Evolution: Difference between revisions

{{Short description|Gradual change in the heritable traits of populations}}

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'''Evolution''' is the change in the [[heritable]] [[Phenotypic trait|characteristics]] of biological populations over successive generations.<ref>{{harvnb|Hall |Hallgrímsson |2008 |pp=[https://books.google.com/books?id=jrDD3cyA09kC&pg=PA4 4–6]}}</ref><ref>{{cite web |title=Evolution Resources |location=Washington, D.C. |publisher=[[National Academies of Sciences, Engineering, and Medicine]] |year=2016 |url=http://www.nas.edu/evolution/index.html |url-status=live |archive-url=https://web.archive.org/web/20160603230514/http://www.nas.edu/evolution/index.html |archive-date=3 June 2016}}</ref> It occurs when evolutionary processes such as [[natural selection]] and [[genetic drift]] act on genetic variation, resulting in certain characteristics becoming more or less common within a population over successive generations.<ref name="Scott-Phillips-2014">{{cite journal |last1=Scott-Phillips |first1=Thomas C. |last2=Laland |first2=Kevin N. |author2-link=Kevin Laland |last3=Shuker |first3=David M. |last4=Dickins |first4=Thomas E. |last5=West |first5=Stuart A. |author-link5=Stuart West |display-authors=3 |date=May 2014 |title=The Niche Construction Perspective: A Critical Appraisal |journal=[[Evolution (journal)|Evolution]] |volume=68 |issue=5 |pages=1231–1243 |doi=10.1111/evo.12332 |issn=0014-3820 |pmid=24325256 |pmc=4261998 |quote=Evolutionary processes are generally thought of as processes by which these changes occur. Four such processes are widely recognized: natural selection (in the broad sense, to include sexual selection), genetic drift, mutation, and migration (Fisher 1930; Haldane 1932). The latter two generate variation; the first two sort it.}}</ref> The process of evolution has given rise to [[biodiversity]] at every level of [[biological organisation]].<ref>{{harvnb|Hall|Hallgrímsson|2008|pp=3–5}}</ref><ref name="Voet-2016">{{harvnb|Voet|Voet|Pratt|2016|pp=1–22|loc=Chapter 1: Introduction to the Chemistry of Life}}</ref>

All life on Earth—including [[Human evolution|humanity]]—shares a [[last universal common ancestor]] (LUCA),<ref name="Kampourakis-2014">{{harvnb|Kampourakis |2014 |pp=[https://archive.org/details/understandingevo0000kamp/page/127 127–129]}}</ref><ref name="Doolittle-2000">{{cite journal |last=Doolittle |first=W. Ford |author-link=Ford Doolittle |date=February 2000 |title=Uprooting the Tree of Life |url=http://shiva.msu.montana.edu/courses/mb437_537_2004_fall/docs/uprooting.pdf |journal=[[Scientific American]] |issn=0036-8733 |volume=282 |issue=2 |pages=90–95 |doi=10.1038/scientificamerican0200-90 |pmid=10710791 |archive-url=https://web.archive.org/web/20060907081933/http://shiva.msu.montana.edu/courses/mb437_537_2004_fall/docs/uprooting.pdf |archive-date=7 September 2006 |access-date=5 April 2015 |bibcode=2000SciAm.282b..90D}}</ref><ref>{{cite journal |last1=Glansdorff |first1=Nicolas |author2=Ying Xu |last3=Labedan |first3=Bernard |date=9 July 2008 |title=The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner |journal=[[Biology Direct]] |volume=3 |page=29 |doi=10.1186/1745-6150-3-29 |issn=1745-6150 |pmc=2478661 |pmid=18613974 |doi-access=free}}</ref> which lived approximately 3.5–3.8&nbsp;billion years ago.<ref name="Schopf-2007" /> The [[fossil]] record includes a progression from early [[biogenic]] [[graphite]]<ref name="Ohtomo-2014" /> to [[microbial mat]] fossils<ref name="Borenstein-2013" /><ref name="Pearlman-2013" /><ref name="Noffke-2013" /> to fossilised [[multicellular organism]]s. Existing patterns of biodiversity have been shaped by repeated formations of new species ([[speciation]]), changes within species ([[anagenesis]]), and loss of species ([[extinction]]) throughout the evolutionary [[history of life]] on Earth.<ref name="Futuyma04">{{harvnb|Futuyma|2004|p=33}}</ref> [[morphology (biology)|Morphological]] and [[biochemical]] traits tend to be more similar among species that share a more [[recent common ancestor]], which historically was used to reconstruct [[phylogenetic tree]]s, although direct comparison of genetic sequences is a more common method today.<ref name="Panno 2005">{{harvnb|Panno|2005|pp=xv-16}}</ref><ref>[[#NAS 2008|NAS 2008]], [http://www.nap.edu/openbook.php?record_id=11876&page=17 p. 17] {{webarchive|url=https://web.archive.org/web/20150630042457/http://www.nap.edu/openbook.php?record_id=11876&page=17 |date=30 June 2015}}</ref>

About half of the mutations in the coding regions of protein-coding genes are deleterious — the other half are neutral. A small percentage of the total mutations in this region confer a fitness benefit.<ref>{{ cite journal |last=Keightley |first=PD |date=2012 |title=Rates and fitness consequences of new mutations in humans |journal=Genetics |volume=190 |issue=2 |pages=295–304 |doi=10.1534/genetics.111.134668 |pmid=22345605 |pmc=3276617}}</ref> Some of the mutations in other parts of the genome are deleterious but the vast majority are neutral. A few are beneficial.

Mutations can involve large sections of a chromosome becoming [[gene duplication|duplicated]] (usually by [[genetic recombination]]), which can introduce extra copies of a gene into a genome.<ref>{{cite journal |last1=Hastings |first1=P. J. |last2=Lupski |first2=James R. |author-link2=James R. Lupski |last3=Rosenberg |first3=Susan M. |last4=Ira |first4=Grzegorz |date=August 2009 |title=Mechanisms of change in gene copy number |journal=Nature Reviews Genetics |volume=10 |issue=8 |pages=551–564 |doi=10.1038/nrg2593 |issn=1471-0056 |pmc=2864001 |pmid=19597530}}</ref> Extra copies of genes are a major source of the raw material needed for new genes to evolve.<ref>{{harvnb|Carroll|Grenier|Weatherbee|2005}}{{page needed|date=December 2014}}</ref> This is important because most new genes evolve within [[gene families]] from pre-existing genes that share common ancestors.<ref>{{cite journal |last1=Harrison |first1=Paul M. |last2=Gerstein |first2=Mark |author-link2=Mark Bender Gerstein |date=17 May 2002 |title=Studying Genomes Through the Aeons: Protein Families, Pseudogenes and Proteome Evolution |journal=[[Journal of Molecular Biology]] |volume=318 |issue=5 |pages=1155–1174 |doi=10.1016/S0022-2836(02)00109-2 |issn=0022-2836 |pmid=12083509}}</ref> For example, the [[human eye]] uses four genes to make structures that sense light: three for [[Cone cell|colour vision]] and one for [[Rod cell|night vision]]; all four are descended from a single ancestral gene.<ref>{{cite journal |last=Bowmaker |first=James K. |s2cid=12851209 |title=Evolution of colour vision in vertebrates |date=May 1998 |journal=Eye |volume=12 |issue=3b |pages=541–547 |doi=10.1038/eye.1998.143 |issn=0950-222X |pmid=9775215 |doi-access=free}}</ref>

New genes can be generated from an ancestral gene when a duplicate copy mutates and acquires a new function. This process is easier once a gene has been duplicated because it increases the [[Gene redundancy|redundancy]] of the system; one gene in the pair can acquire a new function while the other copy continues to perform its original function.<ref>{{cite journal |last1=Gregory |first1=T. Ryan |author-link1=T. Ryan Gregory |last2=Hebert |first2=Paul D. N. |author-link2=Paul D. N. Hebert |date=April 1999 |title=The Modulation of DNA Content: Proximate Causes and Ultimate Consequences |url=http://genome.cshlp.org/content/9/4/317.full |journal=[[Genome Research]] |volume=9 |issue=4 |pages=317–324 |doi=10.1101/gr.9.4.317 |issn=1088-9051 |pmid=10207154 |s2cid=16791399 |access-date=11 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20140823063412/http://genome.cshlp.org/content/9/4/317.full |archive-date=23 August 2014 |doi-access=free}}</ref><ref>{{cite journal |last=Hurles |first=Matthew |title=Gene Duplication: The Genomic Trade in Spare Parts |date=13 July 2004 |journal=[[PLOS Biology]] |volume=2 |issue=7 |page=e206 |doi=10.1371/journal.pbio.0020206 |issn=1545-7885 |pmc=449868 |pmid=15252449 |doi-access=free}}</ref> Other types of mutations can even generate entirely new genes from previously noncoding DNA, a phenomenon termed [[de novo gene birth|''de novo'' gene birth]].<ref>{{cite journal |last1=Liu |first1=Na |last2=Okamura |first2=Katsutomo |last3=Tyler |first3=David M. |last4=Phillips |first4=Michael D. |last5=Chung |first5=Wei-Jen |last6=Lai |first6=Eric C. |date=October 2008 |title=The evolution and functional diversification of animal microRNA genes |journal=Cell Research |volume=18 |issue=10 |pages=985–996 |doi=10.1038/cr.2008.278 |issn=1001-0602 |pmc=2712117 |pmid=18711447 |display-authors=3}}</ref><ref>{{cite journal |last=Siepel |first=Adam |author-link=Adam C. Siepel |date=October 2009 |title=Darwinian alchemy: Human genes from noncoding DNA |journal=Genome Research |volume=19 |issue=10 |pages=1693–1695 |doi=10.1101/gr.098376.109 |issn=1088-9051 |pmc=2765273 |pmid=19797681}}</ref>

The generation of new genes can also involve small parts of several genes being duplicated, with these fragments then recombining to form new combinations with new functions ([[exon shuffling]]).<ref>{{cite journal |last1=Orengo |first1=Christine A. |last2=Thornton |first2=Janet M. |s2cid=7483470 |author-link2=Janet Thornton |date=July 2005 |title=Protein families and their evolution—a structural perspective |journal=[[Annual Review of Biochemistry]] |publisher=[[Annual Reviews (publisher)|Annual Reviews]] |volume=74 |pages=867–900 |doi=10.1146/annurev.biochem.74.082803.133029 |issn=0066-4154 |pmid=15954844}}</ref><ref>{{cite journal |last1=Long |first1=Manyuan |last2=Betrán |first2=Esther |last3=Thornton |first3=Kevin |last4=Wang |first4=Wen |date=November 2003 |title=The origin of new genes: glimpses from the young and old |journal=Nature Reviews Genetics |volume=4 |issue=11 |pages=865–875 |doi=10.1038/nrg1204 |issn=1471-0056 |pmid=14634634 |s2cid=33999892}}</ref> When new genes are assembled from shuffling pre-existing parts, [[protein domain|domains]] act as modules with simple independent functions, which can be mixed together to produce new combinations with new and complex functions.<ref>{{cite journal |last1=Wang |first1=Minglei |last2=Caetano-Anollés |first2=Gustavo |author-link2=Gustavo Caetano-Anolles |date=14 January 2009 |title=The Evolutionary Mechanics of Domain Organization in Proteomes and the Rise of Modularity in the Protein World |journal=[[Structure (journal)|Structure]] |volume=17 |issue=1 |pages=66–78 |doi=10.1016/j.str.2008.11.008 |issn=1357-4310 |pmid=19141283 |doi-access=free}}</ref> For example, [[polyketide synthase]]s are large [[enzyme]]s that make [[antibiotic]]s; they contain up to 100 independent domains that each catalyse one step in the overall process, like a step in an assembly line.<ref>{{cite journal |last1=Weissman |first1=Kira J. |last2=Müller |first2=Rolf |date=14 April 2008 |title=Protein–Protein Interactions in Multienzyme Megasynthetases |journal=[[ChemBioChem]] |volume=9 |issue=6 |pages=826–848 |doi=10.1002/cbic.200700751 |issn=1439-4227 |pmid=18357594 |s2cid=205552778}}</ref>

One example of mutation is [[wild boar]] piglets. They are camouflage coloured and show a characteristic pattern of dark and light longitudinal stripes. However, mutations in the ''[[melanocortin 1 receptor]]'' (''MC1R'') disrupt the pattern. The majority of pig breeds carry MC1R mutations disrupting wild-type colour and different mutations causing dominant black colouring.<ref>{{Cite journal |last=Andersson |first=Leif |date=2020 |title=Mutations in Domestic Animals Disrupting or Creating Pigmentation Patterns |journal=Frontiers in Ecology and Evolution |volume=8 |page=116 |doi=10.3389/fevo.2020.00116 |issn=2296-701X |doi-access=free|bibcode=2020FrEEv...8..116A }}</ref>

Gene transfer between species includes the formation of [[Hybrid (biology)|hybrid]] organisms and [[horizontal gene transfer]]. Horizontal gene transfer is the transfer of genetic material from one organism to another organism that is not its offspring; this is most common among bacteria.<ref>{{cite journal |last1=Boucher |first1=Yan |last2=Douady |first2=Christophe J. |last3=Papke |first3=R. Thane |last4=Walsh |first4=David A. |last5=Boudreau |first5=Mary Ellen R. |last6=Nesbo |first6=Camilla L. |last7=Case |first7=Rebecca J. |last8=Doolittle |first8=W. Ford |date=December 2003 |title=Lateral gene transfer and the origins of prokaryotic groups |journal=[[Annual Review of Genetics]] |volume=37 |pages=283–328 |doi=10.1146/annurev.genet.37.050503.084247 |issn=0066-4197 |pmid=14616063 |display-authors=3}}</ref> In medicine, this contributes to the spread of [[antibiotic resistance]], as when one bacteria acquires resistance genes it can rapidly transfer them to other species.<ref name="Walsh-2006">{{cite journal |last=Walsh |first=Timothy R. |date=October 2006 |title=Combinatorial genetic evolution of multiresistance |journal=[[Current Opinion in Microbiology]] |volume=9 |issue=5 |pages=476–482 |doi=10.1016/j.mib.2006.08.009 |issn=1369-5274 |pmid=16942901}}</ref> Horizontal transfer of genes from bacteria to eukaryotes such as the yeast ''[[Saccharomyces cerevisiae]]'' and the adzuki bean weevil ''[[Callosobruchus chinensis]]'' has occurred.<ref>{{cite journal |last1=Kondo |first1=Natsuko |last2=Nikoh |first2=Naruo |last3=Ijichi |first3=Nobuyuki |last4=Shimada |first4=Masakazu |last5=Fukatsu |first5=Takema |date=29 October 2002 |title=Genome fragment of ''Wolbachia'' endosymbiont transferred to X chromosome of host insect |journal=PNAS |volume=99 |issue=22 |pages=14280–14285 |bibcode=2002PNAS...9914280K |doi=10.1073/pnas.222228199 |issn=0027-8424 |pmc=137875 |pmid=12386340 |display-authors=3 |doi-access=free}}</ref><ref>{{cite journal |last=Sprague |first=George F. Jr. |date=December 1991 |title=Genetic exchange between kingdoms |journal=Current Opinion in Genetics & Development |volume=1 |issue=4 |pages=530–533 |doi=10.1016/S0959-437X(05)80203-5 |issn=0959-437X |pmid=1822285}}</ref> An example of larger-scale transfers are the eukaryotic [[bdelloid rotifers]], which have received a range of genes from bacteria, fungi and plants.<ref>{{cite journal |last1=Gladyshev |first1=Eugene A. |last2=Meselson |first2=Matthew |author-link2=Matthew Meselson |last3=Arkhipova |first3=Irina R. |s2cid=11862013 |date=30 May 2008 |title=Massive Horizontal Gene Transfer in Bdelloid Rotifers |journal=[[Science (journal)|Science]] |volume=320 |issue=5880 |pages=1210–1213 |bibcode=2008Sci...320.1210G |doi=10.1126/science.1156407 |issn=0036-8075 |pmid=18511688 |url=http://nrs.harvard.edu/urn-3:HUL.InstRepos:3120157 |access-date=30 July 2022 |archive-date=30 July 2022 |archive-url=https://web.archive.org/web/20220730090619/https://dash.harvard.edu/handle/1/3120157 |url-status=live|url-access=subscription }}</ref> Viruses can also carry DNA between organisms, allowing transfer of genes even across [[Domain (biology)|biological domains]].<ref>{{cite journal |last1=Baldo |first1=Angela M. |last2=McClure |first2=Marcella A. |date=September 1999 |title=Evolution and Horizontal Transfer of dUTPase-Encoding Genes in Viruses and Their Hosts |journal=[[Journal of Virology]] |volume=73 |issue=9 |pages=7710–7721 |issn=0022-538X |pmc=104298 |pmid=10438861 |doi=10.1128/JVI.73.9.7710-7721.1999}}</ref>

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-2009">{{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]].

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 <em>for</em>. 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 <em>against</em>.<ref name="Lande-1983">{{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}}</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 in Ecology & Evolution]] |volume=23 |issue=11 |pages=602–609 |doi=10.1016/j.tree.2008.06.013 |pmid=18814933 |bibcode=2008TEcoE..23..602C}}</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.{{image reference needed|date=December 2022}} Group A is the original population and Group B is the population after selection.<br />

[[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.{{image reference needed|date=December 2022}}]]

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-1991">{{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=[[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]], 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-2009" /> 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|url-access=subscription }}</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 |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>

* {{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=2318–2342 |doi=10.1093/molbev/msk009 |pmid=16120807 |pmc=1513187 |issn=0737-4038 |ref=none}}</ref>

[[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]]. [[J. B. S. Haldane]]<ref name="Haldane-1927">{{cite journal |last=Haldane |first=J. B. S. |authorlink=J. B. S. Haldane |title=A Mathematical Theory of Natural and Artificial Selection, Part V: Selection and Mutation |journal=[[Mathematical 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 [[Ronald Fisher]]<ref name="Fisher1930">{{harvnb|Fisher|1999}}</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="Yampolsky-2001">{{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="Sueoka-1962">{{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="Freese-1962">{{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="Cox-1967">{{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="Shah-2011">{{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="Bulmer-1991">{{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="Fryxell-2000">{{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 [[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="Duret-2009">{{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="Hershberg-2010">{{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>

Several studies report that the mutations implicated in adaptation reflect common mutation biases<ref name="Stoltzfus-2017">{{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="Payne-2019">{{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="Storz-2019">{{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="Svensson-2019">{{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 |bibcode=2019TEcoE..34..422S |s2cid=125066709}}</ref>

[[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|url-access=subscription }}</ref>]]

Evolution influences every aspect of the form and behaviour of organisms. Most prominent are the specific behavioural and physical adaptations that are the outcome of natural selection. These adaptations increase fitness by aiding activities such as finding food, avoiding [[predators]] or attracting mates. Organisms can also respond to selection by [[Co-operation (evolution)|cooperating]] with each other, usually by aiding their relatives or engaging in mutually beneficial [[symbiosis]]. In the longer term, evolution produces new species through splitting ancestral populations of organisms into new groups that cannot or will not interbreed. These outcomes of evolution are distinguished based on time scale as [[macroevolution]] versus microevolution. Macroevolution refers to evolution that occurs at or above the level of species, in particular speciation and extinction, whereas microevolution refers to smaller evolutionary changes within a species or population, in particular shifts in allele frequency and adaptation.<ref name="Scott-2007">{{cite journal |last1=Scott |first1=Eugenie C. |author-link1=Eugenie Scott |last2=Matzke |first2=Nicholas J. |author-link2=Nick Matzke |date=15 May 2007 |title=Biological design in science classrooms |journal=PNAS |volume=104 |issue=Suppl. 1 |pages=8669–8676 |bibcode=2007PNAS..104.8669S |doi=10.1073/pnas.0701505104 |pmid=17494747 |pmc=1876445 |doi-access=free}}</ref> Macroevolution is the outcome of long periods of microevolution.<ref>{{cite journal |last1=Hendry |first1=Andrew Paul |last2=Kinnison |first2=Michael T. |s2cid=24485535 |date=November 2001 |title=An introduction to microevolution: rate, pattern, process |journal=Genetica |volume=112–113 |issue=1 |pages=1–8 |doi=10.1023/A:1013368628607 |issn=0016-6707 |pmid=11838760}}</ref> Thus, the distinction between micro- and macroevolution is not a fundamental one—the difference is simply the time involved.<ref>{{cite journal |last=Leroi |first=Armand M. |author-link=Armand Marie Leroi |date=March–April 2000 |title=The scale independence of evolution |journal=Evolution & Development |volume=2 |issue=2 |pages=67–77 |doi=10.1046/j.1525-142x.2000.00044.x |issn=1520-541X |pmid=11258392 |citeseerx=10.1.1.120.1020 |s2cid=17289010}}</ref> However, in macroevolution, the traits of the entire species may be important. For instance, a large amount of variation among individuals allows a species to rapidly adapt to new [[habitat]]s, lessening the chance of it going extinct, while a wide geographic range increases the chance of speciation, by making it more likely that part of the population will become isolated. In this sense, microevolution and macroevolution might involve selection at different levels—with microevolution acting on genes and organisms, versus macroevolutionary processes such as [[species selection]] acting on entire species and affecting their rates of speciation and extinction.{{sfn|Gould|2002|pp=657–658}}<ref name="Gould_1994">{{cite journal |last=Gould |first=Stephen Jay |date=19 July 1994 |title=Tempo and mode in the macroevolutionary reconstruction of Darwinism |journal=PNAS |volume=91 |issue=15 |pages=6764–6771 |bibcode=1994PNAS...91.6764G |doi=10.1073/pnas.91.15.6764 |pmc=44281 |pmid=8041695 |doi-access=free}}</ref><ref name="Jablonski-2000">{{cite journal |last=Jablonski |first=David |author-link=David Jablonski |year=2000 |title=Micro- and macroevolution: scale and hierarchy in evolutionary biology and paleobiology |journal=[[Paleobiology (journal)|Paleobiology]] |volume=26 |issue=sp4 |pages=15–52 |doi=10.1666/0094-8373(2000)26[15:MAMSAH]2.0.CO;2 |s2cid=53451360}}</ref>

[[File:Homology vertebrates-en.svg|thumb|upright=1.35|[[Homology (biology)|Homologous]] bones in the limbs of [[tetrapod]]s. The bones of these animals have the same basic structure, but have been [[adapted]] for specific uses.{{image reference needed|date=December 2022}}]]

Adaptation may cause either the gain of a new feature, or the loss of an ancestral feature. An example that shows both types of change is bacterial adaptation to antibiotic selection, with genetic changes causing antibiotic resistance by both modifying the target of the drug, or increasing the activity of transporters that pump the drug out of the cell.<ref>{{cite journal |last1=Nakajima |first1=Akira |last2=Sugimoto |first2=Yohko |last3=Yoneyama |first3=Hiroshi |last4=Nakae |first4=Taiji |display-authors=3 |date=June 2002 |title=High-Level Fluoroquinolone Resistance in ''Pseudomonas aeruginosa'' Due to Interplay of the MexAB-OprM Efflux Pump and the DNA Gyrase Mutation |journal=Microbiology and Immunology |volume=46 |issue=6 |pages=391–395 |doi=10.1111/j.1348-0421.2002.tb02711.x |issn=1348-0421 |pmid=12153116 |s2cid=22593331 |doi-access=free}}</ref> Other striking examples are the bacteria ''[[Escherichia coli]]'' evolving the ability to use [[citric acid]] as a nutrient in a [[E. coli long-term evolution experiment|long-term laboratory experiment]],<ref>{{cite journal |last1=Blount |first1=Zachary D. |last2=Borland |first2=Christina Z. |last3=Lenski |first3=Richard E. |date=10 June 2008 |title=Inaugural Article: Historical contingency and the evolution of a key innovation in an experimental population of ''Escherichia coli'' |journal=PNAS |volume=105 |issue=23 |pages=7899–7906 |bibcode=2008PNAS..105.7899B |doi=10.1073/pnas.0803151105 |issn=0027-8424 |pmc=2430337 |pmid=18524956 |doi-access=free}}</ref> ''[[Flavobacterium]]'' evolving a novel enzyme that allows these bacteria to grow on the by-products of nylon manufacturing,<ref>{{cite journal |last1=Okada |first1=Hirosuke |last2=Negoro |first2=Seiji |last3=Kimura |first3=Hiroyuki |last4=Nakamura |first4=Shunichi |display-authors=3 |s2cid=4364682 |date=10 November 1983 |title=Evolutionary adaptation of plasmid-encoded enzymes for degrading nylon oligomers |journal=Nature |volume=306 |issue=5939 |pages=203–206 |bibcode=1983Natur.306..203O |doi=10.1038/306203a0 |issn=0028-0836 |pmid=6646204}}</ref><ref>{{cite journal |last=Ohno |first=Susumu |author-link=Susumu Ohno |date=April 1984 |title=Birth of a unique enzyme from an alternative reading frame of the preexisted, internally repetitious coding sequence |journal=PNAS |volume=81 |issue=8 |pages=2421–2425 |bibcode=1984PNAS...81.2421O |doi=10.1073/pnas.81.8.2421 |issn=0027-8424 |pmc=345072 |pmid=6585807 |doi-access=free}}</ref> and the soil bacterium ''[[Sphingobium]]'' evolving an entirely new [[metabolic pathway]] that degrades the synthetic [[pesticide]] [[pentachlorophenol]].<ref>{{cite journal |last=Copley |first=Shelley D. |date=June 2000 |title=Evolution of a metabolic pathway for degradation of a toxic xenobiotic: the patchwork approach |journal=[[Trends in Biochemical Sciences]] |volume=25 |issue=6 |pages=261–265 |doi=10.1016/S0968-0004(00)01562-0 |issn=0968-0004 |pmid=10838562}}</ref><ref>{{cite journal |last1=Crawford |first1=Ronald L. |last2=Jung |first2=Carina M. |last3=Strap |first3=Janice L. |date=October 2007 |title=The recent evolution of pentachlorophenol (PCP)-4-monooxygenase (PcpB) and associated pathways for bacterial degradation of PCP |journal=[[Biodegradation (journal)|Biodegradation]] |volume=18 |issue=5 |pages=525–539 |doi=10.1007/s10532-006-9090-6 |issn=0923-9820 |pmid=17123025 |s2cid=8174462}}</ref> An interesting but still controversial idea is that some adaptations might increase the ability of organisms to generate genetic diversity and adapt by natural selection (increasing organisms' evolvability).<ref>{{harvnb|Altenberg|1995|pp=205–259}}</ref><ref>{{cite journal |last1=Masel |first1=Joanna |author-link=Joanna Masel |last2=Bergman |first2=Aviv |date=July 2003 |title=The evolution of the evolvability properties of the yeast prion [PSI+] |url=https://archive.org/details/sim_evolution_2003-07_57_7/page/1498 |journal=Evolution |volume=57 |issue=7 |pages=1498–1512 |doi=10.1111/j.0014-3820.2003.tb00358.x |pmid=12940355 |s2cid=30954684}}</ref><ref>{{Cite journal |last1=Lancaster |first1=Alex K. |last2=Bardill |first2=J. Patrick |last3=True |first3=Heather L. |last4=Masel |first4=Joanna |date=February 2010 |title=The Spontaneous Appearance Rate of the Yeast Prion [''PSI''+] and Its Implications for the Evolution of the Evolvability Properties of the [''PSI''+] System |journal=Genetics |volume=184 |issue=2 |pages=393–400 |doi=10.1534/genetics.109.110213 |issn=0016-6731 |pmc=2828720 |pmid=19917766}}</ref><ref>{{cite journal |last1=Draghi |first1=Jeremy |last2=Wagner |first2=Günter P. |author-link2=Günter P. Wagner |date=February 2008 |title=Evolution of evolvability in a developmental model |journal=Evolution |volume=62 |issue=2 |pages=301–315 |doi=10.1111/j.1558-5646.2007.00303.x |pmid=18031304 |s2cid=11560256}}</ref>

[[File:Whale skeleton.png|upright=1.35|thumb|left|A [[baleen whale]] skeleton. Letters ''a'' and ''b'' label [[flipper (anatomy)|flipper]] bones, which were adapted from front leg bones, while ''c'' indicates [[vestigial]] leg bones, both suggesting an adaptation from land to sea.<ref name="Bejder-2002">{{cite journal |last1=Bejder |first1=Lars |last2=Hall |first2=Brian K. |s2cid=8448387 |author-link2=Brian K. Hall |date=November 2002 |title=Limbs in whales and limblessness in other vertebrates: mechanisms of evolutionary and developmental transformation and loss |journal=Evolution & Development |volume=4 |issue=6 |pages=445–458 |doi=10.1046/j.1525-142X.2002.02033.x |pmid=12492145}}</ref>]]

Adaptation occurs through the gradual modification of existing structures. Consequently, structures with similar internal organisation may have different functions in related organisms. This is the result of a single ancestral structure being adapted to function in different ways. The bones within bat wings, for example, are very similar to those in mice feet and [[primate]] hands, due to the descent of all these structures from a common mammalian ancestor.<ref>{{cite journal |last1=Young |first1=Nathan M. |last2=HallgrÍmsson |first2=Benedikt |s2cid=198156135 |date=December 2005 |title=Serial homology and the evolution of mammalian limb covariation structure |url=https://archive.org/details/sim_evolution_2005-12_59_12/page/2691 |journal=Evolution |volume=59 |issue=12 |pages=2691–2704 |doi=10.1554/05-233.1 |issn=0014-3820 |pmid=16526515}}</ref> However, since all living organisms are related to some extent,<ref name="Penny-1999">{{cite journal |last1=Penny |first1=David |last2=Poole |first2=Anthony |date=December 1999 |title=The nature of the last universal common ancestor |journal=Current Opinion in Genetics & Development |volume=9 |issue=6 |pages=672–677 |doi=10.1016/S0959-437X(99)00020-9 |pmid=10607605}}</ref> even organs that appear to have little or no structural similarity, such as [[arthropod]], [[squid]] and [[vertebrate]] eyes, or the limbs and wings of arthropods and vertebrates, can depend on a common set of homologous genes that control their assembly and function; this is called [[deep homology]].<ref>{{cite journal |last=Hall |first=Brian K. |s2cid=22142786 |date=August 2003 |title=Descent with modification: the unity underlying homology and homoplasy as seen through an analysis of development and evolution |url=https://archive.org/details/sim_biological-reviews_2003-08_78_3/page/409 |journal=Biological Reviews |volume=78 |issue=3 |pages=409–433 |doi=10.1017/S1464793102006097 |issn=1464-7931 |pmid=14558591}}</ref><ref>{{cite journal |last1=Shubin |first1=Neil |author-link1=Neil Shubin |last2=Tabin |first2=Clifford J. |author-link2=Clifford Tabin |last3=Carroll |first3=Sean B. |date=12 February 2009 |title=Deep homology and the origins of evolutionary novelty |url=https://archive.org/details/sim_nature-uk_2009-02-12_457_7231/page/818 |journal=Nature |volume=457 |issue=7231 |pages=818–823 |bibcode=2009Natur.457..818S |doi=10.1038/nature07891 |pmid=19212399 |s2cid=205216390}}</ref>

During evolution, some structures may lose their original function and become vestigial structures.<ref name="Fong-1995">{{cite journal |last1=Fong |first1=Daniel F. |last2=Kane |first2=Thomas C. |last3=Culver |first3=David C. |date=November 1995 |title=Vestigialization and Loss of Nonfunctional Characters |journal=[[Annual Review of Ecology and Systematics]] |volume=26 |issue=1 |pages=249–268 |doi=10.1146/annurev.es.26.110195.001341 |bibcode=1995AnRES..26..249F}}</ref> Such structures may have little or no function in a current species, yet have a clear function in ancestral species, or other closely related species. Examples include [[pseudogene]]s,<ref>{{cite journal |author1=ZhaoLei Zhang |last2=Gerstein |first2=Mark |date=August 2004 |title=Large-scale analysis of pseudogenes in the human genome |journal=Current Opinion in Genetics & Development |volume=14 |issue=4 |pages=328–335 |doi=10.1016/j.gde.2004.06.003 |issn=0959-437X |pmid=15261647}}</ref> the non-functional remains of eyes in blind cave-dwelling fish,<ref>{{cite journal |last1=Jeffery |date=May–June 2005 |first1=William R. |title=Adaptive Evolution of Eye Degeneration in the Mexican Blind Cavefish |journal=Journal of Heredity |volume=96 |issue=3 |pages=185–196 |doi=10.1093/jhered/esi028 |pmid=15653557 |citeseerx=10.1.1.572.6605}}</ref> wings in flightless birds,<ref>{{cite journal |last1=Maxwell |first1=Erin E. |last2=Larsson |first2=Hans C. E. |date=May 2007 |title=Osteology and myology of the wing of the Emu (''Dromaius novaehollandiae'') and its bearing on the evolution of vestigial structures |journal=[[Journal of Morphology]] |volume=268 |issue=5 |pages=423–441 |doi=10.1002/jmor.10527 |issn=0362-2525 |pmid=17390336 |s2cid=12494187}}</ref> the presence of hip bones in whales and snakes,<ref name="Bejder-2002" /> and sexual traits in organisms that reproduce via asexual reproduction.<ref>{{cite journal |last1=van der Kooi |first1=Casper J. |last2=Schwander |first2=Tanja |date=November 2014 |title=On the fate of sexual traits under asexuality |url=https://www.researchgate.net/publication/259824406 |format=PDF |journal=Biological Reviews |volume=89 |issue=4 |pages=805–819 |doi=10.1111/brv.12078 |issn=1464-7931 |pmid=24443922 |s2cid=33644494 |access-date=5 August 2015 |url-status=live |archive-url=https://web.archive.org/web/20150723175840/http://www.researchgate.net/profile/Tanja_Schwander/publication/259824406_On_the_fate_of_sexual_traits_under_asexuality/links/53ff35a50cf283c3583c85f3.pdf |archive-date=23 July 2015}}</ref> Examples of [[Human vestigiality|vestigial structures in humans]] include [[wisdom teeth]],<ref>{{cite journal |last1=Silvestri |first1=Anthony R. Jr. |last2=Singh |first2=Iqbal |date=April 2003 |title=The unresolved problem of the third molar: Would people be better off without it? |url=http://jada.ada.org/cgi/content/full/134/4/450 |journal=[[Journal of the American Dental Association]] |volume=134 |issue=4 |pages=450–455 |doi=10.14219/jada.archive.2003.0194 |pmid=12733778 |archive-url=https://web.archive.org/web/20140823063158/http://jada.ada.org/content/134/4/450.full |archive-date=23 August 2014|url-access=subscription }}</ref> the [[coccyx]],<ref name="Fong-1995" /> the [[vermiform appendix]],<ref name="Fong-1995" /> and other behavioural vestiges such as [[goose bumps]]<ref>{{harvnb|Coyne|2009|p=62}}</ref><ref>{{harvnb|Darwin|1872|pp=101, 103}}</ref> and [[primitive reflexes]].<ref>{{harvnb|Gray|2007|p=66}}</ref><ref>{{harvnb|Coyne|2009|pp=85–86}}</ref><ref>{{harvnb|Stevens|1982|p=87}}</ref>

An area of current investigation in evolutionary developmental biology is the developmental basis of adaptations and exaptations.<ref>{{cite journal |last1=Johnson |first1=Norman A. |last2=Porter |first2=Adam H. |s2cid=1651351 |date=November 2001 |title=Toward a new synthesis: population genetics and evolutionary developmental biology |journal=Genetica |volume=112–113 |issue=1 |pages=45–58 |doi=10.1023/A:1013371201773 |issn=0016-6707 |pmid=11838782}}</ref> This research addresses the origin and evolution of [[Embryogenesis|embryonic development]] and how modifications of development and developmental processes produce novel features.<ref>{{cite journal |last1=Baguñà |first1=Jaume |last2=Garcia-Fernàndez |first2=Jordi |year=2003 |title=Evo-Devo: the long and winding road |url=http://www.ijdb.ehu.es/web/paper.php?doi=14756346 |journal=[[The International Journal of Developmental Biology]] |volume=47 |issue=7–8 |pages=705–713 |issn=0214-6282 |pmid=14756346 |url-status=live |archive-url=https://web.archive.org/web/20141128011936/http://www.ijdb.ehu.es/web/paper.php?doi=14756346 |archive-date=28 November 2014}}

* {{cite journal |last=Love |first=Alan C. |date=March 2003 |title=Evolutionary Morphology, Innovation and the Synthesis of Evolutionary and Developmental Biology |url=https://archive.org/details/sim_biology-philosophy_2003-03_18_2/page/309 |journal=Biology and Philosophy |volume=18 |issue=2 |pages=309–345 |doi=10.1023/A:1023940220348 |s2cid=82307503 |ref=none}}</ref> These studies have shown that evolution can alter development to produce new structures, such as embryonic bone structures that develop into the jaw in other animals instead forming part of the [[Evolution of mammalian auditory ossicles|middle ear in mammals]].<ref>{{cite journal |last=Allin |first=Edgar F. |date=December 1975 |title=Evolution of the mammalian middle ear |journal=Journal of Morphology |volume=147 |issue=4 |pages=403–437 |doi=10.1002/jmor.1051470404 |issn=0362-2525 |pmid=1202224 |s2cid=25886311}}</ref> It is also possible for structures that have been lost in evolution to reappear due to changes in developmental genes, such as a mutation in chickens causing embryos to grow teeth similar to those of crocodiles.<ref>{{cite journal |last1=Harris |first1=Matthew P. |last2=Hasso |first2=Sean M. |last3=Ferguson |first3=Mark W. J. |last4=Fallon |first4=John F. |s2cid=15733491 |date=21 February 2006 |title=The Development of Archosaurian First-Generation Teeth in a Chicken Mutant |journal=Current Biology |volume=16 |issue=4 |pages=371–377 |doi=10.1016/j.cub.2005.12.047 |pmid=16488870 |doi-access=free |bibcode=2006CBio...16..371H}}</ref> It is now becoming clear that most alterations in the form of organisms are due to changes in a small set of conserved genes.<ref>{{cite journal |last=Carroll |first=Sean B. |date=11 July 2008 |title=Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution |journal=[[Cell (journal)|Cell]] |volume=134 |issue=1 |pages=25–36 |doi=10.1016/j.cell.2008.06.030 |pmid=18614008 |s2cid=2513041 |doi-access=free}}</ref>

Speciation is the process where a species diverges into two or more descendant species.<ref name="Gavrilets-2003">{{cite journal |last=Gavrilets |first=Sergey |date=October 2003 |title=Perspective: models of speciation: what have we learned in 40 years? |journal=Evolution |volume=57 |issue=10 |pages=2197–2215 |doi=10.1554/02-727 |pmid=14628909 |s2cid=198158082}}</ref>

Speciation has been observed multiple times under both [[Laboratory experiments of speciation|controlled laboratory conditions]] and in nature.<ref>{{cite journal |last1=Rice |first1=William R. |last2=Hostert |first2=Ellen E. |date=December 1993 |title=Laboratory Experiments on Speciation: What Have We Learned in 40 Years? |journal=Evolution |volume=47 |issue=6 |pages=1637–1653 |doi=10.1111/j.1558-5646.1993.tb01257.x |pmid=28568007 |issn=0014-3820 |jstor=2410209 |s2cid=42100751}}

* {{cite journal |last1=Weinberg |first1=James R. |last2=Starczak |first2=Victoria R. |last3=Jörg |first3=Daniele |date=August 1992 |title=Evidence for Rapid Speciation Following a Founder Event in the Laboratory |url=https://archive.org/details/sim_evolution_1992-08_46_4/page/1214 |journal=Evolution |volume=46 |issue=4 |pages=1214–1220 |doi=10.1111/j.1558-5646.1992.tb00629.x |pmid=28564398 |issn=0014-3820 |jstor=2409766 |ref=none}}</ref> In sexually reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four primary geographic modes of speciation. The most common in animals is [[allopatric speciation]], which occurs in populations initially isolated geographically, such as by [[habitat fragmentation]] or migration. Selection under these conditions can produce very rapid changes in the appearance and behaviour of organisms.<ref>{{cite journal |last1=Herrel |first1=Anthony |last2=Huyghe |first2=Katleen |last3=Vanhooydonck |first3=Bieke |last4=Backeljau |first4=Thierry |last5=Breugelmans |first5=Karin |last6=Grbac |first6=Irena |last7=Van Damme |first7=Raoul |last8=Irschick |first8=Duncan J. |date=25 March 2008 |title=Rapid large-scale evolutionary divergence in morphology and performance associated with exploitation of a different dietary resource |journal=PNAS |volume=105 |issue=12 |pages=4792–4795 |bibcode=2008PNAS..105.4792H |doi=10.1073/pnas.0711998105 |issn=0027-8424 |pmc=2290806 |pmid=18344323 |display-authors=3 |doi-access=free}}</ref><ref name="Losos-1997">{{cite journal |last1=Losos |first1=Jonathan B. |last2=Warhelt |first2=Kenneth I. |last3=Schoener |first3=Thomas W. |date=1 May 1997 |title=Adaptive differentiation following experimental island colonization in ''Anolis'' lizards |url=https://archive.org/details/sim_nature-uk_1997-05-01_387_6628/page/70 |journal=Nature |volume=387 |issue=6628 |pages=70–73 |bibcode=1997Natur.387...70L |doi=10.1038/387070a0 |s2cid=4242248 |issn=0028-0836}}</ref> As selection and drift act independently on populations isolated from the rest of their species, separation may eventually produce organisms that cannot interbreed.<ref>{{cite journal |last1=Hoskin |first1=Conrad J. |last2=Higgle |first2=Megan |last3=McDonald |first3=Keith R. |last4=Moritz |first4=Craig |date=27 October 2005 |title=Reinforcement drives rapid allopatric speciation |url=https://archive.org/details/sim_nature-uk_2005-10-27_437_7063/page/1353 |journal=Nature |pmid=16251964 |volume=437 |issue=7063 |pages=1353–1356 |bibcode=2005Natur.437.1353H |doi=10.1038/nature04004 |s2cid=4417281}}</ref>

The third mode is [[parapatric speciation]]. This is similar to peripatric speciation in that a small population enters a new habitat, but differs in that there is no physical separation between these two populations. Instead, speciation results from the evolution of mechanisms that reduce gene flow between the two populations.<ref name="Gavrilets-2003" /> Generally this occurs when there has been a drastic change in the environment within the parental species' habitat. One example is the grass ''[[Anthoxanthum]] odoratum'', which can undergo parapatric speciation in response to localised metal pollution from mines.<ref>{{cite journal |last=Antonovics |first=Janis |s2cid=12291411 |author-link=Janis Antonovics |date=July 2006 |title=Evolution in closely adjacent plant populations X: long-term persistence of prereproductive isolation at a mine boundary |journal=[[Heredity (journal)|Heredity]] |volume=97 |issue=1 |pages=33–37 |doi=10.1038/sj.hdy.6800835 |issn=0018-067X |pmid=16639420|bibcode=2006Hered..97...33A }}</ref> Here, plants evolve that have resistance to high levels of metals in the soil. Selection against interbreeding with the metal-sensitive parental population produced a gradual change in the flowering time of the metal-resistant plants, which eventually produced complete reproductive isolation. Selection against hybrids between the two populations may cause [[Reinforcement (speciation)|reinforcement]], which is the evolution of traits that promote mating within a species, as well as [[character displacement]], which is when two species become more distinct in appearance.<ref>{{cite journal |last1=Nosil |first1=Patrik |last2=Crespi |first2=Bernard J. |last3=Gries |first3=Regine |last4=Gries |first4=Gerhard |date=March 2007 |title=Natural selection and divergence in mate preference during speciation |url=https://archive.org/details/sim_genetica_2007-03_129_3/page/309 |journal=Genetica |volume=129 |issue=3 |pages=309–327 |doi=10.1007/s10709-006-0013-6 |pmid=16900317 |s2cid=10808041 |issn=0016-6707}}</ref>

One type of sympatric speciation involves [[crossbreed]]ing of two related species to produce a new hybrid species. This is not common in animals as animal hybrids are usually sterile. This is because during [[meiosis]] the [[homologous chromosome]]s from each parent are from different species and cannot successfully pair. However, it is more common in plants because plants often double their number of chromosomes, to form [[polyploids]].<ref>{{cite journal |last1=Wood |first1=Troy E. |last2=Takebayashi |first2=Naoki |last3=Barker |first3=Michael S. |last4=Mayrose |first4=Itay |last5=Greenspoon |first5=Philip B. |last6=Rieseberg |first6=Loren H. |date=18 August 2009 |title=The frequency of polyploid speciation in vascular plants |journal=PNAS |volume=106 |issue=33 |pages=13875–13879 |bibcode=2009PNAS..10613875W |doi=10.1073/pnas.0811575106 |issn=0027-8424 |pmc=2728988 |pmid=19667210 |display-authors=3 |doi-access=free}}</ref> This allows the chromosomes from each parental species to form matching pairs during meiosis, since each parent's chromosomes are represented by a pair already.<ref>{{cite journal |last1=Hegarty |first1=Matthew J. |last2=Hiscock |first2=Simon J. |s2cid=1584282 |date=20 May 2008 |title=Genomic Clues to the Evolutionary Success of Polyploid Plants |journal=Current Biology |volume=18 |issue=10 |pages=R435–R444 |doi=10.1016/j.cub.2008.03.043 |issn=0960-9822 |pmid=18492478 |doi-access=free |bibcode=2008CBio...18.R435H}}</ref> An example of such a speciation event is when the plant species ''[[Arabidopsis thaliana]]'' and ''[[Arabidopsis arenosa]]'' crossbred to give the new species ''Arabidopsis suecica''.<ref>{{cite journal |last1=Jakobsson |first1=Mattias |last2=Hagenblad |first2=Jenny |last3=Tavaré |first3=Simon |author-link3=Simon Tavaré |last4=Säll |first4=Torbjörn |last5=Halldén |first5=Christer |last6=Lind-Halldén |first6=Christina |last7=Nordborg |first7=Magnus |date=June 2006 |title=A Unique Recent Origin of the Allotetraploid Species ''Arabidopsis suecica'': Evidence from Nuclear DNA Markers |journal=Molecular Biology and Evolution |volume=23 |issue=6 |pages=1217–1231 |doi=10.1093/molbev/msk006 |pmid=16549398 |display-authors=3 |url=http://hkr.diva-portal.org/smash/get/diva2:424478/FULLTEXT01 |doi-access=free |access-date=30 July 2022 |archive-date=15 February 2022 |archive-url=https://web.archive.org/web/20220215191506/http://hkr.diva-portal.org/smash/get/diva2:424478/FULLTEXT01 |url-status=live}}</ref> This happened about 20,000 years ago,<ref>{{cite journal |last1=Säll |first1=Torbjörn |last2=Jakobsson |first2=Mattias |last3=Lind-Halldén |first3=Christina |last4=Halldén |first4=Christer |date=September 2003 |title=Chloroplast DNA indicates a single origin of the allotetraploid ''Arabidopsis suecica'' |journal=Journal of Evolutionary Biology |volume=16 |issue=5 |pages=1019–1029 |doi=10.1046/j.1420-9101.2003.00554.x |pmid=14635917 |s2cid=29281998 |doi-access=free}}</ref> and the speciation process has been repeated in the laboratory, which allows the study of the genetic mechanisms involved in this process.<ref>{{cite journal |last1=Bomblies |first1=Kirsten |author-link1=Kirsten Bomblies |last2=Weigel |first2=Detlef |author-link2=Detlef Weigel |date=December 2007 |title=''Arabidopsis''—a model genus for speciation |journal=Current Opinion in Genetics & Development |volume=17 |issue=6 |pages=500–504 |doi=10.1016/j.gde.2007.09.006 |pmid=18006296}}</ref> Indeed, chromosome doubling within a species may be a common cause of reproductive isolation, as half the doubled chromosomes will be unmatched when breeding with undoubled organisms.<ref name="Sémon-2007">{{cite journal |last1=Sémon |first1=Marie |last2=Wolfe |first2=Kenneth H. |date=December 2007 |title=Consequences of genome duplication |journal=Current Opinion in Genetics & Development |volume=17 |issue=6 |pages=505–512 |doi=10.1016/j.gde.2007.09.007 |pmid=18006297}}</ref>

Understanding the changes that have occurred during an organism's evolution can reveal the genes needed to construct parts of the body, genes which may be involved in human [[genetic disorder]]s.<ref>{{cite journal |last=Maher |first=Brendan |s2cid=41648315 |date=8 April 2009 |title=Evolution: Biology's next top model? |journal=Nature |volume=458 |issue=7239 |pages=695–698 |doi=10.1038/458695a |issn=0028-0836 |pmid=19360058 |doi-access=free}}</ref> For example, the [[Mexican tetra]] is an [[albino]] cavefish that lost its eyesight during evolution. Breeding together different populations of this blind fish produced some offspring with functional eyes, since different mutations had occurred in the isolated populations that had evolved in different caves.<ref>{{cite journal |last=Borowsky |first=Richard |s2cid=16967690 |date=8 January 2008 |title=Restoring sight in blind cavefish |journal=Current Biology |volume=18 |issue=1 |pages=R23–R24 |doi=10.1016/j.cub.2007.11.023 |issn=0960-9822 |pmid=18177707 |doi-access=free |bibcode=2008CBio...18..R23B}}</ref> This helped identify genes required for vision and pigmentation.<ref>{{cite journal |last1=Gross |first1=Joshua B. |last2=Borowsky |first2=Richard |last3=Tabin |first3=Clifford J. |date=2 January 2009 |editor1-last=Barsh |editor1-first=Gregory S. |title=A novel role for ''Mc1r'' in the parallel evolution of depigmentation in independent populations of the cavefish ''Astyanax mexicanus'' |journal=PLOS Genetics |volume=5 |issue=1 |page=e1000326 |doi=10.1371/journal.pgen.1000326 |issn=1553-7390 |pmc=2603666 |pmid=19119422 |doi-access=free}}</ref>

Evolutionary theory has many [[Evolutionary therapy|applications in medicine]]. Many human diseases are not static phenomena, but capable of evolution. Viruses, bacteria, fungi and cancers evolve to be resistant to host immune defences, as well as to [[pharmaceutical drug]]s.<ref>{{cite journal |last1=Merlo |first1=Lauren M. F. |last2=Pepper |first2=John W. |last3=Reid |first3=Brian J. |last4=Maley |first4=Carlo C. |author-link4=Carlo Maley |date=December 2006 |title=Cancer as an evolutionary and ecological process |journal=[[Nature Reviews Cancer]] |volume=6 |issue=12 |pages=924–935 |doi=10.1038/nrc2013 |issn=1474-175X |pmid=17109012 |s2cid=8040576}}</ref><ref>{{cite journal |last1=Pan |first1=Dabo |first2=Weiwei |last2=Xue |first3=Wenqi |last3=Zhang |first4=Huanxiang |last4=Liu |first5=Xiaojun |last5=Yao |date=October 2012 |title=Understanding the drug resistance mechanism of hepatitis C virus NS3/4A to ITMN-191 due to R155K, A156V, D168A/E mutations: a computational study |journal=[[Biochimica et Biophysica Acta (BBA) - General Subjects]] |volume=1820 |issue=10 |pages=1526–1534 |doi=10.1016/j.bbagen.2012.06.001 |issn=0304-4165 |pmid=22698669 |display-authors=3}}</ref><ref>{{cite journal |last1=Woodford |first1=Neil |last2=Ellington |first2=Matthew J. |date=January 2007 |title=The emergence of antibiotic resistance by mutation. |journal=Clinical Microbiology and Infection |volume=13 |issue=1 |pages=5–18 |doi=10.1111/j.1469-0691.2006.01492.x |issn=1198-743X |pmid=17184282 |doi-access=free}}</ref> These same problems occur in agriculture with pesticide<ref>{{cite journal |last1=Labbé |first1=Pierrick |last2=Berticat |first2=Claire |last3=Berthomieu |first3=Arnaud |last4=Unal |first4=Sandra |last5=Bernard |first5=Clothilde |last6=Weill |first6=Mylène |last7=Lenormand |first7=Thomas |date=16 November 2007 |title=Forty Years of Erratic Insecticide Resistance Evolution in the Mosquito ''Culex pipiens'' |journal=PLOS Genetics |volume=3 |issue=11 |page=e205 |doi=10.1371/journal.pgen.0030205 |issn=1553-7390 |pmid=18020711 |display-authors=3 |pmc=2077897 |doi-access=free}}</ref> and [[herbicide]]<ref>{{cite journal |last=Neve |first=Paul |date=October 2007 |title=Challenges for herbicide resistance evolution and management: 50 years after Harper |journal=Weed Research |volume=47 |issue=5 |pages=365–369 |doi=10.1111/j.1365-3180.2007.00581.x |issn=0043-1737 |bibcode=2007WeedR..47..365N}}</ref> resistance. It is possible that we are facing the end of the effective life of most of available antibiotics<ref>{{cite journal |last1=Rodríguez-Rojas |first1=Alexandro |last2=Rodríguez-Beltrán |first2=Jerónimo |last3=Couce |first3=Alejandro |last4=Blázquez |first4=Jesús |date=August 2013 |title=Antibiotics and antibiotic resistance: A bitter fight against evolution |journal=[[International Journal of Medical Microbiology]] |volume=303 |issue=6–7 |pages=293–297 |doi=10.1016/j.ijmm.2013.02.004 |issn=1438-4221 |pmid=23517688}}</ref> and predicting the evolution and evolvability<ref>{{cite journal |last1=Schenk |first1=Martijn F. |last2=Szendro |first2=Ivan G. |last3=Krug |first3=Joachim |last4=de Visser |first4=J. Arjan G. M. |date=28 June 2012 |title=Quantifying the Adaptive Potential of an Antibiotic Resistance Enzyme |journal=PLOS Genetics |volume=8 |issue=6 |page=e1002783 |doi=10.1371/journal.pgen.1002783 |issn=1553-7390 |pmid=22761587 |pmc=3386231 |doi-access=free}}</ref> of our pathogens and devising strategies to slow or circumvent it is requiring deeper knowledge of the complex forces driving evolution at the molecular level.<ref>{{cite journal |last1=Read |first1=Andrew F. |last2=Lynch |first2=Penelope A. |last3=Thomas |first3=Matthew B. |date=7 April 2009 |title=How to Make Evolution-Proof Insecticides for Malaria Control |journal=PLOS Biology |volume=7 |issue=4 |page=e1000058 |doi=10.1371/journal.pbio.1000058 |pmid=19355786 |pmc=3279047 |doi-access=free}}</ref>

{{Further|Abiogenesis|Earliest known life forms|Panspermia|RNA world hypothesis}}

The Earth is [[Age of Earth|about 4.54&nbsp;billion years old]].<ref name="USGS-2007">{{cite web |url=http://pubs.usgs.gov/gip/geotime/age.html |title=Age of the Earth |date=9 July 2007 |publisher=[[United States Geological Survey]] |access-date=31 May 2015 |url-status=live |archive-url=https://web.archive.org/web/20051223072700/http://pubs.usgs.gov/gip/geotime/age.html |archive-date=23 December 2005}}</ref><ref name="Dalrymple-2001">{{harvnb|Dalrymple|2001|pp=205–221}}</ref><ref name="Manhesa-1980">{{cite journal |last1=Manhesa |first1=Gérard |last2=Allègre |first2=Claude J. |author-link2=Claude Allègre |last3=Dupréa |first3=Bernard |last4=Hamelin |first4=Bruno |date=May 1980 |title=Lead isotope study of basic-ultrabasic layered complexes: Speculations about the age of the earth and primitive mantle characteristics |url=https://archive.org/details/sim_earth-and-planetary-science-letters_1980-05_47_3/page/370 |journal=[[Earth and Planetary Science Letters]] |volume=47 |issue=3 |pages=370–382 |bibcode=1980E&PSL..47..370M |doi=10.1016/0012-821X(80)90024-2 |issn=0012-821X}}</ref> The earliest undisputed evidence of life on Earth dates from at least 3.5&nbsp;billion years ago,<ref name="Schopf-2007">{{cite journal |last1=Schopf |first1=J. William |author-link1=J. William Schopf |last2=Kudryavtsev |first2=Anatoliy B. |last3=Czaja |first3=Andrew D. |last4=Tripathi |first4=Abhishek B. |date=5 October 2007 |title=Evidence of Archean life: Stromatolites and microfossils |journal=[[Precambrian Research]] |volume=158 |pages=141–155 |issue=3–4 |doi=10.1016/j.precamres.2007.04.009 |issn=0301-9268 |bibcode=2007PreR..158..141S}}</ref><ref name="RavenJohnson2002">{{harvnb|Raven|Johnson|2002|p=68}}</ref> during the [[Eoarchean]] Era after a geological [[Crust (geology)|crust]] started to solidify following the earlier molten [[Hadean]] Eon. Microbial mat fossils have been found in 3.48&nbsp;billion-year-old sandstone in Western Australia.<ref name="Borenstein-2013">{{cite news |last=Borenstein |first=Seth |date=13 November 2013 |title=Oldest fossil found: Meet your microbial mom |url=http://apnews.excite.com/article/20131113/DAA1VSC01.html |work=[[Excite (web portal)|Excite]] |location=Yonkers, New York |publisher=[[Mindspark Interactive Network]] |agency=[[Associated Press]] |access-date=31 May 2015 |url-status=live |archive-url=https://web.archive.org/web/20150629230719/http://apnews.excite.com/article/20131113/DAA1VSC01.html |archive-date=29 June 2015}}</ref><ref name="Pearlman-2013">{{cite news |last=Pearlman |first=Jonathan |date=13 November 2013 |title=Oldest signs of life on Earth found |url=https://www.telegraph.co.uk/news/science/science-news/10445788/Oldest-signs-of-life-on-Earth-found.html |newspaper=[[The Daily Telegraph]] |location=London |access-date=15 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20141216062531/http://www.telegraph.co.uk/news/science/science-news/10445788/Oldest-signs-of-life-on-Earth-found.html |archive-date=16 December 2014}}</ref><ref name="Noffke-2013">{{cite journal |last1=Noffke |first1=Nora |author1-link=Nora Noffke |last2=Christian |first2=Daniel |last3=Wacey |first3=David |last4=Hazen |first4=Robert M. |author-link4=Robert Hazen |date=16 November 2013 |title=Microbially Induced Sedimentary Structures Recording an Ancient Ecosystem in the ''ca.'' 3.48 Billion-Year-Old Dresser Formation, Pilbara, Western Australia |journal=[[Astrobiology (journal)|Astrobiology]] |volume=13 |issue=12 |pages=1103–1124 |bibcode=2013AsBio..13.1103N |doi=10.1089/ast.2013.1030 |issn=1531-1074 |pmc=3870916 |pmid=24205812}}</ref> Other early physical evidence of a biogenic substance is graphite in 3.7&nbsp;billion-year-old [[metasediment]]ary rocks discovered in Western Greenland<ref name="Ohtomo-2014">{{cite journal |last1=Ohtomo |first1=Yoko |last2=Kakegawa |first2=Takeshi |last3=Ishida |first3=Akizumi |last4=Nagase |first4=Toshiro |last5=Rosing |first5=Minik T. |display-authors=3 |date=January 2014 |title=Evidence for biogenic graphite in early Archaean Isua metasedimentary rocks |journal=[[Nature Geoscience]] |volume=7 |issue=1 |pages=25–28 |bibcode=2014NatGe...7...25O |doi=10.1038/ngeo2025 |issn=1752-0894}}</ref> as well as "remains of [[biotic life]]" found in 4.1&nbsp;billion-year-old rocks in Western Australia.<ref name="Borenstein-2015">{{cite news |last=Borenstein |first=Seth |title=Hints of life on what was thought to be desolate early Earth |url=http://apnews.excite.com/article/20151019/us-sci--earliest_life-a400435d0d.html |date=19 October 2015 |work=[[Excite (web portal)|Excite]] |location=Yonkers, NY |publisher=[[Mindspark Interactive Network]] |agency=[[Associated Press]] |archive-url=https://web.archive.org/web/20151023200248/http://apnews.excite.com/article/20151019/us-sci--earliest_life-a400435d0d.html |archive-date=23 October 2015 |access-date=8 October 2018}}</ref><ref name="Bell-2015">{{cite journal |last1=Bell |first1=Elizabeth A. |last2=Boehnike |first2=Patrick |last3=Harrison |first3=T. Mark |last4=Mao |first4=Wendy L. |author4-link=Wendy Mao |date=24 November 2015 |title=Potentially biogenic carbon preserved in a 4.1 billion-year-old zircon |url=http://www.pnas.org/content/early/2015/10/14/1517557112.full.pdf |journal=PNAS |volume=112 |issue=47 |pages=14518–14521 |doi=10.1073/pnas.1517557112 |issn=0027-8424 |access-date=30 December 2015 |pmid=26483481 |pmc=4664351 |bibcode=2015PNAS..11214518B |url-status=live |archive-url=https://web.archive.org/web/20151106021508/http://www.pnas.org/content/early/2015/10/14/1517557112.full.pdf |archive-date=6 November 2015 |doi-access=free}}</ref> Commenting on the Australian findings, [[Stephen Blair Hedges]] wrote: "If life arose relatively quickly on Earth, then it could be common in the universe."<ref name="Borenstein-2015" /><ref>{{cite news |last=Schouten |first=Lucy |date=20 October 2015 |title=When did life first emerge on Earth? Maybe a lot earlier than we thought |url=https://www.csmonitor.com/Science/2015/1020/When-did-life-first-emerge-on-Earth-Maybe-a-lot-earlier-than-we-thought |work=[[The Christian Science Monitor]] |location=Boston, Massachusetts |publisher=[[Christian Science Publishing Society]] |issn=0882-7729 |archive-url=https://web.archive.org/web/20160322214217/http://www.csmonitor.com/Science/2015/1020/When-did-life-first-emerge-on-Earth-Maybe-a-lot-earlier-than-we-thought |archive-date=22 March 2016 |url-status=live |access-date=11 July 2018}}</ref> <!---Nevertheless, [[Late Heavy Bombardment#Geological consequences on Earth|several studies]] suggest that life on Earth may have started even earlier,<ref name="AB-20021014">{{cite web |last=Tenenbaum |first=David |title=When Did Life on Earth Begin? Ask a Rock |url=http://www.astrobio.net/exclusive/293/when-did-life-on-earth-begin-ask-a-rock |date=14 October 2002 |work=Astrobiology Magazine |access-date=13 April 2014 |archive-url=https://web.archive.org/web/20210628022131/https://www.astrobio.net/news-exclusive/when-did-life-on-earth-begin-ask-a-rock/ |archive-date=28 June 2021 |url-status=usurped}}</ref> as early as 4.25 billion years ago according to one study,<ref name="NS-20080702">{{cite web |last=Courtland |first=Rachel |title=Did newborn Earth harbour life? |url=https://www.newscientist.com/article/dn14245-did-newborn-earth-harbour-life.html |date=2 July 2008 |work=[[New Scientist]] |access-date=13 April 2014}}</ref> and 4.4 billion years ago according to another study.<ref name="RN-20090520">{{cite web |last=Steenhuysen |first=Julie |title=Study turns back clock on origins of life on Earth |url=https://www.reuters.com/article/2009/05/20/us-asteroids-idUSTRE54J5PX20090520 |date=20 May 2009 |work=[[Reuters]] |access-date=13 April 2014}}</ref>---> In July 2016, scientists reported identifying a set of 355 [[gene]]s from the [[last universal common ancestor]] (LUCA) of all organisms living on Earth.<ref name="Wade-2016">{{cite news |last=Wade |first=Nicholas |author-link=Nicholas Wade |title=Meet Luca, the Ancestor of All Living Things |url=https://www.nytimes.com/2016/07/26/science/last-universal-ancestor.html |date=25 July 2016 |newspaper=[[The New York Times]] |location=New York |issn=0362-4331 |access-date=25 July 2016 |url-status=live |archive-url=https://web.archive.org/web/20160728053822/http://www.nytimes.com/2016/07/26/science/last-universal-ancestor.html |archive-date=28 July 2016}}</ref>

More than 99% of all species, amounting to over five billion species,<ref name="Book-Biology">{{harvnb|McKinney|1997|p=[https://books.google.com/books?id=4LHnCAAAQBAJ&pg=PA110 110]}}</ref> that ever lived on Earth are estimated to be extinct.<ref name="Stearns-1999" /><ref name="Novacek-2014">{{cite news |last=Novacek |first=Michael J. |date=8 November 2014 |title=Prehistory's Brilliant Future |url=https://www.nytimes.com/2014/11/09/opinion/sunday/prehistorys-brilliant-future.html |newspaper=The New York Times |location=New York |issn=0362-4331 |access-date=25 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20141229225657/http://www.nytimes.com/2014/11/09/opinion/sunday/prehistorys-brilliant-future.html |archive-date=29 December 2014}}</ref> Estimates on the number of Earth's current species range from 10&nbsp;million to 14&nbsp;million,<ref name="Mora-2011">{{cite journal |last1=Mora |first1=Camilo |last2=Tittensor |first2=Derek P. |last3=Adl |first3=Sina |last4=Simpson |first4=Alastair G. B. |last5=Worm |first5=Boris |author-link5=Boris Worm |display-authors=3 |date=23 August 2011 |title=How Many Species Are There on Earth and in the Ocean? |journal=PLOS Biology |volume=9 |issue=8 |page=e1001127 |doi=10.1371/journal.pbio.1001127 |issn=1545-7885 |pmc=3160336 |pmid=21886479 |doi-access=free}}</ref><ref name="Miller">{{harvnb|Miller|Spoolman|2012|p=[https://books.google.com/books?id=NYEJAAAAQBAJ&pg=PA62 62]}}</ref> of which about 1.9&nbsp;million are estimated to have been named<ref name="Chapman2009">{{harvnb|Chapman|2009}}</ref> and 1.6&nbsp;million documented in a central database to date,<ref name="Roskov-2016">{{cite web |url=http://www.catalogueoflife.org/annual-checklist/2016/info/ac |title=Species 2000 & ITIS Catalogue of Life, 2016 Annual Checklist |year=2016 |editor-last=Roskov |editor-first=Y. |editor2-last=Abucay |editor2-first=L. |editor3-last=Orrell |editor3-first=T. |editor4-last=Nicolson |editor4-first=D. |editor5-last=Flann |editor5-first=C. |editor6-last=Bailly |editor6-first=N. |editor7-last=Kirk |editor7-first=P. |editor8-last=Bourgoin |editor8-first=T. |editor9-last=DeWalt |editor9-first=R. E. |editor10-last=Decock |editor10-first=W. |editor11-last=De Wever |editor11-first=A. |display-editors=4 |website=Species 2000 |publisher=[[Naturalis Biodiversity Center]] |location=Leiden, Netherlands |issn=2405-884X |access-date=6 November 2016 |url-status=live |archive-url=https://web.archive.org/web/20161112121623/http://www.catalogueoflife.org/annual-checklist/2016/info/ac |archive-date=12 November 2016}}</ref> leaving at least 80% not yet described.

Past species have also left records of their evolutionary history. Fossils, along with the comparative anatomy of present-day organisms, constitute the morphological, or anatomical, record.<ref name="Jablonski-1999">{{cite journal |last=Jablonski |first=David |s2cid=43388925 |date=25 June 1999 |title=The Future of the Fossil Record |journal=Science |volume=284 |issue=5423 |pages=2114–2116 |pmid=10381868 |doi=10.1126/science.284.5423.2114 |issn=0036-8075}}</ref> By comparing the anatomies of both modern and extinct species, palaeontologists can infer the lineages of those species. However, this approach is most successful for organisms that had hard body parts, such as shells, bones or teeth. Further, as prokaryotes such as bacteria and archaea share a limited set of common morphologies, their fossils do not provide information on their ancestry.

* {{cite journal |last1=Altermann |first1=Wladyslaw |last2=Kazmierczak |first2=Józef |date=November 2003 |title=Archean microfossils: a reappraisal of early life on Earth |journal=Research in Microbiology |volume=154 |issue=9 |pages=611–617 |doi=10.1016/j.resmic.2003.08.006 |pmid=14596897 |ref=none |doi-access=free}}</ref> No obvious changes in morphology or cellular organisation occurred in these organisms over the next few billion years.<ref>{{cite journal |last=Schopf |first=J. William |date=19 July 1994 |title=Disparate rates, differing fates: tempo and mode of evolution changed from the Precambrian to the Phanerozoic |journal=PNAS |volume=91 |issue=15 |pages=6735–6742 |bibcode=1994PNAS...91.6735S |doi=10.1073/pnas.91.15.6735 |pmc=44277 |pmid=8041691 |doi-access=free}}</ref> The eukaryotic cells emerged between 1.6 and 2.7&nbsp;billion years ago. The next major change in cell structure came when bacteria were engulfed by eukaryotic cells, in a cooperative association called [[endosymbiosis]].<ref name="Poole-2007">{{cite journal |last1=Poole |first1=Anthony M. |last2=Penny |first2=David |date=January 2007 |title=Evaluating hypotheses for the origin of eukaryotes |journal=BioEssays |volume=29 |issue=1 |pages=74–84 |doi=10.1002/bies.20516 |issn=0265-9247 |pmid=17187354}}</ref><ref name="Dyall-2004">{{cite journal |last1=Dyall |first1=Sabrina D. |last2=Brown |first2=Mark T. |last3=Johnson |first3=Patricia J. |s2cid=19424594 |author-link3=Patricia J. Johnson |date=9 April 2004 |title=Ancient Invasions: From Endosymbionts to Organelles |journal=Science |volume=304 |issue=5668 |pages=253–257 |bibcode=2004Sci...304..253D |doi=10.1126/science.1094884 |pmid=15073369}}</ref> The engulfed bacteria and the host cell then underwent coevolution, with the bacteria evolving into either mitochondria or [[hydrogenosome]]s.<ref>{{cite journal |last=Martin |first=William |date=October 2005 |title=The missing link between hydrogenosomes and mitochondria |journal=Trends in Microbiology |volume=13 |issue=10 |pages=457–459 |doi=10.1016/j.tim.2005.08.005 |pmid=16109488}}</ref> Another engulfment of [[cyanobacteria]]l-like organisms led to the formation of chloroplasts in algae and plants.<ref>{{cite journal |last1=Lang |first1=B. Franz |last2=Gray |first2=Michael W. |last3=Burger |first3=Gertraud |date=December 1999 |title=Mitochondrial genome evolution and the origin of eukaryotes |journal=[[Annual Review of Genetics]] |volume=33 |pages=351–397 |doi=10.1146/annurev.genet.33.1.351 |issn=0066-4197 |pmid=10690412}}

* {{cite journal |last1=Valentine |first1=James W. |last2=Jablonski |first2=David |title=Morphological and developmental macroevolution: a paleontological perspective |url=http://www.ijdb.ehu.es/web/paper.php?doi=14756327 |year=2003 |journal=The International Journal of Developmental Biology |volume=47 |issue=7–8 |pages=517–522 |issn=0214-6282 |pmid=14756327 |access-date=30 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20141024234611/http://www.ijdb.ehu.es/web/paper.php?doi=14756327 |archive-date=24 October 2014 |ref=none}}</ref>

About 500&nbsp;million years ago, plants and fungi colonised the land and were soon followed by arthropods and other animals.<ref>{{cite journal |last=Waters |first=Elizabeth R. |date=December 2003 |title=Molecular adaptation and the origin of land plants |journal=[[Molecular Phylogenetics and Evolution]] |volume=29 |issue=3 |pages=456–463 |doi=10.1016/j.ympev.2003.07.018 |issn=1055-7903 |pmid=14615186 |bibcode=2003MolPE..29..456W}}</ref> Insects were particularly successful and even today make up the majority of animal species.<ref>{{cite journal |last=Mayhew |first=Peter J. |author-link=Peter Mayhew (biologist) |date=August 2007 |title=Why are there so many insect species? Perspectives from fossils and phylogenies |url=https://archive.org/details/sim_biological-reviews_2007-08_82_3/page/425 |journal=Biological Reviews |volume=82 |issue=3 |pages=425–454 |doi=10.1111/j.1469-185X.2007.00018.x |issn=1464-7931 |pmid=17624962 |s2cid=9356614}}</ref> [[Amphibian]]s first appeared around 364&nbsp;million years ago, followed by early [[amniote]]s and birds around 155&nbsp;million years ago (both from "reptile"-like lineages), [[mammal]]s around 129&nbsp;million years ago, [[Homininae]] around 10&nbsp;million years ago and [[Anatomically modern humans|modern humans]] around 250,000 years ago.<ref>{{cite journal |last=Carroll |first=Robert L. |author-link=Robert L. Carroll |date=May 2007 |title=The Palaeozoic Ancestry of Salamanders, Frogs and Caecilians |journal=[[Zoological Journal of the Linnean Society]] |volume=150 |issue=Supplement s1 |pages=1–140 |doi=10.1111/j.1096-3642.2007.00246.x |issn=1096-3642 |doi-access=free}}</ref><ref>{{cite journal |last1=Wible |first1=John R. |last2=Rougier |first2=Guillermo W. |last3=Novacek |first3=Michael J. |last4=Asher |first4=Robert J. |date=21 June 2007 |title=Cretaceous eutherians and Laurasian origin for placental mammals near the K/T boundary |url=https://archive.org/details/sim_nature-uk_2007-06-21_447_7147/page/1003 |journal=Nature |volume=447 |issue=7147 |pages=1003–1006 |bibcode=2007Natur.447.1003W |doi=10.1038/nature05854 |issn=0028-0836 |pmid=17581585 |s2cid=4334424}}</ref><ref>{{cite journal |last=Witmer |first=Lawrence M. |s2cid=205066360 |author-link=Lawrence Witmer |date=28 July 2011 |title=Palaeontology: An icon knocked from its perch |journal=Nature |volume=475 |issue=7357 |pages=458–459 |doi=10.1038/475458a |issn=0028-0836 |pmid=21796198}}</ref> However, despite the evolution of these large animals, smaller organisms similar to the types that evolved early in this process continue to be highly successful and dominate the Earth, with the majority of both biomass and species being prokaryotes.<ref name="Schloss-2004" />

The [[Scientific revolution|"New Science"]] of the 17th century rejected the Aristotelian approach. It sought to explain natural phenomena in terms of [[physical law]]s that were the same for all visible things and that did not require the existence of any fixed natural categories or divine cosmic order. However, this new approach was slow to take root in the biological sciences: the last bastion of the concept of fixed natural types. [[John Ray]] applied one of the previously more general terms for fixed natural types, "species", to plant and animal types, but he strictly identified each type of living thing as a species and proposed that each species could be defined by the features that perpetuated themselves generation after generation.<ref>{{harvnb|Mayr|1982|pp=256–257}}

In 1880, Marsh caught the attention of the scientific world with the publication of ''Odontornithes: a Monograph on Extinct Birds of North America,'' which included his discoveries of birds with teeth. These skeletons helped bridge the gap between dinosaurs and birds, and provided invaluable support for Darwin's theory of evolution.{{sfnp|McCarren|1993|pp=16–17}} Darwin wrote to Marsh saying, "Your work on these old birds & on the many fossil animals of N. America has afforded the best support to the theory of evolution, which has appeared within the last 20 years" (since Darwin's publication of ''Origin of Species).<ref>Plate, Robert. ''The Dinosaur Hunters: Othniel C. Marsh and Edward D. Cope,'' pp. 210–211, David McKay, New York, 1964.</ref><ref>Cianfaglione, Paul. "O.C. Marsh Odontornithes Monograph Still Relevant Today", 20 July 2016, ''Avian Musings: "going beyond the field mark."''</ref>

The publication of the structure of [[DNA]] by [[James Watson]] and [[Francis Crick]] with contribution of [[Rosalind Franklin]] in 1953 demonstrated a physical mechanism for inheritance.<ref name="Watson-1953">{{cite journal |last1=Watson |first1=J. D. |author-link1=James Watson |last2=Crick |first2=F. H. C. |author-link2=Francis Crick |date=25 April 1953 |title=Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid |url=http://profiles.nlm.nih.gov/SC/B/B/Y/W/_/scbbyw.pdf |journal=[[Nature (journal)|Nature]] |volume=171 |issue=4356 |pages=737–738 |bibcode=1953Natur.171..737W |doi=10.1038/171737a0 |issn=0028-0836 |pmid=13054692 |s2cid=4253007 |access-date=4 December 2014 |quote=It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material. |url-status=dead |archive-url=https://web.archive.org/web/20140823063212/http://profiles.nlm.nih.gov/SC/B/B/Y/W/_/scbbyw.pdf |archive-date=23 August 2014}}</ref> [[Molecular biology]] improved understanding of the relationship between [[genotype]] and [[phenotype]]. Advances were also made in phylogenetic [[systematics]], mapping the transition of traits into a comparative and testable framework through the publication and use of [[evolutionary trees]].<ref name="Hennig99">{{harvnb|Hennig|1999|p=280}}</ref> In 1973, evolutionary biologist [[Theodosius Dobzhansky]] penned that "[[nothing in biology makes sense except in the light of evolution]]", because it has brought to light the relations of what first seemed disjointed facts in natural history into a coherent [[explanatory]] body of knowledge that describes and predicts many observable facts about life on this planet.<ref name="Dobzhansky-1973">{{cite journal |last=Dobzhansky |first=Theodosius |s2cid=207358177 |author-link=Theodosius Dobzhansky |date=March 1973 |title=Nothing in Biology Makes Sense Except in the Light of Evolution |url=http://www.phil.vt.edu/Burian/NothingInBiolChFina.pdf |journal=The American Biology Teacher |volume=35 |issue=3 |pages=125–129 |doi=10.2307/4444260 |url-status=dead |archive-url=https://web.archive.org/web/20151023161423/http://www.phil.vt.edu/Burian/NothingInBiolChFina.pdf |archive-date=23 October 2015 |jstor=4444260 |citeseerx=10.1.1.324.2891}}</ref>

While [[Level of support for evolution#Religious|various religions and denominations]] have reconciled their beliefs with evolution through concepts such as [[theistic evolution]], there are [[creationists]] who believe that evolution is contradicted by the [[creation myth]]s found in their religions and who raise various [[objections to evolution]].<ref name="Scott-2007" /><ref name="Ross-2005">{{cite journal |last=Ross |first=Marcus R. |s2cid=14208021 |author-link=Marcus R. Ross |date=May 2005 |title=Who Believes What? Clearing up Confusion over Intelligent Design and Young-Earth Creationism |url=http://www.nagt.org/files/nagt/jge/abstracts/Ross_v53n3p319.pdf |journal=Journal of Geoscience Education |volume=53 |issue=3 |pages=319–323 |issn=1089-9995 |access-date=28 April 2008 |bibcode=2005JGeEd..53..319R |doi=10.5408/1089-9995-53.3.319 |url-status=live |archive-url=https://web.archive.org/web/20080511204303/http://nagt.org/files/nagt/jge/abstracts/Ross_v53n3p319.pdf |archive-date=11 May 2008 |citeseerx=10.1.1.404.1340}}</ref><ref>{{cite journal |last=Hameed |first=Salman |date=12 December 2008 |title=Bracing for Islamic Creationism |url=http://helios.hampshire.edu/~sahCS/Hameed-Science-Creationism.pdf |journal=Science |volume=322 |issue=5908 |pages=1637–1638 |doi=10.1126/science.1163672 |issn=0036-8075 |pmid=19074331 |s2cid=206515329 |archive-url=https://web.archive.org/web/20141110031233/http://helios.hampshire.edu/~sahCS/Hameed-Science-Creationism.pdf |archive-date=10 November 2014}}</ref> As had been demonstrated by responses to the publication of ''[[Vestiges of the Natural History of Creation]]'' in 1844, the most controversial aspect of evolutionary biology is the implication of [[human evolution]] that humans share common ancestry with apes and that the mental and [[Evolution of morality|moral faculties]] of humanity have the same types of natural causes as other inherited traits in animals.<ref>{{harvnb|Bowler|2003}}</ref> In some countries, notably the United States, these tensions between science and religion have fuelled the current creation–evolution controversy, a religious conflict focusing on politics and [[creation and evolution in public education|public education]].<ref>{{cite journal |last1=Miller |first1=Jon D. |last2=Scott |first2=Eugenie C. |last3=Okamoto |first3=Shinji |s2cid=152990938 |date=11 August 2006 |title=Public Acceptance of Evolution |journal=Science |volume=313 |issue=5788 |pages=765–766 |doi=10.1126/science.1126746 |issn=0036-8075 |pmid=16902112}}</ref> While other scientific fields such as [[physical cosmology|cosmology]]<ref name="Spergel-2003">{{cite journal |last1=Spergel |first1=David Nathaniel |author-link1=David Spergel |last2=Verde |first2=Licia |last3=Peiris |first3=Hiranya V. |last4=Komatsu |first4=Eiichiro |last5=Nolta |first5=Michael R. |last6=Bennett |first6=Charles L. |author-link6=Charles L. Bennett |last7=Halpern |first7=Mark |last8=Hinshaw |first8=Gary |last9=Jarosik |first9=Norman |year=2003 |title=First-Year Wilkinson Microwave Anisotropy Probe (WMAP) Observations: Determination of Cosmological Parameters |journal=The Astrophysical Journal Supplement Series |volume=148 |issue=1 |pages=175–194 |arxiv=astro-ph/0302209 |bibcode=2003ApJS..148..175S |doi=10.1086/377226 |s2cid=10794058 |display-authors=3}}</ref> and [[Earth science]]<ref name="Wilde-2001">{{cite journal |last1=Wilde |first1=Simon A. |last2=Valley |first2=John W. |last3=Peck |first3=William H. |last4=Graham |first4=Colin M. |date=11 January 2001 |title=Evidence from detrital zircons for the existence of continental crust and oceans on the Earth 4.4 Gyr ago |url=https://archive.org/details/sim_nature-uk_2001-01-11_409_6817/page/175 |journal=Nature |volume=409 |issue=6817 |pages=175–178 |doi=10.1038/35051550 |issn=0028-0836 |pmid=11196637 |bibcode=2001Natur.409..175W |s2cid=4319774}}</ref> also conflict with literal interpretations of many [[religious text]]s, evolutionary biology experiences significantly more opposition from religious literalists.

The teaching of evolution in American secondary school biology classes was uncommon in most of the first half of the 20th century. The [[Scopes trial]] decision of 1925 caused the subject to become very rare in American secondary biology textbooks for a generation, but it was gradually re-introduced later and became legally protected with the 1968 ''[[Epperson v. Arkansas]]'' decision. Since then, the competing religious belief of creationism was legally disallowed in secondary school curricula in various decisions in the 1970s and 1980s, but it returned in [[pseudoscientific]] form as [[intelligent design]] (ID), to be excluded once again in the 2005 ''[[Kitzmiller v. Dover Area School District]]'' case.<ref name="Branch-2007">{{cite journal |last=Branch |first=Glenn |s2cid=86665329 |author-link=Glenn Branch |date=March 2007 |title=Understanding Creationism after ''Kitzmiller'' |url=https://archive.org/details/sim_bioscience_2007-03_57_3/page/278 |journal=[[BioScience]] |volume=57 |issue=3 |pages=278–284 |doi=10.1641/B570313 |issn=0006-3568 |doi-access=free}}</ref> The debate over Darwin's ideas did not generate significant controversy in China.<ref name="Xiaoxing-2019">{{cite journal |author=Xiaoxing Jin |date=March 2019 |title=Translation and transmutation: the ''Origin of Species'' in China |journal=The British Journal for the History of Science |location=Cambridge |publisher=Cambridge University Press on behalf of The British Society for the History of Science |volume=52 |issue=1 |pages=117–141 |pmid=30587253 |doi=10.1017/S0007087418000808 |s2cid=58605626}}</ref>