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Do not fill this in! == 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="ScottEC">{{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 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="Jablonski2000">{{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="sciam_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">{{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">{{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.{{imagefact|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 (journals)|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 |doi-access= }}</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="transformation445">{{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="Penny1999">{{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">{{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 |pages=249–268 |doi=10.1146/annurev.es.26.110195.001341}}</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="transformation445" /> 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 tooth|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 }}</ref> the [[coccyx]],<ref name="Fong" /> the [[vermiform appendix]],<ref name="Fong" /> 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="ScottEC" /> 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 |doi-access= }} * {{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">{{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">{{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="Queiroz">{{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="Ereshefsky92">{{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="Queiroz" /> 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="Queiroz" /><ref name="Ereshefsky92" /> [[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 [[gray 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=10.2307/2409766 |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="Losos1997">{{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" /> Generally this occurs when there has been a drastic change in the environment within the parental species' habitat. One example is the grass ''[[Anthoxanthum|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}}</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=719–23 |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 [[polyploidy|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="Semon">{{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|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="StearnsStearns1999">{{harvnb|Stearns|Stearns|1999|p=[https://books.google.com/books?id=0BHeC-tXIB4C&q=99%20percent X]}}</ref><ref name="NYT-20141108-MJN" /> about 1 trillion species are estimated to be on Earth currently with only one-thousandth of 1% described.<ref name="NSF-2016002">{{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" /> 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" /> 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}} Summary: Please note that all contributions to Christianpedia may be edited, altered, or removed by other contributors. 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