Genetic drift

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Genetic drift (also known as allelic drift or the Sewall Wright effect) [1] is the change in the frequency of an existing gene variant (allele) in a population due to random sampling of organisms. [2] 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. [3] Genetic drift may cause gene variants to disappear completely and thereby reduce genetic variation. [4] It can also cause initially rare alleles to become much more frequent and even fixed.

Gene Basic physical and functional unit of heredity

In biology, a gene is a sequence of nucleotides in DNA or RNA that codes for a molecule that has a function. During gene expression, the DNA is first copied into RNA. The RNA can be directly functional or be the intermediate template for a protein that performs a function. The transmission of genes to an organism's offspring is the basis of the inheritance of phenotypic trait. These genes make up different DNA sequences called genotypes. Genotypes along with environmental and developmental factors determine what the phenotypes will be. Most biological traits are under the influence of polygenes as well as gene–environment interactions. Some genetic traits are instantly visible, such as eye color or number of limbs, and some are not, such as blood type, risk for specific diseases, or the thousands of basic biochemical processes that constitute life.

An allele is a variant form of a given gene. Sometimes, the presence of different alleles of the same gene 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 genetic variations result in little or no observable variation.

Probability is a measure quantifying the likelihood that events will occur. See glossary of probability and statistics. Probability quantifies as a number between 0 and 1, where, loosely speaking, 0 indicates impossibility and 1 indicates certainty. The higher the probability of an event, the more likely it is that the event will occur. A simple example is the tossing of a fair (unbiased) coin. Since the coin is fair, the two outcomes are both equally probable; the probability of "heads" equals the probability of "tails"; and since no other outcomes are possible, the probability of either "heads" or "tails" is 1/2.

Contents

When there are few copies of an allele, the effect of genetic drift is larger, and when there are many copies the effect is smaller. In the early 20th century, vigorous debates occurred over the relative importance of natural selection versus neutral processes, including genetic drift. Ronald Fisher, who explained natural selection using Mendelian genetics, [5] held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. In 1968, population geneticist Motoo Kimura rekindled the debate with his neutral theory of molecular evolution, which claims that most instances where a genetic change spreads across a population (although not necessarily changes in phenotypes) are caused by genetic drift acting on neutral mutations. [6] [7]

Natural selection Mechanism of evolution by differential survival and reproduction of individuals

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 in his view is intentional, whereas natural selection is not.

Ronald Fisher British statistician, evolutionary biologist, geneticist, and eugenicist

Sir Ronald Aylmer Fisher 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".

Mendelian inheritance Type of biological inheritance

Mendelian inheritance is a type of biological inheritance that follows the laws originally proposed by Gregor Mendel in 1865 and 1866 and re-discovered in 1900. These laws were initially controversial. When Mendel's theories were integrated with the Boveri–Sutton chromosome theory of inheritance by Thomas Hunt Morgan in 1915, they became the core of classical genetics. Ronald Fisher combined these ideas with the theory of natural selection in his 1930 book The Genetical Theory of Natural Selection, putting evolution onto a mathematical footing and forming the basis for population genetics within the modern evolutionary synthesis.

Analogy with marbles in a jar

The process of genetic drift can be illustrated using 20 marbles in a jar to represent 20 organisms in a population. [8] Consider this jar of marbles as the starting population. Half of the marbles in the jar are red and half are blue, with each colour corresponding to a different allele of one gene in the population. In each new generation the organisms reproduce at random. To represent this reproduction, randomly select a marble from the original jar and deposit a new marble with the same colour into a new jar. This is the "offspring" of the original marble, meaning that the original marble remains in its jar. Repeat this process until there are 20 new marbles in the second jar. The second jar will now contain 20 "offspring", or marbles of various colours. Unless the second jar contains exactly 10 red marbles and 10 blue marbles, a random shift has occurred in the allele frequencies.

If this process is repeated a number of times, the numbers of red and blue marbles picked each generation will fluctuate. Sometimes a jar will have more red marbles than its "parent" jar and sometimes more blue. This fluctuation is analogous to genetic drift – a change in the population's allele frequency resulting from a random variation in the distribution of alleles from one generation to the next.

It is even possible that in any one generation no marbles of a particular colour are chosen, meaning they have no offspring. In this example, if no red marbles are selected, the jar representing the new generation contains only blue offspring. If this happens, the red allele has been lost permanently in the population, while the remaining blue allele has become fixed: all future generations are entirely blue. In small populations, fixation can occur in just a few generations.

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).

In this simulation each black dot on a marble signifies that it has been chosen for copying (reproduction) one time. There is fixation in the blue "allele" within five generations. Random sampling genetic drift.svg
In this simulation each black dot on a marble signifies that it has been chosen for copying (reproduction) one time. There is fixation in the blue "allele" within five generations.

Probability and allele frequency

The mechanisms of genetic drift can be illustrated with a simplified example. Consider a very large colony of bacteria isolated in a drop of solution. The bacteria are genetically identical except for a single gene with two alleles labeled A and B. A and B are neutral alleles meaning that they do not affect the bacteria's ability to survive and reproduce; all bacteria in this colony are equally likely to survive and reproduce. Suppose that half the bacteria have allele A and the other half have allele B. Thus A and B each have allele frequency 1/2.

Bacteria A domain of prokaryotes – single celled organisms without a nucleus

Bacteria are a type of biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a number of shapes, ranging from spheres to rods and spirals. Bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit soil, water, acidic hot springs, radioactive waste, and the deep portions of Earth's crust. Bacteria also live in symbiotic and parasitic relationships with plants and animals. Most bacteria have not been characterised, and only about 27 percent of the bacterial phyla have species that can be grown in the laboratory . The study of bacteria is known as bacteriology, a branch of microbiology.

The drop of solution then shrinks until it has only enough food to sustain four bacteria. All other bacteria die without reproducing. Among the four who survive, there are sixteen possible combinations for the A and B alleles:

In mathematics, a combination is a selection of items from a collection, such that the order of selection does not matter. For example, given three fruits, say an apple, an orange and a pear, there are three combinations of two that can be drawn from this set: an apple and a pear; an apple and an orange; or a pear and an orange. More formally, a k-combination of a set S is a subset of k distinct elements of S. If the set has n elements, the number of k-combinations is equal to the binomial coefficient

(A-A-A-A), (B-A-A-A), (A-B-A-A), (B-B-A-A),
(A-A-B-A), (B-A-B-A), (A-B-B-A), (B-B-B-A),
(A-A-A-B), (B-A-A-B), (A-B-A-B), (B-B-A-B),
(A-A-B-B), (B-A-B-B), (A-B-B-B), (B-B-B-B).

Since all bacteria in the original solution are equally likely to survive when the solution shrinks, the four survivors are a random sample from the original colony. The probability that each of the four survivors has a given allele is 1/2, and so the probability that any particular allele combination occurs when the solution shrinks is

(The original population size is so large that the sampling effectively happens without replacement). In other words, each of the sixteen possible allele combinations is equally likely to occur, with probability 1/16.

Counting the combinations with the same number of A and B, we get the following table.

ABCombinationsProbability
4011/16
3144/16
2266/16
1344/16
0411/16

As shown in the table, the total number of combinations that have the same number of A alleles as of B alleles is six, and the probability of this combination is 6/16. The total number of other combinations is ten, so the probability of unequal number of A and B alleles is 10/16. Thus, although the original colony began with an equal number of A and B alleles, it is very possible that the number of alleles in the remaining population of four members will not be equal. Equal numbers is actually less likely than unequal numbers. In the latter case, genetic drift has occurred because the population's allele frequencies have changed due to random sampling. In this example the population contracted to just four random survivors, a phenomenon known as population bottleneck.

The probabilities for the number of copies of allele A (or B) that survive (given in the last column of the above table) can be calculated directly from the binomial distribution where the "success" probability (probability of a given allele being present) is 1/2 (i.e., the probability that there are k copies of A (or B) alleles in the combination) is given by

where n=4 is the number of surviving bacteria.

Mathematical models

Mathematical models of genetic drift can be designed using either branching processes or a diffusion equation describing changes in allele frequency in an idealised population. [9]

Wright–Fisher model

Consider a gene with two alleles, A or B. In diploid populations consisting of N individuals there are 2N copies of each gene. An individual can have two copies of the same allele or two different alleles. We can call the frequency of one allele p and the frequency of the other q. The Wright–Fisher model (named after Sewall Wright and Ronald Fisher) assumes that generations do not overlap (for example, annual plants have exactly one generation per year) and that each copy of the gene found in the new generation is drawn independently at random from all copies of the gene in the old generation. The formula to calculate the probability of obtaining k copies of an allele that had frequency p in the last generation is then [10] [11]

where the symbol "!" signifies the factorial function. This expression can also be formulated using the binomial coefficient,

Moran model

The Moran model assumes overlapping generations. At each time step, one individual is chosen to reproduce and one individual is chosen to die. So in each timestep, the number of copies of a given allele can go up by one, go down by one, or can stay the same. This means that the transition matrix is tridiagonal, which means that mathematical solutions are easier for the Moran model than for the Wright–Fisher model. On the other hand, computer simulations are usually easier to perform using the Wright–Fisher model, because fewer time steps need to be calculated. In the Moran model, it takes N timesteps to get through one generation, where N is the effective population size. In the Wright–Fisher model, it takes just one. [12]

In practice, the Moran and Wright–Fisher models give qualitatively similar results, but genetic drift runs twice as fast in the Moran model.

Other models of drift

If the variance in the number of offspring is much greater than that given by the binomial distribution assumed by the Wright–Fisher model, then given the same overall speed of genetic drift (the variance effective population size), genetic drift is a less powerful force compared to selection. [13] Even for the same variance, if higher moments of the offspring number distribution exceed those of the binomial distribution then again the force of genetic drift is substantially weakened. [14]

Random effects other than sampling error

Random changes in allele frequencies can also be caused by effects other than sampling error, for example random changes in selection pressure. [15]

One important alternative source of stochasticity, perhaps more important than genetic drift, is genetic draft. [16] Genetic draft is the effect on a locus by selection on linked loci. The mathematical properties of genetic draft are different from those of genetic drift. [17] The direction of the random change in allele frequency is autocorrelated across generations. [2]

Drift and fixation

The Hardy–Weinberg principle states that within sufficiently large populations, the allele frequencies remain constant from one generation to the next unless the equilibrium is disturbed by migration, genetic mutations, or selection. [18]

However, in finite populations, no new alleles are gained from the random sampling of alleles passed to the next generation, but the sampling can cause an existing allele to disappear. Because random sampling can remove, but not replace, an allele, and because random declines or increases in allele frequency influence expected allele distributions for the next generation, genetic drift drives a population towards genetic uniformity over time. When an allele reaches a frequency of 1 (100%) it is said to be "fixed" in the population and when an allele reaches a frequency of 0 (0%) it is lost. Smaller populations achieve fixation faster, whereas in the limit of an infinite population, fixation is not achieved. Once an allele becomes fixed, genetic drift comes to a halt, and the allele frequency cannot change unless a new allele is introduced in the population via mutation or gene flow. Thus even while genetic drift is a random, directionless process, it acts to eliminate genetic variation over time. [19]

Rate of allele frequency change due to drift

Ten simulations of random genetic drift of a single given allele with an initial frequency distribution 0.5 measured over the course of 50 generations, repeated in three reproductively synchronous populations of different sizes. In these simulations, alleles drift to loss or fixation (frequency of 0.0 or 1.0) only in the smallest population. Random genetic drift chart.png
Ten simulations of random genetic drift of a single given allele with an initial frequency distribution 0.5 measured over the course of 50 generations, repeated in three reproductively synchronous populations of different sizes. In these simulations, alleles drift to loss or fixation (frequency of 0.0 or 1.0) only in the smallest population.

Assuming genetic drift is the only evolutionary force acting on an allele, after t generations in many replicated populations, starting with allele frequencies of p and q, the variance in allele frequency across those populations is

[20]

Time to fixation or loss

Assuming genetic drift is the only evolutionary force acting on an allele, at any given time the probability that an allele will eventually become fixed in the population is simply its frequency in the population at that time. [21] For example, if the frequency p for allele A is 75% and the frequency q for allele B is 25%, then given unlimited time the probability A will ultimately become fixed in the population is 75% and the probability that B will become fixed is 25%.

The expected number of generations for fixation to occur is proportional to the population size, such that fixation is predicted to occur much more rapidly in smaller populations. [22] Normally the effective population size, which is smaller than the total population, is used to determine these probabilities. The effective population (Ne) takes into account factors such as the level of inbreeding, the stage of the lifecycle in which the population is the smallest, and the fact that some neutral genes are genetically linked to others that are under selection. [13] The effective population size may not be the same for every gene in the same population. [23]

One forward-looking formula used for approximating the expected time before a neutral allele becomes fixed through genetic drift, according to the Wright–Fisher model, is

where T is the number of generations, Ne is the effective population size, and p is the initial frequency for the given allele. The result is the number of generations expected to pass before fixation occurs for a given allele in a population with given size (Ne) and allele frequency (p). [24]

The expected time for the neutral allele to be lost through genetic drift can be calculated as [10]

When a mutation appears only once in a population large enough for the initial frequency to be negligible, the formulas can be simplified to [25]

for average number of generations expected before fixation of a neutral mutation, and

for the average number of generations expected before the loss of a neutral mutation. [26]

Time to loss with both drift and mutation

The formulae above apply to an allele that is already present in a population, and which is subject to neither mutation nor natural selection. If an allele is lost by mutation much more often than it is gained by mutation, then mutation, as well as drift, may influence the time to loss. If the allele prone to mutational loss begins as fixed in the population, and is lost by mutation at rate m per replication, then the expected time in generations until its loss in a haploid population is given by

where is Euler's constant. [27] The first approximation represents the waiting time until the first mutant destined for loss, with loss then occurring relatively rapidly by genetic drift, taking time Ne  1/m. The second approximation represents the time needed for deterministic loss by mutation accumulation. In both cases, the time to fixation is dominated by mutation via the term 1/m, and is less affected by the effective population size.

Versus natural selection

In natural populations, genetic drift and natural selection do not act in isolation; both forces are always at play, together with mutation and migration. Neutral evolution is the product of both mutation and drift, not of drift alone. Similarly, even when selection overwhelms genetic drift, it can only act on variation that mutation provides.

While natural selection has a direction, guiding evolution towards heritable adaptations to the current environment, genetic drift has no direction and is guided only by the mathematics of chance. [28] As a result, drift acts upon the genotypic frequencies within a population without regard to their phenotypic effects. In contrast, selection favors the spread of alleles whose phenotypic effects increase survival and/or reproduction of their carriers, lowers the frequencies of alleles that cause unfavorable traits, and ignores those that are neutral. [29]

The law of large numbers predicts that when the absolute number of copies of the allele is small (e.g., in small populations), the magnitude of drift on allele frequencies per generation is larger. The magnitude of drift is large enough to overwhelm selection at any allele frequency when the selection coefficient is less than 1 divided by the effective population size. Non-adaptive evolution resulting from the product of mutation and genetic drift is therefore considered to be a consequential mechanism of evolutionary change primarily within small, isolated populations. [30] The mathematics of genetic drift depend on the effective population size, but it is not clear how this is related to the actual number of individuals in a population. [16] Genetic linkage to other genes that are under selection can reduce the effective population size experienced by a neutral allele. With a higher recombination rate, linkage decreases and with it this local effect on effective population size. [31] [32] This effect is visible in molecular data as a correlation between local recombination rate and genetic diversity, [33] and negative correlation between gene density and diversity at noncoding DNA regions. [34] Stochasticity associated with linkage to other genes that are under selection is not the same as sampling error, and is sometimes known as genetic draft in order to distinguish it from genetic drift. [16]

When the allele frequency is very small, drift can also overpower selection even in large populations. For example, while disadvantageous mutations are usually eliminated quickly in large populations, new advantageous mutations are almost as vulnerable to loss through genetic drift as are neutral mutations. Not until the allele frequency for the advantageous mutation reaches a certain threshold will genetic drift have no effect. [29]

Population bottleneck

Changes in a population's allele frequency following a population bottleneck: the rapid and radical decline in population size has reduced the population's genetic variation. Population bottleneck.jpg
Changes in a population's allele frequency following a population bottleneck: the rapid and radical decline in population size has reduced the population's genetic variation.

A population bottleneck is when a population contracts to a significantly smaller size over a short period of time due to some random environmental event. In a true population bottleneck, the odds for survival of any member of the population are purely random, and are not improved by any particular inherent genetic advantage. The bottleneck can result in radical changes in allele frequencies, completely independent of selection. [35]

The impact of a population bottleneck can be sustained, even when the bottleneck is caused by a one-time event such as a natural catastrophe. An interesting example of a bottleneck causing unusual genetic distribution is the relatively high proportion of individuals with total rod cell color blindness (achromatopsia) on Pingelap atoll in Micronesia. After a bottleneck, inbreeding increases. This increases the damage done by recessive deleterious mutations, in a process known as inbreeding depression. The worst of these mutations are selected against, leading to the loss of other alleles that are genetically linked to them, in a process of background selection. [2] For recessive harmful mutations, this selection can be enhanced as a consequence of the bottleneck, due to genetic purging. This leads to a further loss of genetic diversity. In addition, a sustained reduction in population size increases the likelihood of further allele fluctuations from drift in generations to come.

A population's genetic variation can be greatly reduced by a bottleneck, and even beneficial adaptations may be permanently eliminated. [36] The loss of variation leaves the surviving population vulnerable to any new selection pressures such as disease, climate change or shift in the available food source, because adapting in response to environmental changes requires sufficient genetic variation in the population for natural selection to take place. [37] [38]

There have been many known cases of population bottleneck in the recent past. Prior to the arrival of Europeans, North American prairies were habitat for millions of greater prairie chickens. In Illinois alone, their numbers plummeted from about 100 million birds in 1900 to about 50 birds in the 1990s. The declines in population resulted from hunting and habitat destruction, but a consequence has been a loss of most of the species' genetic diversity. DNA analysis comparing birds from the mid century to birds in the 1990s documents a steep decline in the genetic variation in just the latter few decades. Currently the greater prairie chicken is experiencing low reproductive success. [39]

However, the genetic loss caused by bottleneck and genetic drift can increase fitness, as in Ehrlichia . [40]

Over-hunting also caused a severe population bottleneck in the northern elephant seal in the 19th century. Their resulting decline in genetic variation can be deduced by comparing it to that of the southern elephant seal, which were not so aggressively hunted. [41]

Founder effect

When very few members of a population migrate to form a separate new population, the founder effect occurs. For a period after the foundation, the small population experiences intensive drift. In the figure this results in fixation of the red allele. Founder effect with drift.jpg
When very few members of a population migrate to form a separate new population, the founder effect occurs. For a period after the foundation, the small population experiences intensive drift. In the figure this results in fixation of the red allele.

The founder effect is a special case of a population bottleneck, occurring when a small group in a population splinters off from the original population and forms a new one. The random sample of alleles in the just formed new colony is expected to grossly misrepresent the original population in at least some respects. [42] It is even possible that the number of alleles for some genes in the original population is larger than the number of gene copies in the founders, making complete representation impossible. When a newly formed colony is small, its founders can strongly affect the population's genetic make-up far into the future.

A well-documented example is found in the Amish migration to Pennsylvania in 1744. Two members of the new colony shared the recessive allele for Ellis–van Creveld syndrome. Members of the colony and their descendants tend to be religious isolates and remain relatively insular. As a result of many generations of inbreeding, Ellis-van Creveld syndrome is now much more prevalent among the Amish than in the general population. [29] [43]

The difference in gene frequencies between the original population and colony may also trigger the two groups to diverge significantly over the course of many generations. As the difference, or genetic distance, increases, the two separated populations may become distinct, both genetically and phenetically, although not only genetic drift but also natural selection, gene flow, and mutation contribute to this divergence. This potential for relatively rapid changes in the colony's gene frequency led most scientists to consider the founder effect (and by extension, genetic drift) a significant driving force in the evolution of new species. Sewall Wright was the first to attach this significance to random drift and small, newly isolated populations with his shifting balance theory of speciation. [44] Following after Wright, Ernst Mayr created many persuasive models to show that the decline in genetic variation and small population size following the founder effect were critically important for new species to develop. [45] However, there is much less support for this view today since the hypothesis has been tested repeatedly through experimental research and the results have been equivocal at best. [46]

History

The role of random chance in evolution was first outlined by Hagedoorn and Hagedoorn in 1921 [47] . They highlighted that random survival plays a key role in the loss of variation from populations. Fisher (1922) responded to this with the first, albeit marginally incorrect, mathematical treatment of the 'Hagedoorn effect' [48] . Notably, he expected that many natural populations were too large (an N ~10,000) for the effects of drift to be substantial and thought drift would have an insignificant effect on the evolutionary process. The corrected mathematical treatment and term "genetic drift" was later coined by a founder of population genetics, Sewall Wright. His first use of the term "drift" was in 1929, [49] though at the time he was using it in the sense of a directed process of change, or natural selection. Random drift by means of sampling error came to be known as the "Sewall–Wright effect," though he was never entirely comfortable to see his name given to it. Wright referred to all changes in allele frequency as either "steady drift" (e.g., selection) or "random drift" (e.g., sampling error). [50] "Drift" came to be adopted as a technical term in the stochastic sense exclusively. [51] Today it is usually defined still more narrowly, in terms of sampling error, [52] although this narrow definition is not universal. [53] [54] Wright wrote that the "restriction of "random drift" or even "drift" to only one component, the effects of accidents of sampling, tends to lead to confusion." [50] Sewall Wright considered the process of random genetic drift by means of sampling error equivalent to that by means of inbreeding, but later work has shown them to be distinct. [55]

In the early days of the modern evolutionary synthesis, scientists were beginning to blend the new science of population genetics with Charles Darwin's theory of natural selection. Within this framework, Wright focused on the effects of inbreeding on small relatively isolated populations. He introduced the concept of an adaptive landscape in which phenomena such as cross breeding and genetic drift in small populations could push them away from adaptive peaks, which in turn allow natural selection to push them towards new adaptive peaks. [56] Wright thought smaller populations were more suited for natural selection because "inbreeding was sufficiently intense to create new interaction systems through random drift but not intense enough to cause random nonadaptive fixation of genes." [57]

Wright's views on the role of genetic drift in the evolutionary scheme were controversial almost from the very beginning. One of the most vociferous and influential critics was colleague Ronald Fisher. Fisher conceded genetic drift played some role in evolution, but an insignificant one. Fisher has been accused of misunderstanding Wright's views because in his criticisms Fisher seemed to argue Wright had rejected selection almost entirely. To Fisher, viewing the process of evolution as a long, steady, adaptive progression was the only way to explain the ever-increasing complexity from simpler forms. But the debates have continued between the "gradualists" and those who lean more toward the Wright model of evolution where selection and drift together play an important role. [58]

In 1968, Motoo Kimura rekindled the debate with his neutral theory of molecular evolution, which claims that most of the genetic changes are caused by genetic drift acting on neutral mutations. [6] [7]

The role of genetic drift by means of sampling error in evolution has been criticized by John H. Gillespie [59] and William B. Provine, who argue that selection on linked sites is a more important stochastic force.

See also

Notes and references

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Bibliography

Related Research Articles

Evolution Change in the heritable characteristics of biological populations over successive generations

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 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.

Microevolution The change in allele frequencies that occurs over time within a population

Microevolution is the change in allele frequencies that occurs over time within a population. This change is due to four different processes: mutation, selection, gene flow and genetic drift. This change happens over a relatively short amount of time compared to the changes termed macroevolution which is where greater differences in the population occur.

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.

The neutral theory of molecular evolution holds that most evolutionary changes at the molecular level, and most of the variation within and between species, are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin. 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. A neutral mutation is one that does not affect an organism's ability to survive and reproduce. The neutral theory assumes that most mutations that are not deleterious are neutral rather than beneficial. Because only a fraction of gametes are sampled in each generation of a species, the neutral theory suggests that a mutant allele can arise within a population and reach fixation by chance, rather than by selective advantage.

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.

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.

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.

Founder effect Loss of genetic variation that occurs when a new population is established by a very small number of individuals

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.

Motoo Kimura Japanese biologist

Motoo Kimura was a Japanese biologist best known for introducing the neutral theory of molecular evolution in 1968. He became one of the most influential theoretical population geneticists. He is remembered in genetics for his innovative use of diffusion equations to calculate the probability of fixation of beneficial, deleterious, or neutral alleles. Combining theoretical population genetics with molecular evolution data, he also developed the neutral theory of molecular evolution in which genetic drift is the main force changing allele frequencies. James F. Crow, himself a renowned population geneticist, considered Kimura to be one of the two greatest evolutionary geneticists, along with Gustave Malécot, after the great trio of the modern synthesis, Ronald Fisher, J. B. S. Haldane and Sewall Wright.

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 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.

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.

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.

Neutral mutations are changes in DNA sequence that are neither beneficial nor detrimental to the ability of an organism to survive and reproduce. In population genetics, mutations in which natural selection does not affect the spread of the mutation in a species are termed neutral mutations. Neutral mutations that are inheritable and not linked to any genes under selection will either be lost or will replace all other alleles of the gene. This loss or fixation of the gene proceeds based on random sampling known as genetic drift. A neutral mutation that is in linkage disequilibrium with other alleles that are under selection may proceed to loss or fixation via genetic hitchhiking and/or background selection.

In natural selection, negative selection or purifying selection is the selective removal of alleles that are deleterious. This can result in stabilizing selection through the purging of deleterious genetic polymorphisms that arise through random mutations.

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.

Introduction to evolution A non-technical explanation of the basic concepts and principles of biological evolution

Evolution is the process of change in all forms of life over generations, and evolutionary biology is the study of how evolution occurs. Biological populations evolve through genetic changes that correspond to changes in the organisms' observable traits. Genetic changes include mutations, which are caused by damage or replication errors in organisms' DNA. As the genetic variation of a population drifts randomly over generations, natural selection gradually leads traits to become more or less common based on the relative reproductive success of organisms with those traits.

Genetic purging is the reduction of the frequency of a deleterious allele, caused by an increased efficiency of natural selection prompted by inbreeding.