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.
Population genetics was a vital ingredient in the
emergence of the
modern evolutionary synthesis. Its primary founders were
Sewall Wright,
J. B. S. Haldane and
Ronald Fisher, who also laid the foundations for the related discipline of
quantitative genetics. Traditionally a highly mathematical discipline, modern population genetics encompasses theoretical, laboratory, and field work. Population genetic models are used both for
statistical inference from DNA sequence data and for proof/disproof of concept.
What sets population genetics apart from newer, more phenotypic approaches to modelling evolution, such as
evolutionary game theory and
adaptive dynamics, is its emphasis on such genetic phenomena as
dominance,
epistasis, the degree to which
genetic recombination breaks
linkage disequilibrium, and the random phenomena of
mutation and
genetic drift. This makes it appropriate for comparison to
population genomics data.
History
Population genetics began as a reconciliation of
Mendelian inheritance and
biostatistics models.
Natural selection will only cause evolution if there is enough
genetic variation in a population. Before the discovery of
Mendelian genetics, one common hypothesis was
blending inheritance. But with blending inheritance, genetic variance would be rapidly lost, making evolution by natural or sexual selection implausible. The
Hardy–Weinberg principle provides the solution to how variation is maintained in a population with Mendelian inheritance. 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 next key step was the work of the British biologist and statistician
Ronald Fisher. In a series of papers starting in 1918 and culminating in his 1930 book ''
The Genetical Theory of Natural Selection'', 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 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, 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
peppered moth evolution and
industrial melanism, and showed that
selection coefficients could be larger than Fisher assumed, leading to more rapid adaptive evolution as a camouflage strategy following increased pollution.
The American biologist
Sewall Wright, who had a background in
animal breeding experiments, focused on combinations of interacting genes, and the effects of
inbreeding on small, relatively isolated populations that exhibited genetic drift. In 1932 Wright introduced the concept of an
adaptive 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 was Haldane's pupil, whilst
W. D. Hamilton was influenced by the writings of Fisher. The American
George R. Price worked with both Hamilton and Maynard Smith. American
Richard Lewontin and Japanese
Motoo Kimura were influenced by Wright and Haldane.
Gertrude Hauser and Heidi Danker–Hopfe have suggested that
Hubert Walter also contributed to the creation of the subdiscipline population genetics.
Modern synthesis
The mathematics of population genetics were originally developed as the beginning of the
modern synthesis. Authors such as Beatty have asserted that population genetics defines the core of the modern synthesis. For the first few decades of the 20th century, most field naturalists continued to believe that
Lamarckism and
orthogenesis provided the best explanation for the complexity they observed in the living world. During the modern 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, a postdoctoral worker in
T. H. Morgan's lab, had been influenced by the work on
genetic diversity by Russian geneticists such as
Sergei Chetverikov. He helped to bridge the divide between the foundations of
microevolution developed by the population geneticists and the patterns of
macroevolution observed by field biologists, with his 1937 book ''
Genetics and the Origin of Species''. 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.
In Great Britain
E. B. Ford, the pioneer of
ecological genetics, continued throughout the 1930s and 1940s to empirically demonstrate the power of selection due to ecological factors including the ability to maintain genetic diversity through genetic
polymorphisms such as human
blood types. Ford's work, in collaboration with Fisher, contributed to a shift in emphasis during the modern synthesis towards natural selection as the dominant force.
Neutral theory and origin-fixation dynamics
The original, modern synthesis view of population genetics assumes that mutations provide ample raw material, and focuses only on the change in
frequency of alleles within
populations.
The main processes influencing allele frequencies are
natural selection,
genetic drift,
gene flow and recurrent
mutation. Fisher and Wright had some fundamental disagreements about the relative roles of selection and drift.
The availability of molecular data on all genetic differences led to the
neutral theory of molecular evolution. In this view, many mutations are deleterious and so never observed, and most of the remainder are neutral, i.e. are not under selection. With the fate of each neutral mutation left to chance (genetic drift), the direction of evolutionary change is driven by which mutations occur, and so cannot be captured by models of change in the frequency of (existing) alleles alone.
The origin-fixation view of population genetics generalizes this approach beyond strictly neutral mutations, and sees the rate at which a particular change happens as the product of the mutation rate and the
fixation probability.
Four processes
Selection
Natural selection, which includes
sexual selection, is the fact that some
traits make it more likely for an
organism to survive and
reproduce. Population genetics describes natural selection by defining
fitness as a
propensity or probability 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. Natural selection acts on
phenotypes, so population genetic models assume relatively simple relationships to predict the phenotype and hence fitness from the
allele at one or a small number of loci. In this way, natural selection converts differences in the fitness of individuals with different phenotypes into changes in allele frequency in a population over successive generations.
Before the advent of population genetics, many biologists doubted that small differences in fitness were sufficient to make a large difference to evolution.
Population geneticists addressed this concern in part by comparing selection to
genetic drift. Selection can overcome genetic drift when s is greater than 1 divided by the
effective population size. When this criterion is met, the probability that a new advantageous mutant becomes
fixed is approximately equal to 2s. The time until fixation of such an allele depends little on genetic drift, and is approximately proportional to log(sN)/s.
Dominance
Dominance means that the phenotypic and/or fitness effect of one allele at a locus depends on which allele is present in the second copy for that locus. Consider three genotypes at one locus, with the following fitness values
s is the
selection coefficient and h is the dominance coefficient. The value of h yields the following information:
Epistasis
Epistasis means that the phenotypic and/or fitness effect of an allele at one locus depends on which alleles are present at other loci. Selection does not act on a single locus, but on a phenotype that arises through development from a complete genotype. However, many population genetics models of sexual species are "single locus" models, where the fitness of an individual is calculated as the
product of the contributions from each of its loci—effectively assuming no epistasis.
In fact, the
genotype to fitness landscape is more complex. Population genetics must either model this complexity in detail, or capture it by some simpler average rule. Empirically, beneficial mutations tend to have a smaller fitness benefit when added to a genetic background that already has high fitness: this is known as diminishing returns epistasis. When deleterious mutations also have a smaller fitness effect on high fitness backgrounds, this is known as "synergistic epistasis". However, the effect of deleterious mutations tends on average to be very close to multiplicative, or can even show the opposite pattern, known as "antagonistic epistasis".
Synergistic epistasis is central to some theories of the purging of
mutation load and to the
evolution of sexual reproduction.
Mutation
Mutation is the ultimate source of
genetic variation in the form of new alleles. In addition, mutation may influence the direction of evolution when there is mutation bias, i.e. different probabilities for different mutations to occur. For example, recurrent mutation that tends to be in the opposite direction to selection can lead to
mutation–selection balance. At the molecular level, if 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 evolution. For example, according to the
phenotype-first theory of evolution, mutations can eventually cause the
genetic assimilation of traits that were previously
induced by the environment.
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.
Mutation can have no effect, alter the
product of a gene, or prevent the gene from functioning. Studies in the fly ''
Drosophila melanogaster'' 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.
Most loss of function mutations are selected against. But when selection is weak, mutation bias towards loss of function can affect evolution. For example,
pigments 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 ability in a
bacterium 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, indicating that it is driven more by mutation bias than by genetic drift.
Mutations can involve large sections of DNA becoming
duplicated, usually through
genetic recombination. This leads to
copy-number variation within a population. Duplications are a major source of raw material for evolving new genes. Other types of mutation occasionally create new genes from previously noncoding DNA.
Genetic drift
''Genetic drift'' is a change in
allele frequencies caused by
random sampling.
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, 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 are equally likely to make an allele more common as less common.
The effect of genetic drift is larger for alleles present in few copies than when an allele is present in many copies. The population genetics of genetic drift are described using either
branching processes 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
:
Ronald Fisher held the view that genetic drift plays at the most a minor role in evolution, and this remained the dominant view for several decades. No population genetics perspective have ever given genetic drift a central role by itself, but some have made genetic drift important in combination with another non-selective force. The
shifting balance theory of
Sewall Wright held that the combination of population structure and genetic drift was important.
Motoo Kimura's
neutral theory of molecular evolution claims that most genetic differences within and between populations are caused by the combination of 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, who argue that selection on linked sites is a more important stochastic force, doing the work traditionally ascribed to genetic drift by means of sampling error. The mathematical properties of genetic draft are different from those of genetic drift. The direction of the random change in allele frequency is
autocorrelated across generations.
Gene flow

Because of physical barriers to migration, along with the limited tendency for individuals to move or spread (
vagility), and tendency to remain or come back to natal place (
philopatry), natural populations rarely all interbreed as may be assumed in theoretical random models (
panmixy). 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.

Genetic structuring can be caused by migration due to historical
climate change, species
range expansion or current availability of
habitat. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the
Great Wall of China, which has hindered the flow of plant genes.
Gene flow is the exchange of genes between populations or species, breaking down the structure. Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of
pollen. Gene transfer between species includes the formation of
hybrid organisms and
horizontal gene transfer. Population genetic models can be used to identify which populations show significant genetic isolation from one another, and to reconstruct their history.
Subjecting a population to isolation leads to
inbreeding depression. Migration into a population can introduce new genetic variants, potentially contributing to
evolutionary rescue. If a significant proportion of individuals or gametes migrate, it can also change allele frequencies, e.g. giving rise to
migration load.
In the presence of gene flow, other
barriers to hybridization between two diverging populations of an
outcrossing species are required for the populations to
become new species.
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
prokaryotes.
In medicine, this contributes to the spread of
antibiotic resistance, 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'' 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.
Viruses can also carry DNA between organisms, allowing transfer of genes even across
biological domains. Large-scale gene transfer has also occurred between the ancestors of
eukaryotic cells and prokaryotes, during the acquisition of
chloroplasts and
mitochondria.
Linkage
If all genes are in
linkage equilibrium, the effect of an allele at one locus can be averaged across the
gene pool at other loci. In reality, one allele is frequently found in
linkage 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, where an allele at one locus rises to high frequency because it is
linked to an allele under selection at a nearby locus. Linkage also slows down the rate of adaptation, even in sexual populations. The effect of linkage disequilibrium in slowing down the rate of adaptive evolution arises from a combination of the
Hill–Robertson effect (delays in bringing beneficial mutations together) and
background selection (delays in separating beneficial mutations from deleterious
hitchhikers).
Linkage 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 via
selective sweeps.
In the extreme case of an
asexual population, linkage is complete, and population genetic equations can be derived and solved in terms of a travelling
wave of genotype frequencies along a simple
fitness landscape.
Most
microbes, such as
bacteria, are asexual. The population genetics of their
adaptation have two contrasting regimes. When the product of the beneficial mutation rate and population size is small, asexual populations follow a "successional regime" of origin-fixation dynamics, with adaptation rate strongly dependent on this product. When the product is much larger, asexual populations follow a "concurrent mutations" regime with adaptation rate less dependent on the product, characterized by
clonal interference and the appearance of a new beneficial mutation before the last one has
fixed.
Applications
Explaining levels of genetic variation
Neutral theory predicts that the level of
nucleotide diversity in a population will be proportional to the product of the population size and the neutral mutation rate. The fact that levels of genetic diversity vary much less than population sizes do is known as the "paradox of variation". While high levels of genetic diversity were one of the original arguments in favor of neutral theory, the paradox of variation has been one of the strongest arguments against neutral theory.
It is clear that levels of genetic diversity vary greatly within a species as a function of local recombination rate, due to both
genetic hitchhiking and
background selection. Most current solutions to the paradox of variation invoke some level of selection at linked sites.
For example, one analysis suggests that larger populations have more selective sweeps, which remove more neutral genetic diversity. A negative correlation between mutation rate and population size may also contribute.
Life history affects genetic diversity more than population history does, e.g.
r-strategists have more genetic diversity.
Detecting selection
Population genetics models are used to infer which genes are undergoing selection. One common approach is to look for regions of high
linkage disequilibrium and low genetic variance along the chromosome, to detect recent
selective sweeps.
A second common approach is the
McDonald–Kreitman test. The McDonald–Kreitman test compares the amount of variation within a species (
polymorphism) to the divergence between species (substitutions) at two types of sites, one assumed to be neutral. Typically,
synonymous sites are assumed to be neutral.
Genes undergoing positive selection have an excess of divergent sites relative to polymorphic sites. The test can also be used to obtain a genome-wide estimate of the proportion of substitutions that are fixed by positive selection, α.
According to the
neutral theory of molecular evolution, this number should be near zero. High numbers have therefore been interpreted as a genome-wide falsification of neutral theory.
Demographic inference
The simplest test for population structure in a sexually reproducing, diploid species, is to see whether genotype frequencies follow Hardy-Weinberg proportions as a function of allele frequencies. For example, in the simplest case of a single locus with two
alleles denoted A and a at frequencies ''p'' and ''q'', random mating predicts freq(AA) = ''p''
2 for the AA
homozygotes, freq(aa) = ''q''
2 for the aa homozygotes, and freq(Aa) = 2''pq'' for the
heterozygotes. In the absence of population structure, Hardy-Weinberg proportions are reached within 1-2 generations of random mating. More typically, there is an excess of homozygotes, indicative of population structure. The extent of this excess can be quantified as the
inbreeding coefficient, F.
Individuals can be clustered into ''K'' subpopulations. The degree of population structure can then be calculated using
FST, which is a measure of the proportion of genetic variance that can be explained by population structure. Genetic population structure can then be related to geographic structure, and
genetic admixture can be detected.
Coalescent theory relates genetic diversity in a sample to demographic history of the population from which it was taken. It normally assumes
neutrality, and so sequences from more neutrally-evolving portions of genomes are therefore selected for such analyses. It can be used to infer the relationships between species (
phylogenetics), as well as the population structure, demographic history (e.g.
population bottlenecks,
population growth),
biological dispersal,
source–sink dynamics and
introgression within a species.
Another approach to demographic inference relies on the
allele frequency spectrum.
Evolution of genetic systems
By assuming that there are loci that control the genetic system itself, population genetic models are created to describe the
evolution of dominance and other forms of
robustness, the
evolution of sexual reproduction and recombination rates, the evolution of
mutation rates, the evolution of
evolutionary capacitors, the evolution of
costly signalling traits, the
evolution of ageing, and the evolution of
co-operation. For example, most mutations are deleterious, so the optimal
mutation rate for a species may be a trade-off between the damage from a high deleterious mutation rate and the
metabolic costs of maintaining systems to reduce the mutation rate, such as DNA repair enzymes.
One important aspect of such models is that selection is only strong enough to purge deleterious mutations and hence overpower mutational bias towards degradation if the selection coefficient s is greater than the inverse of the
effective population size. This is known as the drift barrier and is related to the
nearly neutral theory of molecular evolution. Drift barrier theory predicts that species with large effective population sizes will have highly streamlined, efficient genetic systems, while those with small population sizes will have bloated and complex
genomes containing for example
introns and
transposable elements. However, somewhat paradoxically, species with large population sizes might be so tolerant to the consequences of certain types of errors that they evolve higher error rates, e.g. in
transcription and
translation, than small populations.
See also
References
External links
Population Genetics TutorialsMolecular population geneticsThe ALlele FREquency Databaseat
Yale UniversityEHSTRAFD.org - Earth Human STR Allele Frequencies DatabaseHistory of population geneticsHow Selection Changes the Genetic Composition of Population video of lecture by
Stephen C. Stearns (
Yale University)
*
National GeographicAtlas of the Human Journey(
Haplogroup-based human migration maps)
{{DEFAULTSORT:Population Genetics
Population genetics
Category:Evolutionary biology
Category:Statistical genetics