAAA), 4p one iii p 2 (AAAB), 6p ane 2 p two 2 (AABB), ivp 1 p ii three (ABBB), and p 4 (BBBB). Similarly, diploid organisms (n = 2) with three segregating alleles (g = 3) are expected to have genotype frequencies of: p i 2 (AA), p two 2 (BB), p 3 2 (CC), 2p one p two (AB), 2p 1 p three (Air-conditioning), and 2p 2 p 3 (BC). Genotype frequencies sum to one for each of the in a higher place scenarios. Although the Hardy–Weinberg principle can too be generalized to include genes located on sex chromosomes (e.g., Ten chromosomes in humans), it is important to notation that it can take multiple generations for genotype frequencies at sex-linked loci to accomplish equilibrium values.

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Genetic Variation : Its Origin and Detection

Lynn B. Jorde PhD , in Medical Genetics , 2020

The Hardy–Weinberg Principle

The instance given for theMN locus presents an platonic situation for gene frequency estimation because, owing to codominance, the 3 genotypes can easily be distinguished and counted. What happens when one of the homozygotes is indistinguishable from the heterozygote (i.e., when there is authority)? Here the basic concepts of probability tin can be used to specify a predictable relationship between cistron frequencies and genotype frequencies.

Imagine a locus that has two alleles, labeledA anda. Suppose that in a population we know the frequency of alleleA, which we volition callp, and the frequency of allelea, which nosotros will callq. From these data we wish to determine the expected population frequencies of each genotype,AA, Aa, andaa. We will assume that individuals in the population mate at random with regard to their genotype at this locus(random mating is also referred to aspanmixia). Thus the genotype has no issue on mate selection. If men and women mate at random, then the assumption of independence is fulfilled. This allows the states to apply the addition and multiplication rules to estimate genotype frequencies.

Suppose that the frequency,p, of alleleA in our population is 0.7. This means that 70% of the sperm cells in the population must have alleleA, equally must 70% of the egg cells. Because the sum of the frequenciesp andq must be 1, 30% of the egg and sperm cells must conduct allelea (i.e.,q = 0.30). Under panmixia, the probability that a sperm prison cell conveyingA will unite with an egg cell carryingA is given past the product of the gene frequencies:p ×p =p 2 = 0.49 (multiplication rule). This is the probability of producing an offspring with theAA genotype. Using the same reasoning, the probability of producing an offspring with theaa genotype is given byq ×q =q ii = 0.09.

What about the frequency of heterozygotes in the population? There are two ways a heterozygote can exist formed. Either a sperm cell carryingA can unite with an egg conveyinga, or a sperm cell carryinga tin unite with an egg conveyingA. The probability of each of these two outcomes is given past the product of the factor frequencies,pq. Because we want to know the overall probability of obtaining a heterozygote (i.e., the first event or the 2d), we can apply the improver rule, calculation the probabilities to obtain a heterozygote frequency of 2pq. These operations are summarized inFig. 3.xxx. The relationship betwixt cistron frequencies and genotype frequencies was established independently past Godfrey Hardy and Wilhelm Weinberg and is termed theHardy–Weinberg principle.

Introductiona

Stephen D. Cederbaum , in Emery and Rimoin's Principles and Practice of Medical Genetics and Genomics (7th Edition), 2019

2.3.5 Statistical, Formal, and Population Genetics

A cornerstone of population genetics is the Hardy–Weinberg principle, named for Godfrey Harold Hardy (1877–1947), distinguished mathematician of Cambridge University, and Wilhelm Weinberg (1862–1937), physician of Stuttgart, Federal republic of germany, each publishing it independently in 1908. Hardy [36] was stimulated to write a short newspaper to explain why a ascendant gene would not, with the passage of generations, go inevitably and progressively more frequent. He published the paper in the American Journal of Science, perhaps considering he considered information technology a trivial contribution and would be embarrassed to publish it in a British journal.

R.A. Fisher, J.B.Southward. Haldane (1892–1964), and Sewall Wright (1889–1988) were the great triumvirate of population genetics. Sewall Wright is noted for the concept and term "random genetic drift." J.B.South. Haldane [37] (Fig. 1.ix) made many contributions, including, with Julia Bell [38], the start endeavor at the quantitation of linkage of two human being traits: color incomprehension and hemophilia. Fisher proposed a multilocus, closely linked hypothesis for Rh claret groups and worked on methods for correcting for the bias of ascertainment affecting segregation analysis of autosomal recessive traits.

Effigy i.nine. J.B.S. Haldane with Helen Spurway and Marcello Siniscalco at the 2nd World Congress of Human Genetics, Rome, 1961.

To test the recessive hypothesis for way of inheritance in a given disorder in humans, the results of different types of matings must exist observed as they are plant, rather than being set upward by blueprint. In those families in which both parents are heterozygous carriers of a rare recessive trait, the presence of the recessive gene is ofttimes not recognizable unless a homozygote is included amongst the offspring. Thus, the ascertained families are a truncated sample of the whole. Furthermore, under the usual social circumstances, families with both parents heterozygous may exist more likely to be ascertained if two, three, or four children are afflicted than they are if just one child is affected. Corrections for these so-called biases of ascertainment were devised by Weinberg (of the Hardy–Weinberg law), Bernstein (of ABO fame), and Fritz Lenz and Lancelot Hogben (whose names are combined in the Lenz–Hogben correction), every bit well as by Fisher, Norman Bailey, and Newton E. Morton. With the development of methods for identifying the presence of the recessive gene biochemically and ultimately past analysis of the DNA itself, such corrections became less oftentimes necessary.

Pre-1956 studies of genetic linkage in the human for the purpose of chromosome mapping are discussed afterward as part of a review of the history of that attribute of human being genetics.

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Population and Mathematical Genetics

Peter D. Turnpenny BSc MB ChB FRCP FRCPCH FRCPath FHEA , in Emery'due south Elements of Medical Genetics and Genomics , 2022

The Hardy-Weinberg Principle

Consider an "platonic" population in which there is an autosomal locus with ii alleles, A and a, that take frequencies of p and q, respectively. These are the only alleles found at this locus, so that p + q=100%, or 1. The frequency of each genotype in the population tin exist adamant by structure of a Punnett square, which shows how the different genes can combine (Fig. 7.1).

FromFig. 7.i, it tin can exist seen that the frequencies of the unlike genotypes are:

Genotype Phenotype Frequency
AA A pii
Aa A 2pq
aa a qtwo

If there is random mating of sperm and ova, the frequencies of the dissimilar genotypes in the first generation will be as shown. If these individuals mate with one some other to produce a second generation, a Punnett square can once again exist used to show the different matings and their frequencies (Fig. seven.2).

FromFig. seven.ii the total frequency for each genotype in the 2d generation can exist derived (Tabular array vii.1 ). This shows that the relative frequency or proportion of each genotype is the same in the second generation as in the beginning. In fact, no matter how many generations are studied, the relative frequencies will remain constant. The bodily numbers of individuals with each genotype will alter as the population size increases or decreases, simply their relative frequencies or proportions remain constant—the fundamental tenet of the Hardy-Weinberg principle. When epidemiological studies confirm that the relative proportions of each genotype remain abiding with frequencies of p2, 2pq and qtwo, then that population is said to exist in Hardy-Weinberg equilibrium for that particular genotype.

Fundamentals of Complex Trait Genetics and Association Studies

Jahad Alghamdi , Sandosh Padmanabhan , in Handbook of Pharmacogenomics and Stratified Medicine, 2014

12.iii.1.ane Hardy-Weinberg Equilibrium

In 1908, two scientists—Godfrey H. Hardy, an English mathematician, and Wilhelm Weinberg, a German language physician—independently worked out a mathematical relationship that related genotypes to allele frequencies chosen the Hardy-Weinberg principle, a crucial concept in population genetics. It predicts how cistron frequencies will exist inherited from generation to generation given a specific set of assumptions. When a population meets all the Hardy-Weinberg conditions, it is said to be in Hardy-Weinberg equilibrium (HWE). Human populations practice not come across all the atmospheric condition of HWE exactly, and their allele frequencies volition change from one generation to the next, so the population evolves. How far a population deviates from HWE can be measured using the "goodness-of-fit" or chi-squared test (χ2) (See Box 12.4).

Box 12.4

Hardy-Weinberg Equilibrium

The distribution of genotypes in a population in Hardy-Weinberg equilibrium can be graphically expressed as shown in the accompanying graph. The x-axis represents a range of possible relative frequencies of A or B alleles. The coordinates at each signal on the iii genotype lines show the expected proportion of each genotype at that particular starting frequency of A and B.

To check for HWE:

Consider a single biallelic locus with 2 alleles A and B with known frequencies (allele A   =   0.6; allele B   =   0.4) that add together up to i.

Possible genotypes: AA, AB and BB

Assume that alleles A and B enter eggs and sperm in proportion to their frequency in the population (i.e., 0.6 and 0.iv)

Assume that the sperm and eggs meet at random (one big gene pool).

Calculate the genotype frequencies every bit follows:

The probability of producing an individual with an AA genotype is the probability that an egg with an A allele is fertilized by a sperm with an A allele, which is 0.6   ×   0.six or 0.36 (the probability that the sperm contains A times the probability that the egg contains A).

Similarly, the frequency of individuals with the BB genotype tin be calculated (0.four   ×   04   =   0.16).

The frequency of individuals with the AB genotype is calculated by the probability that the sperm contains the A allele (0.6) times the probability that the egg contains the B allele (0.4), and the probability that the sperm contains the B allele (0.6) times the probability that the egg contains the A allele. Thus, the probability of AB individuals is (two   ×   0.four   ×   0.6   =   0.48).

Genotypes of the next generation can be given equally shown in the accompanying table.

Allele Allele Frequency Genotype Frequency Counts for 1000
A (p) 0.6 AA 0.36 360
B (q) 0.4 AB 0.48 480
General formula of HW equation: ptwo  +   2pq   +   q2  =   ane BB 0.16 160
Total 1 g

The conclusions from HWE are follows:

Allele frequencies in a population exercise not alter from i generation to the next simply as the result of assortment of alleles and zygote formation.

If the allele frequencies in a genetic pool with ii alleles are given by p and q, the genotype frequencies is given past p2, 2pq, and q2.

The HWE principle identifies the forces that can cause evolution.

If a population is not in HWE, one or more than of the five assumptions is existence violated.

Thus, HWE is based on five assumptions:

Random choice: When individuals with sure genotypes survive better than others, allele frequencies may change from one generation to the next.

No mutation: If new alleles are produced by mutation or if alleles mutate at different rates, allele frequencies may change from one generation to the next.

No migration: Motility of individuals in or out of a population alters allele and genotype frequencies.

No chance events: Luck plays no part in HWE. Eggs and sperm collide at the same frequencies as the actual frequencies of p and q. When this assumption is violated and by chance some individuals contribute more alleles than others to the next generation, allele frequencies may alter. This mechanism of allele modify is called genetic drift.

Individuals select mates at random: If this assumption is violated, allele frequencies do modify, only genotype frequencies may.

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Underdominance

F.A. Reed , ... P.M. Altrock , in Brenner'south Encyclopedia of Genetics (2nd Edition), 2013

Evolutionary Dynamics

Unstable Equilibrium

At an equilibrium, the allele frequency does not alter over time. An equilibrium is stable if pocket-size perturbations lead back to it. It is unstable if minor perturbations pb away, typically toward other, stable equilibria. Heritable fitness differences are expected to lead to evolutionary change in a population over time, driven by natural selection. In the instance of underdominance, heterozygotes are expected to produce fewer offspring in the following generation, corresponding to the fitness disadvantage. According to the Hardy–Weinberg principle (random pairing of alleles), alleles that are rare in a population (low starting frequency) are most often paired with alleles of another type, resulting in a heterozygous genotype. Thus, underdominance is expected to result in a disadvantage of rare alleles, which tend to exist removed from the population by natural selection. However, the same alleles can go on to fixation in a population if they occur every bit homozygotes sufficiently oftentimes, which requires a high starting frequency. In that location is an unstable equilibrium frequency that divides these 2 regimes. The direction of selection in underdominance is thus reverse of the one in overdominance, which is characterized by a stable polymorphic equilibrium frequency (see Figure two ).

Figure ii. Evolution of the frequency of allele A of a single-locus two-allele arrangement with underdominance. For simplification, an infinitely large population with random mating is causeless. The fettle of AA homozygotes is 0.nine and the fitness of BB homozygotes is ane. Heterozygotes have a relative fitness disadvantage of 0.45 (as illustrated in the inset). Trajectories are shown for the five initial allele frequencies 0.2, 0.4, 0.55, 0.six, and 0.eight. For the first two initial conditions, A goes extinct. For the last two initial conditions, A proceeds to fixation. In this example, 0.55 is exactly the unstable equilibrium allele frequency; pocket-size deviations, for example, caused by demographic noise, lead away from it.

Geographic Stability

A geographically stable design can emerge when different alleles leading to underdominance in heterozygotes become established in different populations. Consider two isle populations that substitution a small number of migrant individuals. On the first island, the AA genotype is at loftier frequency. On the 2nd island, the BB genotype is at loftier frequency. If migrants are rare, they tend to mate with the contrary genotype producing less fit heterozygotes in the following generation, which volition exist removed past natural selection. This can result in a migration–pick equilibrium where the departure in allele frequencies betwixt the two populations is maintained by selection as long equally migration rates are beneath disquisitional levels. If migration rates are too loftier, the two island populations substantially reduce to a single mixed population, which tin can just maintain one of the alleles that are in underdominance with each other.

Mutations that can result in underdominance, once established locally, are not necessarily expected to spread nor to exist lost. This may provide a ground for other selective forces to human action, such as mate choice, to strengthen the genetic segmentation between populations.

Office in Speciation

Early on, chromosomal rearrangements resulting in underdominance were appreciated as a possible mechanism to drive the early stages of speciation. This outcome is referred to as 'chromosomal speciation'. The hypothesis later brutal out of favor: information technology was realized that a new (and thus rare and frequently heterozygous) underdominant mutation reaching high frequency in an initial population is exceedingly improbable with increasing fitness disadvantage. Several possible effects have been proposed to help alleviate this, such as meiotic drive of chromosomal rearrangements, or fitness advantages associated with the new allele, but the strength and frequency of these additional effects remained unclear. Nevertheless, potentially underdominant chromosomal rearrangements do accumulate rapidly (on an evolutionary timescale) between closely related species. Hence, there must be some mechanism for these changes to become established at loftier frequency in a population. Some species of flies do non show fitness reduction in individuals with chromosomal inversions that are expected to be underdominant, because recombination appears to be suppressed. Recently, it has likewise been found that translocations affect expression patterns of genes across the genome. This provides the potential for (perhaps locally adaptive) fitness differences that are associated with a chromosomal rearrangement to simultaneously appear with a bulwark to cistron flow. This could help resurrect chromosomal speciation hypotheses. Recent work has besides focused on the cocky-organizing effects of many loci with weak underdominance, which have a higher private likelihood of attaining higher frequencies.

Applications

The field of genetic pest management is focused on using genetic techniques to control or alter populations in the wild. A subset of this field seeks to utilize the effects of underdominance in 2, not mutually sectional, ways. In the starting time case, the aim is to suppress wild populations past producing large numbers of heterozygotes after releases of large numbers of individuals carrying alternative alleles. The 2nd arroyo builds on genetically transforming wild populations with desirable alleles: disease resistance caused by an effector gene can exist linked to an underdominant drive mechanism. Early on work to found underdominance in wing species essentially failed, because the genetically contradistinct homozygotes were likewise unfit to be competitive in the wild. However, new approaches and techniques may allow underdominance to exist used to transform wild populations in a fashion that is not only geographically stable, simply also potentially reversible to the original wild-type state.

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Biological science/DNA

A. Amorim , in Encyclopedia of Forensic Sciences (Second Edition), 2013

Genetic Theory and Probabilities

The foundations of the genetic theory have been laid well-nigh 150 years ago by Gregor Mendel. The field of awarding is limited to characteristics, or observation units (from classical traits such as colour or form, to the outputs of technologically sophisticated methods such as electrophoresis or mass spectrometry) for which the population under study shows discontinuous variation (i.eastward., the individuals announced every bit grouped into discrete classes, called phenotypes). The theory assumes that for each of these characteristics, a pair of genetic information units exists in each individual (genotype), but simply 1 is transmitted to each offspring at a time with equal probability (1/2). Then, for nonhermaphroditic sexually reproducing populations, each member inherits one of these genetic factors (alleles) paternally and the other one maternally; in case of both alleles are of the same type, the individual is said to be a homozygote, and heterozygote in the case the alleles are distinct. The theory farther assumes that for each of the appreciable units (or Mendelian characteristics), there is a genetic determination case (a genetic locus; plural: loci) where the alleles accept identify and that the transmission of information belonging to unlike loci and governing, therefore, singled-out characteristics is independent. It is now known that for some characteristics, the mode of transmission is more than simple and that not every pair of loci is transmitted independently, but the hereditary rules outlined to a higher place apply to the vast majority of cases.

These rules allow us to predict the possible genotypes and their probabilities in the offspring knowing the parents' genotypes or to infer parents' genotypes given the offspring distributions. These predictions or inferences are not limited to cases where information on relatives is available. In fact, presently after the 'rediscovery' of Mendel'south work, a generalization of the theory from the familial to the population level was undertaken embodied in what is now known as the Hardy–Weinberg principle. This formalism states that if an ideal space population with random mating is assumed, and in the absence of mutation, selection, and migration, the squared summation of the allele frequencies equals the genotype distribution. That is, if at a certain locus, the frequencies of alleles A1 and A2 are f1 and f2, respectively, the expected frequency of the heterozygote A1A2 will exist f1   ×   f2   +   f2   ×   f1   =   2f1f2 (note that 'A1A2' and 'A2A1' are duplicate and are collectively represented by convention just as A1A2); conversely, if the frequency of the homozygote for A1 is f1, the allele frequency would be the foursquare root of this frequency (because the expected frequency of this genotype is f1   ×   f1).

In order to apply this theoretical framework to judicial matters, it must exist articulate that 'forensics' implies conflict, a difference of stance, which formally translates into the existence of (at to the lowest degree) two culling explanations for the aforementioned fact. In the simplest state of affairs, the testify is explained to the court as (1) being caused past the doubtable (the prosecution hypothesis) or, alternatively, (ii) resulting from the activity of someone else, co-ordinate to the defence.

In order to understand how genetic expertise can provide ways to differently evaluate the evidence under these hypotheses, a brief digression into the mathematics and statistics involved is therefore required. The first essential concept to be defined is probability itself. The probability of a specific event is the frequency of that outcome, or in more formal terms, probability of an effect is the ratio of the number of cases favorable to it, to the number of all cases possible. It is a convenient manner to summarize quantitatively our previous experience on a specific case and allows us to forecast the likelihood of its future occurrence. But this is not the issue at stake when nosotros motility to the forensic scenario – the event has occurred (both litigants agree upon that) but there is a disagreement on the causes behind it, meaning that the same event can have different probabilities according to its causation.

Let us suppose that a biological sample (a hair, organic fluid, etc.) not belonging to the victim is plant in a homicide scene. When typed for a specific locus, information technology shows the genotype 'xix', as well as the suspect (provider of a 'reference sample'). If allele 19 frequency in the population is ane/100, the probability of finding past chance such a genotype is thus ane/x   000. Therefore, under the prosecutor's hypothesis (the crime scene sample was left by the suspect), the probability of this type of observations (P|H1) is 1/10   000. While assuming the defense force explanation (the law-breaking scene sample was left past someone else), the probability of the same observations (P|H2) would exist 1/10   000   ×   1/x   000. In conclusion, the likelihood ratio takes the value of x   000 (to ane), which means that the occurrence of such an event is 10   000 times more likely if both samples have originated from the same individual than resulting from ii distinct persons (again provided the suspect does not have an identical twin). Annotation that this likelihood ratio is frequently referred as 'probability of identity,' although it is not a probability in the strict sense.

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GENETIC Assay

Raphael Falk , in Philosophy of Biology, 2007

7 POPULATION GENETICS UPHOLDS DARWINISM

Mendel's hypothesis of inheritance of discrete factors that are not diluted should accept resolved a major difficulty that Darwin encountered. Shortly after the publication of his Origin of Species, in 1867, Fleeming Jenkins showed that, adopting Darwin'southward theory of inheritance by mixing pangenes, would wash out any achievement of natural selection (meet Hull [1973, 302-350]). Hugo de Vries and specially William Bateson, considered Mendel'due south Faktoren as indicated by his hypothesis of inheritance to provide a rational basis for the theory of evolution. Although every bit early on as in 1902 Yule showed that, given small enough steps of variation, the Mendelian model reduces to the biometric merits [Yule, 1902], this was largely ignored in the bitter disputes between the Mendelians and the Biometricians [Provine, 1971], (see Tabery [2004]). Hardy'due south [1908] proof that in a large population, the proportion of heterozygotes to homozygotes volition reach equilibrium after ane generation of random mating (provided no mutation or choice interfered), developed in the same year by Weinberg [Stern, 1943 ], became the basic theorem of population genetics — the Hardy-Weinberg principle. It took, nonetheless, another decade for R. A. Fisher to convince that the continuous phenotypic biometric variation reduces to the Mendelian model of polygenes [ Fisher, 1918]. Thus, finally the style was cleared to examine the Darwinian theory of natural evolution on the footing of Mendelian genetic analysis, not only in vivo but too in papyro. As formulated by Fisher in his fundamental theorem of natural selection: "The rate of increase in fitness of any organism at any time is equal to its genetic variance in fitness at that time" [Fisher, 1930, 37].

Whereas Fisher examined primarily the effects of selection of alleles of single genes in indefinitely large population under the supposition of differences in genotypic fitness, J. B. S. Haldane concentrated on the touch of mutations on the rate and direction of evolution of one or few genes (and the influence of population size) [Haldane, 1990]. Sewall Wright in his models of the dynamics of populations wished to be more "realistic", and stressed the influence of finite population size, the limited gene flow between subpopulations, and the heterogeneity of the habitats in which the population and its subpopulations lived [Wright, 1986].

Experimentally, the main British group, led by E. B. Ford adopted a strict Mendelian reductionist approach, emphasizing largely the furnishings of choice on unmarried alleles of specific genes (the evolution of industrial melanism in moths, the development of mimicry in African moth species, the development of seasonal polymorphisms in snails, etc.). The American geneticists, especially Dobzhansky and his school, full-bodied more on issues of whole genotypes, such equally speciation (Sturtevant) and chromosomal polymorphisms (Dobzhansky) in Drosophila.

The triumph of reductionist Mendelism was at the 1940s with the emergence of the "New Synthesis" that defined natural populations and the forces that affect their evolution in terms of gene alleles' frequencies [Huxley, 1943]. This notion dominated population genetics for the next decades. Attempts to emphasize the role of not-genetic constraints, such as the anatomical-physiological factors (east.k. by Goldschmidt [1940]), or the ecology (and evolutionary-historical) constraints (for case by Waddington [1957]) were largely disregarded.

The introduction of the analysis of electrophoretic polymorphisms [Hubby and Lewontin, 1966; Lewontin and Husband, 1966] immune a molecular analysis of allele variation that was too largely independent of the classical morphological and functional genetic markers (see also Lewontin [1991]). Although genes were even so treated as algebraic point entities, inter-genic interacting organisation, such every bit "linkage disequilibrium" were considered [Lewontin and Kojima, 1960]. The New Synthesis was, however, seriously challenged when it was realized that a great bargain of the variation at the molecular level was determined by stochastic processes, rather than because of differences in fitness [Kimura, 1968; King and Jukes, 1969].

This assault on the notion of the New Synthesis was intensified when, in 1972 Gould and Eldridge, 2 paleontologists, suggested a model of evolution past "punctuated equilibrium", or long periods of little evolutionary change interspersed with (geologically) relatively brusque period of fast evolutionary modify. Moreover, in the periods of (relatively) fast evolution big ane-pace "macromutational" changes were established [Eldredge and Gould, 1972]. Although it could be shown that analytically the claims of punctuated equilibrium could exist reduced to those of classical population genetics [Charlesworth et al., 1982], these ideas demanded re-examination of the developmental conceptions that, every bit a dominion, could non have i-pace major developmental changes since these called for disturbance in many systems and hence would have acquired severe disturbances in developmental and reproductive coordination.

The need to reexamine the reductionist assumptions of genetic population analysis and to pay more consideration to constraints on the genetic determinations of intra- and extra-organismal factors coincided with the resurrection of developmental genetics. Withal, the major alter in the analysis of evolution and development came from the molecular perspective. These allowed commencement of all detailed upwardly analysis, from the specific DNA sequences to the early products, rather than the analyses based on end-of-developmental pathway markers. Yet, arguably, the most significant development was the possibility of in-vitro Deoxyribonucleic acid hybridization. This molecular extension of genetic assay sensu stricto finally overcame the empirical impossibility to study (most) in vivo interspecific hybrids. The new methods of Deoxyribonucleic acid hybridization had no taxonomic inhibitions whatsoever, and soon hybrid Dna molecules of, say mosquito, homo and found, were common subjects for research. Genetic applied science, which allowed straight genetic comparison between any species and the transfer of genes from one species to individuals of another, unrelated species, prompted the genetic analysis of the evolution of developmental process, or evo-devo.

Molecular genetic analysis of homeotic mutants, in which one organ is transformed into the likeness of another, unremarkably a homologous 1, revealed stretches of Deoxyribonucleic acid that were virtually identical in other genes with homeotic effects (similar the homeobox of some 180 nucleotides, that appear to be involved in when-and-where particular groups of genes are expressed along the embryo centrality during development [McGinnis et al., 1984a; McGinnis et al., 1984b]). The method of determining homologies by comparing Deoxyribonucleic acid sequences is nowadays done mainly in silico. As suggested many years ago [Ohno, 1970], the abundance of homologous sequences in the same species genome (paralogous sequence that do not necessarily share similar functions whatsoever more than) or in different species (orthologous sequences that 'usually' accept similar functions in different species), signal that the system'due south structural and functional organization have been also causal factors rather than only consequences in the history of the process of evolution.

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FORMALISATIONS OF EVOLUTIONARY BIOLOGY

Paul Thompson , in Philosophy of Biological science, 2007

3.two Formalisation in Population Genetics

The miracle of heredity, although widely accustomed since at least the Greco-Roman period, is extremely complex and an adequate theory proved allusive for several thou years. Indeed, features of heredity seemed almost magical. Breeders from artifact had a sophisticated understanding of the effects of selective breeding but fifty-fifty the nigh accomplished breeders found many aspects of heredity to be capricious. Fifty-fifty Darwin in the middle 19th century knew well the techniques of selective convenance (artificial selection) simply did not have bachelor a satisfactory theory of heredity when he published the Origin of Species [1859]. Although, he realized that his theory of evolution depended on heredity, he was unable to provide an business relationship of it. Instead, he relied on the widely known furnishings of bogus option and by analogy postulated the effects of natural selection in which the alternative of breeders was replaced by forces of nature.

The first major accelerate came from the unproblematic experiments and mathematical description of the dynamics of heredity past Gregor Mendel [1865]. Although Mendel's piece of work went largely unnoticed until the beginning of the 20th century, its smashing forcefulness lay in its mathematical clarification — elementary though that description was. Mendel performed a number of experiments which provided important data merely it was his elementary mathematical description of the underlying dynamics that has had a lasting touch on genetics. His dynamics were uncomplicated. He postulated that a phenotypic characteristic (feature of organisms) is the result of the combination of ii "factors" in the hereditary textile of the organism. Dissimilar characteristics are caused past dissimilar combinations. Focusing on ane characteristic at a time made the problem of heredity tractable. Factors could be dominant or recessive. If two dominant factors combined, the organism would manifest the characteristic controlled by that cistron. If a dominant and a recessive factor combined, the organism would manifest the characteristic of the dominant cistron (that is the sense in which it is dominant). If ii recessive factors combine, the organism will manifest the characteristic of the recessive gene.

Mendel postulated two principles (oft at present referred to every bit Mendel's laws): a principle of segregation and a principal of contained assortment. The principle of segregation states that the factors in a combination will segregate (divide) in the production of gametes. That is gametes volition comprise only one factor from a combination. The principle of independent assortment states that the factors do non blend but remain distinct entities and at that place is no influence of one gene over the other in segregation. The central principle is the law of segregation. The law of independent array can be folded into the law of segregation as function of the definition of segregation. When gametes come together in a fertilised ovum (a zygote), a new combination is fabricated.

Assume A is a dominant gene and a is a recessive factor. 3 combinations are possible AA, Aa and aa. Mendel's experimental piece of work involved convenance AA plants and aa plants. He then crossed the plants which produced only Aa plants. He then bred the Aa plants. What resulted was .25AA, .5Aa and .25aa. His dynamics explains this result. Since the factors A and a exercise non blend and they segregate in the gametes and combine again in the zygote, the results are fully explained. Crossing the AA plants with aa plants volition yield but Aa plants:

Convenance only Aa plants will yield the .25:.5:.25 ratios:

2 of four cells yield Aa that is .v of the possible combinations. Each of AA and aa occupy only 1 jail cell in four, that is, .25 of the possible combinations. In gimmicky population genetics, Mendel'southward factors are called alleles. The location on the chromosome where a pair of alleles is located is chosen a locus. Sometime the term gene is used as a synonym for allele but this usage is far too loose. After, I will explore the defoliation, complexity and controversy over the definition of "gene." Mendel's dynamics assumed diallelic loci: 2 alleles per locus. His dynamics are easily extended to cases where each locus has many alleles any two of which could occupy the locus.

The bones features of Mendel's dynamics were modified and extended early in the 20th century. G. Udny Yule [1902] was amongst the first to explore the implications of Mendel's organisation for populations. In a verbal substitution betwixt Yule and R. C. Punnett in 1908, Yule asserted that a novel dominant allele arising among a 100% recessive alleles would inexorably increase in frequency until it reach 50%. Punnett believing Yule to be wrong only unable to provide a proof, took the problem to Chiliad. H. Hardy. Hardy, a mathematician, quickly produced a proof by using variables where Yule had used specific allelic frequencies. In effect, he developed a elementary mathematical model. He published his results in 1908. What emerged from the proof was a principle that became central to population genetics, namely, afterward the outset generation, allelic frequencies would remain the same for all subsequent generations; an equilibrium would be reached after merely i generation. As well in 1908, Wilhelm Weinberg published similar results and articulated the same principle (the original paper is in German, and English translation is in Boyer [1963 ]). Hence, the principle is known as the Hardy-Weinberg principle or the Hardy-Weinberg equilibrium. 37 In parallel with these mathematical advances was a confirmation of the phenomenon of segregation and recombination in the new field of cytology.

Building on this early work, a sophisticated mathematical model of the complex dynamics of heredity emerged during the 1920s and 1930s, principally through the piece of work of John Haldane [1924; 1931; 1932], Ronald Fisher [1930] and Sewall Wright [1931; 1932]. What has become modern population genetics began during this flow. From that period, the dynamics of heredity in populations has been studied from within a mathematical framework. 38

Equally previously indicated, i of the primal principles of the theory of population genetics, in the form of a mathematical model, is the Hardy-Weinberg Equilibrium. Similar Newton'south Get-go Police, this principle of equilibrium states that after the outset generation if nothing changes so allelic (gene) frequencies will remain abiding. The presence of a principle(south) of equilibrium in the dynamics of a arrangement is of key importance. It defines the conditions under which nothing will alter. All changes, therefore, crave the identification of cause(s) of the change. Newton'south dynamics of movement include an equilibrium principle that states that in absence of unbalanced forces an object will continue in uniform motion or at residual. Hence dispatch, deceleration, modify of direction all crave the presence of an unbalanced forcefulness. In population genetics, in the absence of some perturbing factor, allelic frequencies at a locus will not alter. Factors such as selection, mutation, meiotic bulldoze, and migration are all perturbing factors. Similar many complex systems, population genetics as well has a stochastic perturbing strength, normally telephone call random genetic drift.

In what follows, the key features of the mathematical model of contemporary population genetic theory are fix out. Quite naturally, the exposition begins with the Hardy-Weinberg Equilibrium. It is useful to begin with the exploration of a one locus, two-allele system. In anticipation, withal, of multi allelic loci, nosotros switch from A and a to 'A ane' and 'A2'. Hence, co-ordinate to the Hardy-Weinberg Equilibrium, if there are two dissimilar alleles 'Aane' and 'A2' at a locus and the ratio in generation one is A1:Atwo = p: q, and if there are no perturbing factors, and then in generation 2, and in all subsequent generations, the alleles will exist distributed:

( p ii ) A 1 A one : ( 2 p q ) A 1 A 2 : ( q 2 ) A 2 A 2 .

The ratio of p: q is normalised past requiring that p + q = ane. Hence, q =1 — p and i — p tin can exist substituted for q at all occurrences. The proof of this equilibrium is remarkably merely.

The boxes contain zygote frequencies. In the upper left box, the frequency of the zygote arising from the combination of an A 1 sperm and A 1 egg is p × p, or p 2, since the initial frequency of A 1 is p. In the upper right box, the frequency of the zygote arising from the combination of an A two sperm and A i egg is p × q, or pq, since the initial frequency of an A 2 is q and the initial frequency of A 1 is p.

Sperm

fr(A 1) = p fr(A 2) = p
Ova fr(A 1) = p fr(A oneA1) = p ii fr(AiiA 1) = pq
fr(A 2) = P fr(A i A ii) = pq fr(A2A2) = q2

The lower left box also yields a pq frequency for an A one A two. Since the order doesn't matter, A2Ai is the same every bit A1A2 and hence the sum of frequencies is 2pq.

This proves that a population with A 1: Aii = p:q in an initial generation will in the adjacent generation have a frequency distribution: (p2)AaneA1: (2pq)AoneA2: (qtwo)A2Aii. The second footstep is to show that this distribution is an equilibrium in the absence of perturbing factors. Given the frequency distribution (p2)A1A1: (2pq)A1Atwo: (q2)AiiAtwo, p2 of the alleles volition exist A 1 and one-half of the A 1 A2 combination will be Aane, that is pq. Hence, there will be p 2 + (pq)Ai in this subsequent generation. Since q = (1 — p), we tin substitute (one — p) for q, yielding pii + (p(1 – p)) = p2 + (p – pii) = p. Since the frequency of A one in this generation is the same as in the initial generation (i.eastward., p), the same frequency distribution will occur in the following generation (i.e., (p2)A1Aane: (2pq)A1A2: (q2)AiiA2).

Consequently, if there are no perturbing factors, the frequency of alleles after the offset generation will remain constant. But, of course, there are ever perturbing factors. I fundamental one for Darwinian evolution is choice. Selection can be added to the dynamics by introducing a coefficient of selection. For each genotype (combination of alleles at a locus 39 ) a fitness value can be assigned. Abstractly, AoneA1 has a fitness of Due west 11, AoneA2 has a fitness of Due west12, and AiiAtwo has a fitness of Due west22. Hence, the ratios afterward selection will be:

W xi ( p 2 ) A 1 A one : W 12 ( 2 p q ) A 1 A 2 : W 22 ( q ii ) A ii A 2 .

To calculate the ratio p: q afterward selection this ratio has to exist normalised to brand p + q =one. To do this, the average fitness, westward, is calculated. The average fitness is the sum of the private fitnesses.

due west ¯ = w 11 ( p 2 ) + westward 12 ( 2 p q ) + w 22 ( q 2 ) .

Then each factor in the ratio is divided by due west, to yield:

( ( w 11 ( p two ) ) / w ¯ ) A 1 A 1 : ( ( w 12 ( 2 p q ) / w ¯ ) A 1 A 2 : ( ( w 22 ( q 2 ) / w ¯ ) A 2 A 2 . ) )

Other factors such as meiotic bulldoze tin can be added either as additional parameters in the Hardy-Weinberg equilibrium or as split up ratios or equations.

Against this background, a precise awarding of a X 2-test of goodness of fit can be provided. The post-obit example 40 illustrates the determination the goodness of fit between observed data and the expected data based on the Hardy-Weinberg equilibrium. The human chemokine receptor 41 gene CC-CKR-5codes for a major macrophage co-receptor for the human immunodeficiency virus HIV-1. CC-CKR-5 is part of the receptor structure that allows the entry of HIV-one into macrophages and T-cells. In rare individuals, a 32-base-pair indel 42 results in a non-functional variant of CC-CKR-5. This variant of CC-CKR-5 has a 32-base of operations-pair deletion from the coding region. This results in a frame shift and truncation of the translated protein. The indel results when an private is homozygous for the allele Δ32 43 . These individuals are strongly resistant to HIV-1; the variant CC-CKR-v co-receptor blocks the entry of the virus into macrophages and T-cells.

In a sample of Parisians studied for not-deletion and deletion (+ and Δ32 respectively), Lucotte and Mercier (1998) found the following genotypes:

++: 224 + Δ32: 64 Δ32Δ32: six

Dividing by the populations sample size yields the genotype frequencies:

++: 224/294 = 0.762 + Δ32: 64/294 = 0.218 Δ32Δ32: 6/994 = 0.20

Multiplying the number of homozygotes for an allele by ii and adding the number of heterozygotes yields the number of that allele in the sample. Dividing that past the sample size times 2 (in that location are twice as many alleles every bit individuals) yields the allelic frequency of this sample. Hence:

The frequency of the + allele = 0.871

The frequency of the Δ32 allele = 0.129

What genotype numbers does the hardy-Weinberg equilibrium yield given these allelic frequencies?

( p 2 ) + + : ( ii p q ) + Δ 32 : ( q two ) Δ 32 Δ 32 Yields ( 0 .871 2 ) + + : ( 2 ( 0.871 X 0.129 ) ) + Δ 32 : ( 0.129 ii ) Δ 32 Δ 32 = 0.758641 + + : 0.224718 + Δ 32 : 0.016641 Δ 32 Δ 32

Hence, in a population of 294 individuals, the Hardy-Weinberg equilibrium yields:

+ + : 22.ix + Δ 32 : 66.ii Δ 32 Δ 32 : 4.9

As we would expect these add together up to 294. A comparison of the values expected based on the Hardy-Weinberg equilibrium and those observed yields:

H - D expected : + + : 222 .nine + Δ 32 : 66 .2 Δ 32 Δ 32 : 4 .ix Observed : + + : 224 + Δ 32 : 64 Δ 32 Δ 32 : vi

Now nosotros tin inquire, how proficient is the fit between the H-D expected values based on the specified allelic frequencies and the observed values?

The X 2-test is:

X two = Σ (observed quantity – expected quantity)2/(expected quantity) There are iii genotypes, hence:

Ten2 = ((224 – 222.9)2/222.nine) + ((64 – 66.2)2/66.2) + ((6 – iv.9)2/4.nine)
= (ane.21/222.ix) + (4.84/66.2) + (1.21/four.ix)
= 0.00543 + 0.0731 + 0.2469
= 0.3254

To use this result to assess goodness of fit, information technology is necessary to decide the degrees of freedom for the test.

Degrees of Liberty (df) = (classes of data – 1) – the number of parameters estimated.

Since there are three genotypes, the classes of information is 3. Since p + q = one(hence, q is a function of p; they are not independent parameters), at that place is simply 1 parameter existence estimated. Hence, the degrees of freedom for this exam is:

Using the X 2 result and 1 degree of liberty allows a probability value to be determined.

In this case, the relevant probability is 0.63. This is the probability that hazard alone could have produced the discrepancy between the H-D expected values and the observed values. Since we are measuring the probability that risk alone could have produced the discrepancy (not to be confused with the similarity betwixt the two 44 ), the higher the probability, the more robust one's confidence that there are no factors other than chance causing the discrepancy and, hence, that there is a adept fit between the values expected based on the model and the observed values 45 ; any discrepancy is a function of risk solitary.

The elementary framework sketched above has been expanded to include the Wright-Fisher model of Random Drift, mutations, inbreeding and other causes of non-random breeding, migration speciation, multiple alleles at a locus, multi-loci systems, phenotypic plasticity, etc. One important expansion relates to interdemic option.

The account so far describes intrademic option. That is, selection of individuals within an interbreeding population — a deme. Withal, the mathematical model also permits the exploration of interdemic option (selection between genetically isolated populations) using adaptive landscapes. One outcome of such explorations is a sophisticated account of why and how populations reach sub-maximal, sub-optimal peaks of fitness. Richard Lewontin, building on concepts set up out by Sewell Wright, provided the first mathematical description of this phenomenon.

Consider a population genetic system with two loci and two alleles (here for simplicity I revert to upper and lower case letter of the alphabet for alleles and for say-so and recessiveness). The possible combinations of alleles is:

AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB AaBB AaBb aaBB aaBb
ab AabBb Aabb aaBb aabb

There are 9 different combinations (genotypes). For each genotype a fitness co-efficient Due westi can exist assigned. In addition, for each genotype a frequency can exist assigned based on p1 and q1, p2 and q2 (for locus i and locus 2 respectively). Let that frequency be Zi. The product of the frequency of a genotype and the fitness of that genotype is the contribution to the average fettle of the population w made by that genotype. The sum of the contributions of all the genotypes represented in the population is the average fitness w ¯ of the population. Hence, the average fettle w ¯ for a population

Consider the following calculation for a unmarried population.

Since pane + qi = 1 and ptwo + q2 = ane, the value of q tin can be determined from the value of p. Hence the value of p alone is sufficient to determine the genotype frequencies of the population.

In accordance with the Hardy-Weinberg equilibrium, the genotype frequencies can be calculated by multiplying the frequencies of the allelic combinations at each locus in the 2 loci pair. The resulting frequencies with assigned fitnesses, frequency-fitnesses, and the boilerplate fitness for the population is shown in the following table:

Genotype Frequency Z Fettle Westward Frequencey × Fitness
AABB 0.784 0.85 0.06664
AABb 0.23522 . 0.48 0.108192
AAbb 0.1764 0.54 095256
AaBB 0.0672 0.87 0.058484
AaBb 0.2016 0.65 0.13104
Aabb 0.1512 0.32 0.048384
aaBB 0.0144 0.61 0.008784
aaBb 0.0432 1.2 0.05184
aabb 0.0324 one.13 0.036612
w = 0.605212

Past plotting the average fitness w ¯ of each possible population in a two loci arrangement with the assigned fitness values Wi, an adaptive landscape for the system can be generated. This adaptive landscape is a three dimensional phase infinite (a system with a larger number of loci volition have a correspondingly larger dimensionality):

The plotted point is the average fitness of the population described above. A complete adaptive mural is a surface with adaptive peaks and valleys. An actual population under choice may climb a gradient to an adaptive acme that is sub maximal (i.e., the average fitness of the population is less than the highest average fettle in the organisation). The only way to move to some other slope which leads to a more than maximal or maximal boilerplate fitness is to descend from the meridian. This involves evolving in a management of reduced average fitness that is opposed by stabilizing selection. Hence, the population is stuck on the meridian at a sub maximal average fitness. When several populations are on different sub-maximal average fitness peaks, selection between populations (interdemic selection) can act.

This population genetic clarification has been used extensively to explain situations which cannot exist explained in terms of intrademic selection. For example, body size which may accept high individual fitness, and hence is selected for within a population, tin can reduce the fitness of the population by causing it to achieve a sub maximal average fettle and get out it open to interdemic choice.

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