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. The time until fixation of such an allele is approximately (2 log(sN)+\gamma)/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 of fitness as a function of the number of deleterious mutations. Synergistic epistasis is represented by the red line - each subsequent deleterious mutation has a larger proportionate effect on the organism's fitness. Antagonistic epistasis is in blue. The black line shows the non-epistatic case, where fitness is the
product of the contributions from each of its loci.
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 The genetic process of
mutation takes place within an individual, resulting in heritable changes to the genetic material. This process is often characterized by a description of the starting and ending states, or the kind of change that has happened at the level of DNA (e.g,. a T-to-C mutation, a 1-bp deletion), of genes or proteins (e.g., a null mutation, a loss-of-function mutation), or at a higher phenotypic level (e.g., red-eye mutation). Single-nucleotide changes are frequently the most common type of mutation, but many other types of
mutation are possible, and they occur at widely varying rates that may show systematic asymmetries or biases (
mutation bias). 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. In the
distribution of fitness effects (DFE) for new mutations, only a minority of mutations are beneficial. Mutations with gross effects are typically deleterious. 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. This biological process of mutation is represented in population-genetic models in one of two ways, either as a deterministic pressure of recurrent mutation on allele frequencies, or a source of variation. In deterministic theory, evolution begins with a predetermined set of alleles and proceeds by shifts in continuous frequencies, as if the population is infinite. The occurrence of mutations in individuals is represented by a population-level "force" or "pressure" of mutation, i.e., the force of innumerable events of mutation with a scaled magnitude u applied to shifting frequencies f(A1) to f(A2). For instance, in the classic
mutation–selection balance model, the force of mutation pressure pushes the frequency of an allele upward, and selection against its deleterious effects pushes the frequency downward, so that a balance is reached at equilibrium, given (in the simplest case) by f = u/s. This concept of mutation pressure is mostly useful for considering the implications of deleterious mutation, such as the mutation load and its implications for the evolution of the mutation rate. Transformation of populations by mutation pressure is unlikely. Haldane argued that it would require high mutation rates unopposed by selection, and Kimura concluded even more pessimistically that even this was unlikely, as the process would take too long (see
evolution by mutation pressure). However,
evolution by mutation pressure is possible under some circumstances and has long been suggested as a possible cause for the loss of unused traits. For example,
pigments are no longer useful when animals live in the darkness of caves, and tend to be lost. An experimental example involves the loss of sporulation in experimental populations of
B. subtilis. Sporulation is a complex trait encoded by many loci, such that the mutation rate for loss of the trait was estimated as an unusually high value, \mu = 0.003. Loss of sporulation in this case can occur by recurrent mutation, without requiring selection for the loss of 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 than by genetic drift. The role of mutation as a source of novelty is different from these classical models of mutation pressure. When population-genetic models include a rate-dependent process of mutational introduction or origination, i.e., a process that introduces new alleles including neutral and beneficial ones, then the properties of mutation may have a more direct impact on the rate and direction of evolution, even if the rate of mutation is very low. That is, the spectrum of mutation may become very important, particularly
mutation biases, predictable differences in the rates of occurrence for different types of mutations, because
bias in the introduction of variation can impose biases on the course of evolution. Mutation plays a key role in other classical and recent theories including
Muller%27s ratchet,
subfunctionalization, Eigen's concept of an
error catastrophe and Lynch's
mutational hazard hypothesis.
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 : V_t \approx pq\left(1-\exp\left\{-\frac{t}{2N_e} \right\}\right).
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. 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. is an obstacle to gene flow of some terrestrial species.
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==