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{{Short description|Gradual change in the heritable traits of populations}}
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'''Evolution''' is the change in the [[heredity|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 [[genetic drift]] and [[natural selection]] 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>

The [[scientific theory]] of evolution by natural selection was conceived independently by two British naturalists, [[Charles Darwin]] and [[Alfred Russel Wallace]], in the mid-19th century as an explanation for why organisms are adapted to their physical and biological environments. The theory was first set out in detail in Darwin's book ''[[On the Origin of Species]]''.<ref>{{harvnb|Darwin|1859}}</ref> Evolution by natural selection is established by observable facts about living organisms: (1) more offspring are often produced than can possibly survive; (2) [[phenotypic variation|traits vary]] among individuals with respect to their [[morphology (biology)|morphology]], [[physiology]], and behaviour; (3) different traits confer different rates of survival and reproduction (differential [[Fitness (biology)|fitness]]); and (4) traits can be passed from generation to generation ([[heritability]] of fitness).<ref name="Lewontin-1970">{{cite journal |last=Lewontin |first=Richard C. |author-link=Richard Lewontin |date=November 1970 |title=The Units of Selection |url=http://joelvelasco.net/teaching/167/lewontin%2070%20-%20the%20units%20of%20selection.pdf |journal=[[Annual Review of Ecology and Systematics]] |volume=1 |issue=1 |pages=1–18 |doi=10.1146/annurev.es.01.110170.000245 |jstor=2096764 |bibcode=1970AnRES...1....1L |s2cid=84684420 |url-status=live |archive-url=https://web.archive.org/web/20150206172942/http://joelvelasco.net/teaching/167/lewontin%2070%20-%20the%20units%20of%20selection.pdf |archive-date=6 February 2015 |issn=0066-4162}}</ref> In successive generations, members of a population are therefore more likely to be replaced by the [[offspring]] of parents with favourable characteristics for that environment.

In the early 20th century, [[Alternatives to evolution by natural selection|competing ideas of evolution]] were [[Superseded theories in science|refuted]] and evolution was combined with [[Mendelian inheritance]] and [[population genetics]] to give rise to modern evolutionary theory.<ref name="Futuyma2017a">{{harvnb|Futuyma |Kirkpatrick |2017 |pp=3–26 |loc=Chapter 1: Evolutionary Biology}}</ref> [[Modern synthesis (20th century)|In this synthesis]] the basis for heredity is in [[DNA]] molecules that pass information from generation to generation. The processes that change DNA in a population include natural selection, genetic drift, [[mutation]], and [[gene flow]].<ref name="Scott-Phillips-2014" />

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 |article-number=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>

[[Evolutionary biologists]] have continued to study various aspects of evolution by forming and testing [[hypotheses]] as well as constructing theories based on [[empirical evidence|evidence]] from the field or laboratory and on data generated by the methods of [[mathematical and theoretical biology]]. Their discoveries have influenced not just the development of [[biology]] but also other fields including agriculture, medicine, and [[computer science]].<ref name="Futuyma-1999">{{cite web |url=http://www.rci.rutgers.edu/~ecolevol/fulldoc.pdf |title=Evolution, Science, and Society: Evolutionary Biology and the National Research Agenda |year=1999 |editor-last=Futuyma |editor-first=Douglas J. |editor-link=Douglas J. Futuyma |publisher=[[Rutgers University]] |location=New Brunswick, New Jersey |type=Executive summary |oclc=43422991 |archive-url=https://web.archive.org/web/20120131174727/http://www.rci.rutgers.edu/~ecolevol/fulldoc.pdf |archive-date=31 January 2012 |access-date=24 November 2014}}</ref>
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== Heredity ==
{{further|Introduction to genetics|Genetics|Heredity}}
[[File:ADN static.png|thumb|left|[[DNA]] structure. [[nucleobase|Bases]] are in the centre, surrounded by phosphate–sugar chains in a [[double helix]].]]

Evolution in organisms occurs through changes in heritable characteristics—the inherited characteristics of an organism. In humans, for example, [[eye colour]] is an inherited characteristic and an individual might inherit the "brown-eye trait" from one of their parents.<ref>{{cite journal |last1=Sturm |first1=Richard A. |last2=Frudakis |first2=Tony N. |date=August 2004 |title=Eye colour: portals into pigmentation genes and ancestry |journal=[[Trends in Genetics]] |volume=20 |issue=8 |pages=327–332 |doi=10.1016/j.tig.2004.06.010 |issn=0168-9525 |pmid=15262401}}</ref> Inherited traits are controlled by genes and the complete set of genes within an organism's [[genome]] (genetic material) is called its ''[[genotype]]''.<ref name="Pearson-2006">{{cite journal |last=Pearson |first=Helen |date=25 May 2006 |title=Genetics: What is a gene? |journal=Nature |volume=441 |issue=7092 |pages=398–401 |bibcode=2006Natur.441..398P |doi=10.1038/441398a |issn=0028-0836 |pmid=16724031 |s2cid=4420674 |doi-access=free}}</ref>

The complete set of observable traits that make up the structure and behaviour of an organism is called its ''[[phenotype]]''. Some of these traits come from the interaction of its genotype with the environment while others are neutral.<ref>{{cite journal |last1=Visscher |first1=Peter M. |last2=Hill |first2=William G. |author-link2=William G. Hill |last3=Wray |first3=Naomi R. |author-link3=Naomi Wray |date=April 2008 |title=Heritability in the genomics era — concepts and misconceptions |journal=Nature Reviews Genetics |volume=9 |issue=4 |pages=255–266 |doi=10.1038/nrg2322 |issn=1471-0056 |pmid=18319743 |s2cid=690431}}</ref> Some observable characteristics are not inherited. For example, [[suntanned]] skin comes from the interaction between a person's genotype and sunlight; thus, suntans are not passed on to people's children. The phenotype is the ability of the skin to tan when exposed to sunlight. However, some people tan more easily than others, due to differences in genotypic variation; a striking example are people with the inherited trait of [[albinism]], who do not tan at all and are very sensitive to [[sunburn]].<ref>{{cite journal |last1=Oetting |first1=William S. |last2=Brilliant |first2=Murray H. |last3=King |first3=Richard A. |date=August 1996 |title=The clinical spectrum of albinism in humans |journal=[[Molecular Medicine Today]] |volume=2 |issue=8 |pages=330–335 |doi=10.1016/1357-4310(96)81798-9 |issn=1357-4310 |pmid=8796918}}</ref>

Heritable characteristics are passed from one generation to the next via [[DNA]], a [[molecule]] that encodes genetic information.<ref name="Pearson-2006" /> DNA is a long [[biopolymer]] composed of four types of bases. The sequence of bases along a particular DNA molecule specifies the genetic information, in a manner similar to a sequence of letters spelling out a sentence. Before a cell divides, the DNA is copied, so that each of the resulting two cells will inherit the DNA sequence. Portions of a DNA molecule that specify a single functional unit are called genes; different genes have different sequences of bases. Within cells, each long strand of DNA is called a [[chromosome]]. The specific location of a DNA sequence within a chromosome is known as a [[locus (genetics)|locus]]. If the DNA sequence at a locus varies between individuals, the different forms of this sequence are called alleles. DNA sequences can change through mutations, producing new alleles. If a mutation occurs within a gene, the new allele may affect the trait that the gene controls, altering the phenotype of the organism.<ref name="Futuyma_2005">{{harvnb|Futuyma|2005}}{{page needed|date=December 2014}}</ref> However, while this simple correspondence between an allele and a trait works in some cases, most traits are influenced by multiple genes in a [[quantitative trait loci|quantitative]] or [[epistatic]] manner.<ref>{{cite journal |last=Phillips |first=Patrick C. |date=November 2008 |title=Epistasis—the essential role of gene interactions in the structure and evolution of genetic systems |journal=Nature Reviews Genetics |volume=9 |issue=11 |pages=855–867 |doi=10.1038/nrg2452 |issn=1471-0056 |pmc=2689140 |pmid=18852697}}</ref><ref name="Min Lin-2006">{{cite journal |author1=Rongling Wu |author2=Min Lin |date=March 2006 |title=Functional mapping — how to map and study the genetic architecture of dynamic complex traits |journal=Nature Reviews Genetics |volume=7 |issue=3 |pages=229–237 |doi=10.1038/nrg1804 |issn=1471-0056 |pmid=16485021 |s2cid=24301815}}</ref>

== Sources of variation ==
{{Main|Genetic variation}}
{{further|Genetic diversity|Population genetics}}
{{multiple image|direction=vertical|align=right|image1=Biston.betularia.7200.jpg |image2=Biston.betularia.f.carbonaria.7209.jpg|width=200|caption1=White [[peppered moth]] |caption2=Black morph in [[peppered moth evolution]]}}

Evolution can occur if there is genetic variation within a population. Variation comes from mutations in the genome, reshuffling of genes through [[sexual reproduction]] and migration between populations ([[gene flow]]). Despite the constant introduction of new variation through mutation and gene flow, most of the genome of a species is very similar among all individuals of that species.<ref>{{cite journal |last1=Butlin |first1=Roger K. |last2=Tregenza |first2=Tom |date=28 February 1998 |title=Levels of genetic polymorphism: marker loci versus quantitative traits |journal=Philosophical Transactions of the Royal Society B |volume=353 |issue=1366 |pages=187–198 |doi=10.1098/rstb.1998.0201 |issn=0962-8436 |pmc=1692210 |pmid=9533123}}
* {{cite journal |last1=Butlin |first1=Roger K. |last2=Tregenza |first2=Tom |date=29 December 2000 |title=Correction for Butlin and Tregenza, Levels of genetic polymorphism: marker loci versus quantitative traits |journal=Philosophical Transactions of the Royal Society B |volume=355 |issue=1404 |doi=10.1098/rstb.2000.2000 |issn=0962-8436 |quote=Some of the values in table 1 on p. 193 were given incorrectly. The errors do not affect the conclusions drawn in the paper. The corrected table is reproduced below. |page=1865 |ref=none |doi-access=free}}</ref> However, discoveries in the field of [[evolutionary developmental biology]] have demonstrated that even relatively small differences in genotype can lead to dramatic differences in phenotype both within and between species.

An individual organism's phenotype results from both its genotype and the influence of the environment it has lived in.<ref name="Min Lin-2006" /> The modern evolutionary synthesis defines evolution as the change over time in this genetic variation. The frequency of one particular allele will become more or less prevalent relative to other forms of that gene. Variation disappears when a new allele reaches the point of [[fixation (population genetics)|fixation]]—when it either disappears from the population or replaces the ancestral allele entirely.<ref name="Amos-1998">{{cite journal |last1=Amos |first1=William |last2=Harwood |first2=John |date=28 February 1998 |title=Factors affecting levels of genetic diversity in natural populations |journal=[[Philosophical Transactions of the Royal Society B]] |volume=353 |issue=1366 |pages=177–186 |doi=10.1098/rstb.1998.0200 |issn=0962-8436 |pmc=1692205 |pmid=9533122}}</ref>

=== Mutation ===
{{Main|Mutation}}
[[File:Gene-duplication.svg|thumb|upright|Duplication of part of a [[chromosome]]]]

Mutations are changes in the DNA sequence of a cell's genome and are the ultimate source of genetic variation in all organisms.<ref name="Futuyma2017c">{{harvnb|Futuyma |Kirkpatrick |2017 |pp=79–102 |loc=Chapter 4: Mutation and Variation}}</ref> When mutations occur, they may alter the [[gene product|product of a gene]], or prevent the gene from functioning, or have no effect.

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 |article-number=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 |article-number=116 |doi=10.3389/fevo.2020.00116 |issn=2296-701X |doi-access=free|bibcode=2020FrEEv...8..116A }}</ref>

=== Sex and recombination ===
{{further|Sexual reproduction|Genetic recombination|Evolution of sexual reproduction}}

In [[Asexual reproduction|asexual]] organisms, genes are inherited together, or ''linked'', as they cannot mix with genes of other organisms during reproduction. In contrast, the offspring of sexual organisms contain random mixtures of their parents' chromosomes that are produced through independent assortment. In a related process called [[homologous recombination]], sexual organisms exchange DNA between two matching chromosomes.<ref>{{cite journal |last=Radding |first=Charles M. |date=December 1982 |title=Homologous Pairing and Strand Exchange in Genetic Recombination |journal=[[Annual Review of Genetics]] |volume=16 |pages=405–437 |doi=10.1146/annurev.ge.16.120182.002201 |issn=0066-4197 |pmid=6297377}}</ref> Recombination and reassortment do not alter allele frequencies, but instead change which alleles are associated with each other, producing offspring with new combinations of alleles.<ref name="Agrawal-2006">{{cite journal |last=Agrawal |first=Aneil F. |s2cid=14739487 |date=5 September 2006 |title=Evolution of Sex: Why Do Organisms Shuffle Their Genotypes? |journal=[[Current Biology]] |volume=16 |issue=17 |pages=R696–R704 |doi=10.1016/j.cub.2006.07.063 |issn=0960-9822 |pmid=16950096 |bibcode=2006CBio...16.R696A |citeseerx=10.1.1.475.9645}}</ref> Sex usually increases genetic variation and may increase the rate of evolution.<ref>{{cite journal |last1=Peters |first1=Andrew D. |last2=Otto |first2=Sarah P. |date=June 2003 |title=Liberating genetic variance through sex |journal=[[BioEssays]] |volume=25 |issue=6 |pages=533–537 |doi=10.1002/bies.10291 |issn=0265-9247 |pmid=12766942}}</ref><ref>{{cite journal |last1=Goddard |first1=Matthew R. |last2=Godfray |first2=H. Charles J. |author-link2=Charles Godfray |last3=Burt |first3=Austin |date=31 March 2005 |title=Sex increases the efficacy of natural selection in experimental yeast populations |url=https://archive.org/details/sim_nature-uk_2005-03-31_434_7033/page/636 |journal=Nature |volume=434 |issue=7033 |pages=636–640 |bibcode=2005Natur.434..636G |doi=10.1038/nature03405 |issn=0028-0836 |pmid=15800622 |s2cid=4397491}}</ref>

[[File:Evolsex-dia1a.svg|thumb|upright=1.15|This diagram illustrates the ''twofold cost of sex''. If each individual were to contribute to the same number of offspring (two), ''(a)'' the sexual population remains the same size each generation, where the ''(b)'' [[Asexual reproduction]] population doubles in size each generation.{{image reference needed|date=December 2022}}]]

The two-fold cost of sex was first described by [[John Maynard Smith]].<ref name="maynard">{{harvnb|Maynard Smith|1978}}{{page needed|date=December 2014}}</ref> The first cost is that in sexually dimorphic species only one of the two sexes can bear young. This cost does not apply to hermaphroditic species, like most plants and many [[invertebrate]]s. The second cost is that any individual who reproduces sexually can only pass on 50% of its genes to any individual offspring, with even less passed on as each new generation passes.<ref name="ridley">{{harvnb|Ridley|2004|p=314}}</ref> Yet sexual reproduction is the more common means of reproduction among eukaryotes and multicellular organisms. The [[Red Queen hypothesis]] has been used to explain the significance of sexual reproduction as a means to enable continual evolution and adaptation in response to [[coevolution]] with other species in an ever-changing environment.<ref name="ridley" /><ref name="Van Valen-1973">{{cite journal |last=Van Valen |first=Leigh |author-link=Leigh Van Valen |year=1973 |title=A New Evolutionary Law |url=https://dl.dropboxusercontent.com/u/18310184/evolutionary-theory/vol-01/Vol.1%2CNo.1%2C1-30%2CL.%20Van%20Valen%2C%20A%20new%20evolutionary%20law..pdf |journal=Evolutionary Theory |volume=1 |pages=1–30 |issn=0093-4755 |access-date=24 December 2014 |archive-url=https://web.archive.org/web/20141222094258/https://dl.dropboxusercontent.com/u/18310184/evolutionary-theory/vol-01/Vol.1%2CNo.1%2C1-30%2CL.%20Van%20Valen%2C%20A%20new%20evolutionary%20law..pdf |archive-date=22 December 2014}}</ref><ref name="Hamilton-1990">{{cite journal |last1=Hamilton |first1=W. D. |author-link1=W. D. Hamilton |last2=Axelrod |first2=Robert |author-link2=Robert Axelrod (political scientist) |last3=Tanese |first3=Reiko |date=1 May 1990 |title=Sexual reproduction as an adaptation to resist parasites (a review) |journal=PNAS |volume=87 |issue=9 |pages=3566–3573 |bibcode=1990PNAS...87.3566H |doi=10.1073/pnas.87.9.3566 |issn=0027-8424 |pmid=2185476 |pmc=53943 |doi-access=free}}</ref><ref name="Birdsell">{{harvnb|Birdsell|Wills|2003|pp=113–117}}</ref> Another hypothesis is that sexual reproduction is primarily an adaptation for promoting accurate recombinational repair of damage in germline DNA, and that increased diversity is a byproduct of this process that may sometimes be adaptively beneficial.<ref>Bernstein H, Byerly HC, Hopf FA, Michod RE. Genetic damage, mutation, and the evolution of sex. Science. 1985 Sep 20;229(4719):1277–81. {{doi|10.1126/science.3898363}}. PMID 3898363</ref><ref>Bernstein H, Hopf FA, Michod RE. The molecular basis of the evolution of sex. Adv Genet. 1987;24:323-70. {{doi|10.1016/s0065-2660(08)60012-7}}. PMID 3324702</ref>

=== Gene flow ===
{{further|Gene flow}}

Gene flow is the exchange of genes between populations and between species.<ref name="Morjan-2004">{{cite journal |last1=Morjan |first1=Carrie L. |last2=Rieseberg |first2=Loren H. |author-link2=Loren H. Rieseberg |date=June 2004 |title=How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles |journal=[[Molecular Ecology]] |volume=13 |issue=6 |pages=1341–1356 |pmid=15140081 |doi=10.1111/j.1365-294X.2004.02164.x |issn=0962-1083 |pmc=2600545 |bibcode=2004MolEc..13.1341M}}</ref> It can therefore be a source of variation that is new to a population or to a species. Gene flow can be caused by the movement of individuals between separate populations of organisms, as might be caused by the movement of mice between inland and coastal populations, or the movement of [[pollen]] between heavy-metal-tolerant and heavy-metal-sensitive populations of grasses.

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>

Large-scale gene transfer has also occurred between the ancestors of [[eukaryotic cell]]s and bacteria, during the acquisition of [[chloroplast]]s and [[mitochondria]]. It is possible that eukaryotes themselves originated from horizontal gene transfers between bacteria and [[archaea]].<ref>{{cite journal |last1=Rivera |first1=Maria C. |last2=Lake |first2=James A. |author-link2=James A. Lake |date=9 September 2004 |title=The ring of life provides evidence for a genome fusion origin of eukaryotes |url=https://archive.org/details/sim_nature-uk_2004-09-09_431_7005/page/152 |journal=Nature |volume=431 |issue=7005 |pages=152–155 |bibcode=2004Natur.431..152R |doi=10.1038/nature02848 |issn=0028-0836 |pmid=15356622 |s2cid=4349149}}</ref>

=== Epigenetics ===
{{further|Epigenetics}}

Some heritable changes cannot be explained by changes to the sequence of [[nucleotide]]s in the DNA. These phenomena are classed as epigenetic inheritance systems.<ref name="Jablonka-2009">{{cite journal |last1=Jablonka |first1=Eva |last2=Raz |first2=Gal |date=June 2009 |title=Transgenerational Epigenetic Inheritance: Prevalence, Mechanisms, and Implications for the Study of Heredity and Evolution |journal=The Quarterly Review of Biology |volume=84 |issue=2 |pages=131–176 |doi=10.1086/598822 |issn=0033-5770 |pmid=19606595 |url=http://compgen.unc.edu/wiki/images/d/df/JablonkaQtrRevBio2009.pdf |citeseerx=10.1.1.617.6333 |s2cid=7233550 |access-date=30 July 2022 |archive-date=15 July 2011 |archive-url=https://web.archive.org/web/20110715111243/http://compgen.unc.edu/wiki/images/d/df/JablonkaQtrRevBio2009.pdf |url-status=live}}</ref> [[DNA methylation]] marking [[chromatin]], self-sustaining metabolic loops, gene silencing by [[RNA interference]] and the three-dimensional [[Protein structure|conformation]] of [[protein]]s (such as [[prion]]s) are areas where epigenetic inheritance systems have been discovered at the organismic level.<ref name="Bossdorf-2010">{{cite journal |last1=Bossdorf |first1=Oliver |last2=Arcuri |first2=Davide |last3=Richards |first3=Christina L. |last4=Pigliucci |first4=Massimo |s2cid=15763479 |author-link4=Massimo Pigliucci |date=May 2010 |title=Experimental alteration of DNA methylation affects the phenotypic plasticity of ecologically relevant traits in ''Arabidopsis thaliana'' |journal=Evolutionary Ecology |volume=24 |issue=3 |pages=541–553 |doi=10.1007/s10682-010-9372-7 |bibcode=2010EvEco..24..541B |issn=0269-7653 |url=http://doc.rero.ch/record/318722/files/10682_2010_Article_9372.pdf |access-date=30 July 2022 |archive-date=5 June 2022 |archive-url=https://web.archive.org/web/20220605101316/http://doc.rero.ch/record/318722/files/10682_2010_Article_9372.pdf |url-status=live}}</ref> Developmental biologists suggest that complex interactions in [[genetic networks]] and communication among cells can lead to heritable variations that may underlay some of the mechanics in [[developmental plasticity]] and [[Canalisation (genetics)|canalisation]].<ref name="Jablonka-2002">{{cite journal |last1=Jablonka |first1=Eva |last2=Lamb |first2=Marion J. |date=December 2002 |title=The Changing Concept of Epigenetics |journal=[[Annals of the New York Academy of Sciences]] |volume=981 |issue=1 |pages=82–96 |bibcode=2002NYASA.981...82J |doi=10.1111/j.1749-6632.2002.tb04913.x |issn=0077-8923 |pmid=12547675 |s2cid=12561900}}</ref> Heritability may also occur at even larger scales. For example, ecological inheritance through the process of [[niche construction]] is defined by the regular and repeated activities of organisms in their environment. This generates a legacy of effects that modify and feed back into the selection regime of subsequent generations.<ref name="Laland-2006">{{cite journal |last1=Laland |first1=Kevin N. |last2=Sterelny |first2=Kim |author-link2=Kim Sterelny |date=September 2006 |title=Perspective: Seven Reasons (Not) to Neglect Niche Construction |journal=[[Evolution (journal)|Evolution]] |volume=60 |issue=9 |pages=1751–1762 |doi=10.1111/j.0014-3820.2006.tb00520.x |pmid=17089961 |s2cid=22997236 |issn=0014-3820 |doi-access=free}}</ref> Other examples of heritability in evolution that are not under the direct control of genes include the inheritance of cultural traits and [[symbiogenesis]].<ref name="Chapman-1998">{{cite journal |last1=Chapman |first1=Michael J. |last2=Margulis |first2=Lynn |author-link2=Lynn Margulis |date=December 1998 |title=Morphogenesis by symbiogenesis |url=http://www.im.microbios.org/04december98/14%20Chapman.pdf |journal=[[International Microbiology]] |volume=1 |issue=4 |pages=319–326 |issn=1139-6709 |pmid=10943381 |access-date=9 December 2014 |archive-url=https://web.archive.org/web/20140823062546/http://www.im.microbios.org/04december98/14%20Chapman.pdf |archive-date=23 August 2014}}</ref><ref name="Wilson-2007">{{cite journal |last1=Wilson |first1=David Sloan |author-link1=David Sloan Wilson |last2=Wilson |first2=Edward O. |author-link2=E. O. Wilson |date=December 2007 |title=Rethinking the Theoretical Foundation of Sociobiology |url=http://evolution.binghamton.edu/dswilson/wp-content/uploads/2010/01/Rethinking-sociobiology.pdf |journal=The Quarterly Review of Biology |volume=82 |issue=4 |pages=327–348 |doi=10.1086/522809 |issn=0033-5770 |pmid=18217526 |s2cid=37774648 |archive-url=https://web.archive.org/web/20110511235639/http://evolution.binghamton.edu/dswilson/wp-content/uploads/2010/01/Rethinking-sociobiology.pdf |archive-date=11 May 2011}}</ref>

== Evolutionary forces ==
[[File:Mutation and selection diagram.svg|thumb|upright=1.35|[[Mutation]] followed by natural selection results in a population with darker colouration.]]

From a [[neo-Darwinian]] perspective, evolution occurs when there are changes in the frequencies of alleles within a population of interbreeding organisms,<ref name="Ewens W.J. 2004">{{harvnb|Ewens|2004}}{{page needed|date=December 2014}}</ref> for example, the allele for black colour in a population of moths becoming more common. Mechanisms that can lead to changes in allele frequencies include natural selection, genetic drift, and mutation bias.<!--This is cited in the subsections below.-->

=== Natural selection ===
{{Main|Natural selection}}
{{See also|Dollo's law of irreversibility}}

Evolution by natural selection is the process by which traits that enhance survival and reproduction become more common in successive generations of a population. It embodies three principles:<ref name="Lewontin-1970" />

* Variation exists within populations of organisms with respect to morphology, physiology and behaviour (phenotypic variation).
* Different traits confer different rates of survival and reproduction (differential fitness).
* These traits can be passed from generation to generation (heritability of fitness).

More offspring are produced than can possibly survive, and these conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors are more likely to pass on their traits to the next generation than those with traits that do not confer an advantage.<ref name="Hurst-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]].

The central concept of natural selection is the [[evolutionary fitness]] of an organism.<ref name="Orr-2009">{{cite journal |last=Orr |first=H. Allen |author-link=H. Allen Orr |date=August 2009 |title=Fitness and its role in evolutionary genetics |journal=Nature Reviews Genetics |volume=10 |issue=8 |pages=531–539 |doi=10.1038/nrg2603 |pmc=2753274 |pmid=19546856 |issn=1471-0056}}</ref> Fitness is measured by an organism's ability to survive and reproduce, which determines the size of its genetic contribution to the next generation.<ref name="Orr-2009" /> However, fitness is not the same as the total number of offspring: instead fitness is indicated by the proportion of subsequent generations that carry an organism's genes.<ref name="Haldane-1959">{{cite journal |last=Haldane |first=J. B. S. |s2cid=4185793 |author-link=J. B. S. Haldane |date=14 March 1959 |title=The Theory of Natural Selection To-Day |url=https://archive.org/details/sim_nature-uk_1959-03-14_183_4663/page/710 |journal=Nature |volume=183 |issue=4663 |pages=710–713 |bibcode=1959Natur.183..710H |doi=10.1038/183710a0 |pmid=13644170}}</ref> For example, if an organism could survive well and reproduce rapidly, but its offspring were all too small and weak to survive, this organism would make little genetic contribution to future generations and would thus have low fitness.<ref name="Orr-2009" />

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 />
'''·''' Graph 1 shows [[directional selection]], in which a single extreme [[phenotype]] is favoured.<br />
'''·''' Graph 2 depicts [[stabilising selection]], where the intermediate phenotype is favoured over the extreme traits.<br />
'''·''' Graph 3 shows [[disruptive selection]], in which the extreme phenotypes are favoured over the intermediate.]]

Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorised into three different types. The first is [[directional selection]], which is a shift in the average value of a trait over time—for example, organisms slowly getting taller.<ref>{{cite journal |last1=Hoekstra |first1=Hopi E. |last2=Hoekstra |first2=Jonathan M. |last3=Berrigan |first3=David |last4=Vignieri |first4=Sacha N. |last5=Hoang |first5=Amy |last6=Hill |first6=Caryl E. |last7=Beerli |first7=Peter |last8=Kingsolver |first8=Joel G. |date=31 July 2001 |title=Strength and tempo of directional selection in the wild |journal=PNAS |volume=98 |issue=16 |pages=9157–9160 |bibcode=2001PNAS...98.9157H |doi=10.1073/pnas.161281098 |pmc=55389 |pmid=11470913 |display-authors=3 |doi-access=free}}</ref> Secondly, [[disruptive selection]] is selection for extreme trait values and often results in [[bimodal distribution|two different values]] becoming most common, with selection against the average value. This would be when either short or tall organisms had an advantage, but not those of medium height. Finally, in [[stabilising selection]] there is selection against extreme trait values on both ends, which causes a decrease in [[variance]] around the average value and less diversity.<ref name="Hurst-2009" /><ref>{{cite journal |last=Felsenstein |first=Joseph |author-link=Joseph Felsenstein |date=November 1979 |title=Excursions along the Interface between Disruptive and Stabilizing Selection |journal=Genetics |volume=93 |issue=3 |pages=773–795 |doi=10.1093/genetics/93.3.773 |pmc=1214112 |pmid=17248980}}</ref> This would, for example, cause organisms to eventually have a similar height.

Natural selection most generally makes nature the measure against which individuals and individual traits, are more or less likely to survive. "Nature" in this sense refers to an [[ecosystem]], that is, a system in which organisms interact with every other element, [[Abiotic component|physical]] as well as [[Biotic component|biological]], in their local environment. [[Eugene Odum]], a founder of ecology, defined an ecosystem as: "Any unit that includes all of the organisms...in a given area interacting with the physical environment so that a flow of energy leads to clearly defined trophic structure, biotic diversity, and material cycles (i.e., exchange of materials between living and nonliving parts) within the system...."<ref name="Odum1971">{{harvnb|Odum|1971|p=8}}</ref> Each population within an ecosystem occupies a distinct [[Ecological niche|niche]], or position, with distinct relationships to other parts of the system. These relationships involve the life history of the organism, its position in the [[food chain]] and its geographic range. This broad understanding of nature enables scientists to delineate specific forces which, together, comprise natural selection.

Natural selection can act at [[unit of selection|different levels of organisation]], such as genes, cells, individual organisms, groups of organisms and species.<ref name="Okasha07">{{harvnb|Okasha|2006}}</ref><ref name="Gould-1998">{{cite journal |last=Gould |first=Stephen Jay |author-link=Stephen Jay Gould |date=28 February 1998 |title=Gulliver's further travels: the necessity and difficulty of a hierarchical theory of selection |journal=Philosophical Transactions of the Royal Society B |volume=353 |issue=1366 |pages=307–314 |doi=10.1098/rstb.1998.0211 |issn=0962-8436 |pmc=1692213 |pmid=9533127}}</ref><ref name="Mayr-1997">{{cite journal |last=Mayr |first=Ernst |author-link=Ernst Mayr |date=18 March 1997 |title=The objects of selection |journal=PNAS |volume=94 |issue=6 |pages=2091–2094 |bibcode=1997PNAS...94.2091M |doi=10.1073/pnas.94.6.2091 |issn=0027-8424 |pmc=33654 |pmid=9122151 |doi-access=free}}</ref> Selection can act at multiple levels simultaneously.<ref>{{harvnb|Maynard Smith|1998|pp=203–211; discussion 211–217}}</ref> An example of selection occurring below the level of the individual organism are genes called [[transposons]], which can replicate and spread throughout a genome.<ref>{{cite journal |last=Hickey |first=Donal A. |s2cid=6583945 |year=1992 |title=Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes |journal=[[Genetica]] |volume=86 |issue=1–3 |pages=269–274 |doi=10.1007/BF00133725 |issn=0016-6707 |pmid=1334911}}</ref> Selection at a level above the individual, such as [[group selection]], may allow the evolution of cooperation.<ref>{{cite journal |last1=Gould |first1=Stephen Jay |last2=Lloyd |first2=Elisabeth A. |author-link2=Elisabeth Lloyd |date=12 October 1999 |title=Individuality and adaptation across levels of selection: how shall we name and generalise the unit of Darwinism? |journal=PNAS |volume=96 |issue=21 |pages=11904–11909 |bibcode=1999PNAS...9611904G |doi=10.1073/pnas.96.21.11904 |issn=0027-8424 |pmc=18385 |pmid=10518549 |doi-access=free}}</ref>

=== Genetic drift ===
{{further|Genetic drift|Effective population size}}

[[File:Allele-frequency.png|thumb|Simulation of genetic drift of 20 unlinked alleles in populations of 10 (top) and 100 (bottom). Drift to [[Fixation (population genetics)|fixation]] is more rapid in the smaller population.{{image reference needed|date=December 2022}}]]

Genetic drift is the random fluctuation of [[allele frequencies]] within a population from one generation to the next.<ref name="Futuyma2017b">{{harvnb|Futuyma|Kirkpatrick|2017|pp=55–66|loc=Chapter 3: Natural Selection and Adaptation}}</ref> When selective forces are absent or relatively weak, allele frequencies are equally likely to ''drift'' upward or downward{{clarify|date=November 2022}} in each successive generation because the alleles are subject to [[sampling error]].<ref name="Masel-2011">{{cite journal |last=Masel |first=Joanna |s2cid=17619958 |date=25 October 2011 |title=Genetic drift |journal=Current Biology |volume=21 |issue=20 |pages=R837–R838 |doi=10.1016/j.cub.2011.08.007 |issn=0960-9822 |pmid=22032182 |doi-access=free |bibcode=2011CBio...21.R837M}}</ref> This drift halts when an allele eventually becomes fixed, either by disappearing from the population or by replacing the other alleles entirely. Genetic drift may therefore eliminate some alleles from a population due to chance alone. Even in the absence of selective forces, genetic drift can cause two separate populations that begin with the same genetic structure to drift apart into two divergent populations with different sets of alleles.<ref>{{cite journal |last=Lande |first=Russell |year=1989 |title=Fisherian and Wrightian theories of speciation |url=https://archive.org/details/sim_genome_1989_31_1/page/221 |journal=[[Genome (journal)|Genome]] |volume=31 |issue=1 |pages=221–227 |doi=10.1139/g89-037 |issn=0831-2796 |pmid=2687093}}</ref>

According to the [[neutral theory of molecular evolution]] most evolutionary changes are the result of the fixation of [[neutral mutation]]s by genetic drift.<ref name="Kimura-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>

The time it takes a neutral allele to become fixed by genetic drift depends on population size; fixation is more rapid in smaller populations.<ref>{{cite journal |last1=Otto |first1=Sarah P. |last2=Whitlock |first2=Michael C. |date=June 1997 |title=The Probability of Fixation in Populations of Changing Size |url=http://www.genetics.org/content/146/2/723.full.pdf |journal=Genetics |volume=146 |issue=2 |pages=723–733 |doi=10.1093/genetics/146.2.723 |pmc=1208011 |pmid=9178020 |access-date=18 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20150319042554/http://www.genetics.org/content/146/2/723.full.pdf |archive-date=19 March 2015}}</ref> The number of individuals in a population is not critical, but instead a measure known as the effective population size.<ref name="Charlesworth-2009">{{cite journal |last=Charlesworth |first=Brian |author-link=Brian Charlesworth |date=March 2009 |title=Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation |journal=Nature Reviews Genetics |volume=10 |issue=3 |pages=195–205 |doi=10.1038/nrg2526 |pmid=19204717 |s2cid=205484393}}</ref> The effective population is usually smaller than the total population since it takes into account factors such as the level of inbreeding and the stage of the lifecycle in which the population is the smallest.<ref name="Charlesworth-2009" /> The effective population size may not be the same for every gene in the same population.<ref>{{cite journal |last1=Cutter |first1=Asher D. |last2=Choi |first2=Jae Young |date=August 2010 |title=Natural selection shapes nucleotide polymorphism across the genome of the nematode ''Caenorhabditis briggsae'' |journal=Genome Research |volume=20 |issue=8 |pages=1103–1111 |doi=10.1101/gr.104331.109 |pmc=2909573 |pmid=20508143}}</ref>

It is usually difficult to measure the relative importance of selection and neutral processes, including drift.<ref>{{cite journal |last1=Mitchell-Olds |first1=Thomas |last2=Willis |first2=John H. |last3=Goldstein |first3=David B. |author-link3=David B. Goldstein (geneticist) |date=November 2007 |title=Which evolutionary processes influence natural genetic variation for phenotypic traits? |journal=Nature Reviews Genetics |volume=8 |issue=11 |pages=845–856 |doi=10.1038/nrg2207 |issn=1471-0056 |pmid=17943192 |s2cid=14914998}}</ref> The comparative importance of adaptive and non-adaptive forces in driving evolutionary change is an area of [[Evolutionary biology|current research]].<ref>{{cite journal |last=Nei |first=Masatoshi |author-link=Masatoshi Nei |date=December 2005 |title=Selectionism and Neutralism in Molecular Evolution |journal=[[Molecular Biology and Evolution]] |volume=22 |issue=12 |pages=2318–2342 |doi=10.1093/molbev/msi242 |issn=0737-4038 |pmc=1513187 |pmid=16120807}}
* {{cite journal |last=Nei |first=Masatoshi |date=May 2006 |title=Selectionism and Neutralism in Molecular Evolution |journal=Molecular Biology and Evolution |type=Erratum |volume=23 |issue=5 |pages=2318–2342 |doi=10.1093/molbev/msk009 |pmid=16120807 |pmc=1513187 |issn=0737-4038 |ref=none}}</ref>

=== Mutation bias ===

[[Mutation bias]] is usually conceived as a difference in expected rates for two different kinds of mutation, e.g., transition-transversion bias, GC-AT bias, deletion-insertion bias. This is related to the idea of [[developmental bias]]. [[J. B. S. Haldane]]<ref name="Haldane-1927">{{cite journal |last=Haldane |first=J. B. S. |author-link=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 |article-number=e1001115 |pmid=20838599 |pmc=2936535 |doi=10.1371/journal.pgen.1001115 |doi-access=free}}</ref>

Contemporary thinking about the role of mutation biases reflects a different theory from that of Haldane and Fisher. More recent work<ref name="Yampolsky-2001" /> showed that the original "pressures" theory assumes that evolution is based on standing variation: when evolution depends on events of mutation that introduce new alleles, mutational and developmental [[Bias in the introduction of variation|biases in the introduction of variation]] (arrival biases) can impose biases on evolution without requiring neutral evolution or high mutation rates.<ref name="Yampolsky-2001" /><ref name="Stoltzfus-2019">{{cite book |author=A. Stoltzfus |chapter=Understanding bias in the introduction of variation as an evolutionary cause |editor1-last=Uller |editor1-first=T. |editor2-last=Laland |editor2-first=K. N. |title=Evolutionary Causation: Biological and Philosophical Reflections |date=2019 |publisher=MIT Press |location=Cambridge, MA}}</ref>
Several studies report that the mutations implicated in adaptation reflect common mutation biases<ref name="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 |article-number=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 |article-number=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>

==== Genetic hitchhiking ====
{{Further|Genetic hitchhiking|Hill–Robertson effect|Selective sweep}}

Recombination allows alleles on the same strand of DNA to become separated. However, the rate of recombination is low (approximately two events per chromosome per generation). As a result, genes close together on a chromosome may not always be shuffled away from each other and genes that are close together tend to be inherited together, a phenomenon known as [[genetic linkage|linkage]].<ref>{{cite journal |last1=Lien |first1=Sigbjørn |last2=Szyda |first2=Joanna |last3=Schechinger |first3=Birgit |last4=Rappold |first4=Gudrun |last5=Arnheim |first5=Norm |date=February 2000 |title=Evidence for Heterogeneity in Recombination in the Human Pseudoautosomal Region: High Resolution Analysis by Sperm Typing and Radiation-Hybrid Mapping |journal=[[American Journal of Human Genetics]] |volume=66 |issue=2 |pages=557–566 |doi=10.1086/302754 |issn=0002-9297 |pmc=1288109 |pmid=10677316 |display-authors=3}}</ref> This tendency is measured by finding how often two alleles occur together on a single chromosome compared to [[independence (probability theory)|expectations]], which is called their [[linkage disequilibrium]]. A set of alleles that is usually inherited in a group is called a [[haplotype]]. This can be important when one allele in a particular haplotype is strongly beneficial: natural selection can drive a [[selective sweep]] that will also cause the other alleles in the haplotype to become more common in the population; this effect is called genetic hitchhiking or genetic draft.<ref>{{cite journal |last=Barton |first=Nicholas H. |author-link=Nick Barton |date=29 November 2000 |title=Genetic hitchhiking |journal=Philosophical Transactions of the Royal Society B |volume=355 |issue=1403 |pages=1553–1562 |doi=10.1098/rstb.2000.0716 |issn=0962-8436 |pmc=1692896 |pmid=11127900}}</ref> Genetic draft caused by the fact that some neutral genes are genetically linked to others that are under selection can be partially captured by an appropriate effective population size.<ref name="Gillespie-2001" />

==== Sexual selection ====
{{further|Sexual selection}}
[[File:Rana arvalis2.jpg|thumb|Male [[moor frog]]s become blue during the height of mating season. Blue reflectance may be a form of intersexual communication. It is hypothesised that males with brighter blue coloration may signal greater sexual and genetic fitness.<ref name="Ries-2008">{{Cite journal |last1=Ries |first1=C |last2=Spaethe |first2=J |last3=Sztatecsny |first3=M |last4=Strondl |first4=C |last5=Hödl |first5=W |date=20 October 2008 |title=Turning blue and ultraviolet: sex-specific colour change during the mating season in the Balkan moor frog |url=https://zslpublications.onlinelibrary.wiley.com/doi/epdf/10.1111/j.1469-7998.2008.00456.x |journal=Journal of Zoology |volume=276 |issue=3 |pages=229–236 |doi=10.1111/j.1469-7998.2008.00456.x |via=Google Scholar|url-access=subscription }}</ref>]]

A special case of natural selection is sexual selection, which is selection for any trait that increases mating success by increasing the attractiveness of an organism to potential mates.<ref>{{cite journal |last1=Andersson |first1=Malte |last2=Simmons |first2=Leigh W. |date=June 2006 |title=Sexual selection and mate choice |journal=Trends in Ecology & Evolution |volume=21 |issue=6 |pages=296–302 |pmid=16769428 |doi=10.1016/j.tree.2006.03.015 |issn=0169-5347 |url=http://academic.reed.edu/biology/professors/srenn/pages/teaching/2008_syllabus/2008_readings/2_anderson-simmons_2006.pdf |url-status=live |archive-url=https://web.archive.org/web/20130309112854/http://academic.reed.edu/biology/professors/srenn/pages/teaching/2008_syllabus/2008_readings/2_Anderson-Simmons_2006.pdf |archive-date=9 March 2013 |citeseerx=10.1.1.595.4050}}</ref> Traits that evolved through sexual selection are particularly prominent among males of several animal species. Although sexually favoured, traits such as cumbersome antlers, mating calls, large body size and bright colours often attract predation, which compromises the survival of individual males.<ref>{{cite journal |last1=Kokko |first1=Hanna |author-link1=Hanna Kokko |last2=Brooks |first2=Robert |last3=McNamara |first3=John M. |last4=Houston |first4=Alasdair I. |date=7 July 2002 |title=The sexual selection continuum |journal=[[Proceedings of the Royal Society B]] |volume=269 |issue=1498 |pages=1331–1340 |doi=10.1098/rspb.2002.2020 |issn=0962-8452 |pmc=1691039 |pmid=12079655}}</ref><ref name="Quinn-2001">{{cite journal |last1=Quinn |first1=Thomas P. |last2=Hendry |first2=Andrew P. |last3=Buck |first3=Gregory B. |year=2001 |title=Balancing natural and sexual selection in sockeye salmon: interactions between body size, reproductive opportunity and vulnerability to predation by bears |url=http://redpath-staff.mcgill.ca/hendry/QuinnetalEvolEcolRes2001.pdf |journal=Evolutionary Ecology Research |volume=3 |pages=917–937 |issn=1522-0613 |access-date=15 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20160305092304/http://redpath-staff.mcgill.ca/hendry/QuinnetalEvolEcolRes2001.pdf |archive-date=5 March 2016}}</ref> This survival disadvantage is balanced by higher reproductive success in males that show these [[Handicap principle|hard-to-fake]], sexually selected traits.<ref>{{cite journal |last1=Hunt |first1=John |last2=Brooks |first2=Robert |last3=Jennions |first3=Michael D. |last4=Smith |first4=Michael J. |last5=Bentsen |first5=Caroline L. |last6=Bussière |first6=Luc F. |date=23 December 2004 |title=High-quality male field crickets invest heavily in sexual display but die young |journal=Nature |volume=432 |issue=7020 |pages=1024–1027 |bibcode=2004Natur.432.1024H |doi=10.1038/nature03084 |issn=0028-0836 |pmid=15616562 |s2cid=4417867 |display-authors=3}}</ref>

== Natural outcomes ==

[[File:Kishony lab-The Evolution of Bacteria on a Mega-Plate.webm|thumb|upright=1.5|thumbtime=106|A visual demonstration of rapid [[antibiotic resistance]] evolution by ''E. coli'' growing across a plate with increasing concentrations of [[trimethoprim]]<ref>{{Cite journal |last1=Baym |first1=Michael |last2=Lieberman |first2=Tami D. |last3=Kelsic |first3=Eric D. |last4=Chait |first4=Remy |last5=Gross |first5=Rotem |last6=Yelin |first6=Idan |last7=Kishony |first7=Roy |display-authors=3 |date=9 September 2016 |title=Spatiotemporal microbial evolution on antibiotic landscapes |journal=Science |language=en |volume=353 |issue=6304 |pages=1147–1151 |doi=10.1126/science.aag0822 |issn=0036-8075 |pmid=27609891 |pmc=5534434 |bibcode=2016Sci...353.1147B}}</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>

A common misconception is that evolution has goals, long-term plans, or an innate tendency for "progress", as expressed in beliefs such as [[orthogenesis]] and evolutionism; realistically, however, evolution has no long-term goal and does not necessarily produce greater complexity.<ref name="Dougherty-1998">{{cite journal |last=Dougherty |first=Michael J. |date=20 July 1998 |title=Is the human race evolving or devolving? |url=http://www.scientificamerican.com/article/is-the-human-race-evolvin/ |journal=Scientific American |issn=0036-8733 |access-date=11 September 2015 |url-status=live |archive-url=https://wayback.archive-it.org/all/20140506224205/http://www.scientificamerican.com/article/is-the-human-race-evolvin/ |archive-date=6 May 2014}}</ref><ref>{{cite web |url=http://www.talkorigins.org/indexcc/CB/CB932.html |title=Claim CB932: Evolution of degenerate forms |date=22 July 2003 |editor-last=Isaak |editor-first=Mark |website=[[TalkOrigins Archive]] |publisher=The TalkOrigins Foundation |location=Houston, Texas |access-date=19 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20140823062949/http://www.talkorigins.org/indexcc/CB/CB932.html |archive-date=23 August 2014}}</ref><ref>{{harvnb|Lane|1996|p=61}}</ref> Although [[Evolution of biological complexity|complex species]] have evolved, they occur as a side effect of the overall number of organisms increasing, and simple forms of life still remain more common in the biosphere.<ref name="Carroll-2001">{{cite journal |last=Carroll |first=Sean B. |author-link=Sean B. Carroll |date=22 February 2001 |title=Chance and necessity: the evolution of morphological complexity and diversity |url=https://archive.org/details/sim_nature-uk_2001-02-22_409_6823/page/1102 |journal=Nature |volume=409 |issue=6823 |pages=1102–1109 |bibcode=2001Natur.409.1102C |doi=10.1038/35059227 |pmid=11234024 |s2cid=4319886}}</ref> For example, the overwhelming majority of species are microscopic [[prokaryote]]s, which form about half the world's [[Biomass (ecology)|biomass]] despite their small size<ref>{{cite journal |last1=Whitman |first1=William B. |last2=Coleman |first2=David C. |last3=Wiebe |first3=William J. |date=9 June 1998 |title=Prokaryotes: The unseen majority |journal=PNAS |volume=95 |issue=12 |pages=6578–6583 |bibcode=1998PNAS...95.6578W |doi=10.1073/pnas.95.12.6578 |issn=0027-8424 |pmc=33863 |pmid=9618454 |doi-access=free}}</ref> and constitute the vast majority of Earth's biodiversity.<ref name="Schloss-2004">{{cite journal |last1=Schloss |first1=Patrick D. |last2=Handelsman |first2=Jo |author-link2=Jo Handelsman |date=December 2004 |title=Status of the Microbial Census |journal=[[Microbiology and Molecular Biology Reviews]] |volume=68 |issue=4 |pages=686–691 |doi=10.1128/MMBR.68.4.686-691.2004 |pmc=539005 |pmid=15590780}}</ref> Simple organisms have therefore been the dominant form of life on Earth throughout its history and continue to be the main form of life up to the present day, with complex life only appearing more diverse because it is [[Sampling bias|more noticeable]].<ref>{{cite journal |last=Nealson |first=Kenneth H. |s2cid=12289639 |date=January 1999 |title=Post-Viking microbiology: new approaches, new data, new insights |url=https://archive.org/details/sim_origins-of-life-and-evolution-of-biospheres_1999-01_29_1/page/73 |journal=[[Origins of Life and Evolution of Biospheres]] |volume=29 |issue=1 |pages=73–93 |doi=10.1023/A:1006515817767 |issn=0169-6149 |pmid=11536899 |bibcode=1999OLEB...29...73N}}</ref> Indeed, the evolution of microorganisms is particularly important to evolutionary research since their rapid reproduction allows the study of [[experimental evolution]] and the observation of evolution and adaptation in real time.<ref name="Buckling-2009">{{cite journal |last1=Buckling |first1=Angus |last2=MacLean |first2=R. Craig |last3=Brockhurst |first3=Michael A. |last4=Colegrave |first4=Nick |s2cid=205216404 |date=12 February 2009 |title=The Beagle in a bottle |url=https://archive.org/details/sim_nature-uk_2009-02-12_457_7231/page/824 |journal=Nature |volume=457 |issue=7231 |pages=824–829 |bibcode=2009Natur.457..824B |doi=10.1038/nature07892 |issn=0028-0836 |pmid=19212400}}</ref><ref>{{cite journal |last1=Elena |first1=Santiago F. |last2=Lenski |first2=Richard E. |author-link2=Richard Lenski |date=June 2003 |title=Evolution experiments with microorganisms: the dynamics and genetic bases of adaptation |journal=Nature Reviews Genetics |volume=4 |issue=6 |pages=457–469 |doi=10.1038/nrg1088 |issn=1471-0056 |pmid=12776215 |s2cid=209727}}</ref>

=== Adaptation ===
{{further|Adaptation}}

[[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 is the process that makes organisms better suited to their habitat.<ref>{{harvnb|Mayr|1982|p=483}}: "Adaptation... could no longer be considered a static condition, a product of a creative past and became instead a continuing dynamic process."</ref><ref>The sixth edition of the ''Oxford Dictionary of Science'' (2010) defines ''adaptation'' as "Any change in the structure or functioning of successive generations of a population that makes it better suited to its environment."</ref> Also, the term adaptation may refer to a trait that is important for an organism's survival. For example, the adaptation of horses' teeth to the grinding of grass. By using the term ''adaptation'' for the evolutionary process and ''adaptive trait'' for the product (the bodily part or function), the two senses of the word may be distinguished. Adaptations are produced by natural selection.<ref>{{cite journal |last=Orr |first=H. Allen |date=February 2005 |title=The genetic theory of adaptation: a brief history |journal=Nature Reviews Genetics |volume=6 |issue=2 |pages=119–127 |doi=10.1038/nrg1523 |issn=1471-0056 |pmid=15716908 |s2cid=17772950}}</ref> The following definitions are due to Theodosius Dobzhansky:

# ''Adaptation'' is the evolutionary process whereby an organism becomes better able to live in its habitat or habitats.<ref>{{harvnb|Dobzhansky|1968|pp=1–34}}</ref>
# ''Adaptedness'' is the state of being adapted: the degree to which an organism is able to live and reproduce in a given set of habitats.<ref>{{harvnb|Dobzhansky|1970|pp=4–6, 79–82, 84–87}}</ref>
# An ''adaptive trait'' is an aspect of the developmental pattern of the organism which enables or enhances the probability of that organism surviving and reproducing.<ref>{{cite journal |last=Dobzhansky |first=Theodosius |date=March 1956 |title=Genetics of Natural Populations. XXV. Genetic Changes in Populations of ''Drosophila pseudoobscura'' and ''Drosophila persimilis'' in Some Localities in California |url=https://archive.org/details/sim_evolution_1956-03_10_1/page/82 |journal=Evolution |volume=10 |issue=1 |pages=82–92 |doi=10.2307/2406099 |issn=0014-3820 |jstor=2406099}}</ref>

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>

However, many traits that appear to be simple adaptations are in fact [[exaptation]]s: structures originally adapted for one function, but which coincidentally became somewhat useful for some other function in the process.{{sfn|Gould|2002|pp=1235–1236}} One example is the African lizard ''Holaspis guentheri'', which developed an extremely flat head for hiding in crevices, as can be seen by looking at its near relatives. However, in this species, the head has become so flattened that it assists in gliding from tree to tree—an exaptation.{{sfn|Gould|2002|pp=1235–1236}} Within cells, [[molecular machine]]s such as the bacterial [[flagella]]<ref>{{cite journal |last1=Pallen |first1=Mark J. |last2=Matzke |first2=Nicholas J. |date=October 2006 |title=From ''The Origin of Species'' to the origin of bacterial flagella |url=https://www.ocf.berkeley.edu/~matzke/matzke_cv/_pubs/Pallen_Matzke_2006_NRM_origin_flagella.pdf |type=PDF |journal=Nature Reviews Microbiology |volume=4 |issue=10 |pages=784–790 |doi=10.1038/nrmicro1493 |issn=1740-1526 |pmid=16953248 |s2cid=24057949 |access-date=25 December 2014 |archive-url=https://web.archive.org/web/20141226013207/https://www.ocf.berkeley.edu/~matzke/matzke_cv/_pubs/Pallen_Matzke_2006_NRM_origin_flagella.pdf |archive-date=26 December 2014}}</ref> and [[translocase of the inner membrane|protein sorting machinery]]<ref>{{cite journal |last1=Clements |first1=Abigail |last2=Bursac |first2=Dejan |last3=Gatsos |first3=Xenia |last4=Perry |first4=Andrew J. |last5=Civciristov |first5=Srgjan |last6=Celik |first6=Nermin |last7=Likic |first7=Vladimir A. |last8=Poggio |first8=Sebastian |last9=Jacobs-Wagner |first9=Christine |last10=Strugnell |first10=Richard A. |last11=Lithgow |first11=Trevor |date=15 September 2009 |title=The reducible complexity of a mitochondrial molecular machine |journal=PNAS |volume=106 |issue=37 |pages=15791–15795 |bibcode=2009PNAS..10615791C |doi=10.1073/pnas.0908264106 |pmid=19717453 |pmc=2747197 |display-authors=3 |doi-access=free}}</ref> evolved by the recruitment of several pre-existing proteins that previously had different functions.<ref name="Scott-2007" /> Another example is the recruitment of enzymes from [[glycolysis]] and [[xenobiotic metabolism]] to serve as structural proteins called [[crystallin]]s within the lenses of organisms' eyes.<ref>{{harvnb|Piatigorsky|Kantorow|Gopal-Srivastava|Tomarev|1994|pp=241–250}}</ref><ref>{{cite journal |last=Wistow |first=Graeme |date=August 1993 |title=Lens crystallins: gene recruitment and evolutionary dynamism |url=https://archive.org/details/sim_trends-in-biochemical-sciences_1993-08_18_8/page/301 |journal=Trends in Biochemical Sciences |volume=18 |issue=8 |pages=301–306 |doi=10.1016/0968-0004(93)90041-K |issn=0968-0004 |pmid=8236445}}</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>

=== Coevolution ===
{{Further|Coevolution}}
[[File:Thamnophis sirtalis sirtalis Wooster.jpg|thumb|The [[common garter snake]] has evolved resistance to the [[anti-predator adaptation|defensive substance]] [[tetrodotoxin]] in its amphibian prey.]]

Interactions between organisms can produce both conflict and cooperation. When the interaction is between pairs of species, such as a [[pathogen]] and a [[host (biology)|host]], or a predator and its prey, these species can develop matched sets of adaptations. Here, the evolution of one species causes adaptations in a second species. These changes in the second species then, in turn, cause new adaptations in the first species. This cycle of selection and response is called coevolution.<ref>{{cite journal |last=Wade |first=Michael J. |s2cid=36705246 |author-link=Michael J. Wade |date=March 2007 |title=The co-evolutionary genetics of ecological communities |journal=Nature Reviews Genetics |volume=8 |issue=3 |pages=185–195 |doi=10.1038/nrg2031 |pmid=17279094}}</ref> An example is the production of [[tetrodotoxin]] in the [[rough-skinned newt]] and the evolution of tetrodotoxin resistance in its predator, the [[common garter snake]]. In this predator-prey pair, an [[evolutionary arms race]] has produced high levels of toxin in the newt and correspondingly high levels of toxin resistance in the snake.<ref>{{cite journal |last1=Geffeney |first1=Shana |last2=Brodie |first2=Edmund D. Jr. |last3=Ruben |first3=Peter C. |last4=Brodie |first4=Edmund D. III |s2cid=8816337 |date=23 August 2002 |title=Mechanisms of Adaptation in a Predator-Prey Arms Race: TTX-Resistant Sodium Channels |journal=Science |volume=297 |issue=5585 |pages=1336–1339 |bibcode=2002Sci...297.1336G |doi=10.1126/science.1074310 |pmid=12193784}}
* {{cite journal |last1=Brodie |first1=Edmund D. Jr. |last2=Ridenhour |first2=Benjamin J. |last3=Brodie |first3=Edmund D. III |date=October 2002 |title=The evolutionary response of predators to dangerous prey: hotspots and coldspots in the geographic mosaic of coevolution between garter snakes and newts |url=https://archive.org/details/sim_evolution_2002-10_56_10/page/2067 |journal=Evolution |volume=56 |issue=10 |pages=2067–2082 |doi=10.1554/0014-3820(2002)056[2067:teropt]2.0.co;2 |pmid=12449493 |s2cid=8251443 |ref=none}}
* {{cite news |last=Carroll |first=Sean B. |date=21 December 2009 |title=Whatever Doesn't Kill Some Animals Can Make Them Deadly |url=https://www.nytimes.com/2009/12/22/science/22creature.html |url-access=subscription |newspaper=The New York Times |location=New York |access-date=26 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20150423075609/http://www.nytimes.com/2009/12/22/science/22creature.html |archive-date=23 April 2015 |ref=none}}</ref>

=== Cooperation ===
{{Further|Co-operation (evolution)}}

Not all co-evolved interactions between species involve conflict.<ref>{{cite journal |last=Sachs |first=Joel L. |date=September 2006 |title=Cooperation within and among species |journal=Journal of Evolutionary Biology |volume=19 |issue=5 |pages=1415–1418; discussion 1426–1436 |doi=10.1111/j.1420-9101.2006.01152.x |pmid=16910971 |s2cid=4828678}}
* {{cite journal |last=Nowak |first=Martin A. |author-link=Martin Nowak |date=8 December 2006 |title=Five Rules for the Evolution of Cooperation |journal=Science |volume=314 |issue=5805 |pages=1560–1563 |bibcode=2006Sci...314.1560N |doi=10.1126/science.1133755 |pmc=3279745 |pmid=17158317 |ref=none}}</ref> Many cases of mutually beneficial interactions have evolved. For instance, an extreme cooperation exists between plants and the [[mycorrhiza]]l fungi that grow on their roots and aid the plant in absorbing nutrients from the soil.<ref>{{cite journal |last=Paszkowski |first=Uta |date=August 2006 |title=Mutualism and parasitism: the yin and yang of plant symbioses |journal=Current Opinion in Plant Biology |volume=9 |issue=4 |pages=364–370 |doi=10.1016/j.pbi.2006.05.008 |issn=1369-5266 |pmid=16713732 |bibcode=2006COPB....9..364P}}</ref> This is a [[Reciprocity (evolution)|reciprocal]] relationship as the plants provide the fungi with sugars from [[photosynthesis]]. Here, the fungi actually grow inside plant cells, allowing them to exchange nutrients with their hosts, while sending [[signal transduction|signals]] that suppress the plant [[immune system]].<ref>{{cite journal |last1=Hause |first1=Bettina |last2=Fester |first2=Thomas |s2cid=20082902 |date=May 2005 |title=Molecular and cell biology of arbuscular mycorrhizal symbiosis |journal=[[Planta (journal)|Planta]] |volume=221 |issue=2 |pages=184–196 |doi=10.1007/s00425-004-1436-x |pmid=15871030 |bibcode=2005Plant.221..184H}}</ref>

Coalitions between organisms of the same species have also evolved. An extreme case is the [[eusociality]] found in social insects, such as [[bee]]s, [[termite]]s and [[ant]]s, where sterile insects feed and guard the small number of organisms in a [[Colony (biology)|colony]] that are able to reproduce. On an even smaller scale, the somatic cells that make up the body of an animal limit their reproduction so they can maintain a stable organism, which then supports a small number of the animal's germ cells to produce offspring. Here, somatic cells respond to specific signals that instruct them whether to grow, remain as they are, or die. If cells ignore these signals and multiply inappropriately, their uncontrolled growth [[carcinogenesis|causes cancer]].<ref name="Bertram-2000">{{cite journal |last=Bertram |first=John S. |date=December 2000 |title=The molecular biology of cancer |journal=[[Molecular Aspects of Medicine]] |volume=21 |issue=6 |pages=167–223 |doi=10.1016/S0098-2997(00)00007-8 |pmid=11173079 |s2cid=24155688}}</ref>

Such cooperation within species may have evolved through the process of [[kin selection]], which is where one organism acts to help raise a relative's offspring.<ref>{{cite journal |last1=Reeve |first1=H. Kern |last2=Hölldobler |first2=Bert |author-link2=Bert Hölldobler |date=5 June 2007 |title=The emergence of a superorganism through intergroup competition |journal=PNAS |volume=104 |issue=23 |pages=9736–9740 |bibcode=2007PNAS..104.9736R |doi=10.1073/pnas.0703466104 |issn=0027-8424 |pmc=1887545 |pmid=17517608 |doi-access=free}}</ref> This activity is selected for because if the ''helping'' individual contains alleles which promote the helping activity, it is likely that its kin will ''also'' contain these alleles and thus those alleles will be passed on.<ref>{{cite journal |last1=Axelrod |first1=Robert |last2=Hamilton |first2=W. D. |date=27 March 1981 |title=The evolution of cooperation |url=https://archive.org/details/sim_science_1981-03-27_211_4489/page/1390 |journal=Science |volume=211 |issue=4489 |pages=1390–1396 |bibcode=1981Sci...211.1390A |doi=10.1126/science.7466396 |pmid=7466396}}</ref> Other processes that may promote cooperation include group selection, where cooperation provides benefits to a group of organisms.<ref>{{cite journal |last1=Wilson |first1=Edward O. |last2=Hölldobler |first2=Bert |date=20 September 2005 |title=Eusociality: Origin and consequences |journal=PNAS |volume=102 |issue=38 |pages=13367–1371 |bibcode=2005PNAS..10213367W |doi=10.1073/pnas.0505858102 |pmc=1224642 |pmid=16157878 |doi-access=free}}</ref>

=== Speciation ===
{{Main|Speciation}}
{{further|Assortative mating|Panmixia}}

[[File:Speciation modes edit.svg|left|thumb|upright=1.6|The four geographic modes of [[speciation]]]]

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>

There are multiple ways to define the concept of "species". The choice of definition is dependent on the particularities of the species concerned.<ref name="de Queiroz-2005">{{cite journal |last=de Queiroz |first=Kevin |date=3 May 2005 |title=Ernst Mayr and the modern concept of species |journal=PNAS |volume=102 |issue=Suppl. 1 |pages=6600–6607 |bibcode=2005PNAS..102.6600D |doi=10.1073/pnas.0502030102 |pmc=1131873 |pmid=15851674 |doi-access=free}}</ref> For example, some species concepts apply more readily toward sexually reproducing organisms while others lend themselves better toward asexual organisms. Despite the diversity of various species concepts, these various concepts can be placed into one of three broad philosophical approaches: interbreeding, ecological and phylogenetic.<ref name="Ereshefsky-1992">{{cite journal |last=Ereshefsky |first=Marc |author-link=Marc Ereshefsky |date=December 1992 |title=Eliminative pluralism |url=https://archive.org/details/sim_philosophy-of-science_1992-12_59_4/page/671 |journal=[[Philosophy of Science (journal)|Philosophy of Science]] |volume=59 |issue=4 |pages=671–690 |doi=10.1086/289701 |jstor=188136 |s2cid=224829314}}</ref> The Biological Species Concept (BSC) is a classic example of the interbreeding approach. Defined by evolutionary biologist [[Ernst Mayr]] in 1942, the BSC states that "species are groups of actually or potentially interbreeding natural populations, which are reproductively isolated from other such groups."<ref>{{harvnb|Mayr|1942|p=120}}</ref> Despite its wide and long-term use, the BSC like other species concepts is not without controversy, for example, because genetic recombination among prokaryotes is not an intrinsic aspect of reproduction;<ref>{{cite journal |last1=Fraser |first1=Christophe |last2=Alm |first2=Eric J. |last3=Polz |first3=Martin F. |last4=Spratt |first4=Brian G. |last5=Hanage |first5=William P. |s2cid=15763831 |date=6 February 2009 |title=The Bacterial Species Challenge: Making Sense of Genetic and Ecological Diversity |journal=Science |volume=323 |issue=5915 |pages=741–746 |bibcode=2009Sci...323..741F |doi=10.1126/science.1159388 |pmid=19197054 |display-authors=3}}</ref> this is called the [[species problem]].<ref name="de Queiroz-2005" /> Some researchers have attempted a unifying monistic definition of species, while others adopt a pluralistic approach and suggest that there may be different ways to logically interpret the definition of a species.<ref name="de Queiroz-2005" /><ref name="Ereshefsky-1992" />

[[Reproductive isolation|Barriers to reproduction]] between two diverging sexual populations are required for the populations to become new species. Gene flow may slow this process by spreading the new genetic variants also to the other populations. Depending on how far two species have diverged since their [[most recent common ancestor]], it may still be possible for them to produce offspring, as with horses and donkeys mating to produce [[mule]]s.<ref>{{cite journal |last=Short |first=Roger Valentine |date=October 1975 |title=The contribution of the mule to scientific thought |journal=Journal of Reproduction and Fertility. Supplement |issue=23 |pages=359–364 |oclc=1639439 |pmid=1107543}}</ref> Such hybrids are generally [[infertile]]. In this case, closely related species may regularly interbreed, but hybrids will be selected against and the species will remain distinct. However, viable hybrids are occasionally formed and these new species can either have properties intermediate between their parent species, or possess a totally new phenotype.<ref>{{cite journal |last1=Gross |first1=Briana L. |last2=Rieseberg |first2=Loren H. |date=May–June 2005 |title=The Ecological Genetics of Homoploid Hybrid Speciation |journal=Journal of Heredity |volume=96 |issue=3 |pages=241–252 |doi=10.1093/jhered/esi026 |issn=0022-1503 |pmc=2517139 |pmid=15618301}}</ref> The importance of hybridisation in producing [[hybrid speciation|new species]] of animals is unclear, although cases have been seen in many types of animals,<ref>{{cite journal |last1=Burke |first1=John M. |last2=Arnold |first2=Michael L. |s2cid=26683922 |date=December 2001 |title=Genetics and the fitness of hybrids |journal=[[Annual Review of Genetics]] |volume=35 |pages=31–52 |doi=10.1146/annurev.genet.35.102401.085719 |issn=0066-4197 |pmid=11700276}}</ref> with the [[grey tree frog]] being a particularly well-studied example.<ref>{{cite journal |last=Vrijenhoek |first=Robert C. |s2cid=11657663 |date=4 April 2006 |title=Polyploid Hybrids: Multiple Origins of a Treefrog Species |journal=Current Biology |volume=16 |issue=7 |pages=R245–R247 |doi=10.1016/j.cub.2006.03.005 |issn=0960-9822 |pmid=16581499 |doi-access=free |bibcode=2006CBio...16.R245V}}</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=Jiggins |first1=Chris D. |last2=Bridle |first2=Jon R. |date=March 2004 |title=Speciation in the apple maggot fly: a blend of vintages? |journal=Trends in Ecology & Evolution |volume=19 |issue=3 |pages=111–114 |doi=10.1016/j.tree.2003.12.008 |pmid=16701238 |issn=0169-5347 |ref=none}}
* {{cite web |url=http://www.talkorigins.org/faqs/faq-speciation.html |title=Observed Instances of Speciation |last=Boxhorn |first=Joseph |date=1 September 1995 |website=TalkOrigins Archive |publisher=The TalkOrigins Foundation, Inc. |location=Houston, Texas |access-date=26 December 2008 |url-status=live |archive-url=https://web.archive.org/web/20090122211743/http://talkorigins.org/faqs/faq-speciation.html |archive-date=22 January 2009 |ref=none}}
* {{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 second mode of speciation is [[peripatric speciation]], which occurs when small populations of organisms become isolated in a new environment. This differs from allopatric speciation in that the isolated populations are numerically much smaller than the parental population. Here, the [[founder effect]] causes rapid speciation after an increase in [[inbreeding]] increases selection on homozygotes, leading to rapid genetic change.<ref>{{cite journal |last=Templeton |first=Alan R. |author-link=Alan Templeton |date=April 1980 |title=The Theory of Speciation ''VIA'' the Founder Principle |url=http://www.genetics.org/content/94/4/1011.full.pdf+html |journal=Genetics |volume=94 |issue=4 |pages=1011–1038 |doi=10.1093/genetics/94.4.1011 |pmid=6777243 |pmc=1214177 |access-date=29 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20140823063455/http://www.genetics.org/content/94/4/1011.full.pdf+html |archive-date=23 August 2014}}</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>

[[File:Darwin's finches.jpeg|frame|[[Geographical isolation]] of [[Darwin's finches|finches]] on the [[Galápagos Islands]] produced over a dozen new species.]]

Finally, in [[sympatric speciation]] species diverge without geographic isolation or changes in habitat. This form is rare since even a small amount of gene flow may remove genetic differences between parts of a population.<ref>{{cite journal |author1-link=Vincent Savolainen |last1=Savolainen |first1=Vincent |last2=Anstett |first2=Marie-Charlotte |last3=Lexer |first3=Christian |last4=Hutton |first4=Ian |last5=Clarkson |first5=James J. |last6=Norup |first6=Maria V. |last7=Powell |first7=Martyn P. |last8=Springate |first8=David |last9=Salamin |first9=Nicolas |last10=Baker |first10=William J. |date=11 May 2006 |title=Sympatric speciation in palms on an oceanic island |url=https://archive.org/details/sim_nature-uk_2006-05-11_441_7090/page/210 |journal=Nature |volume=441 |issue=7090 |pages=210–213 |bibcode=2006Natur.441..210S |doi=10.1038/nature04566 |issn=0028-0836 |pmid=16467788 |s2cid=867216 |display-authors=3}}
* {{cite journal |last1=Barluenga |first1=Marta |last2=Stölting |first2=Kai N. |last3=Salzburger |first3=Walter |last4=Muschick |first4=Moritz |last5=Meyer |first5=Axel |s2cid=3165729 |author-link5=Axel Meyer |date=9 February 2006 |title=Sympatric speciation in Nicaraguan crater lake cichlid fish |journal=Nature |volume=439 |issue=7077 |pages=719–723 |bibcode=2006Natur.439..719B |doi=10.1038/nature04325 |issn=0028-0836 |pmid=16467837 |display-authors=3 |url=http://nbn-resolving.de/urn:nbn:de:bsz:352-opus-34004 |ref=none |access-date=30 July 2022 |archive-date=30 July 2022 |archive-url=https://web.archive.org/web/20220730090843/http://kops.uni-konstanz.de/handle/123456789/6577 |url-status=live}}</ref> Generally, sympatric speciation in animals requires the evolution of both [[Polymorphism (biology)|genetic differences]] and nonrandom mating, to allow reproductive isolation to evolve.<ref>{{cite journal |last=Gavrilets |first=Sergey |date=21 March 2006 |title=The Maynard Smith model of sympatric speciation |journal=Journal of Theoretical Biology |volume=239 |issue=2 |pages=172–182 |doi=10.1016/j.jtbi.2005.08.041 |issn=0022-5193 |pmid=16242727 |bibcode=2006JThBi.239..172G}}</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>

Speciation events are important in the theory of [[punctuated equilibrium]], which accounts for the pattern in the fossil record of short "bursts" of evolution interspersed with relatively long periods of stasis, where species remain relatively unchanged.<ref>{{harvnb|Eldredge|Gould|1972|pp=82–115}}</ref> In this theory, speciation and [[Contemporary evolution|rapid evolution]] are linked, with natural selection and genetic drift acting most strongly on organisms undergoing speciation in novel habitats or small populations. As a result, the periods of stasis in the fossil record correspond to the parental population and the organisms undergoing speciation and rapid evolution are found in small populations or geographically restricted habitats and therefore rarely being preserved as fossils.<ref name="Gould_1994" />

=== Extinction ===
{{Further|Extinction}}
[[File:Palais de la Decouverte Tyrannosaurus rex p1050042.jpg|thumb|left|''[[Tyrannosaurus rex]]''. Non-[[bird|avian]] dinosaurs died out in the [[Cretaceous–Paleogene extinction event]] at the end of the [[Cretaceous]] period.]]

Extinction is the disappearance of an entire species. Extinction is not an unusual event, as species regularly appear through speciation and disappear through extinction.<ref>{{cite journal |last1=Benton |first1=Michael J. |author-link=Michael Benton |date=7 April 1995 |title=Diversification and extinction in the history of life |url=https://archive.org/details/sim_science_1995-04-07_268_5207/page/52 |journal=Science |volume=268 |issue=5207 |pages=52–58 |bibcode=1995Sci...268...52B |doi=10.1126/science.7701342 |issn=0036-8075 |pmid=7701342}}</ref> Nearly all animal and plant species that have lived on Earth are now extinct,<ref>{{cite journal |last=Raup |first=David M. |s2cid=23012011 |author-link=David M. Raup |date=28 March 1986 |title=Biological extinction in Earth history |journal=Science |volume=231 |issue=4745 |pages=1528–1533 |bibcode=1986Sci...231.1528R |doi=10.1126/science.11542058 |pmid=11542058}}</ref> and extinction appears to be the ultimate fate of all species.<ref>{{cite journal |last1=Avise |first1=John C. |last2=Hubbell |first2=Stephen P. |author-link2=Stephen P. Hubbell |last3=Ayala |first3=Francisco J. |date=12 August 2008 |title=In the light of evolution II: Biodiversity and extinction |journal=PNAS |volume=105 |issue=Suppl. 1 |pages=11453–11457 |bibcode=2008PNAS..10511453A |doi=10.1073/pnas.0802504105 |pmc=2556414 |pmid=18695213 |doi-access=free}}</ref> These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass [[extinction event]]s.<ref name="Raup-1994">{{cite journal |last=Raup |first=David M. |date=19 July 1994 |title=The role of extinction in evolution |journal=PNAS |volume=91 |issue=15 |pages=6758–6763 |bibcode=1994PNAS...91.6758R |doi=10.1073/pnas.91.15.6758 |pmc=44280 |pmid=8041694 |doi-access=free}}</ref> The [[Cretaceous–Paleogene extinction event]], during which the non-avian dinosaurs became extinct, is the most well-known, but the earlier [[Permian–Triassic extinction event]] was even more severe, with approximately 96% of all marine species driven to extinction.<ref name="Raup-1994" /> The [[Holocene extinction]] event is an ongoing mass extinction associated with humanity's expansion across the globe over the past few thousand years. Present-day extinction rates are 100–1000 times greater than the background rate and up to 30% of current species may be extinct by the mid 21st century.<ref>{{cite journal |last1=Novacek |first1=Michael J. |last2=Cleland |first2=Elsa E. |date=8 May 2001 |title=The current biodiversity extinction event: scenarios for mitigation and recovery |doi=10.1073/pnas.091093698 |journal=PNAS |volume=98 |issue=10 |pages=5466–5470 |bibcode=2001PNAS...98.5466N |issn=0027-8424 |pmc=33235 |pmid=11344295 |doi-access=free}}</ref> Human activities are now the primary cause of the ongoing extinction event;<ref>{{cite journal |last1=Pimm |first1=Stuart |author-link1=Stuart Pimm |last2=Raven |first2=Peter |author-link2=Peter H. Raven |last3=Peterson |first3=Alan |last4=Şekercioğlu |first4=Çağan H. |last5=Ehrlich |first5=Paul R. |author-link5=Paul R. Ehrlich |date=18 July 2006 |title=Human impacts on the rates of recent, present and future bird extinctions |journal=PNAS |volume=103 |issue=29 |pages=10941–10946 |bibcode=2006PNAS..10310941P |doi=10.1073/pnas.0604181103 |issn=0027-8424 |pmc=1544153 |pmid=16829570 |display-authors=3 |doi-access=free}}</ref><ref>{{cite journal |last1=Barnosky |first1=Anthony D. |author-link1=Anthony David Barnosky |last2=Koch |first2=Paul L. |last3=Feranec |first3=Robert S. |last4=Wing |first4=Scott L. |last5=Shabel |first5=Alan B. |date=1 October 2004 |title=Assessing the Causes of Late Pleistocene Extinctions on the Continents |journal=Science |volume=306 |issue=5693 |pages=70–75 |bibcode=2004Sci...306...70B |doi=10.1126/science.1101476 |issn=0036-8075 |pmid=15459379 |display-authors=3 |citeseerx=10.1.1.574.332 |s2cid=36156087}}</ref> [[global warming]] may further accelerate it in the future.<ref>{{cite journal |last1=Lewis |first1=Owen T. |date=29 January 2006 |title=Climate change, species–area curves and the extinction crisis |journal=Philosophical Transactions of the Royal Society B |volume=361 |issue=1465 |pages=163–171 |doi=10.1098/rstb.2005.1712 |issn=0962-8436 |pmc=1831839 |pmid=16553315}}</ref> Despite the estimated extinction of more than 99% of all species that ever lived on Earth,<ref name="Stearns-1999">{{harvnb|Stearns|Stearns|1999|p=[https://books.google.com/books?id=0BHeC-tXIB4C&q=99%20percent X]}}</ref><ref name="Novacek-2014" /> about 1&nbsp;trillion species are estimated to be on Earth currently with only one-thousandth of 1% described.<ref name="NSF-2016">{{cite web |url=https://www.nsf.gov/news/news_summ.jsp?cntn_id=138446 |title=Researchers find that Earth may be home to 1 trillion species |author=<!--Not stated--> |date=2 May 2016 |website=[[National Science Foundation]] |location=Arlington County, Virginia |access-date=6 May 2016 |url-status=live |archive-url=https://web.archive.org/web/20160504111108/https://www.nsf.gov/news/news_summ.jsp?cntn_id=138446 |archive-date=4 May 2016}}</ref>

The role of extinction in evolution is not very well understood and may depend on which type of extinction is considered.<ref name="Raup-1994" /> The causes of the continuous "low-level" extinction events, which form the majority of extinctions, may be the result of competition between species for limited resources (the [[competitive exclusion principle]]).<ref name="Kutschera-2004" /> If one species can out-compete another, this could produce species selection, with the fitter species surviving and the other species being driven to extinction.<ref name="Gould-1998" /> The intermittent mass extinctions are also important, but instead of acting as a selective force, they drastically reduce diversity in a nonspecific manner and promote bursts of rapid evolution and speciation in survivors.<ref>{{cite journal |last=Jablonski |first=David |date=8 May 2001 |title=Lessons from the past: Evolutionary impacts of mass extinctions |journal=PNAS |volume=98 |issue=10 |pages=5393–5398 |bibcode=2001PNAS...98.5393J |doi=10.1073/pnas.101092598 |pmc=33224 |pmid=11344284 |doi-access=free}}</ref>
{{Clear}}

== Applications ==
{{Main|Applications of evolution|Selective breeding|Evolutionary computation}}

Concepts and models used in evolutionary biology, such as natural selection, have many applications.<ref name="Bull-2001">{{cite journal |last1=Bull |first1=James J. |author-link1=James J. Bull |last2=Wichman |first2=Holly A. |date=November 2001 |title=Applied evolution |journal=Annual Review of Ecology and Systematics |volume=32 |issue=1 |pages=183–217 |doi=10.1146/annurev.ecolsys.32.081501.114020 |bibcode=2001AnRES..32..183B |issn=1545-2069}}</ref>

Artificial selection is the intentional selection of traits in a population of organisms. This has been used for thousands of years in the [[domestication]] of plants and animals.<ref>{{cite journal |last1=Doebley |first1=John F. |last2=Gaut |first2=Brandon S. |last3=Smith |first3=Bruce D. |author-link3=Bruce D. Smith |date=29 December 2006 |title=The Molecular Genetics of Crop Domestication |journal=Cell |volume=127 |issue=7 |pages=1309–1321 |doi=10.1016/j.cell.2006.12.006 |issn=0092-8674 |pmid=17190597 |s2cid=278993 |doi-access=free}}</ref> More recently, such selection has become a vital part of [[genetic engineering]], with [[selectable marker]]s such as antibiotic resistance genes being used to manipulate DNA. Proteins with valuable properties have evolved by repeated rounds of mutation and selection (for example modified enzymes and new [[antibodies]]) in a process called [[directed evolution]].<ref>{{cite journal |last1=Jäckel |first1=Christian |last2=Kast |first2=Peter |last3=Hilvert |first3=Donald |date=June 2008 |title=Protein Design by Directed Evolution |journal=[[Annual Review of Biophysics]] |volume=37 |pages=153–173 |doi=10.1146/annurev.biophys.37.032807.125832 |issn=1936-122X |pmid=18573077}}</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 |article-number=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 |article-number=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 |article-number=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 |article-number=e1000058 |doi=10.1371/journal.pbio.1000058 |pmid=19355786 |pmc=3279047 |doi-access=free}}</ref>

In [[computer science]], simulations of evolution using [[evolutionary algorithm]]s and [[artificial life]] started in the 1960s and were extended with simulation of artificial selection.<ref>{{cite journal |last=Fraser |first=Alex S. |s2cid=4211563 |author-link=Alex Fraser (scientist) |date=18 January 1958 |title=Monte Carlo Analyses of Genetic Models |url=https://archive.org/details/sim_nature-uk_1958-01-18_181_4603/page/208 |journal=Nature |volume=181 |issue=4603 |pages=208–209 |bibcode=1958Natur.181..208F |doi=10.1038/181208a0 |issn=0028-0836 |pmid=13504138}}</ref> Artificial evolution became a widely recognised optimisation method as a result of the work of [[Ingo Rechenberg]] in the 1960s. He used [[evolution strategies]] to solve complex engineering problems.<ref>{{harvnb|Rechenberg|1973}}</ref> [[Genetic algorithm]]s in particular became popular through the writing of [[John Henry Holland]].<ref>{{harvnb|Holland|1975}}</ref> Practical applications also include [[genetic programming|automatic evolution of computer programmes]].<ref>{{harvnb|Koza|1992}}</ref> Evolutionary algorithms are now used to solve multi-dimensional problems more efficiently than software produced by human designers and also to optimise the design of systems.<ref>{{cite journal |last=Jamshidi |first=Mo |s2cid=34259612 |date=15 August 2003 |title=Tools for intelligent control: fuzzy controllers, neural networks and genetic algorithms |journal=[[Philosophical Transactions of the Royal Society A]] |volume=361 |issue=1809 |pages=1781–1808 |bibcode=2003RSPTA.361.1781J |doi=10.1098/rsta.2003.1225 |pmid=12952685}}</ref>

== Evolutionary history of life ==

{{align|right|{{Life timeline}} }}
{{Main|Evolutionary history of life}}
{{See also|Timeline of the evolutionary history of life}}

=== Origin of life ===
{{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=https://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 |article-number=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.

Highly energetic chemistry is thought to have produced a self-replicating molecule around 4&nbsp;billion years ago, and half a billion years later the last common ancestor of all life existed.<ref name="Doolittle-2000" /> The current scientific consensus is that the complex biochemistry that makes up life came from simpler chemical reactions.<ref>{{cite journal |last=Peretó |first=Juli |date=March 2005 |title=Controversies on the origin of life |url=http://www.im.microbios.org/0801/0801023.pdf |journal=International Microbiology |volume=8 |issue=1 |pages=23–31 |issn=1139-6709 |pmid=15906258 |archive-url=https://web.archive.org/web/20150824074726/http://www.im.microbios.org/0801/0801023.pdf |archive-date=24 August 2015}}</ref><ref name="BBC-20201111">{{cite news |last=Marshall |first=Michael |title=Charles Darwin's hunch about early life was probably right – In a few scrawled notes to a friend, biologist Charles Darwin theorised how life began. Not only was it probably correct, his theory was a century ahead of its time. |url=https://www.bbc.com/future/article/20201110-charles-darwin-early-life-theory |date=11 November 2020 |work=[[BBC News]] |access-date=11 November 2020 |archive-date=11 November 2020 |archive-url=https://web.archive.org/web/20201111015900/https://www.bbc.com/future/article/20201110-charles-darwin-early-life-theory |url-status=live}}</ref> The beginning of life may have included self-replicating molecules such as [[RNA]]<ref>{{cite journal |last=Joyce |first=Gerald F. |author-link=Gerald Joyce |date=11 July 2002 |title=The antiquity of RNA-based evolution |journal=Nature |volume=418 |issue=6894 |pages=214–221 |bibcode=2002Natur.418..214J |doi=10.1038/418214a |pmid=12110897 |s2cid=4331004}}</ref> and the assembly of simple cells.<ref>{{cite journal |last1=Trevors |first1=Jack T. |last2=Psenner |first2=Roland |date=December 2001 |title=From self-assembly of life to present-day bacteria: a possible role for nanocells |journal=FEMS Microbiology Reviews |volume=25 |issue=5 |pages=573–582 |doi=10.1111/j.1574-6976.2001.tb00592.x |issn=1574-6976 |pmid=11742692 |doi-access=free}}</ref>

=== Common descent ===
{{Further|Common descent|Evidence of common descent}}

All organisms on Earth are descended from a common ancestor or ancestral [[gene pool]].<ref name="Penny-1999" /><ref>{{cite journal |last=Theobald |first=Douglas L. |date=13 May 2010 |title=A formal test of the theory of universal common ancestry |url=https://archive.org/details/sim_nature-uk_2010-05-13_465_7295/page/219 |journal=Nature |volume=465 |issue=7295 |pages=219–222 |bibcode=2010Natur.465..219T |doi=10.1038/nature09014 |issn=0028-0836 |pmid=20463738 |s2cid=4422345}}</ref> Current species are a stage in the process of evolution, with their diversity the product of a long series of speciation and extinction events.<ref>{{cite journal |last1=Bapteste |first1=Eric |last2=Walsh |first2=David A. |date=June 2005 |title=Does the 'Ring of Life' ring true? |journal=[[Trends in Microbiology]] |volume=13 |issue=6 |pages=256–261 |doi=10.1016/j.tim.2005.03.012 |issn=0966-842X |pmid=15936656}}</ref> The common descent of organisms was first deduced from four simple facts about organisms: First, they have geographic distributions that cannot be explained by local adaptation. Second, the diversity of life is not a set of completely unique organisms, but organisms that share morphological similarities. Third, [[vestigial trait]]s with no clear purpose resemble functional ancestral traits. Fourth, organisms can be classified using these similarities into a hierarchy of nested groups, similar to a family tree.<ref>{{harvnb|Darwin|1859|p=[http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=16 1]}}</ref>

[[File:Ape skeletons.png|upright=1.5|thumb|left|The [[hominoids]] are descendants of a [[common ancestor]].]]

Due to horizontal gene transfer, this "tree of life" may be more complicated than a simple branching tree, since some genes have spread independently between distantly related species.<ref>{{cite journal |last1=Doolittle |first1=W. Ford |last2=Bapteste |first2=Eric |date=13 February 2007 |title=Pattern pluralism and the Tree of Life hypothesis |journal=PNAS |volume=104 |issue=7 |pages=2043–2049 |bibcode=2007PNAS..104.2043D |doi=10.1073/pnas.0610699104 |issn=0027-8424 |pmc=1892968 |pmid=17261804 |doi-access=free}}</ref><ref>{{cite journal |last1=Kunin |first1=Victor |last2=Goldovsky |first2=Leon |last3=Darzentas |first3=Nikos |last4=Ouzounis |first4=Christos A. |date=July 2005 |title=The net of life: Reconstructing the microbial phylogenetic network |journal=Genome Research |volume=15 |issue=7 |pages=954–959 |doi=10.1101/gr.3666505 |issn=1088-9051 |pmid=15965028 |pmc=1172039}}</ref> To solve this problem and others, some authors prefer to use the "[[Coral of life]]" as a metaphor or a mathematical model to illustrate the evolution of life. This view dates back to an idea briefly mentioned by Darwin but later abandoned.<ref name="Bnotebook">{{harvnb|Darwin|1837|p=[http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=CUL-DAR121.-&pageseq=27 25]}}</ref>

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.

More recently, evidence for common descent has come from the study of biochemical similarities between organisms. For example, all living cells use the same basic set of nucleotides and [[amino acid]]s.<ref>{{cite journal |last=Mason |first=Stephen F. |date=6 September 1984 |title=Origins of biomolecular handedness |url=https://archive.org/details/sim_nature-uk_1984-09-06_311_5981/page/19 |journal=Nature |volume=311 |issue=5981 |pages=19–23 |bibcode=1984Natur.311...19M |doi=10.1038/311019a0 |issn=0028-0836 |pmid=6472461 |s2cid=103653}}</ref> The development of [[molecular genetics]] has revealed the record of evolution left in organisms' genomes: dating when species diverged through the [[molecular clock]] produced by mutations.<ref>{{cite journal |last1=Wolf |first1=Yuri I. |last2=Rogozin |first2=Igor B. |last3=Grishin |first3=Nick V. |last4=Koonin |first4=Eugene V. |author-link4=Eugene Koonin |date=1 September 2002 |title=Genome trees and the tree of life |url=https://archive.org/details/sim_trends-in-genetics_2002-09_18_9/page/472 |journal=Trends in Genetics |volume=18 |issue=9 |pages=472–479 |doi=10.1016/S0168-9525(02)02744-0 |issn=0168-9525 |pmid=12175808}}</ref> For example, these DNA sequence comparisons have revealed that humans and chimpanzees share 98% of their genomes and analysing the few areas where they differ helps shed light on when the common ancestor of these species existed.<ref>{{cite journal |last1=Varki |first1=Ajit |author-link1=Ajit Varki |last2=Altheide |first2=Tasha K. |date=December 2005 |title=Comparing the human and chimpanzee genomes: searching for needles in a haystack |journal=Genome Research |volume=15 |issue=12 |pages=1746–1758 |doi=10.1101/gr.3737405 |issn=1088-9051 |pmid=16339373 |citeseerx=10.1.1.673.9212}}</ref>

=== Evolution of life ===
{{Main|Evolutionary history of life|Timeline of evolutionary history of life}}

{{PhylomapA|size=320px|align=right|caption=[[Evolutionary tree]] showing the divergence of modern species from their common ancestor in the centre.<ref name="Ciccarelli-2006">{{cite journal |last1=Ciccarelli |first1=Francesca D. |last2=Doerks |first2=Tobias |last3=von Mering |first3=Christian |last4=Creevey |first4=Christopher J. |last5=Snel |first5=Berend |last6=Bork |first6=Peer |s2cid=1615592 |author-link6=Peer Bork |date=3 March 2006 |title=Toward Automatic Reconstruction of a Highly Resolved Tree of Life |journal=Science |volume=311 |issue=5765 |pages=1283–1287 |bibcode=2006Sci...311.1283C |doi=10.1126/science.1123061 |issn=0036-8075 |pmid=16513982 |display-authors=3 |url=http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf |url-status=live |archive-url=https://web.archive.org/web/20160304035346/http://bioinformatics.bio.uu.nl/pdf/Ciccarelli.s06-311.pdf |archive-date=4 March 2016 |citeseerx=10.1.1.381.9514}}</ref> The three [[Domain (biology)|domains]] are coloured, with bacteria blue, [[archaea]] green and [[eukaryote]]s red.}}
Prokaryotes inhabited the Earth from approximately 3–4&nbsp;billion years ago.<ref name="Cavalier-Smith-2006">{{cite journal |last=Cavalier-Smith |first=Thomas |author-link=Thomas Cavalier-Smith |date=29 June 2006 |title=Cell evolution and Earth history: stasis and revolution |journal=Philosophical Transactions of the Royal Society B |volume=361 |issue=1470 |pages=969–1006 |doi=10.1098/rstb.2006.1842 |issn=0962-8436 |pmc=1578732 |pmid=16754610}}</ref><ref>{{cite journal |last=Schopf |first=J. William |date=29 June 2006 |title=Fossil evidence of Archaean life |journal=Philosophical Transactions of the Royal Society B |volume=361 |issue=1470 |pages=869–885 |doi=10.1098/rstb.2006.1834 |pmc=1578735 |pmid=16754604}}
* {{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 |last=McFadden |first=Geoffrey Ian |date=1 December 1999 |title=Endosymbiosis and evolution of the plant cell |journal=Current Opinion in Plant Biology |volume=2 |issue=6 |pages=513–519 |doi=10.1016/S1369-5266(99)00025-4 |pmid=10607659 |bibcode=1999COPB....2..513M |ref=none}}</ref>

The history of life was that of the [[unicellular]] eukaryotes, prokaryotes and archaea until around 1.7&nbsp;billion years ago, when [[multicellular organism]]s began to appear, with [[cellular differentiation|differentiated cells]] performing specialised functions.<ref name="Bonner1999">{{cite journal |last=Bonner |first=John Tyler |author-link=John Tyler Bonner |date=7 January 1998 |title=The origins of multicellularity |journal=[[Integrative Biology]] |volume=1 |issue=1 |pages=27–36 |doi=10.1002/(SICI)1520-6602(1998)1:1<27::AID-INBI4>3.0.CO;2-6 |issn=1757-9694}}</ref> The [[evolution of multicellularity]] occurred in multiple independent events, in organisms as diverse as [[sponge]]s, [[brown algae]], cyanobacteria, [[slime moulds]] and [[myxobacteria]].<ref>{{cite journal |last=Kaiser |first=Dale |s2cid=18276422 |author-link=A. Dale Kaiser |date=December 2001 |title=Building a multicellular organism |journal=[[Annual Review of Genetics]] |volume=35 |pages=103–123 |doi=10.1146/annurev.genet.35.102401.090145 |issn=0066-4197 |pmid=11700279}}</ref> In January 2016, scientists reported that, about 800&nbsp;million years ago, a minor genetic change in a single molecule called GK-PID may have allowed organisms to go from a single cell organism to one of many cells.<ref name="Zimmer-2016">{{cite news |last=Zimmer |first=Carl |author-link=Carl Zimmer |title=Genetic Flip Helped Organisms Go From One Cell to Many |url=https://www.nytimes.com/2016/01/12/science/genetic-flip-helped-organisms-go-from-one-cell-to-many.html |date=7 January 2016 |newspaper=The New York Times |issn=0362-4331 |access-date=7 January 2016 |url-status=live |archive-url=https://web.archive.org/web/20160107204432/http://www.nytimes.com/2016/01/12/science/genetic-flip-helped-organisms-go-from-one-cell-to-many.html |archive-date=7 January 2016}}</ref>

Approximately 538.8&nbsp;million years ago, a remarkable amount of biological diversity appeared over a span of around 10&nbsp;million years in what is called the [[Cambrian explosion]]. Here, the majority of [[Phylum|types]] of modern animals appeared in the fossil record, as well as unique lineages that subsequently became extinct.<ref name="Valentine-1999">{{cite journal |last1=Valentine |first1=James W. |author-link1=James W. Valentine |last2=Jablonski |first2=David |last3=Erwin |first3=Douglas H. |author-link3=Douglas Erwin |date=1 March 1999 |title=Fossils, molecules and embryos: new perspectives on the Cambrian explosion |url=http://dev.biologists.org/content/126/5/851.full.pdf+html |journal=[[Development (journal)|Development]] |volume=126 |issue=5 |pages=851–859 |doi=10.1242/dev.126.5.851 |issn=0950-1991 |pmid=9927587 |access-date=30 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20150301063309/http://dev.biologists.org/content/126/5/851.full.pdf+html |archive-date=1 March 2015|url-access=subscription }}</ref> Various triggers for the Cambrian explosion have been proposed, including the accumulation of oxygen in the atmosphere from photosynthesis.<ref>{{cite journal |last=Ohno |first=Susumu |s2cid=21879320 |date=January 1997 |title=The reason for as well as the consequence of the Cambrian explosion in animal evolution |journal=Journal of Molecular Evolution |volume=44 |issue=Suppl. 1 |pages=S23–S27 |doi=10.1007/PL00000055 |issn=0022-2844 |pmid=9071008 |bibcode=1997JMolE..44S..23O}}
* {{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" />

== History of evolutionary thought ==
<!-- Note, this section is too long to be presented first, so it has been moved down. If it is shortened to three paragraphs or fewer it could be moved back up. See the lead of History of evolutionary thought for ideas on how to do that. -->

{{Main|History of evolutionary thought}}
{{further|History of speciation}}

[[File:Lucretius Rome.jpg|thumb|upright|[[Lucretius]]]]
[[File:Alfred-Russel-Wallace-c1895.jpg|thumb|upright|[[Alfred Russel Wallace]]]]
[[File:Thomas Robert Malthus Wellcome L0069037 -crop.jpg|thumb|upright|[[Thomas Robert Malthus]]]]
[[File:Charles Darwin aged 51.jpg|thumb|upright|In 1842, [[Charles Darwin]] penned his first sketch of ''[[On the Origin of Species]]''.<ref>{{harvnb|Darwin|1909|p=53}}</ref>]]

=== Classical antiquity ===

The proposal that one type of organism could descend from another type goes back to some of the first [[pre-Socratic]] Greek philosophers, such as [[Anaximander#Origin of humankind|Anaximander]] and [[Empedocles#Cosmogony|Empedocles]].<ref>{{harvnb|Kirk|Raven|Schofield|1983|pp=100–142, 280–321}}</ref> Such proposals survived into Roman times. The poet and philosopher [[Lucretius]] followed Empedocles in his masterwork ''[[De rerum natura]]'' ({{lit|On the Nature of Things}}).<ref>{{harvnb|Lucretius}}</ref><ref>{{cite journal |last=Sedley |first=David |author-link=David Sedley |year=2003 |title=Lucretius and the New Empedocles |url=http://lics.leeds.ac.uk/2003/200304.pdf |journal=Leeds International Classical Studies |volume=2 |issue=4 |issn=1477-3643 |access-date=25 November 2014 |archive-url=https://web.archive.org/web/20140823062637/http://lics.leeds.ac.uk/2003/200304.pdf |archive-date=23 August 2014}}</ref>

=== Middle Ages ===

In contrast to these [[Materialism|materialistic]] views, [[Aristotelianism]] had considered all natural things as [[potentiality and actuality|actualisations]] of fixed natural possibilities, known as [[Theory of forms|forms]].<ref name="Torrey-1937">{{cite journal |last1=Torrey |first1=Harry Beal |last2=Felin |first2=Frances |date=March 1937 |title=Was Aristotle an Evolutionist? |url=https://archive.org/details/sim_quarterly-review-of-biology_1937-03_12_1/page/1 |journal=[[The Quarterly Review of Biology]] |volume=12 |issue=1 |pages=1–18 |doi=10.1086/394520 |issn=0033-5770 |jstor=2808399 |s2cid=170831302}}</ref><ref name="Hull-1967">{{cite journal |last=Hull |first=David L. |author-link=David Hull (philosopher) |date=December 1967 |title=The Metaphysics of Evolution |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=3 |issue=4 |pages=309–337 |doi=10.1017/S0007087400002892 |jstor=4024958 |s2cid=170328394}}</ref> This became part of a medieval [[teleological]] understanding of [[Nature (philosophy)|nature]] in which all things have an intended role to play in a [[divine]] [[cosmos|cosmic]] order. Variations of this idea became the standard understanding of the [[Middle Ages]] and were integrated into Christian learning, but Aristotle did not demand that real types of organisms always correspond one-for-one with exact metaphysical forms and specifically gave examples of how new types of living things could come to be.<ref>{{harvnb|Mason|1962|pp=43–44}}</ref>

A number of Arab Muslim scholars wrote about evolution, most notably [[Ibn Khaldun]], who wrote the book ''[[Muqaddimah]]'' in 1377, in which he asserted that humans developed from "the world of the monkeys", in a process by which "species become more numerous".<ref name="Kiros-2001">Kiros, Teodros. ''Explorations in African Political Thought''. 2001, page 55</ref>

=== Pre-Darwinian ===

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}}
* {{harvnb|Ray|1686}}</ref> The [[biological classification]] introduced by [[Carl Linnaeus]] in 1735 explicitly recognised the hierarchical nature of species relationships, but still viewed species as fixed according to a divine plan.<ref>{{cite web |url=http://www.ucmp.berkeley.edu/history/linnaeus.html |title=Carl Linnaeus (1707–1778) |last=Waggoner |first=Ben |date=7 July 2000 |website=Evolution |publisher=[[University of California Museum of Paleontology]] |location=Berkeley, California |type=Online exhibit |access-date=11 February 2012 |url-status=live |archive-url=https://web.archive.org/web/20110430160025/http://www.ucmp.berkeley.edu/history/linnaeus.html |archive-date=30 April 2011}}</ref>

Other [[naturalists]] of this time speculated on the evolutionary change of species over time according to natural laws. In 1751, [[Pierre Louis Maupertuis]] wrote of natural modifications occurring during reproduction and accumulating over many generations to produce new species.<ref>{{harvnb|Bowler|2003|pp=73–75}}</ref> [[Georges-Louis Leclerc, Comte de Buffon]], suggested that species could degenerate into different organisms, and [[Erasmus Darwin]] proposed that all warm-blooded animals could have descended from a single microorganism (or "filament").<ref>{{cite web |url=http://www.ucmp.berkeley.edu/history/Edarwin.html |title=Erasmus Darwin (1731–1802) |date=4 October 1995 |website=Evolution |publisher=University of California Museum of Paleontology |location=Berkeley, California |type=Online exhibit |access-date=11 February 2012 |url-status=live |archive-url=https://web.archive.org/web/20120119004316/http://www.ucmp.berkeley.edu/history/Edarwin.html |archive-date=19 January 2012}}</ref> The first full-fledged evolutionary scheme was [[Jean-Baptiste Lamarck]]'s "transmutation" theory of 1809,<ref>{{harvnb|Lamarck|1809}}</ref> which envisaged [[spontaneous generation]] continually producing simple forms of life that developed greater complexity in parallel lineages with an inherent progressive tendency, and postulated that on a local level, these lineages adapted to the environment by inheriting changes caused by their use or disuse in parents.<ref name="Nardon_Grenier91">{{harvnb|Nardon|Grenier|1991|p=162}}</ref> (The latter process was later called [[Lamarckism]].)<ref name="Nardon_Grenier91" /><ref name="Ghiselin-1994">{{cite journal |last=Ghiselin |first=Michael T. |author-link=Michael Ghiselin |date=September–October 1994 |title=The Imaginary Lamarck: A Look at Bogus 'History' in Schoolbooks |url=http://www.textbookleague.org/54marck.htm |journal=The Textbook Letter |oclc=23228649 |access-date=23 January 2008 |url-status=usurped |archive-url=https://web.archive.org/web/20080212174536/http://www.textbookleague.org/54marck.htm |archive-date=12 February 2008}}</ref><ref name="Jablonka-2007">{{cite journal |last1=Jablonka |first1=Eva |author-link1=Eva Jablonka |last2=Lamb |first2=Marion J. |s2cid=15879804 |author-link2=Marion J. Lamb |date=August 2007 |title=Précis of Evolution in Four Dimensions |journal=[[Behavioral and Brain Sciences]] |volume=30 |issue=4 |pages=353–365 |doi=10.1017/S0140525X07002221 |pmid=18081952 |issn=0140-525X}}</ref> These ideas were condemned by established naturalists as speculation lacking empirical support. In particular, [[Georges Cuvier]] insisted that species were unrelated and fixed, their similarities reflecting divine design for functional needs. In the meantime, Ray's ideas of benevolent design had been developed by [[William Paley]] into the ''[[Natural Theology or Evidences of the Existence and Attributes of the Deity]]'' (1802), which proposed complex adaptations as evidence of divine design and which was admired by Charles Darwin.<ref name="Darwin91">{{harvnb|Burkhardt|Smith|1991}}
* {{cite news |url=http://www.darwinproject.ac.uk/letter/entry-2532 |title=Darwin, C. R. to Lubbock, John |website=[[Correspondence of Charles Darwin#Darwin Correspondence Project website|Darwin Correspondence Project]] |publisher=[[University of Cambridge]] |location=Cambridge |access-date=1 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20141215213940/http://www.darwinproject.ac.uk/letter/entry-2532 |archive-date=15 December 2014}} Letter 2532, 22 November 1859.</ref><ref name="Sulloway-2009">{{cite journal |last=Sulloway |first=Frank J. |s2cid=12289290 |author-link=Frank Sulloway |date=June 2009 |title=Why Darwin rejected intelligent design |journal=[[Journal of Biosciences]] |volume=34 |issue=2 |pages=173–183 |doi=10.1007/s12038-009-0020-8 |issn=0250-5991 |pmid=19550032}}</ref>

=== Darwinian revolution ===

The crucial break from the concept of constant typological classes or types in biology came with the theory of evolution through natural selection, which was formulated by [[Charles Darwin]] and [[Alfred Wallace]] in terms of variable populations. Darwin used the expression ''descent with modification'' rather than ''evolution''.<ref>{{Cite web |url=http://darwin-online.org.uk/content/search-results?pagesize=50&sort=date-ascending&pageno=0&freetext=descent+with+modification&allfields=&searchid=&name=Darwin+Charles+Robert&dateafter=&datebefore=&searchtitle=&description=&place=&publisher=&periodical= |title=Search results for "descent with modification" – The Complete Work of Charles Darwin Online |access-date=30 July 2022 |archive-date=5 June 2022 |archive-url=https://web.archive.org/web/20220605101314/http://darwin-online.org.uk/content/search-results?pagesize=50&sort=date-ascending&pageno=0&freetext=descent+with+modification&allfields=&searchid=&name=Darwin+Charles+Robert&dateafter=&datebefore=&searchtitle=&description=&place=&publisher=&periodical= |url-status=live}}</ref> Partly influenced by ''[[An Essay on the Principle of Population]]'' (1798) by [[Thomas Robert Malthus]], Darwin noted that population growth would lead to a "struggle for existence" in which favourable variations prevailed as others perished. In each generation, many offspring fail to survive to an age of reproduction because of limited resources. This could explain the diversity of plants and animals from a common ancestry through the working of natural laws in the same way for all types of organism.<ref name="Sober-2009">{{cite journal |last=Sober |first=Elliott |author-link=Elliott Sober |date=16 June 2009 |title=Did Darwin write the ''Origin'' backwards? |journal=[[PNAS]] |volume=106 |issue=Suppl. 1 |pages=10048–10055 |bibcode=2009PNAS..10610048S |doi=10.1073/pnas.0901109106 |issn=0027-8424 |pmid=19528655 |pmc=2702806 |doi-access=free}}</ref><ref>{{harvnb|Mayr|2002|p=165}}</ref><ref>{{harvnb|Bowler|2003|pp=145–146}}</ref><ref>{{cite journal |last1=Sokal |first1=Robert R. |author-link1=Robert R. Sokal |last2=Crovello |first2=Theodore J. |date=March–April 1970 |title=The Biological Species Concept: A Critical Evaluation |journal=[[The American Naturalist]] |volume=104 |issue=936 |pages=127–153 |doi=10.1086/282646 |issn=0003-0147 |jstor=2459191 |bibcode=1970ANat..104..127S |s2cid=83528114}}</ref> Darwin developed his theory of "natural selection" from 1838 onwards and was writing up his "big book" on the subject when [[Alfred Russel Wallace]] sent him a version of virtually the same theory in 1858. Their [[On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection|separate papers]] were presented together at an 1858 meeting of the [[Linnean Society of London]].<ref>{{cite journal |last1=Darwin |first1=Charles |author-link1=Charles Darwin |last2=Wallace |first2=Alfred |author-link2=Alfred Russel Wallace |date=20 August 1858 |title=On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection |url=http://darwin-online.org.uk/content/frameset?itemID=F350&viewtype=text&pageseq=1 |journal=[[Journal of the Proceedings of the Linnean Society of London. Zoology]] |volume=3 |issue=9 |pages=45–62 |doi=10.1111/j.1096-3642.1858.tb02500.x |issn=1096-3642 |access-date=13 May 2007 |url-status=live |archive-url=https://web.archive.org/web/20070714042318/http://darwin-online.org.uk/content/frameset?itemID=F350&viewtype=text&pageseq=1 |archive-date=14 July 2007 |doi-access=free}}</ref> At the end of 1859, Darwin's publication of his "abstract" as ''On the Origin of Species'' explained natural selection in detail and in a way that led to an increasingly wide acceptance of [[Darwinism|Darwin's concepts of evolution]] at the expense of [[Alternatives to evolution by natural selection|alternative theories]]. [[Thomas Henry Huxley]] applied Darwin's ideas to humans, using [[palaeontology]] and [[comparative anatomy]] to provide strong evidence that humans and [[ape]]s shared a common ancestry. Some were disturbed by this since it implied that humans did not have a special place in the [[universe]].<ref>{{cite encyclopedia |last=Desmond |first=Adrian J. |author-link=Adrian Desmond |encyclopedia=[[Encyclopædia Britannica Online]] |url=https://www.britannica.com/EBchecked/topic/277746/Thomas-Henry-Huxley |title=Thomas Henry Huxley |access-date=2 December 2014 |date=17 July 2014 |url-status=live |archive-url=https://web.archive.org/web/20150119231241/https://www.britannica.com/EBchecked/topic/277746/Thomas-Henry-Huxley |archive-date=19 January 2015}}</ref>

[[Othniel C. Marsh]], America's first palaeontologist, was the first to provide solid fossil evidence to support Darwin's theory of evolution by unearthing the ancestors of the modern horse.<ref>Plate, Robert. ''The Dinosaur Hunters: Othniel C. Marsh and Edward D. Cope,'' pp. 69, 203–205, David McKay, New York, 1964.</ref> In 1877, Marsh delivered a very influential speech before the annual meeting of the American Association for the Advancement of Science, providing a demonstrative argument for evolution. For the first time, Marsh traced the evolution of vertebrates from fish all the way through humans. Sparing no detail, he listed a wealth of fossil examples of past life forms. The significance of this speech was immediately recognised by the scientific community, and it was printed in its entirety in several scientific journals.<ref>McCarren, Mark J. ''The Scientific Contributions of Othniel Charles Marsh,'' pp. 37–39, Peabody Museum of Natural History, Yale University, New Haven, Connecticut, 1993. {{ISBN|0-912532-32-7}}</ref><ref>Plate, Robert. ''The Dinosaur Hunters: Othniel C. Marsh and Edward D. Cope,'' pp. 188–189, David McKay, New York, 1964.</ref>
[[File:Hesperornis Regalis - Project Gutenberg eText 16474.jpg|thumb|left|''Hesperornis regalis,'' a species of ancient flightless bird with teeth, as drawn by [[Othniel Charles Marsh|Othniel Marsh]], and published in his book, ''Odontornithes: A Monograph on the Extinct Toothed Birds of North America.'']]

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>

=== Pangenesis and heredity ===

The mechanisms of reproductive heritability and the origin of new traits remained a mystery. Towards this end, Darwin developed his provisional theory of [[pangenesis]].<ref name="Liu-2009">{{cite journal |author1=Y.-S. Liu |author2=X. M. Zhou |author3=M. X. Zhi |author4=X. J. Li |author5=Q. L. Wang |s2cid=19919317 |date=September 2009 |title=Darwin's contributions to genetics |journal=Journal of Applied Genetics |volume=50 |issue=3 |pages=177–184 |doi=10.1007/BF03195671 |issn=1234-1983 |pmid=19638672}}</ref> In 1865, [[Gregor Mendel]] reported that traits were inherited in a predictable manner through the [[independent assortment]] and segregation of elements (later known as genes). Mendel's laws of inheritance eventually supplanted most of Darwin's pangenesis theory.<ref name="Weiling-1991">{{cite journal |last=Weiling |first=Franz |date=July 1991 |title=Historical study: Johann Gregor Mendel 1822–1884 |journal=[[American Journal of Medical Genetics]] |volume=40 |issue=1 |pages=1–25; discussion 26 |doi=10.1002/ajmg.1320400103 |pmid=1887835}}</ref> [[August Weismann]] made the important distinction between [[germ cell]]s that give rise to [[gamete]]s (such as [[sperm]] and [[egg cell]]s) and the [[somatic cell]]s of the body, demonstrating that heredity passes through the germ line only. [[Hugo de Vries]] connected Darwin's pangenesis theory to Weismann's germ/soma cell distinction and proposed that Darwin's pangenes were concentrated in the [[cell nucleus]] and when expressed they could move into the [[cytoplasm]] to change the [[Cell (biology)|cell]]'s structure. De Vries was also one of the researchers who made Mendel's work well known, believing that Mendelian traits corresponded to the transfer of heritable variations along the germline.<ref name="Wright84">{{harvnb|Wright|1984|p=480}}</ref> To explain how new variants originate, de Vries developed [[Mutationism|a mutation theory]] that led to a temporary rift between those who accepted Darwinian evolution and biometricians who allied with de Vries.<ref>{{harvnb|Provine|1971}}</ref><ref>{{cite journal |last1=Stamhuis |first1=Ida H. |last2=Meijer |first2=Onno G. |last3=Zevenhuizen |first3=Erik J. A. |date=June 1999 |title=Hugo de Vries on Heredity, 1889–1903: Statistics, Mendelian Laws, Pangenes, Mutations |url=https://archive.org/details/sim_isis_1999-06_90_2/page/238 |volume=90 |issue=2 |pages=238–267 |journal=[[Isis (journal)|Isis]] |doi=10.1086/384323 |jstor=237050 |pmid=10439561 |s2cid=20200394}}</ref> In the 1930s, pioneers in the field of [[population genetics]], such as [[Ronald Fisher]], [[Sewall Wright]] and [[J. B. S. Haldane]] set the foundations of evolution onto a robust statistical philosophy. The false contradiction between Darwin's theory, genetic mutations, and [[Mendelian inheritance]] was thus reconciled.{{sfn|Bowler|1989|pp=307–318}}

=== The 'modern synthesis' ===
{{Main|Modern synthesis (20th century)}}

In the 1920s and 1930s, the [[modern synthesis]] connected natural selection and population genetics, based on Mendelian inheritance, into a unified theory that included random genetic drift, mutation, and gene flow. This new version of evolutionary theory focused on changes in allele frequencies in population. It explained patterns observed across species in populations, through [[Transitional fossil|fossil transitions]] in palaeontology.{{sfn|Bowler|1989|pp=307–318}}

=== Further syntheses ===

Since then, further syntheses have extended evolution's explanatory power in the light of numerous discoveries, to cover biological phenomena across the whole of the [[Biological organisation|biological hierarchy]] from genes to populations.{{sfn|Levinson|2019}}

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. |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 |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>

One extension, known as [[evolutionary developmental biology]] and informally called "evo-devo", emphasises how changes between generations (evolution) act on patterns of change within individual organisms ([[Developmental biology|development]]).<ref name="Kutschera-2004">{{cite journal |last1=Kutschera |first1=Ulrich |author-link1=Ulrich Kutschera |last2=Niklas |first2=Karl J. |author-link2=Karl J. Niklas |date=June 2004 |title=The modern theory of biological evolution: an expanded synthesis |journal=[[Naturwissenschaften]] |volume=91 |issue=6 |pages=255–276 |bibcode=2004NW.....91..255K |doi=10.1007/s00114-004-0515-y |issn=1432-1904 |pmid=15241603 |s2cid=10731711}}</ref><ref name="Avise10">{{cite journal |last1=Avise |first1=John C. |author-link1=John Avise |last2=Ayala |first2=Francisco J. |author-link2=Francisco J. Ayala |date=11 May 2010 |title=In the light of evolution IV: The human condition |url=http://faculty.sites.uci.edu/johncavise/files/2011/03/311-intro-to-ILE-IV.pdf |journal=PNAS |volume=107 |issue=Suppl. 2 |pages=8897–8901 |doi=10.1073/pnas.1003214107 |pmid=20460311 |pmc=3024015 |issn=0027-8424 |access-date=29 December 2014 |url-status=live |archive-url=https://web.archive.org/web/20140823063532/http://faculty.sites.uci.edu/johncavise/files/2011/03/311-intro-to-ILE-IV.pdf |archive-date=23 August 2014 |doi-access=free}}</ref> Since the beginning of the 21st century, some biologists have argued for an [[extended evolutionary synthesis]], which would account for the effects of non-genetic inheritance modes, such as [[epigenetics]], [[Maternal effect|parental effects]], ecological inheritance and [[Dual inheritance theory|cultural inheritance]], and [[evolvability]].<ref name="Danchin-2011">{{cite journal |last1=Danchin |first1=Étienne |last2=Charmantier |first2=Anne |last3=Champagne |first3=Frances A. |author-link3=Frances Champagne |last4=Mesoudi |first4=Alex |last5=Pujol |first5=Benoit |last6=Blanchet |first6=Simon |date=June 2011 |title=Beyond DNA: integrating inclusive inheritance into an extended theory of evolution |journal=[[Nature Reviews Genetics]] |volume=12 |issue=7 |pages=475–486 |doi=10.1038/nrg3028 |issn=1471-0056 |pmid=21681209 |s2cid=8837202|url=https://durham-repository.worktribe.com/output/1497583 }}</ref><ref name="eesbook">{{harvnb|Pigliucci|Müller|2010}}</ref>

== Social and cultural responses ==
{{further|Social effects of evolutionary theory|1860 Oxford evolution debate|Acceptance of evolution by religious groups|Rejection of evolution by religious groups|Objections to evolution|Evolution in fiction}}

[[File:Editorial cartoon depicting Charles Darwin as an ape (1871).jpg|upright|thumb|As evolution became widely accepted in the 1870s, [[caricature]]s of Charles Darwin with an [[ape]] or monkey body symbolised evolution.<ref>{{harvnb|Browne|2003|pp=376–379}}</ref>]]

In the 19th century, particularly after the publication of ''On the Origin of Species'' in 1859, the idea that life had evolved was an active source of academic debate centred on the philosophical, social and religious implications of evolution. Today, the modern evolutionary synthesis is accepted by a vast majority of scientists.<ref name="Kutschera-2004" /> However, evolution remains a contentious concept for some [[theists]].<ref>For an overview of the philosophical, religious and cosmological controversies, see:
* {{harvnb|Dennett|1995}}
For the scientific and social reception of evolution in the 19th and early 20th centuries, see:
* {{cite book |last=Johnston |first=Ian C. |author-link=Ian C. Johnston |year=1999 |chapter=Section Three: The Origins of Evolutionary Theory |chapter-url=https://malvma.viu.ca/~johnstoi/darwin/sect3.htm |title=... And Still We Evolve: A Handbook for the Early History of Modern Science |url=https://malvma.viu.ca/~johnstoi/darwin/title.htm |edition=3rd revised |location=Nanaimo, BC |publisher=Liberal Studies Department, [[Malaspina University-College]] |access-date=1 January 2015 |url-status=live |archive-url=https://web.archive.org/web/20160416050826/http://records.viu.ca/~johnstoi/darwin/title.htm |archive-date=16 April 2016 |ref=none}}
* {{harvnb|Bowler|2003}}
* {{cite journal |last=Zuckerkandl |first=Emile |author-link=Emile Zuckerkandl |date=30 December 2006 |title=Intelligent design and biological complexity |journal=[[Gene (journal)|Gene]] |volume=385 |pages=2–18 |pmid=17011142 |doi=10.1016/j.gene.2006.03.025 |issn=0378-1119 |ref=none}}</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>
{{Clear}}

== See also ==
* {{annotated link|Devolution (biology)}}
* [[Chronospecies]]

== References ==
{{reflist}}

== Bibliography ==
{{Refbegin|30em}}
* {{cite book |last=Altenberg |first=Lee |author-link=Lee Altenberg |year=1995 |chapter=Genome growth and the evolution of the genotype–phenotype map |editor1-last=Banzhaf |editor1-first=Wolfgang |editor2-last=Eeckman |editor2-first=Frank H. |title=Evolution and Biocomputation: Computational Models of Evolution |series=Lecture Notes in Computer Science |volume=899 |pages=205–259 |location=Berlin; New York |publisher=[[Springer-Verlag Berlin Heidelberg]] |doi=10.1007/3-540-59046-3_11 |issn=0302-9743 |isbn=978-3-540-59046-0 |lccn=95005970 |oclc=32049812 |citeseerx=10.1.1.493.6534}}
* {{cite book |last1=Birdsell |first1=John A. |last2=Wills |first2=Christopher |author-link2=Christopher Wills |year=2003 |chapter=The Evolutionary Origin and Maintenance of Sexual Recombination: A Review of Contemporary Models |editor1-last=MacIntyre |editor1-first=Ross J. |editor2-last=Clegg |editor2-first=Michael T. |title=Evolutionary Biology |volume=33 |location=New York |publisher=[[Springer Science+Business Media]] |isbn=978-1-4419-3385-0 |issn=0071-3260 |oclc=751583918}}
* {{cite book |last=Bowler |first=Peter J. |author-link=Peter J. Bowler |year=1989 |title=The Mendelian Revolution: The Emergence of Hereditarian Concepts in Modern Science and Society |location=Baltimore, Maryland |publisher=Johns Hopkins University Press |isbn=978-0-8018-3888-0 |lccn=89030914 |oclc=19322402}}
* {{cite book |last=Bowler |first=Peter J. |author-link=Peter J. Bowler |year=2003 |title=Evolution: The History of an Idea |edition=3rd completely rev. and expanded |location=Berkeley, California |publisher=[[University of California Press]] |isbn=978-0-520-23693-6 |lccn=2002007569 |oclc=49824702 |url-access=registration |url=https://archive.org/details/evolutionhistory0000bowl_n7y8}}
* {{cite book |last=Browne |first=Janet |author-link=Janet Browne |year=2003 |title=Charles Darwin: The Power of Place |volume=2 |location=London |publisher=[[Random House|Pimlico]] |isbn=978-0-7126-6837-8 |lccn=94006598 |oclc=52327000}}
* {{cite book |editor1-last=Burkhardt |editor1-first=Frederick |editor1-link=Frederick Burkhardt |editor2-last=Smith |editor2-first=Sydney |year=1991 |title=The Correspondence of Charles Darwin |volume='''7''': 1858–1859 |location=Cambridge |publisher=[[Cambridge University Press]] |isbn=978-0-521-38564-0 |lccn=84045347 |oclc=185662993}}
* {{cite book |last1=Carroll |first1=Sean B. |author-link1=Sean B. Carroll |last2=Grenier |first2=Jennifer K. |last3=Weatherbee |first3=Scott D. |year=2005 |title=From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design |edition=2nd |location=Malden, Massachusetts |publisher=[[Wiley-Blackwell|Blackwell Publishing]] |isbn=978-1-4051-1950-4 |lccn=2003027991 |oclc=53972564}}
* {{cite book |last=Chapman |first=Arthur D. |year=2009 |title=Numbers of Living Species in Australia and the World |edition=2nd |url=https://www.environment.gov.au/science/abrs/publications/other/numbers-living-species/ |access-date=6 November 2016 |url-status=live |archive-url=https://web.archive.org/web/20161225064434/http://www.environment.gov.au/science/abrs/publications/other/numbers-living-species |archive-date=25 December 2016 |location=Canberra |publisher=[[Department of the Environment, Water, Heritage and the Arts]]: [[Australian Biological Resources Study]] |isbn=978-0-642-56860-1 |oclc=780539206}}
* {{cite book |last=Coyne |first=Jerry A. |author-link=Jerry Coyne |year=2009 |title=Why Evolution is True |location=New York |publisher=[[Viking Press|Viking]] |isbn=978-0-670-02053-9 |lccn=2008033973 |oclc=233549529 |url=https://archive.org/details/whyevolutionistr00coyn}}
* {{cite book |last=Dalrymple |first=G. Brent |author-link=Brent Dalrymple |year=2001 |chapter=The age of the Earth in the twentieth century: a problem (mostly) solved |editor1-last=Lewis |editor1-first=C. L. E. |editor2-last=Knell |editor2-first=S. J. |title=The Age of the Earth: from 4004 BC to AD 2002 |series=Geological Society Special Publication |volume=190 |issue=1 |pages=205–221 |bibcode=2001GSLSP.190..205D |doi=10.1144/gsl.sp.2001.190.01.14 |isbn=978-1-86239-093-5 |s2cid=130092094 |lccn=2003464816 |oclc=48570033}}
* {{cite book |last=Darwin |first=Charles |author-link=Charles Darwin |title="B" Notebook |date=1837}} The notebook is available from [http://darwin-online.org.uk/content/frameset?itemID=CUL-DAR121.-&viewtype=side&pageseq=1 The Complete Work of Charles Darwin Online] {{Webarchive|url=https://web.archive.org/web/20220318093920/http://darwin-online.org.uk/content/frameset?viewtype=side&itemID=CUL-DAR121.-&pageseq=1 |date=18 March 2022 }}. Retrieved 2019-10-09.
* {{cite book |last=Darwin |first=Charles |author-link=Charles Darwin |year=1859 |title=On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life |edition=1st |location=London |publisher=[[John Murray (publishing house)|John Murray]] |lccn=06017473 |oclc=741260650 |title-link=On the Origin of Species}} The book is available from [http://darwin-online.org.uk/content/frameset?pageseq=1&itemID=F373&viewtype=side The Complete Work of Charles Darwin Online] {{Webarchive|url=https://web.archive.org/web/20150127124331/http://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=side&pageseq=1 |date=27 January 2015 }}. Retrieved 2014-11-21.
* {{cite book |last=Darwin |first=Charles |author-link=Charles Darwin |date=1872 |title=The Expression of the Emotions in Man and Animals |location=London |publisher=John Murray |lccn=04002793 |oclc=1102785 |title-link=The Expression of the Emotions in Man and Animals}}
* {{cite book |editor-last=Darwin |editor-first=Francis |editor-link=Francis Darwin |year=1909 |title=The foundations of The origin of species, a sketch written in 1842 |url=http://darwin-online.org.uk/converted/pdf/1909_Foundations_F1555.pdf |location=Cambridge |publisher=Printed at the University Press |lccn=61057537 |oclc=1184581 |access-date=27 November 2014 |archive-date=4 March 2016 |archive-url=https://web.archive.org/web/20160304111606/http://darwin-online.org.uk/converted/pdf/1909_Foundations_F1555.pdf |url-status=live}}
* {{cite book |last=Dennett |first=Daniel |author-link=Daniel Dennett |year=1995 |title=Darwin's Dangerous Idea: Evolution and the Meanings of Life |location=New York |publisher=[[Simon & Schuster]] |isbn=978-0-684-80290-9 |lccn=94049158 |oclc=31867409 |title-link=Darwin's Dangerous Idea}}
* {{cite book |last=Dobzhansky |first=Theodosius |title=Evolutionary Biology |author-link1=Theodosius Dobzhansky |year=1968 |chapter=On Some Fundamental Concepts of Darwinian Biology |editor1-last=Dobzhansky |editor1-first=Theodosius |editor2-last=Hecht |editor2-first=Max K. |editor3-last=Steere |editor3-first=William C. |pages=1–34 |edition=1st |location=New York |publisher=[[Appleton-Century-Crofts]] |doi=10.1007/978-1-4684-8094-8_1 |oclc=24875357 |isbn=978-1-4684-8096-2}}
* {{cite book |last=Dobzhansky |first=Theodosius |author-link1=Theodosius Dobzhansky |year=1970 |title=Genetics of the Evolutionary Process |location=New York |publisher=[[Columbia University Press]] |isbn=978-0-231-02837-0 |lccn=72127363 |oclc=97663}}
* {{cite book |last1=Eldredge |first1=Niles |author-link1=Niles Eldredge |last2=Gould |first2=Stephen Jay |author-link2=Stephen Jay Gould |year=1972 |chapter=Punctuated equilibria: an alternative to phyletic gradualism |editor1-last=Schopf |editor1-first=Thomas J. M. |title=Models in Paleobiology |location=San Francisco, California |publisher=Freeman, Cooper |isbn=978-0-87735-325-6 |lccn=72078387 |oclc=572084}}
* {{cite book |last=Eldredge |first=Niles |year=1985 |title=Time Frames: The Rethinking of Darwinian Evolution and the Theory of Punctuated Equilibria |url=https://archive.org/details/timeframesrethin0000eldr |location=New York |publisher=[[Simon & Schuster]] |isbn=978-0-671-49555-8 |lccn=84023632 |oclc=11443805 |ref=none}}
* {{cite book |last=Ewens |first=Warren J. |author-link=Warren Ewens |year=2004 |title=Mathematical Population Genetics |series=Interdisciplinary Applied Mathematics |volume=I. Theoretical Introduction |edition=2nd |location=New York |publisher=[[Springer-Verlag New York]] |isbn=978-0-387-20191-7 |lccn=2003065728 |oclc=53231891}}
* {{cite book |last=Fisher |first=Ronald A. |author-link=Ronald Fisher |date=1999 |orig-date=1930 |title=The Genetical Theory of Natural Selection |editor=J. H. Bennett |location=Oxford |publisher=[[Oxford University Press]] |isbn=978-0-19-850440-5 |lccn=30029177 |oclc=45308589}}
* {{cite book |last=Futuyma |first=Douglas J. |author-link=Douglas J. Futuyma |year=2004 |chapter=The Fruit of the Tree of Life: Insights into Evolution and Ecology |editor1-last=Cracraft |editor1-first=Joel |editor2-last=Donoghue |editor2-first=Michael J. |title=Assembling the Tree of Life |location=Oxford; New York |publisher=[[Oxford University Press]] |isbn=978-0-19-517234-8 |lccn=2003058012 |oclc=61342697}} "Proceedings of a symposium held at the American Museum of Natural History in New York, 2002."
* {{cite book |last=Futuyma |first=Douglas J. |year=2005 |title=Evolution |location=Sunderland, Massachusetts |publisher=[[Sinauer Associates]] |isbn=978-0-87893-187-3 |lccn=2004029808 |oclc=57311264 |url=https://archive.org/details/evolution0000futu}}
* {{cite book |last1=Futuyma |first1=Douglas J. |last2=Kirkpatrick |first2=Mark |year=2017 |title=Evolution |edition=Fourth |location=Sunderland, Massachusetts |publisher=Sinauer Associates |isbn=978-1-60535-605-1 |lccn=2017000562 |oclc=969439375}}
* {{cite book |last=Gould |first=Stephen Jay |year=2002 |title=The Structure of Evolutionary Theory |location=[[Cambridge, Massachusetts]] |publisher=[[Belknap Press of Harvard University Press]] |isbn=978-0-674-00613-3 |lccn=2001043556 |oclc=47869352 |title-link=The Structure of Evolutionary Theory}}
* {{cite book |last=Gray |first=Peter |author-link=Peter Gray (psychologist) |year=2007 |title=Psychology |edition=5th |location=New York |publisher=[[Macmillan Publishers (United States)|Worth Publishers]] |isbn=978-0-7167-0617-5 |lccn=2006921149 |oclc=76872504 |url=https://archive.org/details/psychology0000gray}}
* {{cite book |last1=Hall |first1=Brian K. |author-link1=Brian K. Hall |last2=Hallgrímsson |first2=Benedikt |title=Strickberger's Evolution |url=https://archive.org/details/strickbergersevo0000hall |url-access=registration |year=2008 |edition=4th |location=Sudbury, Massachusetts |publisher=Jones and Bartlett Publishers |isbn=978-0-7637-0066-9 |lccn=2007008981 |oclc=85814089}}
* {{cite book |last=Hennig |first=Willi |author-link=Willi Hennig |year=1999 |orig-date=Originally published 1966 (reprinted 1979); translated from the author's unpublished revision of ''Grundzüge einer Theorie der phylogenetischen Systematik'', published in 1950 |title=Phylogenetic Systematics |others=Translation by D. Dwight Davis and Rainer Zangerl; foreword by Donn E. Rosen, Gareth Nelson, and [[Colin Patterson (biologist)|Colin Patterson]] |edition=Reissue |location=Urbana, Illinois |publisher=[[University of Illinois Press]] |isbn=978-0-252-06814-0 |lccn=78031969 |oclc=722701473}}
* {{cite book |last=Holland |first=John H. |author-link=John Henry Holland |year=1975 |title=Adaptation in Natural and Artificial Systems: An Introductory Analysis with Applications to Biology, Control, and Artificial Intelligence |url=https://archive.org/details/adaptationinnatu0000holl |location=Ann Arbor, Michigan |publisher=[[University of Michigan Press]] |isbn=978-0-472-08460-9 |lccn=74078988 |oclc=1531617}}
* {{cite book |last=Kampourakis |first=Kostas |year=2014 |title=Understanding Evolution |location=Cambridge; New York |publisher=Cambridge University Press |isbn=978-1-107-03491-4 |lccn=2013034917 |oclc=855585457 |url-access=registration |url=https://archive.org/details/understandingevo0000kamp}}
* {{cite book |last1=Kirk |first1=Geoffrey |author-link1=Geoffrey Kirk |last2=Raven |first2=John |author-link2=John Raven |last3=Schofield |first3=Malcolm |year=1983 |title=The Presocratic Philosophers: A Critical History with a Selection of Texts |edition=2nd |location=Cambridge; New York |publisher=Cambridge University Press |isbn=978-0-521-27455-5 |lccn=82023505 |oclc=9081712}}
* {{cite book |last=Koza |first=John R. |author-link=John Koza |year=1992 |title=Genetic Programming: On the Programming of Computers by Means of Natural Selection |series=Complex Adaptive Systems |location=Cambridge, Massachusetts |publisher=MIT Press |isbn=978-0-262-11170-6 |lccn=92025785 |oclc=26263956}}
* {{cite book |last=Lamarck |first=Jean-Baptiste |author-link=Jean-Baptiste Lamarck |year=1809 |title=Philosophie Zoologique |location=Paris |publisher=Dentu et L'Auteur |oclc=2210044 |title-link=Philosophie Zoologique}} {{Internet Archive|id=philosophiezool06unkngoog|name=Philosophie zoologique (1809)}}. Retrieved 2014-11-29.
* {{cite book |last=Lane |first=David H. |year=1996 |title=The Phenomenon of Teilhard: Prophet for a New Age |edition=1st |location=Macon, Georgia |publisher=[[Mercer University Press]] |isbn=978-0-86554-498-7 |lccn=96008777 |oclc=34710780}}
* {{cite book |title=Rethinking Evolution: The Revolution That's Hiding in Plain Sight |url=https://rethinkingevolution.com/ |last=Levinson |first=Gene |location=Hackensack, New Jersey |publisher=[[World Scientific]] |year=2019 |isbn=978-1-78634-726-8 |lccn=2019013762 |oclc=1138095098 |access-date=30 July 2022 |archive-date=21 May 2022 |archive-url=https://web.archive.org/web/20220521082753/https://rethinkingevolution.com/ |url-status=live}}
* {{cite book |author=Lucretius |author-link=Lucretius |chapter=Book V, lines 855–877 |chapter-url=https://www.perseus.tufts.edu/hopper/text?doc=Perseus%3Atext%3A1999.02.0131%3Abook%3D5%3Acard%3D855 |title=De Rerum Natura |via=[[Perseus Digital Library]] |others=Edited and translated by [[William Ellery Leonard]] (1916) |location=Medford/Somerville, Massachusetts |publisher=[[Tufts University]] |oclc=33233743 |access-date=25 November 2014 |url-status=live |archive-url=https://web.archive.org/web/20140904053325/http://www.perseus.tufts.edu/hopper/text?doc=Perseus%3Atext%3A1999.02.0131%3Abook%3D5%3Acard%3D855 |archive-date=4 September 2014 |title-link=De rerum natura}}
* {{cite book |last=McCarren |first=Mark J. |year=1993 |title=The Scientific Contributions of Othniel Charles Marsh: Birds, Bones, and Brontotheres |publisher=Peabody Museum of Natural History |isbn=978-0-912532-32-5}}
* {{cite book |last=Mason |first=Stephen F. |year=1962 |title=A History of the Sciences |url=https://archive.org/details/historyofscience00maso |url-access=registration |series=Collier Books. Science Library, CS9 |edition=New rev. |location=New York |publisher=[[Collier Books]] |lccn=62003378 |oclc=568032626}}
* {{cite book |last=Maynard Smith |first=John |author-link=John Maynard Smith |year=1978 |title=The Evolution of Sex |url=https://archive.org/details/evolutionofsex0000mayn |url-access=registration |location=Cambridge; New York |publisher=Cambridge University Press |isbn=978-0-521-29302-0 |lccn=77085689 |oclc=3413793}}
* {{cite book |last=Maynard Smith |first=John |year=1998 |chapter=The Units of Selection |editor1-last=Bock |editor1-first=Gregory R. |editor2-last=Goode |editor2-first=Jamie A. |title=The Limits of Reductionism in Biology |series=Novartis Foundation Symposia |volume=213 |pages=203–221 |location=[[Chichester]]; New York |publisher=[[John Wiley & Sons]] |doi=10.1002/9780470515488.ch15 |isbn=978-0-471-97770-4 |lccn=98002779 |oclc=38311600 |pmid=9653725}} "Papers from the Symposium on the Limits of Reductionism in Biology, held at the Novartis Foundation, London, May 13–15, 1997."
* {{cite book |last=Mayr |first=Ernst |author-link=Ernst Mayr |year=1942 |title=Systematics and the Origin of Species from the Viewpoint of a Zoologist |series=Columbia Biological Series |volume=13 |location=New York |publisher=Columbia University Press |lccn=43001098 |oclc=766053 |title-link=Systematics and the Origin of Species}}
* {{cite book |last=Mayr |first=Ernst |year=1982 |title=The Growth of Biological Thought: Diversity, Evolution, and Inheritance |others=Translation of [[John Ray]] by E. Silk |location=Cambridge, Massachusetts |publisher=[[Harvard University Press|Belknap Press]] |isbn=978-0-674-36445-5 |lccn=81013204 |oclc=7875904 |title-link=The Growth of Biological Thought}}
* {{cite book |last=Mayr |first=Ernst |year=2002 |orig-date=Originally published 2001; New York: [[Basic Books]] |title=What Evolution Is |series=Science Masters |location=London |publisher=[[Weidenfeld & Nicolson]] |isbn=978-0-297-60741-0 |lccn=2001036562 |oclc=248107061}}
* {{cite book |last=McKinney |first=Michael L. |year=1997 |chapter=How do rare species avoid extinction? A palaeontological view |editor1-last=Kunin |editor1-first=William E. |editor2-last=Gaston |editor2-first=Kevin J. |title=The Biology of Rarity: Causes and consequences of rare—common differences |edition=1st |location=London; New York |publisher=[[Chapman & Hall]] |isbn=978-0-412-63380-5 |lccn=96071014 |oclc=36442106}}
* {{cite book |last1=Miller |first1=G. Tyler |last2=Spoolman |first2=Scott E. |year=2012 |title=Environmental Science |url=https://books.google.com/books?id=NYEJAAAAQBAJ&pg=PA62 |edition=14th |location=Belmont, California |publisher=[[Brooks/Cole]] |isbn=978-1-111-98893-7 |lccn=2011934330 |oclc=741539226 |access-date=27 December 2014 |archive-date=2 May 2019 |archive-url=https://web.archive.org/web/20190502055246/https://books.google.com/books?id=NYEJAAAAQBAJ&pg=PA62 |url-status=live}}
* {{cite book |last1=Nardon |first1=Paul |last2=Grenier |first2=Anne-Marie |year=1991 |chapter=Serial Endosymbiosis Theory and Weevil Evolution: The Role of Symbiosis |editor1-last=Margulis |editor1-first=Lynn |editor2-last=Fester |editor2-first=René |title=Symbiosis as a Source of Evolutionary Innovation: Speciation and Morphogenesis |location=Cambridge, Massachusetts |publisher=MIT Press |isbn=978-0-262-13269-5 |lccn=90020439 |oclc=22597587}} "Based on a conference held in Bellagio, Italy, June 25–30, 1989"
* {{cite book |author1=National Academy of Sciences |author-link1=National Academy of Sciences |author2=Institute of Medicine |author-link2=Institute of Medicine |year=2008 |title=Science, Evolution, and Creationism |url=https://archive.org/details/isbn_9780309105866 |location=Washington, DC |publisher=National Academy Press |isbn=978-0-309-10586-6 |lccn=2007015904 |oclc=123539346 |access-date=22 November 2014 |ref=NAS 2008}}
* {{cite book |last=Odum |first=Eugene P. |author-link=Eugene Odum |year=1971 |title=Fundamentals of Ecology |url=https://archive.org/details/fundamentalsofec0000odum |url-access=registration |edition=3rd |location=Philadelphia, Pennsylvania |publisher=[[Saunders (imprint)|Saunders]] |isbn=978-0-7216-6941-0 |lccn=76081826 |oclc=154846}}
* {{cite book |last=Okasha |first=Samir |year=2006 |title=Evolution and the Levels of Selection |location=Oxford; New York |publisher=Oxford University Press |isbn=978-0-19-926797-2 |lccn=2006039679 |oclc=70985413}}
* {{cite book |last=Panno |first=Joseph |title=The Cell: Evolution of the First Organism |year=2005 |series=Facts on File science library |location=New York |publisher=[[Facts on File]] |isbn=978-0-8160-4946-2 |lccn=2003025841 |oclc=53901436}}
* {{cite book |last1=Piatigorsky |first1=Joram |last2=Kantorow |first2=Marc |last3=Gopal-Srivastava |first3=Rashmi |last4=Tomarev |first4=Stanislav I. |year=1994 |chapter=Recruitment of enzymes and stress proteins as lens crystallins |editor1-last=Jansson |editor1-first=Bengt |editor2-last=Jörnvall |editor2-first=Hans |editor3-last=Rydberg |editor3-first=Ulf |editor4-last=Terenius |editor4-first=Lars |editor5-last=Vallee |editor5-first=Bert L. |display-editors=3 |title=Toward a Molecular Basis of Alcohol Use and Abuse |series=Experientia |volume=71 |pages=241–250 |location=Basel; Boston |publisher=[[Birkhäuser]] Verlag |doi=10.1007/978-3-0348-7330-7_24 |isbn=978-3-7643-2940-2 |lccn=94010167 |oclc=30030941 |pmid=8032155}}
* {{cite book |editor1-last=Pigliucci |editor1-first=Massimo |editor1-link=Massimo Pigliucci |editor2-last=Müller |editor2-first=Gerd B. |editor2-link=Gerd B. Müller |year=2010 |title=Evolution, the Extended Synthesis |url=http://muse.jhu.edu/books/9780262315142 |url-status=live |archive-url=https://web.archive.org/web/20150918231401/http://muse.jhu.edu/books/9780262315142 |archive-date=18 September 2015 |location=Cambridge, Massachusetts |publisher=MIT Press |isbn=978-0-262-51367-8 |lccn=2009024587 |oclc=804875316}}
* {{cite book |last=Provine |first=William B. |author-link=Will Provine |year=1971 |title=The Origins of Theoretical Population Genetics |url=https://archive.org/details/originsoftheoret00prov |url-access=registration |series=Chicago History of Science and Medicine |edition=2nd |location=Chicago, Illinois |publisher=[[University of Chicago Press]] |isbn=978-0-226-68464-2 |lccn=2001027561 |oclc=46660910}}
* {{cite book |last1=Raven |first1=Peter H. |author-link1=Peter H. Raven |last2=Johnson |first2=George B. |author-link2=George B. Johnson |year=2002 |title=Biology |url=https://archive.org/details/biologyrave00rave |url-access=registration |edition=6th |location=Boston, Massachusetts |publisher=[[McGraw-Hill]] |isbn=978-0-07-112261-0 |lccn=2001030052 |oclc=45806501}}
* {{cite book |last=Ray |first=John |author-link=John Ray |year=1686 |title=Historia Plantarum |trans-title=History of Plants |volume=I |location=Londini |publisher=Typis Mariæ Clark |lccn=agr11000774 |oclc=2126030}}
* {{cite book |last=Rechenberg |first=Ingo |author-link=Ingo Rechenberg |year=1973 |title=Evolutionsstrategie; Optimierung technischer Systeme nach Prinzipien der biologischen Evolution |type=PhD thesis |series=Problemata |language=de |volume=15 |others=Afterword by [[Manfred Eigen]] |location=Stuttgart-Bad Cannstatt |publisher=Frommann-Holzboog |isbn=978-3-7728-0373-4 |lccn=74320689 |oclc=9020616}}
* {{cite book |last=Ridley |first=Mark |year=2004 |title=Evolution |location=Oxford |publisher=Blackwell |isbn=978-1-4051-0345-9}}
* {{cite book |last1=Stearns |first1=Beverly Peterson |last2=Stearns |first2=Stephen C. |author-link2=Stephen C. Stearns |year=1999 |title=Watching, from the Edge of Extinction |url=https://archive.org/details/isbn_9780300084696 |url-access=registration |location=New Haven, Connecticut |publisher=[[Yale University Press]] |isbn=978-0-300-08469-6 |lccn=98034087 |oclc=803522914}}
* {{cite book |last=Stevens |first=Anthony |author-link=Anthony Stevens (Jungian analyst) |year=1982 |title=Archetype: A Natural History of the Self |location=London |publisher=[[Routledge]] & Kegan Paul |isbn=978-0-7100-0980-7 |lccn=84672250 |oclc=10458367}}
* {{cite book |last1=Voet |first1=Donald |author-link1=Donald Voet |last2=Voet |first2=Judith G. |author-link2=Judith G. Voet |last3=Pratt |first3=Charlotte W. |author-link3=Charlotte W. Pratt |year=2016 |title=Fundamentals of Biochemistry: Life at the Molecular Level |edition=Fifth |location=[[Hoboken, New Jersey]] |publisher=[[John Wiley & Sons]] |isbn=978-1-118-91840-1 |lccn=2016002847 |oclc=939245154}}
* {{cite book |last=Wright |first=Sewall |author-link=Sewall Wright |year=1984 |title=Genetic and Biometric Foundations |series=Evolution and the Genetics of Populations |volume=1 |location=Chicago, Illinois |publisher=University of Chicago Press |isbn=978-0-226-91038-3 |lccn=67025533 |oclc=246124737 |url-access=registration |url=https://archive.org/details/evolutiongenetic0003wrig_b9l5}}
{{Refend}}

== Further reading ==
{{further|Bibliography of biology}}
{{Library resources box |onlinebooks=yes |by=no |lcheading=Evolution (Biology) |label=Evolution}}
{{refbegin}}

;Introductory reading

* {{cite book |editor1-last=Barrett |editor1-first=Paul H. |editor2-last=Weinshank |editor2-first=Donald J. |editor3-last=Gottleber |editor3-first=Timothy T. |year=1981 |title=A Concordance to Darwin's Origin of Species, First Edition |location=Ithaca, New York |publisher=[[Cornell University Press]] |isbn=978-0-8014-1319-3 |lccn=80066893 |oclc=610057960 |ref=none}}
* {{cite book |last=Carroll |first=Sean B. |year=2005 |title=Endless Forms Most Beautiful: The New Science of Evo Devo and the Making of the Animal Kingdom |others=illustrations by Jamie W. Carroll, Josh P. Klaiss, Leanne M. Olds |edition=1st |location=New York |publisher=W. W. Norton |isbn=978-0-393-06016-4 |lccn=2004029388 |oclc=57316841 |url=https://archive.org/details/endlessformsmost00carr_0 |ref=none}}
* {{cite book |last1=Charlesworth |first1=Brian |author-link1=Brian Charlesworth |last2=Charlesworth |first2=Deborah |author-link2=Deborah Charlesworth |year=2003 |title=Evolution: A Very Short Introduction |series=Very Short Introductions |location=Oxford; New York |publisher=Oxford University Press |isbn=978-0-19-280251-4 |lccn=2003272247 |oclc=51668497 |url-access=registration |url=https://archive.org/details/evolutionverysho0000char |ref=none}}
* {{cite book |last=Gould |first=Stephen Jay |year=1989 |title=Wonderful Life: The Burgess Shale and the Nature of History |edition=1st |location=New York |publisher=W. W. Norton |isbn=978-0-393-02705-1 |lccn=88037469 |oclc=18983518 |title-link=Wonderful Life (book) |ref=none}}
* {{cite book |last=Jones |first=Steve |author-link=Steve Jones (biologist) |year=1999 |title=Almost Like a Whale: The Origin of Species Updated |location=London; New York |publisher=[[Doubleday (publisher)|Doubleday]] |isbn=978-0-385-40985-8 |lccn=2002391059 |oclc=41420544 |title-link=Almost Like a Whale |ref=none}}
** {{cite book |last=Jones |first=Steve |year=2000 |title=Darwin's Ghost: The Origin of Species Updated |url=https://archive.org/details/darwinsghostorig0000jone |url-access=registration |edition=1st |location=New York |publisher=[[Random House]] |isbn=978-0-375-50103-6 |lccn=99053246 |oclc=42690131 |author-mask=2 |ref=none}} American version.
* {{cite book |last=Mader |first=Sylvia S. |title=Biology |year=2007 |others=Significant contributions by Murray P. Pendarvis |edition=9th |location=Boston, Massachusetts |publisher=[[McGraw-Hill Higher Education]] |isbn=978-0-07-246463-4 |lccn=2005027781 |oclc=61748307 |ref=none}}
* {{cite book |last=Maynard Smith |first=John |year=1993 |title=The Theory of Evolution |edition=Canto |location=Cambridge; New York |publisher=Cambridge University Press |isbn=978-0-521-45128-4 |lccn=93020358 |oclc=27676642 |title-link=The Theory of Evolution |ref=none}}
* {{cite book |last=Pallen |first=Mark J. |year=2009 |title=The Rough Guide to Evolution |url=https://archive.org/details/roughguidetoevol0000pall |series=Rough Guides Reference Guides |location=London; New York |publisher=[[Rough Guides]] |isbn=978-1-85828-946-5 |lccn=2009288090 |oclc=233547316 |ref=none}}

;Advanced reading

* {{cite book |last1=Barton |first1=Nicholas H. |author-link1=Nick Barton |last2=Briggs |first2=Derek E. G. |author-link2=Derek Briggs |last3=Eisen |first3=Jonathan A. |author-link3=Jonathan Eisen |last4=Goldstein |first4=David B. |last5=Patel |first5=Nipan H. |year=2007 |title=Evolution |location=Cold Spring Harbor, New York |publisher=Cold Spring Harbor Laboratory Press |isbn=978-0-87969-684-9 |lccn=2007010767 |oclc=86090399 |display-authors=3 |ref=none}}
* {{cite book |last1=Coyne |first1=Jerry A. |last2=Orr |first2=H. Allen |author-link2=H. Allen Orr |year=2004 |title=Speciation |location=Sunderland, Massachusetts |publisher=Sinauer Associates |isbn=978-0-87893-089-0 |lccn=2004009505 |oclc=55078441 |ref=none}}
* {{cite book |last1=Bergstrom |first1=Carl T. |author-link1=Carl Bergstrom |last2=Dugatkin |first2=Lee Alan |year=2012 |title=Evolution |edition=1st |location=New York |publisher=W. W. Norton |isbn=978-0-393-91341-5 |lccn=2011036572 |oclc=729341924 |ref=none}}
* {{cite book |editor1-last=Hall |editor1-first=Brian K. |editor2-last=Olson |editor2-first=Wendy |year=2003 |title=Keywords and Concepts in Evolutionary Developmental Biology |url=https://archive.org/details/keywordsconcepts0000unse |location=Cambridge, Massachusetts |publisher=Harvard University Press |isbn=978-0-674-00904-2 |lccn=2002192201 |oclc=50761342 |ref=none}}
* {{cite book |last=Kauffman |first=Stuart A. |author-link1=Stuart Kauffman |year=1993 |title=The Origins of Order: Self-organization and Selection in Evolution |url=https://archive.org/details/originsoforderse0000kauf |url-access=registration |location=New York; Oxford |publisher=Oxford University Press |isbn=978-0-19-507951-7 |lccn=91011148 |oclc=895048122 |ref=none}}
* {{cite book |last1=Maynard Smith |first1=John |last2=Szathmáry |first2=Eörs |author-link2=Eörs Szathmáry |year=1995 |title=The Major Transitions in Evolution |location=Oxford; New York |publisher=W. H. Freeman Spektrum |isbn=978-0-7167-4525-9 |lccn=94026965 |oclc=30894392 |title-link=The Major Transitions in Evolution |ref=none}}
* {{cite book |last=Mayr |first=Ernst |year=2001 |title=What Evolution Is |url=https://archive.org/details/whatevolutionis0000mayr |url-access=registration |location=New York |publisher=Basic Books |isbn=978-0-465-04426-9 |lccn=2001036562 |oclc=47443814 |ref=none}}
* {{cite book |last=Minelli |first=Alessandro |author-link=Alessandro Minelli (biologist) |year=2009 |title=Forms of Becoming: The Evolutionary Biology of Development |others=Translation by Mark Epstein |location=Princeton, New Jersey; Oxford |publisher=[[Princeton University Press]] |isbn=978-0-691-13568-7 |lccn=2008028825 |oclc=233030259 |ref=none}}
{{refend}}

== External links ==
<!-- IMPORTANT! Please do not add any links before discussing them on the talk page. -->
{{Spoken Wikipedia|Evolution.ogg|date=18 April 2005}} <!-- updated changed sections 2005-04-18 -->
{{Sister project links|auto=1|wikt=y|n=y|s=y|b=y|v=y}}

;General information

* {{In Our Time|"Evolution"|p00545gl}}
* {{cite web |url=http://nationalacademies.org/evolution/ |title=Evolution Resources from the National Academies |publisher=[[National Academy of Sciences]] |location=Washington, D.C. |access-date=30 May 2011}}
* {{cite web |url=http://evolution.berkeley.edu/ |title=Understanding Evolution: your one-stop resource for information on evolution |publisher=[[University of California, Berkeley]] |location=Berkeley, California |access-date=30 May 2011}}
* {{cite web |url=https://www.nsf.gov/news/special_reports/darwin/textonly/index.jsp |title=Evolution of Evolution – 150 Years of Darwin's 'On the Origin of Species' |publisher=[[National Science Foundation]] |location=Arlington County, Virginia |access-date=30 May 2011 |archive-date=19 May 2011 |archive-url=https://web.archive.org/web/20110519131450/http://www.nsf.gov/news/special_reports/darwin/textonly/index.jsp}}
* {{cite web |url=http://humanorigins.si.edu/evidence/human-evolution-timeline-interactive |title=Human Evolution Timeline Interactive |publisher=[[Smithsonian Institution]], [[National Museum of Natural History]] |access-date=14 July 2018 |date=28 January 2010}} Adobe Flash required.
* "[https://www.salon.com/2021/08/24/more-americans-believe-in-evolution/ History of Evolution in the United States]". [[Salon.com|Salon]]. Retrieved 2021-08-24.
* {{youTube|gZpsVSVRsZk|Video (1980; Cosmos animation; 8:01): "Evolution" – Carl Sagan}}

;Experiments

* {{cite web |url=http://myxo.css.msu.edu/index.html |title=Experimental Evolution |last=Lenski |first=Richard E. |author-link=Richard Lenski |publisher=[[Michigan State University]] |location=East Lansing, Michigan |access-date=31 July 2013 |ref=none}}
* {{cite journal |last1=Chastain |first1=Erick |last2=Livnat |first2=Adi |last3=Papadimitriou |first3=Christos |author-link3=Christos Papadimitriou |last4=Vazirani |first4=Umesh |author-link4=Umesh Vazirani |date=22 July 2014 |title=Algorithms, games, and evolution |journal=[[PNAS]] |volume=111 |issue=29 |pages=10620–10623 |bibcode=2014PNAS..11110620C |doi=10.1073/pnas.1406556111 |pmid=24979793 |issn=0027-8424 |pmc=4115542 |ref=none |doi-access=free}}

;Online lectures

* {{cite news |url=https://online-learning.harvard.edu/course/evolution-matters-lecture-series-0 |title=Evolution Matters Lecture Series |newspaper=Harvard Online Learning |publisher=[[Harvard University]] |location=Cambridge, Massachusetts |archive-url=https://web.archive.org/web/20171218132454/https://online-learning.harvard.edu/course/evolution-matters-lecture-series-0 |archive-date=18 December 2017 |access-date=15 July 2018 |ref=none}}
* {{cite web |url=https://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122 |title=EEB 122: Principles of Evolution, Ecology and Behavior |last=Stearns |first=Stephen C. |author-link=Stephen C. Stearns |website=[[Open Yale Courses]] |publisher=[[Yale University]] |location=New Haven, Connecticut |access-date=14 July 2018 |archive-url=https://web.archive.org/web/20171201233654/https://oyc.yale.edu/ecology-and-evolutionary-biology/eeb-122 |url-status=live |archive-date=1 December 2017 |ref=none}}

{{Evolution|state=uncollapsed}}
{{Authority control}}

[[Category:Evolution| ]]
[[Category:Biological evolution| ]]
[[Category:Biology theories]]
[[Category:Evolutionary biology|*]]