Negative selection (natural selection)

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In natural selection, negative selection [1] or purifying selection is the selective removal of alleles that are deleterious. This can result in stabilising selection through the purging of deleterious genetic polymorphisms that arise through random mutations. [2] [3]

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Purging of deleterious alleles can be achieved on the population genetics level, with as little as a single point mutation being the unit of selection. In such a case, carriers of the harmful point mutation have fewer offspring each generation, reducing the frequency of the mutation in the gene pool.

In the case of strong negative selection on a locus, the purging of deleterious variants will result in the occasional removal of linked variation, producing a decrease in the level of variation surrounding the locus under selection. The incidental purging of non-deleterious alleles due to such spatial proximity to deleterious alleles is called background selection . [4] This effect increases with lower mutation rate but decreases with higher recombination rate. [5]

Purifying selection can be split into purging by non-random mating (assortative mating) and purging by genetic drift. Purging by genetic drift can remove primarily deeply recessive alleles, whereas natural selection can remove any type of deleterious alleles. [6]

Negative selection in haploid compared to diploid tissue

The idea that those genes of an organism that are expressed in the haploid stage are under more efficient natural selection than those genes expressed exclusively in the diploid stage is referred to as the “masking theory”. [7] This theory implies that purifying selection is more efficient in the haploid stage of the life cycle where fitness effects are more fully expressed than in the diploid stage of the life cycle. Evidence supporting the masking theory has been reported in the single-celled yeast Saccharomyces cerevisiae . [8] Further evidence of strong purifying selection in haploid tissue-specific genes, in support of the masking theory, has been reported for the plant, Scots Pine. [7]

See also

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<span class="mw-page-title-main">Neutral theory of molecular evolution</span> Theory of evolution by changes at the molecular level

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<span class="mw-page-title-main">Evolution of sexual reproduction</span>

Evolution of sexual reproduction describes how sexually reproducing animals, plants, fungi and protists could have evolved from a common ancestor that was a single-celled eukaryotic species. Sexual reproduction is widespread in eukaryotes, though a few eukaryotic species have secondarily lost the ability to reproduce sexually, such as Bdelloidea, and some plants and animals routinely reproduce asexually without entirely having lost sex. The evolution of sexual reproduction contains two related yet distinct themes: its origin and its maintenance. Bacteria and Archaea (prokaryotes) have processes that can transfer DNA from one cell to another, but it is unclear if these processes are evolutionarily related to sexual reproduction in Eukaryotes. In eukaryotes, true sexual reproduction by meiosis and cell fusion is thought to have arisen in the last eukaryotic common ancestor, possibly via several processes of varying success, and then to have persisted.

The effective population size (Ne) is the size of an idealised population that would experience the same rate of genetic drift or increase in inbreeding as the real population. Idealised populations are based on unrealistic but convenient assumptions including random mating, simultaneous birth of each new generation, and constant population size. For most quantities of interest and most real populations, Ne is smaller than the census population size N of a real population. The same population may have multiple effective population sizes for different properties of interest, including genetic drift and inbreeding.

In population genetics and population ecology, population size is a countable quantity representing the number of individual organisms in a population. Population size is directly associated with amount of genetic drift, and is the underlying cause of effects like population bottlenecks and the founder effect. Genetic drift is the major source of decrease of genetic diversity within populations which drives fixation and can potentially lead to speciation events.

Genetic load is the difference between the fitness of an average genotype in a population and the fitness of some reference genotype, which may be either the best present in a population, or may be the theoretically optimal genotype. The average individual taken from a population with a low genetic load will generally, when grown in the same conditions, have more surviving offspring than the average individual from a population with a high genetic load. Genetic load can also be seen as reduced fitness at the population level compared to what the population would have if all individuals had the reference high-fitness genotype. High genetic load may put a population in danger of extinction.

Mutation–selection balance is an equilibrium in the number of deleterious alleles in a population that occurs when the rate at which deleterious alleles are created by mutation equals the rate at which deleterious alleles are eliminated by selection. The majority of genetic mutations are neutral or deleterious; beneficial mutations are relatively rare. The resulting influx of deleterious mutations into a population over time is counteracted by negative selection, which acts to purge deleterious mutations. Setting aside other factors, the equilibrium number of deleterious alleles is then determined by a balance between the deleterious mutation rate and the rate at which selection purges those mutations.

Complementation refers to a genetic process when two strains of an organism with different homozygous recessive mutations that produce the same mutant phenotype have offspring that express the wild-type phenotype when mated or crossed. Complementation will ordinarily occur if the mutations are in different genes. Complementation may also occur if the two mutations are at different sites within the same gene, but this effect is usually weaker than that of intergenic complementation. When the mutations are in different genes, each strain's genome supplies the wild-type allele to "complement" the mutated allele of the other strain's genome. Since the mutations are recessive, the offspring will display the wild-type phenotype. A complementation test can test whether the mutations in two strains are in different genes. Complementation is usually weaker or absent if the mutations are in the same gene. The convenience and essence of this test is that the mutations that produce a phenotype can be assigned to different genes without the exact knowledge of what the gene product is doing on a molecular level. American geneticist Edward B. Lewis developed the complementation test.

Inbreeding depression is the reduced biological fitness that has the potential to result from inbreeding. The loss of genetic diversity that is seen due to inbreeding, results from small population size. Biological fitness refers to an organism's ability to survive and perpetuate its genetic material. Inbreeding depression is often the result of a population bottleneck. In general, the higher the genetic variation or gene pool within a breeding population, the less likely it is to suffer from inbreeding depression, though inbreeding and outbreeding depression can simultaneously occur.

Coalescent theory is a model of how alleles sampled from a population may have originated from a common ancestor. In the simplest case, coalescent theory assumes no recombination, no natural selection, and no gene flow or population structure, meaning that each variant is equally likely to have been passed from one generation to the next. The model looks backward in time, merging alleles into a single ancestral copy according to a random process in coalescence events. Under this model, the expected time between successive coalescence events increases almost exponentially back in time. Variance in the model comes from both the random passing of alleles from one generation to the next, and the random occurrence of mutations in these alleles.

Genetic hitchhiking, also called genetic draft or the hitchhiking effect, is when an allele changes frequency not because it itself is under natural selection, but because it is near another gene that is undergoing a selective sweep and that is on the same DNA chain. When one gene goes through a selective sweep, any other nearby polymorphisms that are in linkage disequilibrium will tend to change their allele frequencies too. Selective sweeps happen when newly appeared mutations are advantageous and increase in frequency. Neutral or even slightly deleterious alleles that happen to be close by on the chromosome 'hitchhike' along with the sweep. In contrast, effects on a neutral locus due to linkage disequilibrium with newly appeared deleterious mutations are called background selection. Both genetic hitchhiking and background selection are stochastic (random) evolutionary forces, like genetic drift.

<span class="mw-page-title-main">Mating in fungi</span> Combination of genetic material between compatible mating types

Fungi are a diverse group of organisms that employ a huge variety of reproductive strategies, ranging from fully asexual to almost exclusively sexual species. Most species can reproduce both sexually and asexually, alternating between haploid and diploid forms. This contrasts with most multicellular eukaryotes such as mammals, where the adults are usually diploid and produce haploid gametes which combine to form the next generation. In fungi, both haploid and diploid forms can reproduce – haploid individuals can undergo asexual reproduction while diploid forms can produce gametes that combine to give rise to the next generation.

<span class="mw-page-title-main">Haplodiploidy</span> Biological system where sex is determined by the number of sets of chromosomes

Haplodiploidy is a sex-determination system in which males develop from unfertilized eggs and are haploid, and females develop from fertilized eggs and are diploid. Haplodiploidy is sometimes called arrhenotoky.

Out-crossing or out-breeding is the technique of crossing between different breeds. This is the practice of introducing distantly related genetic material into a breeding line, thereby increasing genetic diversity.

Background selection describes the loss of genetic diversity at a locus due to negative selection against deleterious alleles with which it is in linkage disequilibrium. The name emphasizes the fact that the genetic background, or genomic environment, of a mutation has a significant impact on whether it will be preserved versus lost from a population. Background selection contradicts the assumption of the neutral theory of molecular evolution that the fixation or loss of a neutral allele can be described by one-locus models of genetic drift, independently from other loci. As well as reducing neutral nucleotide diversity, background selection reduces the fixation probability of beneficial mutations, and increases the fixation probability of deleterious mutations.

In population genetics, fixation is the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) in a given population to a situation where only one of the alleles remains. That is, the allele becomes fixed. In the absence of mutation or heterozygote advantage, any allele must eventually either be lost completely from the population, or fixed, i.e. permanently established at 100% frequency in the population. Whether a gene will ultimately be lost or fixed is dependent on selection coefficients and chance fluctuations in allelic proportions. Fixation can refer to a gene in general or particular nucleotide position in the DNA chain (locus).

Genetic purging is the increased pressure of natural selection against deleterious alleles prompted by inbreeding.

<span class="mw-page-title-main">Epistasis</span> Dependence of a gene mutations phenotype on mutations in other genes

Epistasis is a phenomenon in genetics in which the effect of a gene mutation is dependent on the presence or absence of mutations in one or more other genes, respectively termed modifier genes. In other words, the effect of the mutation is dependent on the genetic background in which it appears. Epistatic mutations therefore have different effects on their own than when they occur together. Originally, the term epistasis specifically meant that the effect of a gene variant is masked by that of different gene.

References

  1. ↑ Loewe L (2008). "Negative selection". Nature Education. 1 (1): 59.
  2. ↑ Tien NS, Sabelis MW, Egas M (March 2015). "Inbreeding depression and purging in a haplodiploid: gender-related effects". Heredity. 114 (3): 327–32. doi:10.1038/hdy.2014.106. PMC   4815584 . PMID   25407077.
  3. ↑ Gulisija D, Crow JF (May 2007). "Inferring purging from pedigree data". Evolution; International Journal of Organic Evolution. 61 (5): 1043–51. doi:10.1111/j.1558-5646.2007.00088.x. PMID   17492959. S2CID   24302475.
  4. ↑ Charlesworth B, Morgan MT, Charlesworth D (August 1993). "The effect of deleterious mutations on neutral molecular variation". Genetics. 134 (4): 1289–303. doi:10.1093/genetics/134.4.1289. PMC   1205596 . PMID   8375663.
  5. ↑ Hudson RR, Kaplan NL (December 1995). "Deleterious background selection with recombination". Genetics. 141 (4): 1605–17. doi:10.1093/genetics/141.4.1605. PMC   1206891 . PMID   8601498.
  6. ↑ Glémin S (December 2003). "How are deleterious mutations purged? Drift versus nonrandom mating". Evolution; International Journal of Organic Evolution. 57 (12): 2678–87. doi: 10.1111/j.0014-3820.2003.tb01512.x . PMID   14761049.
  7. 1 2 Cervantes S, Kesälahti R, Kumpula TA, Mattila TM, Helanterä H, Pyhäjärvi T (August 2023). "Strong Purifying Selection in Haploid Tissue-Specific Genes of Scots Pine Supports the Masking Theory". Mol Biol Evol. 40 (8). doi:10.1093/molbev/msad183. PMC   10457172 . PMID   37565532.
  8. ↑ Gerstein AC, Cleathero LA, Mandegar MA, Otto SP (March 2011). "Haploids adapt faster than diploids across a range of environments". J Evol Biol. 24 (3): 531–40. doi:10.1111/j.1420-9101.2010.02188.x. PMID   21159002.


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