Population genetics
Encyclopedia
Population genetics is the study of allele frequency
Allele frequency
Allele frequency or Gene frequency is the proportion of all copies of a gene that is made up of a particular gene variant . In other words, it is the number of copies of a particular allele divided by the number of copies of all alleles at the genetic place in a population. It can be expressed for...

 distribution and change under the influence of the four main evolutionary processes: natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

, genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.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...

, mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

 and gene flow
Gene flow
In population genetics, gene flow is the transfer of alleles of genes from one population to another.Migration into or out of a population may be responsible for a marked change in allele frequencies...

. It also takes into account the factors of recombination
Recombination
Recombination may refer to:* Recombination , the process by which genetic material is broken and joined to other genetic material* Recombination , in semiconductors, the elimination of mobile charge carriers...

, population subdivision and population structure
Population structure
Population structure may refer to many aspects of population ecology:* Population stratification* Population pyramid* Age class structure* F-statistics* Population density* Population distribution* Population dynamics and population growth...

. It attempts to explain such phenomena as adaptation and speciation
Speciation
Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...

.

Population genetics was a vital ingredient in the emergence of the modern evolutionary synthesis
Modern evolutionary synthesis
The modern evolutionary synthesis is a union of ideas from several biological specialties which provides a widely accepted account of evolution...

. Its primary founders were Sewall Wright
Sewall Wright
Sewall Green Wright was an American geneticist known for his influential work on evolutionary theory and also for his work on path analysis. With R. A. Fisher and J.B.S. Haldane, he was a founder of theoretical population genetics. He is the discoverer of the inbreeding coefficient and of...

, J. B. S. Haldane
J. B. S. Haldane
John Burdon Sanderson Haldane FRS , known as Jack , was a British-born geneticist and evolutionary biologist. A staunch Marxist, he was critical of Britain's role in the Suez Crisis, and chose to leave Oxford and moved to India and became an Indian citizen...

 and R. A. Fisher
Ronald Fisher
Sir Ronald Aylmer Fisher FRS was an English statistician, evolutionary biologist, eugenicist and geneticist. Among other things, Fisher is well known for his contributions to statistics by creating Fisher's exact test and Fisher's equation...

, who also laid the foundations for the related discipline of quantitative genetics
Quantitative genetics
Quantitative genetics is the study of continuous traits and their underlying mechanisms. It is effectively an extension of simple Mendelian inheritance in that the combined effects of one or more genes and the environments in which they are expressed give rise to continuous distributions of...

.

Fundamentals

Population genetics is the study of the frequency and interaction of alleles and genes in populations. A sexual population is a set of organisms in which any pair of members can breed
Breeding in the wild
Breeding in the wild is the natural process of animal reproduction occurring in the natural habitat of a given species. This terminology is distinct from animal husbandry or breeding of species in captivity...

 together. This implies that all members belong to the same species and live near each other.

For example, all of the moths of the same species living in an isolated forest are a population. A gene in this population may have several alternate forms, which account for variations between the phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...

s of the organisms. An example might be a gene for coloration in moths that has two allele
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...

s: black and white. A gene pool
Gene pool
In population genetics, a gene pool is the complete set of unique alleles in a species or population.- Description :A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection...

 is the complete set of alleles for a gene in a single population; the allele frequency
Allele frequency
Allele frequency or Gene frequency is the proportion of all copies of a gene that is made up of a particular gene variant . In other words, it is the number of copies of a particular allele divided by the number of copies of all alleles at the genetic place in a population. It can be expressed for...

 for an allele is the fraction of the genes in the pool that is composed of that allele (for example, what fraction of moth coloration genes are the black allele). Evolution
Evolution
Evolution is any change across successive generations in the heritable characteristics of biological populations. Evolutionary processes give rise to diversity at every level of biological organisation, including species, individual organisms and molecules such as DNA and proteins.Life on Earth...

 occurs when there are changes in the frequencies of alleles within a population; for example, the allele for black color in a population of moths becoming more common.

Hardy–Weinberg principle

Natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

 will only cause evolution if there is enough genetic variation
Genetic variation
Genetic variation, variation in alleles of genes, occurs both within and among populations. Genetic variation is important because it provides the “raw material” for natural selection. Genetic variation is brought about by mutation, a change in a chemical structure of a gene. Polyploidy is an...

 in a population. Before the discovery of Mendelian genetics, one common hypothesis was blending inheritance
Blending inheritance
Many biologists and other academics held to the idea of blending inheritance during the 19th century, prior to the discovery of genetics. Blending inheritance was merely a widespread hypothetical model, rather than a formalized scientific theory , in...

. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural selection implausible. The Hardy-Weinberg principle
Hardy-Weinberg principle
The Hardy–Weinberg principle states that both allele and genotype frequencies in a population remain constant—that is, they are in equilibrium—from generation to generation unless specific disturbing influences are introduced...

provides the solution to how variation is maintained in a population with Mendelian inheritance
Mendelian inheritance
Mendelian inheritance is a scientific description of how hereditary characteristics are passed from parent organisms to their offspring; it underlies much of genetics...

. According to this principle, the frequencies of alleles (variations in a gene) will remain constant in the absence of selection, mutation, migration and genetic drift. The Hardy-Weinberg "equilibrium" refers to this stability of allele frequencies over time.

A second component of the Hardy-Weinberg principle concerns the effects of a single generation of random mating. In this case, the genotype frequencies can be predicted from the allele frequencies. For example, in the simplest case of a single locus with two allele
Allele
An allele is one of two or more forms of a gene or a genetic locus . "Allel" is an abbreviation of allelomorph. Sometimes, different alleles can result in different observable phenotypic traits, such as different pigmentation...

s: the dominant allele is denoted A and the recessive
Recessive
In genetics, the term "recessive gene" refers to an allele that causes a phenotype that is only seen in a homozygous genotype and never in a heterozygous genotype. Every person has two copies of every gene on autosomal chromosomes, one from mother and one from father...

 a and their frequencies are denoted by p and q; freq(A) = p; freq(a) = q; p + q = 1. If the genotype frequencies are in Hardy-Weinberg proportions resulting from random mating, then we will have freq(AA) = p2 for the AA homozygotes in the population, freq(aa) = q2 for the aa homozygotes, and freq(Aa) = 2pq for the heterozygotes.

Natural selection

Natural selection is the fact that some traits
Trait (biology)
A trait is a distinct variant of a phenotypic character of an organism that may be inherited, environmentally determined or be a combination of the two...

 make it more likely for an organism
Organism
In biology, an organism is any contiguous living system . In at least some form, all organisms are capable of response to stimuli, reproduction, growth and development, and maintenance of homoeostasis as a stable whole.An organism may either be unicellular or, as in the case of humans, comprise...

 to survive and reproduce. Population genetics describes natural selection by defining fitness
Fitness (biology)
Fitness is a central idea in evolutionary theory. It can be defined either with respect to a genotype or to a phenotype in a given environment...

 as a propensity or probability
Propensity probability
The propensity theory of probability is one interpretation of the concept of probability. Theorists who adopt this interpretation think of probability as a physical propensity, or disposition, or tendency of a given type of physical situation to yield an outcome of a certain kind, or to yield a...

 of survival and reproduction in a particular environment. The fitness is normally given by the symbol w=1+s where s is the selection coefficient
Selection coefficient
In population genetics, the selection coefficient is a measure of the relative fitness of a phenotype. Usually denoted by the letter s, it compares the fitness of a phenotype to another favored phenotype, and is the proportional amount that the considered phenotype is less fit as measured by...

. Natural selection acts on phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...

s, or the observable characteristics of organisms, but the genetically heritable
Heritability
The Heritability of a population is the proportion of observable differences between individuals that is due to genetic differences. Factors including genetics, environment and random chance can all contribute to the variation between individuals in their observable characteristics...

 basis of any phenotype which gives a reproductive advantage will become more common in a population (see allele frequency
Allele frequency
Allele frequency or Gene frequency is the proportion of all copies of a gene that is made up of a particular gene variant . In other words, it is the number of copies of a particular allele divided by the number of copies of all alleles at the genetic place in a population. It can be expressed for...

). In this way, natural selection converts differences in fitness into changes in allele frequency in a population
Population
A population is all the organisms that both belong to the same group or species and live in the same geographical area. The area that is used to define a sexual population is such that inter-breeding is possible between any pair within the area and more probable than cross-breeding with individuals...

 over successive generations.

Before the advent of population genetics, many biologists doubted that small difference in fitness were sufficient to make a large difference to evolution. Population geneticists addressed this concern in part by comparing selection to genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.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...

. Selection can overcome genetic drift when s is greater than 1 divided by the effective population size
Effective population size
In population genetics, the concept of effective population size Ne was introduced by the American geneticist Sewall Wright, who wrote two landmark papers on it...

. When this criterion is met, the probability that a new advantageous mutant becomes fixed
Fixation (population genetics)
In population genetics, fixation is the change in a gene pool from a situation where there exist at least two variants of a particular gene to a situation where only one of the alleles remains...

 is approximately equal to s. The time until fixation of such an allele depends little on genetic drift, and is approximately proportional to log(sN)/s.

Genetic drift

Genetic drift is a change in allele frequencies
Allele frequency
Allele frequency or Gene frequency is the proportion of all copies of a gene that is made up of a particular gene variant . In other words, it is the number of copies of a particular allele divided by the number of copies of all alleles at the genetic place in a population. It can be expressed for...

 caused by random sampling
Sampling (statistics)
In statistics and survey methodology, sampling is concerned with the selection of a subset of individuals from within a population to estimate characteristics of the whole population....

. That is, the alleles in the offspring are a random sample of those in the parents. Genetic drift may cause gene variants to disappear completely, and thereby reduce genetic variability. In contrast to natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

, which makes gene variants more common or less common depending on their reproductive success, the changes due to genetic drift are not driven by environmental or adaptive pressures, and may be beneficial, neutral, or detrimental to reproductive success.

The effect of genetic drift is larger for alleles present in a smaller number of copies, and smaller when an allele is present in many copies. Vigorous debates wage among scientists over the relative importance of genetic drift compared with natural selection. Ronald Fisher
Ronald Fisher
Sir Ronald Aylmer Fisher FRS was an English statistician, evolutionary biologist, eugenicist and geneticist. Among other things, Fisher is well known for his contributions to statistics by creating Fisher's exact test and Fisher's equation...

 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 Motoo Kimura
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...

 rekindled the debate with his neutral theory of molecular evolution
Neutral theory of molecular evolution
The neutral theory of molecular evolution states that the vast majority of evolutionary changes at the molecular level are caused by random drift of selectively neutral mutants . The theory was introduced by Motoo Kimura in the late 1960s and early 1970s...

 which claims that most of the changes in the genetic material are caused by neutral mutations and genetic drift. The role of genetic drift by means of sampling error in evolution has been criticized by John H Gillespie and Will Provine
Will Provine
William B. Provine is an American historian of science, particularly of evolutionary biology and population genetics. He is the Andrew H. and James S. Tisch Distinguished University Professor at Cornell University and is a professor in the Departments of History, Science and Technology Studies,...

, who argue that selection on linked sites is a more important stochastic force.

The population genetics of genetic drift are described using either branching process
Branching process
In probability theory, a branching process is a Markov process that models a population in which each individual in generation n produces some random number of individuals in generation n + 1, according to a fixed probability distribution that does not vary from individual to...

es or a diffusion equation describing changes in allele frequency. These approaches are usually applied to the Wright-Fisher and Moran models of population genetics. 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

Mutation

Mutation is the ultimate source of genetic variation
Genetic variation
Genetic variation, variation in alleles of genes, occurs both within and among populations. Genetic variation is important because it provides the “raw material” for natural selection. Genetic variation is brought about by mutation, a change in a chemical structure of a gene. Polyploidy is an...

 in the form of new alleles. Mutation can result in several different types of change in DNA sequences; these can either have no effect, alter the product of a gene
Gene product
A gene product is the biochemical material, either RNA or protein, resulting from expression of a gene. A measurement of the amount of gene product is sometimes used to infer how active a gene is. Abnormal amounts of gene product can be correlated with disease-causing alleles, such as the...

, or prevent the gene from functioning. Studies in the fly Drosophila melanogaster
Drosophila melanogaster
Drosophila melanogaster is a species of Diptera, or the order of flies, in the family Drosophilidae. The species is known generally as the common fruit fly or vinegar fly. Starting from Charles W...

suggest that if a mutation changes a protein produced by a gene, this will probably be harmful, with about 70 percent of these mutations having damaging effects, and the remainder being either neutral or weakly beneficial.

Mutations can involve large sections of DNA becoming duplicated
Gene duplication
Gene duplication is any duplication of a region of DNA that contains a gene; it may occur as an error in homologous recombination, a retrotransposition event, or duplication of an entire chromosome.The second copy of the gene is often free from selective pressure — that is, mutations of it have no...

, usually through genetic recombination
Genetic recombination
Genetic recombination is a process by which a molecule of nucleic acid is broken and then joined to a different one. Recombination can occur between similar molecules of DNA, as in homologous recombination, or dissimilar molecules, as in non-homologous end joining. Recombination is a common method...

. These duplications are a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. Most genes belong to larger families of genes
Gene family
A gene family is a set of several similar genes, formed by duplication of a single original gene, and generally with similar biochemical functions...

 of shared ancestry
Homology (biology)
Homology forms the basis of organization for comparative biology. In 1843, Richard Owen defined homology as "the same organ in different animals under every variety of form and function". Organs as different as a bat's wing, a seal's flipper, a cat's paw and a human hand have a common underlying...

. Novel genes are produced by several methods, commonly through the duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. Here, domains
Protein domain
A protein domain is a part of protein sequence and structure that can evolve, function, and exist independently of the rest of the protein chain. Each domain forms a compact three-dimensional structure and often can be independently stable and folded. Many proteins consist of several structural...

 act as modules, each with a particular and independent function, that can be mixed together to produce genes encoding new proteins with novel properties. For example, the human eye uses four genes to make structures that sense light: three for color vision
Cone cell
Cone cells, or cones, are photoreceptor cells in the retina of the eye that are responsible for color vision; they function best in relatively bright light, as opposed to rod cells that work better in dim light. If the retina is exposed to an intense visual stimulus, a negative afterimage will be...

 and one for night vision
Rod cell
Rod cells, or rods, are photoreceptor cells in the retina of the eye that can function in less intense light than can the other type of visual photoreceptor, cone cells. Named for their cylindrical shape, rods are concentrated at the outer edges of the retina and are used in peripheral vision. On...

; all four arose from a single ancestral gene. Another advantage of duplicating a gene (or even an entire genome
Polyploidy
Polyploid is a term used to describe cells and organisms containing more than two paired sets of chromosomes. Most eukaryotic species are diploid, meaning they have two sets of chromosomes — one set inherited from each parent. However polyploidy is found in some organisms and is especially common...

) is that this increases redundancy
Redundancy (engineering)
In engineering, redundancy is the duplication of critical components or functions of a system with the intention of increasing reliability of the system, usually in the case of a backup or fail-safe....

; this allows one gene in the pair to acquire a new function while the other copy performs the original function. Other types of mutation occasionally create new genes from previously noncoding DNA.

In addition to being a major source of variation, mutation may also function as a mechanism of evolution when there are different probabilities at the molecular level for different mutations to occur, a process known as mutation bias. If two genotypes, for example one with the nucleotide G and another with the nucleotide A in the same position, have the same fitness, but mutation from G to A happens more often than mutation from A to G, then genotypes with A will tend to evolve. Different insertion vs. deletion mutation biases in different taxa can lead to the evolution of different genome sizes. Developmental or mutational biases have also been observed in morphological
Morphology (biology)
In biology, morphology is a branch of bioscience dealing with the study of the form and structure of organisms and their specific structural features....

 evolution. For example, according to the phenotype-first theory of evolution
Baldwin effect
The Baldwin effect, also known as Baldwinian evolution or ontogenic evolution, is a theory of a possible evolutionary processes that was originally put forward in 1896 in a paper, "A New Factor in Evolution," by American psychologist James Mark Baldwin. The paper proposed a mechanism for specific...

, mutations can eventually cause the genetic assimilation
Genetic assimilation
Note: Genetic assimilation is sometimes used to describe "eventual extinction of a natural species as massive pollen flow occurs from another related species and the older crop becomes more like the new crop." This usage is unrelated to the usage below....

 of traits that were previously induced by the environment
Phenotypic plasticity
Phenotypic plasticity is the ability of an organism to change its phenotype in response to changes in the environment. Such plasticity in some cases expresses as several highly morphologically distinct results; in other cases, a continuous norm of reaction describes the functional interrelationship...

.

Mutation bias effects are superimposed on other processes. If selection would favor either one out of two mutations, but there is no extra advantage to having both, then the mutation that occurs the most frequently is the one that is most likely to become fixed in a population. Mutations leading to the loss of function of a gene are much more common than mutations that produce a new, fully functional gene. Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution. For example, pigment
Pigment
A pigment is a material that changes the color of reflected or transmitted light as the result of wavelength-selective absorption. This physical process differs from fluorescence, phosphorescence, and other forms of luminescence, in which a material emits light.Many materials selectively absorb...

s are no longer useful when animals live in the darkness of caves, and tend to be lost. This kind of loss of function can occur because of mutation bias, and/or because the function had a cost, and once the benefit of the function disappeared, natural selection leads to the loss. Loss of sporulation
Endospore
An endospore is a dormant, tough, and temporarily non-reproductive structure produced by certain bacteria from the Firmicute phylum. The name "endospore" is suggestive of a spore or seed-like form , but it is not a true spore . It is a stripped-down, dormant form to which the bacterium can reduce...

 ability in a bacterium
Bacillus subtilis
Bacillus subtilis, known also as the hay bacillus or grass bacillus, is a Gram-positive, catalase-positive bacterium commonly found in soil. A member of the genus Bacillus, B. subtilis is rod-shaped, and has the ability to form a tough, protective endospore, allowing the organism to tolerate...

 during laboratory evolution appears to have been caused by mutation bias, rather than natural selection against the cost of maintaining sporulation ability. When there is no selection for loss of function, the speed at which loss evolves depends more on the mutation rate than it does on the effective population size
Effective population size
In population genetics, the concept of effective population size Ne was introduced by the American geneticist Sewall Wright, who wrote two landmark papers on it...

, indicating that it is driven more by mutation bias than by genetic drift.

Evolution of mutation rate

Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as DNA repair
DNA repair
DNA repair refers to a collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome. In human cells, both normal metabolic activities and environmental factors such as UV light and radiation can cause DNA damage, resulting in as many as 1...

 to remove mutations. Therefore, the optimal mutation rate for a species is a trade-off between costs of a high mutation rate, such as deleterious mutations, and the metabolic
Metabolism
Metabolism is the set of chemical reactions that happen in the cells of living organisms to sustain life. These processes allow organisms to grow and reproduce, maintain their structures, and respond to their environments. Metabolism is usually divided into two categories...

 costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes. Viruses that use RNA as their genetic material have rapid mutation rates, which can be an advantage since these viruses will evolve constantly and rapidly, and thus evade the defensive responses of e.g. the human immune system
Immune system
An immune system is a system of biological structures and processes within an organism that protects against disease by identifying and killing pathogens and tumor cells. It detects a wide variety of agents, from viruses to parasitic worms, and needs to distinguish them from the organism's own...

.

Gene Flow & Transfer

Gene flow
Gene flow
In population genetics, gene flow is the transfer of alleles of genes from one population to another.Migration into or out of a population may be responsible for a marked change in allele frequencies...

 is the exchange of genes between populations, which are usually of the same species. Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of pollen
Pollen
Pollen is a fine to coarse powder containing the microgametophytes of seed plants, which produce the male gametes . Pollen grains have a hard coat that protects the sperm cells during the process of their movement from the stamens to the pistil of flowering plants or from the male cone to the...

. Gene transfer between species includes the formation of hybrid organisms and horizontal gene transfer
Horizontal gene transfer
Horizontal gene transfer , also lateral gene transfer , is any process in which an organism incorporates genetic material from another organism without being the offspring of that organism...

.

Migration into or out of a population can change allele frequencies, as well as introducing genetic variation into a population. Immigration may add new genetic material to the established gene pool
Gene pool
In population genetics, a gene pool is the complete set of unique alleles in a species or population.- Description :A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection...

 of a population. Conversely, emigration may remove genetic material.

Reproductive isolation

As barriers to reproduction
Reproductive isolation
The mechanisms of reproductive isolation or hybridization barriers are a collection of mechanisms, behaviors and physiological processes that prevent the members of two different species that cross or mate from producing offspring, or which ensure that any offspring that may be produced is not...

 between two diverging populations are required for the populations to become new species
Speciation
Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...

, gene flow may slow this process by spreading genetic differences between the populations. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the Great Wall of China
Great Wall of China
The Great Wall of China is a series of stone and earthen fortifications in northern China, built originally to protect the northern borders of the Chinese Empire against intrusions by various nomadic groups...

, which has hindered the flow of plant genes.

Depending on how far two species have diverged since their most recent common ancestor
Most recent common ancestor
In genetics, the most recent common ancestor of any set of organisms is the most recent individual from which all organisms in the group are directly descended...

, it may still be possible for them to produce offspring, as with horse
Horse
The horse is one of two extant subspecies of Equus ferus, or the wild horse. It is a single-hooved mammal belonging to the taxonomic family Equidae. The horse has evolved over the past 45 to 55 million years from a small multi-toed creature into the large, single-toed animal of today...

s and donkey
Donkey
The donkey or ass, Equus africanus asinus, is a domesticated member of the Equidae or horse family. The wild ancestor of the donkey is the African Wild Ass, E...

s mating to produce mule
Mule
A mule is the offspring of a male donkey and a female horse. Horses and donkeys are different species, with different numbers of chromosomes. Of the two F1 hybrids between these two species, a mule is easier to obtain than a hinny...

s. Such hybrids are generally infertile
Infertility
Infertility primarily refers to the biological inability of a person to contribute to conception. Infertility may also refer to the state of a woman who is unable to carry a pregnancy to full term...

, due to the two different sets of chromosomes being unable to pair up during meiosis
Meiosis
Meiosis is a special type of cell division necessary for sexual reproduction. The cells produced by meiosis are gametes or spores. The animals' gametes are called sperm and egg cells....

. In this case, closely related species may regularly interbreed, but hybrids will be selected against and the species will remain distinct. However, viable hybrids are occasionally formed and these new species can either have properties intermediate between their parent species, or possess a totally new phenotype. The importance of hybridization in creating new species
Hybrid speciation
Hybrid speciation is the process wherein hybridization between two different closely related species leads to a distinct phenotype. This phenotype in very rare cases can also be fitter than the parental lineage and as such natural selection may then favor these individuals. Eventually, if...

 of animals is unclear, although cases have been seen in many types of animals, with the gray tree frog being a particularly well-studied example.

Hybridization is, however, an important means of speciation in plants, since polyploidy
Polyploidy
Polyploid is a term used to describe cells and organisms containing more than two paired sets of chromosomes. Most eukaryotic species are diploid, meaning they have two sets of chromosomes — one set inherited from each parent. However polyploidy is found in some organisms and is especially common...

 (having more than two copies of each chromosome) is tolerated in plants more readily than in animals. Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis. Polyploids also have more genetic diversity, which allows them to avoid inbreeding depression
Inbreeding depression
Inbreeding depression is the reduced fitness in a given population as a result of breeding of related individuals. It is often the result of a population bottleneck...

 in small populations.

Genetic structure

Because of physical barriers to migration, along with limited tendency for individuals to move or spread (vagility), and tendency to remain or come back to natal place (philopatry
Philopatry
Broadly, philopatry is the behaviour of remaining in, or returning to, an individual's birthplace. More specifically, in ecology philopatry is the behaviour of elder offspring sharing the parental burden in the upbringing of their siblings, a classic example of kin selection...

), natural populations rarely all interbreed as convenient in theoretical random models (panmixy) (Buston et al., 2007). There is usually a geographic range within which individuals are more closely related to one another than those randomly selected from the general population. This is described as the extent to which a population is genetically structured (Repaci et al., 2007). Genetic structuring can be caused by migration due to historical climate change
Climate change
Climate change is a significant and lasting change in the statistical distribution of weather patterns over periods ranging from decades to millions of years. It may be a change in average weather conditions or the distribution of events around that average...

, species range expansion or current availability of habitat
Habitat
* Habitat , a place where a species lives and grows*Human habitat, a place where humans live, work or play** Space habitat, a space station intended as a permanent settlement...

.

Horizontal Gene Transfer

Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

. In medicine, this contributes to the spread of antibiotic resistance
Antibiotic resistance
Antibiotic resistance is a type of drug resistance where a microorganism is able to survive exposure to an antibiotic. While a spontaneous or induced genetic mutation in bacteria may confer resistance to antimicrobial drugs, genes that confer resistance can be transferred between bacteria in a...

, as when one bacteria acquires resistance genes it can rapidly transfer them to other species. Horizontal transfer of genes from bacteria to eukaryotes such as the yeast Saccharomyces cerevisiae
Saccharomyces cerevisiae
Saccharomyces cerevisiae is a species of yeast. It is perhaps the most useful yeast, having been instrumental to baking and brewing since ancient times. It is believed that it was originally isolated from the skin of grapes...

and the adzuki bean beetle Callosobruchus chinensis may also have occurred. An example of larger-scale transfers are the eukaryotic bdelloid rotifers, which appear to have received a range of genes from bacteria, fungi, and plants. Virus
Virus
A virus is a small infectious agent that can replicate only inside the living cells of organisms. Viruses infect all types of organisms, from animals and plants to bacteria and archaea...

es can also carry DNA between organisms, allowing transfer of genes even across biological domains
Domain (biology)
In biological taxonomy, a domain is the highest taxonomic rank of organisms, higher than a kingdom. According to the three-domain system of Carl Woese, introduced in 1990, the Tree of Life consists of three domains: Archaea, Bacteria and Eukarya...

. Large-scale gene transfer has also occurred between the ancestors of eukaryotic cells
Eukaryote
A eukaryote is an organism whose cells contain complex structures enclosed within membranes. Eukaryotes may more formally be referred to as the taxon Eukarya or Eukaryota. The defining membrane-bound structure that sets eukaryotic cells apart from prokaryotic cells is the nucleus, or nuclear...

 and prokaryotes, during the acquisition of chloroplast
Chloroplast
Chloroplasts are organelles found in plant cells and other eukaryotic organisms that conduct photosynthesis. Chloroplasts capture light energy to conserve free energy in the form of ATP and reduce NADP to NADPH through a complex set of processes called photosynthesis.Chloroplasts are green...

s and mitochondria
Mitochondrion
In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These organelles range from 0.5 to 1.0 micrometers in diameter...

.

Complications

Basic models of population genetics consider only one gene locus at a time. In practice, epistatic
Epistasis
In genetics, epistasis is the phenomenon where the effects of one gene are modified by one or several other genes, which are sometimes called modifier genes. The gene whose phenotype is expressed is called epistatic, while the phenotype altered or suppressed is called hypostatic...

 and linkage
Linkage
Linkage generally means "the manner or style of being united", and can refer to:*Genetic linkage, the tendency of certain genes to be inherited together*Flux linkage, the total flux passing through a surface formed by a closed conducting loop...

 relationships between loci may also be important.

Epistasis

Because of epistasis
Epistasis
In genetics, epistasis is the phenomenon where the effects of one gene are modified by one or several other genes, which are sometimes called modifier genes. The gene whose phenotype is expressed is called epistatic, while the phenotype altered or suppressed is called hypostatic...

, the phenotypic effect of an allele at one locus may depend on which alleles are present at many other loci. Selection does not act on a single locus, but on a phenotype that arises through development from a complete genotype.

According to Lewontin
Richard Lewontin
Richard Charles "Dick" Lewontin is an American evolutionary biologist, geneticist and social commentator. A leader in developing the mathematical basis of population genetics and evolutionary theory, he pioneered the notion of using techniques from molecular biology such as gel electrophoresis to...

 (1974), the theoretical task for population genetics is a process in two spaces: a "genotypic space" and a "phenotypic space". The challenge of a complete theory of population genetics is to provide a set of laws that predictably map a population of genotype
Genotype
The genotype is the genetic makeup of a cell, an organism, or an individual usually with reference to a specific character under consideration...

s (G1) to a phenotype
Phenotype
A phenotype is an organism's observable characteristics or traits: such as its morphology, development, biochemical or physiological properties, behavior, and products of behavior...

 space (P1), where selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

 takes place, and another set of laws that map the resulting population (P2) back to genotype space (G2) where Mendelian genetics can predict the next generation of genotypes, thus completing the cycle. Even leaving aside for the moment the non-Mendelian aspects of molecular genetics
Molecular genetics
Molecular genetics is the field of biology and genetics that studies the structure and function of genes at a molecular level. The field studies how the genes are transferred from generation to generation. Molecular genetics employs the methods of genetics and molecular biology...

, this is clearly a gargantuan task. Visualizing this transformation schematically:


(adapted from Lewontin 1974, p. 12). XD

T1 represents the genetic and epigenetic laws, the aspects of functional biology, or development
Developmental biology
Developmental biology is the study of the process by which organisms grow and develop. Modern developmental biology studies the genetic control of cell growth, differentiation and "morphogenesis", which is the process that gives rise to tissues, organs and anatomy.- Related fields of study...

, that transform a genotype into phenotype. We will refer to this as the "genotype-phenotype map". T2 is the transformation due to natural selection, T3 are epigenetic relations that predict genotypes based on the selected phenotypes and finally T4 the rules of Mendelian genetics.

In practice, there are two bodies of evolutionary theory that exist in parallel, traditional population genetics operating in the genotype space and the biometric theory used in plant
Plant breeding
Plant breeding is the art and science of changing the genetics of plants in order to produce desired characteristics. Plant breeding can be accomplished through many different techniques ranging from simply selecting plants with desirable characteristics for propagation, to more complex molecular...

 and animal breeding
Animal breeding
Animal breeding is a branch of animal science that addresses the evaluation of the genetic value of domestic livestock...

, operating in phenotype space. The missing part is the mapping between the genotype and phenotype space. This leads to a "sleight of hand" (as Lewontin terms it) whereby variables in the equations of one domain, are considered parameters or constants, where, in a full-treatment they would be transformed themselves by the evolutionary process and are in reality functions of the state variables in the other domain. The "sleight of hand" is assuming that we know this mapping. Proceeding as if we do understand it is enough to analyze many cases of interest. For example, if the phenotype is almost one-to-one with genotype (sickle-cell disease
Sickle-cell disease
Sickle-cell disease , or sickle-cell anaemia or drepanocytosis, is an autosomal recessive genetic blood disorder with overdominance, characterized by red blood cells that assume an abnormal, rigid, sickle shape. Sickling decreases the cells' flexibility and results in a risk of various...

) or the time-scale is sufficiently short, the "constants" can be treated as such; however, there are many situations where it is inaccurate.

Linkage

If all genes are in linkage equilibrium, the effect of an allele at one locus can be averaged across the gene pool
Gene pool
In population genetics, a gene pool is the complete set of unique alleles in a species or population.- Description :A large gene pool indicates extensive genetic diversity, which is associated with robust populations that can survive bouts of intense selection...

 at other loci. In reality, one allele is frequently found in linkage disequilibrium
Linkage disequilibrium
In population genetics, linkage disequilibrium is the non-random association of alleles at two or more loci, not necessarily on the same chromosome. It is also referred to as to as gametic phase disequilibrium , or simply gametic disequilibrium...

 with genes at other loci, especially with genes located nearby on the same chromosome. Recombination breaks up this linkage disequilibrium too slowly to avoid genetic hitchhiking
Genetic hitchhiking
Genetic hitchhiking is the process by which an allele may increase in frequency by virtue of being linked to a gene that is positively selected. Proximity on a chromosome may allow genes to be dragged along with a selective sweep experienced by an advantageous gene nearby...

, where an allele at one locus rises to high frequency because it is linked
Genetic linkage
Genetic linkage is the tendency of certain loci or alleles to be inherited together. Genetic loci that are physically close to one another on the same chromosome tend to stay together during meiosis, and are thus genetically linked.-Background:...

 to an allele under selection at a nearby locus. This is a problem for population genetic models that treat one gene locus at a time. It can, however, be exploited as a method for detecting the action of natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

 via selective sweep
Selective sweep
A selective sweep is the reduction or elimination of variation among the nucleotides in neighboring DNA of a mutation as the result of recent and strong positive natural selection....

s.

In the extreme case of primarily asexual populations
Asexual reproduction
Asexual reproduction is a mode of reproduction by which offspring arise from a single parent, and inherit the genes of that parent only, it is reproduction which does not involve meiosis, ploidy reduction, or fertilization. A more stringent definition is agamogenesis which is reproduction without...

, linkage is complete, and different population genetic equations can be derived and solved, which behave quite differently to the sexual case. Most microbes, such as bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...

, are asexual. The population genetics of microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...

s lays the foundations for tracking the origin and evolution of antibiotic resistance
Antibiotic resistance
Antibiotic resistance is a type of drug resistance where a microorganism is able to survive exposure to an antibiotic. While a spontaneous or induced genetic mutation in bacteria may confer resistance to antimicrobial drugs, genes that confer resistance can be transferred between bacteria in a...

 and deadly infectious pathogen
Pathogen
A pathogen gignomai "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host...

s. Population genetics of microorganisms is also an essential factor for devising strategies for the conservation and better utilization of beneficial microbes (Xu, 2010).

History

Population genetics began as a reconciliation of the Mendelian
Mendelian inheritance
Mendelian inheritance is a scientific description of how hereditary characteristics are passed from parent organisms to their offspring; it underlies much of genetics...

 and biometrician
Biostatistics
Biostatistics is the application of statistics to a wide range of topics in biology...

 models. A key step was the work of the British biologist and statistician R.A. Fisher
Ronald Fisher
Sir Ronald Aylmer Fisher FRS was an English statistician, evolutionary biologist, eugenicist and geneticist. Among other things, Fisher is well known for his contributions to statistics by creating Fisher's exact test and Fisher's equation...

. In a series of papers starting in 1918 and culminating in his 1930 book The Genetical Theory of Natural Selection
The Genetical Theory of Natural Selection
The Genetical Theory of Natural Selection is a book by R.A. Fisher first published in 1930 by Clarendon. It is one of the most important books of the modern evolutionary synthesis and is commonly cited in biology books.-Editions:...

, Fisher showed that the continuous variation measured by the biometricians could be produced by the combined action of many discrete genes, and that natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

 could change allele frequencies in a population, resulting in evolution. In a series of papers beginning in 1924, another British geneticist, J.B.S. Haldane
J. B. S. Haldane
John Burdon Sanderson Haldane FRS , known as Jack , was a British-born geneticist and evolutionary biologist. A staunch Marxist, he was critical of Britain's role in the Suez Crisis, and chose to leave Oxford and moved to India and became an Indian citizen...

 worked out the mathematics of allele frequency change at a single gene locus under a broad range of conditions. Haldane also applied statistical analysis to real-world examples of natural selection, such as the evolution of industrial melanism in peppered moths
Peppered moth evolution
The evolution of the peppered moth over the last two hundred years has been studied in detail. Originally, the vast majority of peppered moths had light colouration, which effectively camouflaged them against the light-coloured trees and lichens which they rested upon...

, and showed that selection coefficient
Selection coefficient
In population genetics, the selection coefficient is a measure of the relative fitness of a phenotype. Usually denoted by the letter s, it compares the fitness of a phenotype to another favored phenotype, and is the proportional amount that the considered phenotype is less fit as measured by...

s could be larger than Fisher assumed, leading to more rapid adaptive evolution.

The American biologist Sewall Wright
Sewall Wright
Sewall Green Wright was an American geneticist known for his influential work on evolutionary theory and also for his work on path analysis. With R. A. Fisher and J.B.S. Haldane, he was a founder of theoretical population genetics. He is the discoverer of the inbreeding coefficient and of...

, who had a background in animal breeding
Animal breeding
Animal breeding is a branch of animal science that addresses the evaluation of the genetic value of domestic livestock...

 experiments, focused on combinations of interacting genes, and the effects of inbreeding on small, relatively isolated populations that exhibited genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.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...

. In 1932, Wright introduced the concept of an adaptive landscape
Fitness landscape
In evolutionary biology, fitness landscapes or adaptive landscapes are used to visualize the relationship between genotypes and reproductive success. It is assumed that every genotype has a well-defined replication rate . This fitness is the "height" of the landscape...

 and argued that genetic drift and inbreeding could drive a small, isolated sub-population away from an adaptive peak, allowing natural selection to drive it towards different adaptive peaks.

The work of Fisher, Haldane and Wright founded the discipline of population genetics. This integrated natural selection with Mendelian genetics, which was the critical first step in developing a unified theory of how evolution worked. John Maynard Smith
John Maynard Smith
John Maynard Smith,His surname was Maynard Smith, not Smith, nor was it hyphenated. F.R.S. was a British theoretical evolutionary biologist and geneticist. Originally an aeronautical engineer during the Second World War, he took a second degree in genetics under the well-known biologist J.B.S....

 was Haldane's pupil, whilst W.D. Hamilton was heavily influenced by the writings of Fisher. The American George R. Price
George R. Price
George Robert Price was an American population geneticist. Originally a physical chemist and later a science journalist, he moved to London in 1967, where he worked in theoretical biology at the Galton Laboratory, making three important contributions: first, rederiving W.D...

 worked with both Hamilton and Maynard Smith. American Richard Lewontin
Richard Lewontin
Richard Charles "Dick" Lewontin is an American evolutionary biologist, geneticist and social commentator. A leader in developing the mathematical basis of population genetics and evolutionary theory, he pioneered the notion of using techniques from molecular biology such as gel electrophoresis to...

 and Japanese Motoo Kimura
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...

 were heavily influenced by Wright.

Modern evolutionary synthesis

The mathematics of population genetics were originally developed as the beginning of the modern evolutionary synthesis
Modern evolutionary synthesis
The modern evolutionary synthesis is a union of ideas from several biological specialties which provides a widely accepted account of evolution...

. According to Beatty (1986), population genetics defines the core of the modern synthesis. In the first few decades of the 20th century, most field naturalists continued to believe that Lamarckian and orthogenic mechanisms of evolution provided the best explanation for the complexity they observed in the living world. However, as the field of genetics continued to develop, those views became less tenable. During the modern evolutionary synthesis, these ideas were purged, and only evolutionary causes that could be expressed in the mathematical framework of population genetics were retained. Consensus was reached as to which evolutionary factors might influence evolution, but not as to the relative importance of the various factors.

Theodosius Dobzhansky
Theodosius Dobzhansky
Theodosius Grygorovych Dobzhansky ForMemRS was a prominent geneticist and evolutionary biologist, and a central figure in the field of evolutionary biology for his work in shaping the unifying modern evolutionary synthesis...

, a postdoctoral worker in T. H. Morgan's lab, had been influenced by the work on genetic diversity by Russia
Russia
Russia or , officially known as both Russia and the Russian Federation , is a country in northern Eurasia. It is a federal semi-presidential republic, comprising 83 federal subjects...

n geneticists such as Sergei Chetverikov
Sergei Chetverikov
Sergei Sergeevich Chetverikov was one of the early contributors to the development of the field of genetics...

. He helped to bridge the divide between the foundations of microevolution
Microevolution
Microevolution is the changes in allele frequencies that occur over time within a population. This change is due to four different processes: mutation, selection , gene flow, and genetic drift....

 developed by the population geneticists and the patterns of macroevolution
Macroevolution
Macroevolution is evolution on a scale of separated gene pools. Macroevolutionary studies focus on change that occurs at or above the level of species, in contrast with microevolution, which refers to smaller evolutionary changes within a species or population.The process of speciation may fall...

 observed by field biologists, with his 1937 book Genetics and the Origin of Species
Genetics and the Origin of Species
Genetics and the Origin of Species is a 1937 book by the twentieth century Ukrainian-American evolutionary biologist Theodosius Dobzhansky and one of the important books of the modern evolutionary synthesis. The book describes the Modern Synthesis of Evolution Theory, also known as Synthetic...

. Dobzhansky examined the genetic diversity of wild populations and showed that, contrary to the assumptions of the population geneticists, these populations had large amounts of genetic diversity, with marked differences between sub-populations. The book also took the highly mathematical work of the population geneticists and put it into a more accessible form. Many more biologists were influenced by population genetics via Dobzhansky than were able to read the highly mathematical works in the original.

Selection vs. genetic drift

Fisher and Wright had some fundamental disagreements and a controversy about the relative roles of selection and drift continued for much of the century between the Americans and the British.

In Great Britain E.B. Ford
E.B. Ford
Edmund Brisco "Henry" Ford FRS Hon. FRCP was a British ecological geneticist. He was a leader among those British biologists who investigated the role of natural selection in nature. As a schoolboy Ford became interested in lepidoptera, the group of insects which includes butterflies and moths...

, the pioneer of ecological genetics
Ecological genetics
Ecological genetics is the study of genetics in natural populations.This contrasts with classical genetics, which works mostly on crosses between laboratory strains, and DNA sequence analysis, which studies genes at the molecular level....

, continued throughout the 1930s and 1940s to demonstrate the power of selection due to ecological factors including the ability to maintain genetic diversity through genetic polymorphisms
Polymorphism (biology)
Polymorphism in biology occurs when two or more clearly different phenotypes exist in the same population of a species — in other words, the occurrence of more than one form or morph...

 such as human blood types. Ford's work, in collaboration with Fisher, contributed to a shift in emphasis during the course of the modern synthesis towards natural selection
Natural selection
Natural selection is the nonrandom process by which biologic traits become either more or less common in a population as a function of differential reproduction of their bearers. It is a key mechanism of evolution....

 over genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.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...

.

Recent studies of eukaryotic transposable elements, and of their impact on speciation
Speciation
Speciation is the evolutionary process by which new biological species arise. The biologist Orator F. Cook seems to have been the first to coin the term 'speciation' for the splitting of lineages or 'cladogenesis,' as opposed to 'anagenesis' or 'phyletic evolution' occurring within lineages...

, point again to a major role of nonadaptive processes such as mutation
Mutation
In molecular biology and genetics, mutations are changes in a genomic sequence: the DNA sequence of a cell's genome or the DNA or RNA sequence of a virus. They can be defined as sudden and spontaneous changes in the cell. Mutations are caused by radiation, viruses, transposons and mutagenic...

 and genetic drift
Genetic drift
Genetic drift or allelic drift is the change in the frequency of a gene variant in a population due to random sampling.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...

. Mutation and genetic drift are also viewed as major factors in the evolution of genome complexity

External links

  • The ALlele FREquency Database at Yale University
    Yale University
    Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...

  • EHSTRAFD.org - Earth Human STR Allele Frequencies Database
  • History of population genetics
  • How Selection Changes the Genetic Composition of Population, video of lecture by Stephen C. Stearns
    Stephen C. Stearns
    Stephen C. Stearns is an American biologist, the Edward P. Bass Professor of Ecology and Evolutionary Biology at Yale University...

     (Yale University
    Yale University
    Yale University is a private, Ivy League university located in New Haven, Connecticut, United States. Founded in 1701 in the Colony of Connecticut, the university is the third-oldest institution of higher education in the United States...

    )
  • National Geographic: Atlas of the Human Journey (Haplogroup
    Haplogroup
    In the study of molecular evolution, a haplogroup is a group of similar haplotypes that share a common ancestor having the same single nucleotide polymorphism mutation in both haplotypes. Because a haplogroup consists of similar haplotypes, this is what makes it possible to predict a haplogroup...

    -based human migration maps)
  • Monash Virtual Laboratory - Simulations of habitat fragmentation and population genetics online at Monash University's Virtual Laboratory.
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