Muller's ratchet

Last updated
Illustration of chromosome crossover during genetic recombination Morgan crossover 1.jpg
Illustration of chromosome crossover during genetic recombination

In evolutionary genetics, Muller's ratchet (named after Hermann Joseph Muller, by analogy with a ratchet effect) is a process which, in the absence of recombination (especially in an asexual population), results in an accumulation of irreversible deleterious mutations. [1] [2] This happens because in the absence of recombination, and assuming reverse mutations are rare, offspring bear at least as much mutational load as their parents. [2] Muller proposed this mechanism as one reason why sexual reproduction may be favored over asexual reproduction, as sexual organisms benefit from recombination and consequent elimination of deleterious mutations. The negative effect of accumulating irreversible deleterious mutations may not be prevalent in organisms which, while they reproduce asexually, also undergo other forms of recombination. This effect has also been observed in those regions of the genomes of sexual organisms that do not undergo recombination.

Contents

Etymology

Although Muller discussed the advantages of sexual reproduction in his 1932 talk, it does not contain the word "ratchet". Muller first introduced the term "ratchet" in his 1964 paper, [2] and the phrase "Muller's ratchet" was coined by Joe Felsenstein in his 1974 paper, "The Evolutionary Advantage of Recombination". [3]

Explanation

Asexual reproduction compels genomes to be inherited as indivisible blocks so that once the least mutated genomes in an asexual population begin to carry at least one deleterious mutation, no genomes with fewer such mutations can be expected to be found in future generations (except as a result of back mutation). This results in an eventual accumulation of mutations known as genetic load. In theory, the genetic load carried by asexual populations eventually becomes so great that the population goes extinct. [4] Also, laboratory experiments have confirmed the existence of the ratchet and the consequent extinction of populations in many organisms (under intense drift and when recombinations are not allowed) including RNA viruses, bacteria, and eukaryotes. [5] [6] [7] In sexual populations, the process of genetic recombination allows the genomes of the offspring to be different from the genomes of the parents. In particular, progeny (offspring) genomes with fewer mutations can be generated from more highly mutated parental genomes by putting together mutation-free portions of parental chromosomes. Also, purifying selection, to some extent, unburdens a loaded population when recombination results in different combinations of mutations. [2]

Among protists and prokaryotes, a plethora of supposedly asexual organisms exists. More and more are being shown to exchange genetic information through a variety of mechanisms. In contrast, the genomes of mitochondria and chloroplasts do not recombine and would undergo Muller's ratchet were they not as small as they are (see Birdsell and Wills [pp. 93–95]). [8] Indeed, the probability that the least mutated genomes in an asexual population end up carrying at least one (additional) mutation depends heavily on the genomic mutation rate and this increases more or less linearly with the size of the genome (more accurately, with the number of base pairs present in active genes). However, reductions in genome size, especially in parasites and symbionts, can also be caused by direct selection to get rid of genes that have become unnecessary. Therefore, a smaller genome is not a sure indication of the action of Muller's ratchet. [9]

In sexually reproducing organisms, nonrecombining chromosomes or chromosomal regions such as the mammalian Y chromosome (with the exception of multicopy sequences which do engage intrachromosomal recombination and gene conversion [4] ) should also be subject to the effects of Muller's ratchet. Such nonrecombining sequences tend to shrink and evolve quickly. However, this fast evolution might also be due to these sequences' inability to repair DNA damage via template-assisted repair, which is equivalent to an increase in the mutation rate for these sequences. Ascribing cases of genome shrinkage or fast evolution to Muller's ratchet alone is not easy.

Muller's ratchet relies on genetic drift, and turns faster in smaller populations because in such populations deleterious mutations have a better chance of fixation. Therefore, it sets the limits to the maximum size of asexual genomes and to the long-term evolutionary continuity of asexual lineages. [4] However, some asexual lineages are thought to be quite ancient; Bdelloid rotifers, for example, appear to have been asexual for nearly 40 million years. [10] However, rotifers were found to possess a substantial number of foreign genes from possible horizontal gene transfer events. [11] Furthermore, a vertebrate fish, Poecilia formosa , seems to defy the ratchet effect, having existed for 500,000 generations. This has been explained by maintenance of genomic diversity through parental introgression and a high level of heterozygosity resulting from the hybrid origin of this species. [12]

Calculation of the fittest class

In 1978, John Haigh used a Wright–Fisher model to analyze the effect of Muller's ratchet in an asexual population. [13] If the ratchet is operating the fittest class (least loaded individuals) is small and prone to extinction by the effect of genetic drift. In his paper Haigh derives the equation that calculates the frequency of individuals carrying mutations for the population with stationary distribution:

where, is the number of individual carrying mutations, is the population size, is the mutation rate and is the selection coefficient.

Thus, the frequency of the individuals of the fittest class () is:

In an asexual population which suffers from ratchet the frequency of fittest individuals would be small, and go extinct after few generations. [13] This is called a click of the ratchet. Following each click, the rate of accumulation of deleterious mutation would increase, and ultimately results in the extinction of the population.

The antiquity of recombination and Muller's ratchet

It has been argued that recombination was an evolutionary development as ancient as life on Earth. [14] Early RNA replicators capable of recombination may have been the ancestral sexual source from which asexual lineages could periodically emerge. [14] Recombination in the early sexual lineages may have provided a means for coping with genome damage. [15] Muller's ratchet under such ancient conditions would likely have impeded the evolutionary persistence of the asexual lineages that were unable to undergo recombination. [14]

Muller's ratchet and mutational meltdown

Since deleterious mutations are harmful by definition, accumulation of them would result in loss of individuals and a smaller population size. Small populations are more susceptible to the ratchet effect and more deleterious mutations would be fixed as a result of genetic drift. This creates a positive feedback loop which accelerates extinction of small asexual populations. This phenomenon has been called mutational meltdown. [16] It appears that mutational meltdown due to Muller’s ratchet can be avoided by a little bit of sex as in the common apomictic asexual flowering plant Ranunculus auricomus . [17]

See also

Related Research Articles

<span class="mw-page-title-main">Mutation</span> Alteration in the nucleotide sequence of a genome

In biology, a mutation is an alteration in the nucleic acid sequence of the genome of an organism, virus, or extrachromosomal DNA. Viral genomes contain either DNA or RNA. Mutations result from errors during DNA or viral replication, mitosis, or meiosis or other types of damage to DNA, which then may undergo error-prone repair, cause an error during other forms of repair, or cause an error during replication. Mutations may also result from substitution, insertion or deletion of segments of DNA due to mobile genetic elements.

<span class="mw-page-title-main">Rotifer</span> Phylum of pseudocoelomate invertebrates

The rotifers, sometimes called wheel animals or wheel animalcules, make up a phylum of microscopic and near-microscopic pseudocoelomate animals.

<span class="mw-page-title-main">Genetic recombination</span> Production of offspring with combinations of traits that differ from those found in either parent

Genetic recombination is the exchange of genetic material between different organisms which leads to production of offspring with combinations of traits that differ from those found in either parent. In eukaryotes, genetic recombination during meiosis can lead to a novel set of genetic information that can be further passed on from parents to offspring. Most recombination occurs naturally and can be classified into two types: (1) interchromosomal recombination, occurring through independent assortment of alleles whose loci are on different but homologous chromosomes ; & (2) intrachromosomal recombination, occurring through crossing over.

<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.

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.

In evolutionary genetics, mutational meltdown is a sub class of extinction vortex in which the environment and genetic predisposition mutually reinforce each other. Mutational meltdown is the accumulation of harmful mutations in a small population, which leads to loss of fitness and decline of the population size, which may lead to further accumulation of deleterious mutations due to fixation by genetic drift.

<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.

Evolvability is defined as the capacity of a system for adaptive evolution. Evolvability is the ability of a population of organisms to not merely generate genetic diversity, but to generate adaptive genetic diversity, and thereby evolve through natural selection.

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.

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.

Michael Lynch is an American geneticist who is the Director of the Biodesign Institute for Mechanisms of Evolution at Arizona State University, Tempe, Arizona.

Enquiry into the evolution of ageing, or aging, aims to explain why a detrimental process such as ageing would evolve, and why there is so much variability in the lifespans of organisms. The classical theories of evolution suggest that environmental factors, such as predation, accidents, disease, and/or starvation, ensure that most organisms living in natural settings will not live until old age, and so there will be very little pressure to conserve genetic changes that increase longevity. Natural selection will instead strongly favor genes which ensure early maturation and rapid reproduction, and the selection for genetic traits which promote molecular and cellular self-maintenance will decline with age for most organisms.

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.

The Red Queen's hypothesis is a hypothesis in evolutionary biology proposed in 1973, that species must constantly adapt, evolve, and proliferate in order to survive while pitted against ever-evolving opposing species. The hypothesis was intended to explain the constant (age-independent) extinction probability as observed in the paleontological record caused by co-evolution between competing species; however, it has also been suggested that the Red Queen hypothesis explains the advantage of sexual reproduction at the level of individuals, and the positive correlation between speciation and extinction rates in most higher taxa.

<span class="mw-page-title-main">Clonal interference</span> Phenomenon in evolutionary biology

Clonal interference is a phenomenon in evolutionary biology, related to the population genetics of organisms with significant linkage disequilibrium, especially asexually reproducing organisms. The idea of clonal interference was introduced by American geneticist Hermann Joseph Muller in 1932. It explains why beneficial mutations can take a long time to get fixated or even disappear in asexually reproducing populations. As the name suggests, clonal interference occurs in an asexual lineage ("clone") with a beneficial mutation. This mutation would be likely to get fixed if it occurred alone, but it may fail to be fixed, or even be lost, if another beneficial-mutation lineage arises in the same population; the multiple clones interfere with each other.

Experimental evolution studies are a means of testing evolutionary theory under carefully designed, reproducible experiments. Given enough time, space, and money, any organism could be used for experimental evolution studies. However, those with rapid generation times, high mutation rates, large population sizes, and small sizes increase the feasibility of experimental studies in a laboratory context. For these reasons, bacteriophages are especially favored by experimental evolutionary biologists. Bacteriophages, and microbial organisms, can be frozen in stasis, facilitating comparison of evolved strains to ancestors. Additionally, microbes are especially labile from a molecular biologic perspective. Many molecular tools have been developed to manipulate the genetic material of microbial organisms, and because of their small genome sizes, sequencing the full genomes of evolved strains is trivial. Therefore, comparisons can be made for the exact molecular changes in evolved strains during adaptation to novel conditions.

Wagner's gene network model is a computational model of artificial gene networks, which explicitly modeled the developmental and evolutionary process of genetic regulatory networks. A population with multiple organisms can be created and evolved from generation to generation. It was first developed by Andreas Wagner in 1996 and has been investigated by other groups to study the evolution of gene networks, gene expression, robustness, plasticity and epistasis.

<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.

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. It has been designed as a companion to Glossary of cellular and molecular biology, which contains many overlapping and related terms; other related glossaries include Glossary of biology and Glossary of ecology.

A mutation accumulation (MA) experiment is a genetic experiment in which isolated and inbred lines of organisms are maintained such that the effect of natural selection is minimized, with the aim of quantitatively estimating the rates at which spontaneous mutations occur in the studied organism. Spontaneous mutation rates may be directly estimated using molecular techniques such as DNA sequencing, or indirectly estimated using phenotypic assays.

References

  1. ↑ Muller HJ (1932). "Some genetic aspects of sex". American Naturalist . 66 (703): 118–138. doi:10.1086/280418. S2CID   84301227. (Muller's original 1932 paper)
  2. 1 2 3 4 Muller HJ (May 1964). "The relation of recombination to mutational advance". Mutation Research. 106: 2–9. doi:10.1016/0027-5107(64)90047-8. PMID   14195748. (original paper as cited by, e.g.: Smith JM, Szathmary E (1997). The major transitions in evolution. Oxford, New York, Tokyo: Oxford University Press. ; Futuyma DJ (1998). Evolutionary biology (3rd ed.). Sunderland, Mass.: Sinauer Associates.)
  3. ↑ Felsenstein J (October 1974). "The evolutionary advantage of recombination". Genetics. 78 (2): 737–56. doi:10.1093/genetics/78.2.737. PMC   1213231 . PMID   4448362.
  4. 1 2 3 Freeman S, Herron JC (2007). Evolutionary Analysis, 4th edition. San Francisco: Benjamin Cummings. pp. 308–309. ISBN   978-0-13-227584-2.
  5. ↑ Chao L (November 1990). "Fitness of RNA virus decreased by Muller's ratchet". Nature. 348 (6300): 454–5. Bibcode:1990Natur.348..454C. doi:10.1038/348454a0. PMID   2247152. S2CID   4235839.
  6. ↑ Andersson DI, Hughes D (January 1996). "Muller's ratchet decreases fitness of a DNA-based microbe". Proceedings of the National Academy of Sciences of the United States of America. 93 (2): 906–7. Bibcode:1996PNAS...93..906A. doi: 10.1073/pnas.93.2.906 . PMC   40156 . PMID   8570657.
  7. ↑ Zeyl C, Mizesko M, de Visser JA (May 2001). "Mutational meltdown in laboratory yeast populations". Evolution; International Journal of Organic Evolution. 55 (5): 909–17. doi:10.1554/0014-3820(2001)055[0909:MMILYP]2.0.CO;2. PMID   11430651. S2CID   198152956.
  8. ↑ Birdsell JA, Wills C (2003). The evolutionary origin and maintenance of sexual recombination: A review of contemporary models. Evolutionary Biology Series >> Evolutionary Biology, Vol. 33 pp. 27-137. MacIntyre, Ross J.; Clegg, Michael, T (Eds.), Springer. Hardcover ISBN   978-0306472619, ISBN   0306472619 Softcover ISBN   978-1-4419-3385-0.
  9. ↑ Moran NA (April 1996). "Accelerated evolution and Muller's rachet in endosymbiotic bacteria". Proceedings of the National Academy of Sciences of the United States of America. 93 (7): 2873–8. Bibcode:1996PNAS...93.2873M. doi: 10.1073/pnas.93.7.2873 . PMC   39726 . PMID   8610134. (An article that discusses Muller's ratchet in the context of endosymbiotic bacteria.)
  10. ↑ Milius S. "Bdelloids: No sex for over 40 million years". TheFreeLibrary. ScienceNews. Retrieved 30 April 2011.
  11. ↑ Boschetti C, Carr A, Crisp A, Eyres I, Wang-Koh Y, Lubzens E, et al. (November 15, 2012). "Biochemical diversification through foreign gene expression in bdelloid rotifers". PLOS Genetics. 8 (11): e1003035. doi: 10.1371/journal.pgen.1003035 . PMC   3499245 . PMID   23166508.
  12. ↑ Warren WC, García-Pérez R, Xu S, Lampert KP, Chalopin D, Stöck M, et al. (April 2018). "Clonal polymorphism and high heterozygosity in the celibate genome of the Amazon molly". Nature Ecology & Evolution. 2 (4): 669–679. doi: 10.1038/s41559-018-0473-y . PMC   5866774 . PMID   29434351.
  13. 1 2 Haigh J (October 1978). "The accumulation of deleterious genes in a population--Muller's Ratchet". Theoretical Population Biology. 14 (2): 251–67. doi:10.1016/0040-5809(78)90027-8. PMID   746491.
  14. 1 2 3 Lehman N (June 2003). "A case for the extreme antiquity of recombination". Journal of Molecular Evolution. 56 (6): 770–7. Bibcode:2003JMolE..56..770L. doi:10.1007/s00239-003-2454-1. PMID   12911039. S2CID   33130898.
  15. ↑ Bernstein H, Byerly HC, Hopf FA, Michod RE (October 1984). "Origin of sex". Journal of Theoretical Biology. 110 (3): 323–51. Bibcode:1984JThBi.110..323B. doi:10.1016/s0022-5193(84)80178-2. PMID   6209512.
  16. ↑ Gabriel W, Lynch M, Bürger R (December 1993). "Muller's Ratchet and Mutational Meltdowns" (PDF). Evolution; International Journal of Organic Evolution. 47 (6): 1744–1757. doi: 10.1111/j.1558-5646.1993.tb01266.x . PMID   28567994. S2CID   1323281.
  17. ↑ Hojsgaard D, Hörandl E (2015). "A little bit of sex matters for genome evolution in asexual plants". Front Plant Sci. 6: 82. doi: 10.3389/fpls.2015.00082 . PMC   4335465 . PMID   25750646.
This page is based on this Wikipedia article
Text is available under the CC BY-SA 4.0 license; additional terms may apply.
Images, videos and audio are available under their respective licenses.