Fixed allele

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In population genetics, a fixed allele is an allele that is the only variant that exists for that gene in a population. A fixed allele is homozygous for all members of the population. [1] The process by which alleles become fixed is called fixation.

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For this hypothetical species, the population in the topmost frame exhibits no fixed allele for "color". In contrast, the populations depicted in the latter frames exhibit fixed alleles for "color" black, red and purple respectively. Fixed alleles illustration.png
For this hypothetical species, the population in the topmost frame exhibits no fixed allele for "color". In contrast, the populations depicted in the latter frames exhibit fixed alleles for "color" black, red and purple respectively.

A population of a hypothetical species can be conceived to exemplify the concept of fixed alleles. If an allele is fixed in the population, then all organisms can have only that allele for the gene in question. Suppose that genotype corresponds directly to the phenotype of body color, then all organisms of the population would exhibit the same body color.

An allele in a population being fixed necessarily entails the phenotypic traits corresponding to that allele to be identical for all organisms in the population (if those genotypes correspond directly to a certain phenotype), as it follows logically from the definition of relevant concepts. However, identical phenotypic traits exhibited in a population does not necessarily entail the allele(s) corresponding to those traits to be fixed, as exemplified by the case of genetic dominance being apposite in a species' population. [2]

Low genetic diversity is accompanied by allele fixation, which can potentially lead to lower adaptibility to changing environmental conditions for a population as a whole. For example, often having certain alleles make an organism more susceptible to a disease than having other alleles; if an allele highly susceptible to a disease with a prevalent cause is fixed in a population, most organisms of the population might be affected. Hence, generally, populations exhibiting a significant range of fixed alleles are often at risk for extinction. [3] [4]

Fixed alleles were first defined by Motoo Kimura in 1962. [5] Kimura discussed how fixed alleles could arise within populations and was the first to generalize the topic. He credits the works of Haldane in 1927 [6] and Fisher in 1922 [7] as being important in providing foundational information that allowed him to come to his conclusion.

The evolution of fixed alleles in populations

While there are many possibilities for how a fixed allele can develop, often multiple factors come into play simultaneously and guide the process, consequently determining the end result.

The two key driving forces behind fixation are natural selection and genetic drift. Natural selection was postulated by Charles Darwin and encompasses many processes that lead to the differential survival of organisms due to genetic or phenotypic differences. Genetic drift is the process by which allele frequencies fluctuate within populations. Natural selection and genetic drift propel evolution forward, and through evolution, alleles can become fixed. [8] [9]

Processes of natural selection such as sexual, convergent, divergent, or stabilizing selection pave the way for allele fixation. One way some of these natural selection processes cause fixation is through one specific genotype or phenotype being favored, which leads to the convergence of the variability until one allele becomes fixed. Natural selection can work the other way, where two alleles become fixed through two specific genotypes or phenotypes being favored, leading to divergence within the population until the populations become so separate that they are now two species each with their own fixed allele.

Selective pressures can favor certain genotypes or phenotypes. A commonly known example of this is the process of antibiotic resistance within bacterial populations. As antibiotics are used to kill bacteria, a small number of them with favorable mutations can survive and repopulate in an environment that is now free of competition. The allele for antibiotic resistance then becomes a fixed allele within the surviving and future populations. This is an example of the bottleneck effect. A bottleneck occurs when a population is put under strong selective pressure, and only certain individuals survive. These surviving individuals have a decreased number of alleles present within their population than were present in the initial population, however, these remaining alleles are the only ones left in future populations assuming no mutation or migration. This bottleneck effect can also be seen in natural disasters, as shown in the rabbit example above. [10]

This image shows how though successive generations random allele fluctuations, or genetic drift, can lead to the fixation or loss of certain alleles within a population. Allele-frequency.png
This image shows how though successive generations random allele fluctuations, or genetic drift, can lead to the fixation or loss of certain alleles within a population.

Similar to the bottleneck effect, the founder's effect can also cause allele fixation. The founder effect occurs when a small founding population is moved to a new area and propagates the future population. This can be seen in the Alces alces moose population in Newfoundland, Canada. Moose are not native to Newfoundland, and in 1878 and 1904 six total moose were introduced to the island. The six founding moose propagated the current population of an estimated 4000-6000 moose. This has had dramatic effects on the offspring of the founding moose and has led to a great decrease in genetic variability within the Newfoundland moose population as compared to the mainland population. [11] [12]

Other random processes such as genetic drift can lead to fixation. Through these random processes, some random individuals or alleles are removed from the population. These random fluctuations within the allele frequencies can lead to the fixation or loss of certain alleles within a population. To the right is an image that shows through successive generations; the allele frequencies fluctuate randomly within a population. The smaller the population size, the faster fixation or loss of alleles will occur. However, all populations are driven to allele fixation and it is inevitable; it just takes varying amounts of time for this to occur due to population size.

Some other causes of allele fixation are inbreeding, as this decreases the genetic variability of the population and therefore decreases the effective population size. [11] [13] This allows genetic drift to cause fixation faster than anticipated.

Isolation can also cause fixation, as it prevents the influx of new variable alleles into the population. This can often be seen on island populations, where the populations have a limited set of alleles. The only variability that can be added to these populations is through mutations. [11] [12]

Examples

One example of a fixed allele is the DGAT-1 exon 8 in Anatolian buffalo. This is a non-conservative mutation in the DGAT-1 allele, which produces a protein with a lysine at position 232 instead of an alanine. This mutation produces a protein different from the wild type of protein. This mutation in cattle affects milk production. Investigation into three water buffalo populations revealed four different haplotypes each having a single nucleotide polymorphism (SNP), however, all of these SNPs were conservative mutations, causing no change in protein production. All populations of Anatolian buffalo studied had the non-conservative lysine mutation at 232, leading to the conclusion that this DGAT-1 allele mutation is fixed within the populations. [14]

The Parnassius apollo butterfly is classified as a threatened species, having many disjointed populations in the Western Palaearctic region. The population in the Mosel Valley of Germany has been genetically characterized and had been shown to have six long-term monomorphic microsatellites. Six microsatellites were examined by looking at the current population in 2008 as well as museum samples from 1895 to 1989. One of the microsatellite alleles examined has become fixed within the population before1895. For the current population, all six microsatellites as well as all sixteen alloenzymes analyzed were fixed. [15]

Fixed alleles can often be deleterious to populations, especially when there is small population size and low genetic variability. For example, the California Channel Island Fox ( Urocyon littoralis ) has the most monomorphic population ever reported for a sexually reproducing animal. [15] During the 1990s the Island Fox experienced disastrous population decline, leading to near extinction. [3] This population decline was caused in part by the canine distemper virus. The foxes were susceptible to this virus, and many were killed due to their genetic similarity. The introduction of a predator, the golden eagle, was also attributed to this population decline. With current conservation efforts, the population is in recovery. [4]

See also

Related Research Articles

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

Genetic drift, also known as random genetic drift, allelic drift or the Wright effect, is the change in the frequency of an existing gene variant (allele) in a population due to random chance.

Small populations can behave differently from larger populations. They are often the result of population bottlenecks from larger populations, leading to loss of heterozygosity and reduced genetic diversity and loss or fixation of alleles and shifts in allele frequencies. A small population is then more susceptible to demographic and genetic stochastic events, which can impact the long-term survival of the population. Therefore, small populations are often considered at risk of endangerment or extinction, and are often of conservation concern.

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

The neutral theory of molecular evolution holds that most evolutionary changes occur at the molecular level, and most of the variation within and between species are due to random genetic drift of mutant alleles that are selectively neutral. The theory applies only for evolution at the molecular level, and is compatible with phenotypic evolution being shaped by natural selection as postulated by Charles Darwin.

Fitness is a quantitative representation of individual reproductive success. It is also equal to the average contribution to the gene pool of the next generation, made by the same individuals of the specified genotype or phenotype. Fitness can be defined either with respect to a genotype or to a phenotype in a given environment or time. The fitness of a genotype is manifested through its phenotype, which is also affected by the developmental environment. The fitness of a given phenotype can also be different in different selective environments.

Population genetics is a subfield of genetics that deals with genetic differences within and among populations, and is a part of evolutionary biology. Studies in this branch of biology examine such phenomena as adaptation, speciation, and population structure.

<span class="mw-page-title-main">Polymorphism (biology)</span> Occurrence of two or more clearly different morphs or forms in the population of a species

In biology, polymorphism is the occurrence of two or more clearly different morphs or forms, also referred to as alternative phenotypes, in the population of a species. To be classified as such, morphs must occupy the same habitat at the same time and belong to a panmictic population.

<span class="mw-page-title-main">Index of evolutionary biology articles</span>

This is a list of topics in evolutionary biology.

<span class="mw-page-title-main">Motoo Kimura</span> Japanese biologist

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

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.

<span class="mw-page-title-main">Conservation genetics</span> Interdisciplinary study of extinction avoidance

Conservation genetics is an interdisciplinary subfield of population genetics that aims to understand the dynamics of genes in a population for the purpose of natural resource management, conservation of genetic diversity, and the prevention of species extinction. Scientists involved in conservation genetics come from a variety of fields including population genetics, research in natural resource management, molecular ecology, molecular biology, evolutionary biology, and systematics. The genetic diversity within species is one of the three fundamental components of biodiversity, so it is an important consideration in the wider field of conservation biology.

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.

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.

<i>The Neutral Theory of Molecular Evolution</i>

The Neutral Theory of Molecular Evolution is an influential monograph written in 1983 by Japanese evolutionary biologist Motoo Kimura. While the neutral theory of molecular evolution existed since his article in 1968, Kimura felt the need to write a monograph with up-to-date information and evidences showing the importance of his theory in evolution.

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

In 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).

The history of molecular evolution starts in the early 20th century with "comparative biochemistry", but the field of molecular evolution came into its own in the 1960s and 1970s, following the rise of molecular biology. The advent of protein sequencing allowed molecular biologists to create phylogenies based on sequence comparison, and to use the differences between homologous sequences as a molecular clock to estimate the time since the last common ancestor. In the late 1960s, the neutral theory of molecular evolution provided a theoretical basis for the molecular clock, though both the clock and the neutral theory were controversial, since most evolutionary biologists held strongly to panselectionism, with natural selection as the only important cause of evolutionary change. After the 1970s, nucleic acid sequencing allowed molecular evolution to reach beyond proteins to highly conserved ribosomal RNA sequences, the foundation of a reconceptualization of the early history of life.

Weak selection in evolutionary biology is when individuals with different phenotypes possess similar fitness, i.e. one phenotype is weakly preferred over the other. Weak selection, therefore, is an evolutionary theory to explain the maintenance of multiple phenotypes in a stable population.

The stepwise mutation model (SMM) is a mathematical theory, developed by Motoo Kimura and Tomoko Ohta, that allows for investigation of the equilibrium distribution of allelic frequencies in a finite population where neutral alleles are produced in step-wise fashion.

This glossary of genetics and evolutionary biology is a list of definitions of terms and concepts used in the study of genetics and evolutionary biology, as well as sub-disciplines and related fields, with an emphasis on classical genetics, quantitative genetics, population biology, phylogenetics, speciation, and systematics. Overlapping and related terms can be found in Glossary of cellular and molecular biology, Glossary of ecology, and Glossary of biology.

References

  1. ↑ "fixed allele definition". www.biochem.northwestern.edu. Archived from the original on 2010-06-14. Retrieved 2008-10-07.
  2. ↑ "Genotype & Phenotype". biomed.brown.edu. Retrieved 2023-05-25.
  3. 1 2 Coonan, Timothy; Schwemma, Catherin; Roemerb, Gary; Garcelonc, David; Munsond, Linda (Mar 2005). "Decline of an Island Fox Subspecies to Near Extinction". The Southwestern Naturalist. 50: 32–41. doi:10.1894/0038-4909(2005)050<0032:DOAIFS>2.0.CO;2.
  4. 1 2 "Friends of the Island Fox: About Island Fox". www1.islandfox.org. Retrieved 2016-02-07.
  5. ↑ Kimura, Motoo (1962-06-01). "On the Probability of Fixation of Mutant Genes in a Population". Genetics. 47 (6): 713–719. ISSN   0016-6731. PMC   1210364 . PMID   14456043.
  6. ↑ Haldane, J. B. S. (1927-07-01). "A Mathematical Theory of Natural and Artificial Selection, Part V: Selection and Mutation". Mathematical Proceedings of the Cambridge Philosophical Society. 23 (7): 838–844. Bibcode:1927PCPS...23..838H. doi:10.1017/S0305004100015644. ISSN   1469-8064.
  7. ↑ Fisher, R. A. (1990-01-01). "On the dominance ratio". Bulletin of Mathematical Biology. 52 (1–2): 297–318. doi:10.1007/BF02459576. ISSN   0092-8240. PMID   2185862.
  8. ↑ Hartwell, Leland (2011). Genetics: From Genes to Genomes. New York: McGraw-Hill. pp. 655–697. ISBN   978-0-07-352526-6.
  9. ↑ Kimura, Motoo (1983). The Neutral Theory of Molecular Evolution - Cambridge Books Online - Cambridge University Press. doi:10.1017/cbo9780511623486. ISBN   9780511623486.
  10. ↑ Molles, Manuel (2013). Ecology Concepts and Applications. New York: McGraw-Hill. ISBN   978-0-07353249-3.
  11. 1 2 3 Broders, H. G.; Mahoney, S. P.; Montevecchi, W. A.; Davidson, W. S. (1999-08-01). "Population genetic structure and the effect of founder events on the genetic variability of moose, Alces alces, in Canada" (PDF). Molecular Ecology. 8 (8): 1309–1315. doi:10.1046/j.1365-294x.1999.00695.x. ISSN   0962-1083. PMID   10447871.
  12. 1 2 Frankham, R. (1997-03-01). "Heredity - Abstract of article: Do island populations have less genetic variation than mainland populations?". Heredity. 78 (3): 311–327. doi: 10.1038/hdy.1997.46 . ISSN   0018-067X. PMID   9119706.
  13. ↑ Keller, Lukas F.; Waller, Donald M. (2002-05-01). "Inbreeding effects in wild populations". Trends in Ecology & Evolution. 17 (5): 230–241. doi:10.1016/S0169-5347(02)02489-8. ISSN   0169-5347.
  14. ↑ Özdil, Fulya; Ilhan, Fatma (21 July 2012). "DGAT1-exon8 polymorphism in Anatolian buffalo" (PDF). Livestock Science. 149 (1–2): 83–87. doi:10.1016/j.livsci.2012.06.030 . Retrieved 6 Feb 2016.
  15. 1 2 Habel, Jan Christian; Zachos, Frank Emmanuel; Finger, Aline; Meyer, Marc; Louy, Dirk; Assmann, Thorsten; Schmitt, Thomas (December 2009). "Unprecedented long-term genetic monomorphism in an endangered relict butterfly species". Conservation Genetics. 10 (6): 1659–1665. doi:10.1007/s10592-008-9744-5.
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