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! === 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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