Evolution Warning: You are not logged in. Your IP address will be publicly visible if you make any edits. If you log in or create an account, your edits will be attributed to your username, along with other benefits.Anti-spam check. Do not fill this in! == Evolutionary forces == [[File:Mutation and selection diagram.svg|thumb|upright=1.35|[[Mutation]] followed by natural selection results in a population with darker colouration.]] From a [[Neo-Darwinism|neo-Darwinian]] perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms,<ref name="Ewens W.J. 2004">{{harvnb|Ewens|2004}}{{page needed|date=December 2014}}</ref> for example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, and mutation bias.<!--This is cited in the subsections below.--> === Natural selection === {{main|Natural selection}} {{See also|Dollo's law of irreversibility}} Evolution by natural selection is the process by which traits that enhance survival and reproduction become more common in successive generations of a population. It embodies three principles:<ref name="Lewontin70" /> * Variation exists within populations of organisms with respect to morphology, physiology and behaviour (phenotypic variation). * Different traits confer different rates of survival and reproduction (differential fitness). * These traits can be passed from generation to generation (heritability of fitness). More offspring are produced than can possibly survive, and these conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors are more likely to pass on their traits to the next generation than those with traits that do not confer an advantage.<ref name="Hurst">{{cite journal |last=Hurst |first=Laurence D. |author-link=Laurence Hurst |title=Fundamental concepts in genetics: genetics and the understanding of selection |date=February 2009 |journal=Nature Reviews Genetics |volume=10 |issue=2 |pages=83–93 |doi=10.1038/nrg2506 |pmid=19119264 |s2cid=1670587 }}</ref> This [[teleonomy]] is the quality whereby the process of natural selection creates and preserves traits that are [[teleology in biology|seemingly fitted]] for the [[function (biology)|functional]] roles they perform.<ref>{{harvnb|Darwin|1859|loc=[http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=477 Chapter XIV]}}</ref> Consequences of selection include [[Assortative mating|nonrandom mating]]<ref>{{Cite journal |last1=Otto |first1=Sarah P. |author-link1=Sarah Otto |last2=Servedio |first2=Maria R. |author-link2=Maria Servedio|last3=Nuismer |first3=Scott L. |title=Frequency-Dependent Selection and the Evolution of Assortative Mating |journal=Genetics |date=August 2008 |volume=179 |issue=4 |pages=2091–2112 |doi=10.1534/genetics.107.084418 |pmc=2516082 |pmid=18660541}}</ref> and [[genetic hitchhiking]]. The central concept of natural selection is the [[fitness (biology)|evolutionary fitness]] of an organism.<ref name="Orr">{{cite journal |last=Orr |first=H. Allen |author-link=H. Allen Orr |date=August 2009 |title=Fitness and its role in evolutionary genetics |journal=Nature Reviews Genetics |volume=10 |issue=8 |pages=531–539 |doi=10.1038/nrg2603 |pmc=2753274 |pmid=19546856 |issn=1471-0056}}</ref> Fitness is measured by an organism's ability to survive and reproduce, which determines the size of its genetic contribution to the next generation.<ref name="Orr" /> However, fitness is not the same as the total number of offspring: instead fitness is indicated by the proportion of subsequent generations that carry an organism's genes.<ref name="Haldane">{{cite journal |last=Haldane |first=J. B. S. |s2cid=4185793 |author-link=J. B. S. Haldane |date=14 March 1959 |title=The Theory of Natural Selection To-Day |url=https://archive.org/details/sim_nature-uk_1959-03-14_183_4663/page/710 |journal=Nature |volume=183 |issue=4663 |pages=710–713 |bibcode=1959Natur.183..710H |doi=10.1038/183710a0 |pmid=13644170}}</ref> For example, if an organism could survive well and reproduce rapidly, but its offspring were all too small and weak to survive, this organism would make little genetic contribution to future generations and would thus have low fitness.<ref name="Orr"/> If an allele increases fitness more than the other alleles of that gene, then with each generation this allele has a higher probability of becoming common within the population. These traits are said to be "selected ''for''." Examples of traits that can increase fitness are enhanced survival and increased [[fecundity]]. Conversely, the lower fitness caused by having a less beneficial or deleterious allele results in this allele likely becoming rarer—they are "selected ''against''."<ref name="Lande">{{cite journal |last1=Lande |first1=Russell |author-link1=Russell Lande |last2=Arnold |first2=Stevan J. |date=November 1983 |title=The Measurement of Selection on Correlated Characters |journal=Evolution |volume=37 |issue=6 |pages=1210–1226 |doi=10.1111/j.1558-5646.1983.tb00236.x |pmid=28556011 |issn=0014-3820 |jstor=2408842|s2cid=36544045 |doi-access= }}</ref> Importantly, the fitness of an allele is not a fixed characteristic; if the environment changes, previously neutral or harmful traits may become beneficial and previously beneficial traits become harmful.<ref name="Futuyma_2005" /> However, even if the direction of selection does reverse in this way, traits that were lost in the past may not re-evolve in an identical form.<ref>{{cite journal |last1=Goldberg |first1=Emma E. |last2=Igić |first2=Boris |date=November 2008 |title=On phylogenetic tests of irreversible evolution |journal=Evolution |volume=62 |issue=11 |pages=2727–2741 |doi=10.1111/j.1558-5646.2008.00505.x |issn=0014-3820 |pmid=18764918|s2cid=30703407 }}</ref><ref>{{cite journal |last1=Collin |first1=Rachel |last2=Miglietta |first2=Maria Pia |date=November 2008 |title=Reversing opinions on Dollo's Law |journal=[[Trends (journals)|Trends in Ecology & Evolution]] |volume=23 |issue=11 |pages=602–609 |doi=10.1016/j.tree.2008.06.013 |pmid=18814933}}</ref> However, a re-activation of dormant genes, as long as they have not been eliminated from the genome and were only suppressed perhaps for hundreds of generations, can lead to the re-occurrence of traits thought to be lost like hindlegs in dolphins, teeth in chickens, wings in wingless stick insects, tails and additional nipples in humans etc. "Throwbacks" such as these are known as [[atavism]]s.<ref>{{cite journal |last1=Tomić |first1=Nenad |last2=Meyer-Rochow |first2=Victor Benno |s2cid=40851098 |year=2011 |title=Atavisms: Medical, Genetic, and Evolutionary Implications |url=https://archive.org/details/sim_perspectives-in-biology-and-medicine_summer-2011_54_3/page/332 |journal=[[Perspectives in Biology and Medicine]] |volume=54 |issue=3 |pages=332–353 |doi=10.1353/pbm.2011.0034 |pmid=21857125}}</ref> [[File:Genetic Distribution.svg|thumb|left|upright=1.45|These charts depict the different types of genetic selection. On each graph, the x-axis variable is the type of [[phenotypic trait]] and the y-axis variable is the number of organisms.{{imagefact|date=December 2022}} Group A is the original population and Group B is the population after selection.<br /> '''·''' Graph 1 shows [[directional selection]], in which a single extreme [[phenotype]] is favoured.<br /> '''·''' Graph 2 depicts [[stabilizing selection]], where the intermediate phenotype is favoured over the extreme traits.<br /> '''·''' Graph 3 shows [[disruptive selection]], in which the extreme phenotypes are favoured over the intermediate.]] Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorised into three different types. The first is [[directional selection]], which is a shift in the average value of a trait over time—for example, organisms slowly getting taller.<ref>{{cite journal |last1=Hoekstra |first1=Hopi E. |last2=Hoekstra |first2=Jonathan M. |last3=Berrigan |first3=David |last4=Vignieri |first4=Sacha N. |last5=Hoang |first5=Amy |last6=Hill |first6=Caryl E. |last7=Beerli |first7=Peter |last8=Kingsolver |first8=Joel G. |date=31 July 2001 |title=Strength and tempo of directional selection in the wild |journal=PNAS |volume=98 |issue=16 |pages=9157–9160 |bibcode=2001PNAS...98.9157H |doi=10.1073/pnas.161281098 |pmc=55389 |pmid=11470913 |display-authors=3|doi-access=free }}</ref> Secondly, [[disruptive selection]] is selection for extreme trait values and often results in [[bimodal distribution|two different values]] becoming most common, with selection against the average value. This would be when either short or tall organisms had an advantage, but not those of medium height. Finally, in [[stabilising selection]] there is selection against extreme trait values on both ends, which causes a decrease in [[variance]] around the average value and less diversity.<ref name="Hurst" /><ref>{{cite journal |last=Felsenstein |first=Joseph |author-link=Joseph Felsenstein |date=November 1979 |title=Excursions along the Interface between Disruptive and Stabilizing Selection |journal=Genetics |volume=93 |issue=3 |pages=773–795 |doi=10.1093/genetics/93.3.773 |pmc=1214112 |pmid=17248980}}</ref> This would, for example, cause organisms to eventually have a similar height. Natural selection most generally makes nature the measure against which individuals and individual traits, are more or less likely to survive. "Nature" in this sense refers to an [[ecosystem]], that is, a system in which organisms interact with every other element, [[Abiotic component|physical]] as well as [[Biotic component|biological]], in their local environment. [[Eugene Odum]], a founder of ecology, defined an ecosystem as: "Any unit that includes all of the organisms...in a given area interacting with the physical environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity, and material cycles (i.e., exchange of materials between living and nonliving parts) within the system...."<ref name="Odum1971">{{harvnb|Odum|1971|p=8}}</ref> Each population within an ecosystem occupies a distinct [[Ecological niche|niche]], or position, with distinct relationships to other parts of the system. These relationships involve the life history of the organism, its position in the [[food chain]] and its geographic range. This broad understanding of nature enables scientists to delineate specific forces which, together, comprise natural selection. Natural selection can act at [[unit of selection|different levels of organisation]], such as genes, cells, individual organisms, groups of organisms and species.<ref name="Okasha07">{{harvnb|Okasha|2006}}</ref><ref name="Gould">{{cite journal |last=Gould |first=Stephen Jay |author-link=Stephen Jay Gould |date=28 February 1998 |title=Gulliver's further travels: the necessity and difficulty of a hierarchical theory of selection |journal=Philosophical Transactions of the Royal Society B |volume=353 |issue=1366 |pages=307–314 |doi=10.1098/rstb.1998.0211 |issn=0962-8436 |pmc=1692213 |pmid=9533127}}</ref><ref name="Mayr1997">{{cite journal |last=Mayr |first=Ernst |author-link=Ernst Mayr |date=18 March 1997 |title=The objects of selection |journal=PNAS |volume=94 |issue=6 |pages=2091–2094 |bibcode=1997PNAS...94.2091M |doi=10.1073/pnas.94.6.2091 |issn=0027-8424 |pmc=33654 |pmid=9122151|doi-access=free }}</ref> Selection can act at multiple levels simultaneously.<ref>{{harvnb|Maynard Smith|1998|pp=203–211; discussion 211–217}}</ref> An example of selection occurring below the level of the individual organism are genes called [[Transposable element|transposons]], which can replicate and spread throughout a genome.<ref>{{cite journal |last=Hickey |first=Donal A. |s2cid=6583945 |year=1992 |title=Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes |journal=[[Genetica]] |volume=86 |issue=1–3 |pages=269–274 |doi=10.1007/BF00133725 |issn=0016-6707 |pmid=1334911}}</ref> Selection at a level above the individual, such as [[group selection]], may allow the evolution of cooperation.<ref>{{cite journal |last1=Gould |first1=Stephen Jay |last2=Lloyd |first2=Elisabeth A. |author-link2=Elisabeth Lloyd |date=12 October 1999 |title=Individuality and adaptation across levels of selection: how shall we name and generalise the unit of Darwinism? |journal=PNAS |volume=96 |issue=21 |pages=11904–11909 |bibcode=1999PNAS...9611904G |doi=10.1073/pnas.96.21.11904 |issn=0027-8424 |pmc=18385 |pmid=10518549 |doi-access=free }}</ref> === Genetic drift === {{further|Genetic drift|Effective population size}} [[File:Allele-frequency.png|thumb|Simulation of genetic drift of 20 unlinked alleles in populations of 10 (top) and 100 (bottom). Drift to [[Fixation (population genetics)|fixation]] is more rapid in the smaller population.{{imagefact|date=December 2022}}]] Genetic drift is the random fluctuation of [[allele frequency|allele frequencies]] within a population from one generation to the next.<ref name="Futuyma2017b">{{harvnb|Futuyma|Kirkpatrick|2017|pp=55–66|loc=Chapter 3: Natural Selection and Adaptation}}</ref> When selective forces are absent or relatively weak, allele frequencies are equally likely to ''drift'' upward or downward{{clarify|date=November 2022}} in each successive generation because the alleles are subject to [[sampling error]].<ref name="Masel 2011">{{cite journal |last=Masel |first=Joanna |s2cid=17619958 |date=25 October 2011 |title=Genetic drift |journal=Current Biology |volume=21 |issue=20 |pages=R837–R838 |doi=10.1016/j.cub.2011.08.007 |issn=0960-9822 |pmid=22032182|doi-access=free |bibcode=2011CBio...21.R837M }}</ref> This drift halts when an allele eventually becomes fixed, either by disappearing from the population or by replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations that begin with the same genetic structure to drift apart into two divergent populations with different sets of alleles.<ref>{{cite journal |last=Lande |first=Russell |year=1989 |title=Fisherian and Wrightian theories of speciation |url=https://archive.org/details/sim_genome_1989_31_1/page/221 |journal=[[Genome (journal)|Genome]] |volume=31 |issue=1 |pages=221–227 |doi=10.1139/g89-037 |issn=0831-2796 |pmid=2687093}}</ref> According to the [[neutral theory of molecular evolution]] most evolutionary changes are the result of the fixation of [[neutral mutation]]s by genetic drift.<ref name="Kimura M 1991 367–86">{{cite journal |last=Kimura |first=Motoo |author-link=Motoo Kimura |year=1991 |title=The neutral theory of molecular evolution: a review of recent evidence |journal=[[Journal of Human Genetics|Japanese Journal of Human Genetics]] |volume=66 |issue=4 |pages=367–386 |doi=10.1266/jjg.66.367 |pmid=1954033 |url=https://www.jstage.jst.go.jp/article/jjg/66/4/66_4_367/_pdf |doi-access=free |archive-date=5 June 2022 |archive-url=https://web.archive.org/web/20220605101314/https://www.jstage.jst.go.jp/article/jjg/66/4/66_4_367/_pdf |url-status=live }}</ref> In this model, most genetic changes in a population are thus the result of constant mutation pressure and genetic drift.<ref>{{cite journal |last=Kimura |first=Motoo |year=1989 |title=The neutral theory of molecular evolution and the world view of the neutralists |journal=Genome |volume=31 |issue=1 |pages=24–31 |doi=10.1139/g89-009 |issn=0831-2796 |pmid=2687096}}</ref> This form of the neutral theory has been debated since it does not seem to fit some genetic variation seen in nature.<ref>{{cite journal |last=Kreitman |first=Martin |author-link=Martin Kreitman |date=August 1996 |title=The neutral theory is dead. Long live the neutral theory |url=https://archive.org/details/sim_bioessays_1996-08_18_8/page/678 |journal=BioEssays |volume=18 |issue=8 |pages=678–683; discussion 683 |doi=10.1002/bies.950180812 |issn=0265-9247 |pmid=8760341}}</ref><ref>{{cite journal |last=Leigh | first=E. G. Jr. |date=November 2007 |title=Neutral theory: a historical perspective |journal=[[Journal of Evolutionary Biology]] |volume=20 |issue=6 |pages=2075–2091 |doi=10.1111/j.1420-9101.2007.01410.x |issn=1010-061X |pmid=17956380 |s2cid=2081042 |doi-access=free }}</ref> A better-supported version of this model is the [[nearly neutral theory of molecular evolution|nearly neutral theory]], according to which a mutation that would be effectively neutral in a small population is not necessarily neutral in a large population.<ref name="Hurst" /> Other theories propose that genetic drift is dwarfed by other [[stochastic]] forces in evolution, such as genetic hitchhiking, also known as genetic draft.<ref name="Masel 2011"/><ref name="gillespie 2001">{{cite journal |last=Gillespie |first=John H. |author-link=John H. Gillespie |date=November 2001 |title=Is the population size of a species relevant to its evolution? |journal=Evolution |volume=55 |issue=11 |pages=2161–2169 |doi=10.1111/j.0014-3820.2001.tb00732.x |issn=0014-3820 |pmid=11794777|s2cid=221735887 |doi-access=free }}</ref><ref>{{Cite journal |last1=Neher |first1=Richard A. |last2=Shraiman |first2=Boris I. |date=August 2011 |title=Genetic Draft and Quasi-Neutrality in Large Facultatively Sexual Populations |journal=Genetics |volume=188 |issue=4 |pages=975–996 |doi=10.1534/genetics.111.128876 |pmc=3176096 |pmid=21625002 |arxiv=1108.1635 |bibcode=2011arXiv1108.1635N }}</ref> Another concept is [[constructive neutral evolution]] (CNE), which explains that complex systems can emerge and spread into a population through neutral transitions due to the principles of excess capacity, presuppression, and ratcheting,<ref>{{cite journal |last=Stoltzfus |first=Arlin |date=1999 |title=On the Possibility of Constructive Neutral Evolution |url=http://link.springer.com/10.1007/PL00006540|journal=Journal of Molecular Evolution |volume=49 |issue=2 |pages=169–181 |doi=10.1007/PL00006540 |pmid=10441669 |bibcode=1999JMolE..49..169S |s2cid=1743092 |access-date=30 July 2022 |archive-date=30 July 2022 |archive-url=https://web.archive.org/web/20220730090616/https://link.springer.com/article/10.1007/PL00006540|url-status=live}}</ref><ref>{{Cite journal |last=Stoltzfus |first=Arlin |date=13 October 2012 |title=Constructive neutral evolution: exploring evolutionary theory's curious disconnect |journal=Biology Direct |volume=7 |issue=1 |page=35 |doi=10.1186/1745-6150-7-35 |pmc=3534586 |pmid=23062217 |doi-access=free }}</ref><ref>{{Cite journal |last1=Muñoz-Gómez |first1=Sergio A. |last2=Bilolikar |first2=Gaurav |last3=Wideman |first3=Jeremy G. |last4=Geiler-Samerotte |first4=Kerry |display-authors=3 |date=1 April 2021 |title=Constructive Neutral Evolution 20 Years Later |journal=Journal of Molecular Evolution |volume=89 |issue=3 |pages=172–182 |doi=10.1007/s00239-021-09996-y |pmc=7982386 |pmid=33604782 |bibcode=2021JMolE..89..172M }}</ref> and it has been applied in areas ranging from the origins of the [[spliceosome]] to the complex interdependence of [[Microbial consortium|microbial communities]].<ref>{{Cite journal |last1=Lukeš |first1=Julius |last2=Archibald |first2=John M.|last3=Keeling|first3=Patrick J.|last4=Doolittle |first4=W. Ford |last5=Gray |first5=Michael W. |display-authors=3 |date=2011|title=How a neutral evolutionary ratchet can build cellular complexity |url=https://onlinelibrary.wiley.com/doi/10.1002/iub.489 |journal=IUBMB Life |volume=63 |issue=7 |pages=528–537 |doi=10.1002/iub.489 |pmid=21698757 |s2cid=7306575}}</ref><ref>{{cite journal |last1=Vosseberg |first1=Julian |last2=Snel |first2=Berend |date=1 December 2017 |title=Domestication of self-splicing introns during eukaryogenesis: the rise of the complex spliceosomal machinery |journal=Biology Direct |volume=12 |issue=1 |page=30 |doi=10.1186/s13062-017-0201-6 |pmc=5709842 |pmid=29191215 |doi-access=free }}</ref><ref>{{Cite journal |last1=Brunet |first1=T. D. P. |last2=Doolittle |first2=W. Ford |date=19 March 2018 |title=The generality of Constructive Neutral Evolution |journal=Biology & Philosophy |volume=33 |issue=1 |page=2|doi=10.1007/s10539-018-9614-6 |s2cid=90290787 }}</ref> The time it takes a neutral allele to become fixed by genetic drift depends on population size; fixation is more rapid in smaller populations.<ref>{{cite journal |last1=Otto |first1=Sarah P. |last2=Whitlock |first2=Michael C. |date=June 1997 |title=The Probability of Fixation in Populations of Changing Size |url=http://www.genetics.org/content/146/2/723.full.pdf |journal=Genetics |volume=146 |issue=2 |pages=723–733 |doi=10.1093/genetics/146.2.723 |pmc=1208011 |pmid=9178020 |access-date=18 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20150319042554/http://www.genetics.org/content/146/2/723.full.pdf |archive-date=19 March 2015}}</ref> The number of individuals in a population is not critical, but instead a measure known as the effective population size.<ref name="Charlesworth">{{cite journal |last=Charlesworth |first=Brian |author-link=Brian Charlesworth |date=March 2009 |title=Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation |journal=Nature Reviews Genetics |volume=10 |issue=3 |pages=195–205 |doi=10.1038/nrg2526 |pmid=19204717|s2cid=205484393 }}</ref> The effective population is usually smaller than the total population since it takes into account factors such as the level of inbreeding and the stage of the lifecycle in which the population is the smallest.<ref name="Charlesworth" /> The effective population size may not be the same for every gene in the same population.<ref>{{cite journal |last1=Cutter |first1=Asher D. |last2=Choi |first2=Jae Young |date=August 2010 |title=Natural selection shapes nucleotide polymorphism across the genome of the nematode ''Caenorhabditis briggsae'' |journal=Genome Research |volume=20 |issue=8 |pages=1103–1111 |doi=10.1101/gr.104331.109 |pmc=2909573 |pmid=20508143}}</ref> It is usually difficult to measure the relative importance of selection and neutral processes, including drift.<ref>{{cite journal |last1=Mitchell-Olds |first1=Thomas |last2=Willis |first2=John H. |last3=Goldstein |first3=David B. |author-link3=David B. Goldstein (geneticist) |date=November 2007 |title=Which evolutionary processes influence natural genetic variation for phenotypic traits? |journal=Nature Reviews Genetics |volume=8 |issue=11 |pages=845–856 |doi=10.1038/nrg2207 |issn=1471-0056 |pmid=17943192|s2cid=14914998 }}</ref> The comparative importance of adaptive and non-adaptive forces in driving evolutionary change is an area of [[Evolutionary biology|current research]].<ref>{{cite journal |last=Nei |first=Masatoshi |author-link=Masatoshi Nei |date=December 2005 |title=Selectionism and Neutralism in Molecular Evolution |journal=[[Molecular Biology and Evolution]] |volume=22 |issue=12 |pages=2318–2342 |doi=10.1093/molbev/msi242 |issn=0737-4038 |pmc=1513187 |pmid=16120807}} * {{cite journal |last=Nei |first=Masatoshi |date=May 2006 |title=Selectionism and Neutralism in Molecular Evolution |journal=Molecular Biology and Evolution |type=Erratum |volume=23 |issue=5 |pages=2318–42 |doi=10.1093/molbev/msk009 |pmid=16120807 |pmc=1513187 |issn=0737-4038 |ref=none}}</ref> === Mutation bias === [[Mutation bias]] is usually conceived as a difference in expected rates for two different kinds of mutation, e.g., transition-transversion bias, GC-AT bias, deletion-insertion bias. This is related to the idea of [[developmental bias]]. Haldane<ref name="Haldane1927">{{cite journal |last=Haldane |first=J.B.S. |title=A Mathematical Theory of Natural and Artificial Selection, Part V: Selection and Mutation |journal=[[Mathematical Proceedings of the Cambridge Philosophical Society|Proceedings of the Cambridge Philosophical Society]] |date=July 1927 |volume=26 |issue=7 |pages=838–844 |doi=10.1017/S0305004100015644|bibcode=1927PCPS...23..838H |s2cid=86716613 }}</ref> and Fisher<ref name="Fisher1930">{{harvnb|Fisher|1930}}</ref> argued that, because mutation is a weak pressure easily overcome by selection, tendencies of mutation would be ineffectual except under conditions of neutral evolution or extraordinarily high mutation rates. This opposing-pressures argument was long used to dismiss the possibility of internal tendencies in evolution,<ref name="YampolskyStoltzfus2001">{{cite journal |last1=Yampolsky |first1=Lev Y.|last2=Stoltzfus |first2=Arlin |date=20 December 2001 |title=Bias in the introduction of variation as an orienting factor in evolution |journal=[[Evolution & Development]] |volume=3 |issue=2 |pages=73–83 |doi=10.1046/j.1525-142x.2001.003002073.x |pmid=11341676|s2cid=26956345}}</ref> until the molecular era prompted renewed interest in neutral evolution. Noboru Sueoka<ref name="Sueoka1962">{{cite journal |last=Sueoka |first=Noboru |date=1 April 1962 |title=On the Genetic Basis of Variation and Heterogeneity of DNA Base Composition |journal=PNAS |volume=48 |issue=4 |pages=582–592 |doi=10.1073/pnas.48.4.582|pmid=13918161 |pmc=220819 |bibcode=1962PNAS...48..582S |doi-access=free }}</ref> and [[Ernst Freese]]<ref name="Freese1962">{{cite journal |last=Freese |first=Ernst |author-link=Ernst Freese |title=On the Evolution of the Base Composition of DNA |date=July 1962 |journal=[[Journal of Theoretical Biology]] |volume=3 |issue=1 |pages=82–101 |doi=10.1016/S0022-5193(62)80005-8|bibcode=1962JThBi...3...82F }}</ref> proposed that systematic biases in mutation might be responsible for systematic differences in genomic GC composition between species. The identification of a GC-biased ''E. coli'' mutator strain in 1967,<ref name="CoxYanofsky1967">{{cite journal |last1=Cox |first1=Edward C. |last2=Yanofsky |first2=Charles |author-link2=Charles Yanofsky |title=Altered base ratios in the DNA of an Escherichia coli mutator strain |date=1 November 1967 |journal=Proc. Natl. Acad. Sci. USA |volume=58 |issue=5 |pages=1895–1902 |doi=10.1073/pnas.58.5.1895|pmid=4866980 |pmc=223881 |bibcode=1967PNAS...58.1895C |doi-access=free }}</ref> along with the proposal of the [[Neutral theory of molecular evolution|neutral theory]], established the plausibility of mutational explanations for molecular patterns, which are now common in the molecular evolution literature. For instance, mutation biases are frequently invoked in models of codon usage.<ref name="ShahGilchrist2011">{{cite journal |last1=Shah |first1=Premal |last2=Gilchrist |first2=Michael A. |title=Explaining complex codon usage patterns with selection for translational efficiency, mutation bias, and genetic drift |date=21 June 2011 |journal=PNAS |volume=108 |issue=25 |pages=10231–10236 |doi=10.1073/pnas.1016719108 |pmid=21646514 |pmc=3121864 |bibcode=2011PNAS..10810231S |doi-access=free }}</ref> Such models also include effects of selection, following the mutation-selection-drift model,<ref name="Bulmer1991">{{cite journal |last=Bulmer |first=Michael G. |author-link=Michael Bulmer |title=The selection-mutation-drift theory of synonymous codon usage |date=November 1991 |journal=[[Genetics (journal)|Genetics]] |volume=129 |issue=3 |pages=897–907 |doi=10.1093/genetics/129.3.897 |pmid=1752426 |pmc=1204756 }}</ref> which allows both for mutation biases and differential selection based on effects on translation. Hypotheses of mutation bias have played an important role in the development of thinking about the evolution of genome composition, including isochores.<ref name="FryxellZuckerkandl2000">{{cite journal |last1=Fryxell |first1=Karl J. |last2=Zuckerkandl |first2=Emile |author-link2=Emile Zuckerkandl |title=Cytosine Deamination Plays a Primary Role in the Evolution of Mammalian Isochores |date=September 2000 |journal=Molecular Biology and Evolution |volume=17 |issue=9 |pages=1371–1383 |doi=10.1093/oxfordjournals.molbev.a026420 |pmid=10958853 |doi-access=free }}</ref> Different insertion vs. deletion biases in different [[Taxon|taxa]] can lead to the evolution of different genome sizes.<ref>{{cite journal |last1=Petrov |first1=Dmitri A. |last2=Sangster |first2=Todd A. |last3=Johnston |first3=J. Spencer |last4=Hartl |first4=Daniel L. |last5=Shaw |first5=Kerry L. |s2cid=12021662 |date=11 February 2000 |title=Evidence for DNA Loss as a Determinant of Genome Size |journal=[[Science (journal)|Science]] |volume=287 |issue=5455 |pages=1060–1062 |bibcode=2000Sci...287.1060P |doi=10.1126/science.287.5455.1060 |issn=0036-8075 |pmid=10669421 |display-authors=3}}</ref><ref>{{cite journal |last=Petrov |first=Dmitri A. |s2cid=5314242 |date=May 2002 |title=DNA loss and evolution of genome size in ''Drosophila'' |url=https://archive.org/details/sim_genetica_2002-05_115_1/page/81 |journal=Genetica |volume=115 |issue=1 |pages=81–91 |doi=10.1023/A:1016076215168 |issn=0016-6707 |pmid=12188050}}</ref> The hypothesis of Lynch regarding genome size relies on mutational biases toward increase or decrease in genome size. However, mutational hypotheses for the evolution of composition suffered a reduction in scope when it was discovered that (1) GC-biased gene conversion makes an important contribution to composition in diploid organisms such as mammals<ref name="Duret2009">{{cite journal |last1=Duret |first1=Laurent |last2=Galtier |first2=Nicolas |s2cid=9126286 |title=Biased Gene Conversion and the Evolution of Mammalian Genomic Landscapes |date=September 2009 |journal=Annual Review of Genomics and Human Genetics |publisher=Annual Reviews |volume=10 |pages=285–311 |doi=10.1146/annurev-genom-082908-150001 |pmid=19630562 }}</ref> and (2) bacterial genomes frequently have AT-biased mutation.<ref name="Hershberg2010">{{cite journal |last1=Hershberg |first1=Ruth |last2=Petrov |first2=Dmitri A. |author-link2=Dmitri Petrov |title=Evidence That Mutation Is Universally Biased towards AT in Bacteria |date=9 September 2010 |journal=[[PLOS Genetics]] |volume=6 |issue=9 |page=e1001115 |pmid=20838599 |pmc=2936535 |doi=10.1371/journal.pgen.1001115 |doi-access=free }}</ref> Contemporary thinking about the role of mutation biases reflects a different theory from that of Haldane and Fisher. More recent work<ref name="YampolskyStoltzfus2001" /> showed that the original "pressures" theory assumes that evolution is based on standing variation: when evolution depends on events of mutation that introduce new alleles, mutational and developmental [[Bias_in_the_introduction_of_variation|biases in the introduction of variation]] (arrival biases) can impose biases on evolution without requiring neutral evolution or high mutation rates.<ref name="YampolskyStoltzfus2001" /><ref name=Stoltzfus2019>{{cite book |author=A. Stoltzfus | chapter=Understanding bias in the introduction of variation as an evolutionary cause |editor1-last=Uller |editor1-first=T. |editor2-last=Laland |editor2-first=K.N. |title=Evolutionary Causation: Biological and Philosophical Reflections |date=2019 |publisher=MIT Press |location=Cambridge, MA}}</ref> Several studies report that the mutations implicated in adaptation reflect common mutation biases<ref name="StoltzfusMcCandlish2017">{{cite journal |last1=Stoltzfus |first1=Arlin |last2=McCandlish |first2=David M. |title=Mutational Biases Influence Parallel Adaptation |journal= Molecular Biology and Evolution|date=September 2017 |volume=34 |issue=9 |pages=2163–2172 |doi=10.1093/molbev/msx180|pmid=28645195 |pmc=5850294 }}</ref><ref name="Payne2019">{{cite journal |last1=Payne |first1=Joshua L. |last2=Menardo |first2=Fabrizio |last3=Trauner |first3=Andrej |last4=Borrell |first4=Sonia |last5=Gygli |first5=Sebastian M. |last6=Loiseau |first6=Chloe |last7=Gagneux |first7=Sebastien |last8=Hall |first8=Alex R. |display-authors=3 |title=Transition bias influences the evolution of antibiotic resistance in ''Mycobacterium tuberculosis'' |date=13 May 2019 |journal=PLOS Biology |volume=17 |issue=5 |page=e3000265 |pmid=31083647 |pmc=6532934 |doi=10.1371/journal.pbio.3000265 |doi-access=free }}</ref><ref name="Storz2019">{{cite journal |last1=Storz |first1=Jay F. |last2=Natarajan |first2=Chandrasekhar |last3=Signore |first3=Anthony V. |last4=Witt |first4=Christopher C. |last5=McCandlish |first5=David M. |last6=Stoltzfus |first6=Arlin |display-authors=3 |title=The role of mutation bias in adaptive molecular evolution: insights from convergent changes in protein function |date=22 July 2019 |journal=Philosophical Transactions of the Royal Society B |volume=374 |issue=1777 |page=20180238 |pmid=31154983 |pmc=6560279 |doi=10.1098/rstb.2018.0238}}</ref> though others dispute this interpretation.<ref name="SvenssonBerger2019">{{cite journal |last1=Svensson |first1=Erik I. |last2=Berger |first2=David |title=The Role of Mutation Bias in Adaptive Evolution |journal=Trends in Ecology & Evolution |date=1 May 2019 |volume=34 |issue=5 |pages=422–434 |doi=10.1016/j.tree.2019.01.015|pmid=31003616 |s2cid=125066709 }}</ref> ==== Genetic hitchhiking ==== {{Further|Genetic hitchhiking|Hill–Robertson effect|Selective sweep}} Recombination allows alleles on the same strand of DNA to become separated. However, the rate of recombination is low (approximately two events per chromosome per generation). As a result, genes close together on a chromosome may not always be shuffled away from each other and genes that are close together tend to be inherited together, a phenomenon known as [[genetic linkage|linkage]].<ref>{{cite journal |last1=Lien |first1=Sigbjørn |last2=Szyda |first2=Joanna |last3=Schechinger |first3=Birgit |last4=Rappold |first4=Gudrun |last5=Arnheim |first5=Norm |date=February 2000 |title=Evidence for Heterogeneity in Recombination in the Human Pseudoautosomal Region: High Resolution Analysis by Sperm Typing and Radiation-Hybrid Mapping |journal=[[American Journal of Human Genetics]] |volume=66 |issue=2 |pages=557–566 |doi=10.1086/302754 |issn=0002-9297 |pmc=1288109 |pmid=10677316 |display-authors=3}}</ref> This tendency is measured by finding how often two alleles occur together on a single chromosome compared to [[independence (probability theory)|expectations]], which is called their [[linkage disequilibrium]]. A set of alleles that is usually inherited in a group is called a [[haplotype]]. This can be important when one allele in a particular haplotype is strongly beneficial: natural selection can drive a [[selective sweep]] that will also cause the other alleles in the haplotype to become more common in the population; this effect is called genetic hitchhiking or genetic draft.<ref>{{cite journal |last=Barton |first=Nicholas H. |author-link=Nick Barton |date=29 November 2000 |title=Genetic hitchhiking |journal=Philosophical Transactions of the Royal Society B |volume=355 |issue=1403 |pages=1553–1562 |doi=10.1098/rstb.2000.0716 |issn=0962-8436 |pmc=1692896 |pmid=11127900}}</ref> Genetic draft caused by the fact that some neutral genes are genetically linked to others that are under selection can be partially captured by an appropriate effective population size.<ref name="gillespie 2001" /> ==== Sexual selection ==== {{further|Sexual selection}} [[File:Rana arvalis2.jpg|thumb|Male [[moor frog]]s become blue during the height of mating season. Blue reflectance may be a form of intersexual communication. It is hypothesised that males with brighter blue coloration may signal greater sexual and genetic fitness.<ref name="Ries-2008">{{Cite journal |last1=Ries |first1=C |last2=Spaethe |first2=J |last3=Sztatecsny |first3=M |last4=Strondl |first4=C |last5=Hödl |first5=W |date=20 October 2008 |title=Turning blue and ultraviolet: sex-specific colour change during the mating season in the Balkan moor frog |url=https://zslpublications.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-7998.2008.00456.x |journal=Journal of Zoology |volume=276 |issue=3 |pages=229–236 |doi=10.1111/j.1469-7998.2008.00456.x |via=Google Scholar}}</ref>]] A special case of natural selection is sexual selection, which is selection for any trait that increases mating success by increasing the attractiveness of an organism to potential mates.<ref>{{cite journal |last1=Andersson |first1=Malte |last2=Simmons |first2=Leigh W. |date=June 2006 |title=Sexual selection and mate choice |journal=Trends in Ecology & Evolution |volume=21 |issue=6 |pages=296–302 |pmid=16769428 |doi=10.1016/j.tree.2006.03.015 |issn=0169-5347 |url=http://academic.reed.edu/biology/professors/srenn/pages/teaching/2008_syllabus/2008_readings/2_anderson-simmons_2006.pdf |url-status=live |archive-url=https://web.archive.org/web/20130309112854/http://academic.reed.edu/biology/professors/srenn/pages/teaching/2008_syllabus/2008_readings/2_Anderson-Simmons_2006.pdf |archive-date=9 March 2013|citeseerx=10.1.1.595.4050}}</ref> Traits that evolved through sexual selection are particularly prominent among males of several animal species. Although sexually favoured, traits such as cumbersome antlers, mating calls, large body size and bright colours often attract predation, which compromises the survival of individual males.<ref>{{cite journal |last1=Kokko |first1=Hanna |author-link1=Hanna Kokko |last2=Brooks |first2=Robert |last3=McNamara |first3=John M. |last4=Houston |first4=Alasdair I. |date=7 July 2002 |title=The sexual selection continuum |journal=[[Proceedings of the Royal Society B]] |volume=269 |issue=1498 |pages=1331–1340 |doi=10.1098/rspb.2002.2020 |issn=0962-8452 |pmc=1691039 |pmid=12079655}}</ref><ref name="Balancing">{{cite journal |last1=Quinn |first1=Thomas P. |last2=Hendry |first2=Andrew P. |last3=Buck |first3=Gregory B. |year=2001 |title=Balancing natural and sexual selection in sockeye salmon: interactions between body size, reproductive opportunity and vulnerability to predation by bears |url=http://redpath-staff.mcgill.ca/hendry/QuinnetalEvolEcolRes2001.pdf |journal=Evolutionary Ecology Research |volume=3 |pages=917–937 |issn=1522-0613 |access-date=15 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20160305092304/http://redpath-staff.mcgill.ca/hendry/QuinnetalEvolEcolRes2001.pdf |archive-date=5 March 2016}}</ref> This survival disadvantage is balanced by higher reproductive success in males that show these [[Handicap principle|hard-to-fake]], sexually selected traits.<ref>{{cite journal |last1=Hunt |first1=John |last2=Brooks |first2=Robert |last3=Jennions |first3=Michael D. |last4=Smith |first4=Michael J. |last5=Bentsen |first5=Caroline L. |last6=Bussière |first6=Luc F. |date=23 December 2004 |title=High-quality male field crickets invest heavily in sexual display but die young |journal=Nature |volume=432 |issue=7020 |pages=1024–1027 |bibcode=2004Natur.432.1024H |doi=10.1038/nature03084 |issn=0028-0836 |pmid=15616562 |s2cid=4417867 |display-authors=3}}</ref> Summary: Please note that all contributions to Christianpedia may be edited, altered, or removed by other contributors. 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