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To understand the mechanisms that cause a population to evolve, it is useful to consider what conditions are required for a population not to evolve. The ''[[Hardy-Weinberg principle]]'' states that the frequencies of alleles (variations in a gene) in a sufficiently large population will remain constant if the only forces acting on that population are the random reshuffling of alleles during the formation of the sperm or egg, and the random combination of the alleles in these sex cells during [[Fertilisation|fertilization]].<ref name=oneil>{{cite web |url=http://anthro.palomar.edu/synthetic/synth_2.htm|title= Hardy-Weinberg Equilibrium Model|accessdate=2008-01-06 |last= O'Neil |first=Dennis |year=2008 |work= The synthetic theory of evolution: An introduction to modern evolutionary concepts and theories|publisher=Behavioral Sciences Department, Palomar College }}</ref> Such a population is said to be in ''Hardy-Weinberg equilibrium'' - it is not evolving.<ref name= Teach2>{{cite web |url=http://www.evoled.org/lessons/speciation.htm|title= Causes of evolution|accessdate=2007-12-30 |last= Bright |first=Kerry |year=2006 |work= Teach Evolution and Make It Relevant |publisher=National Science Foundation}}</ref>
== Mechanisms ==
The three main mechanisms that produce evolution are [[natural selection]], [[genetic drift]], and [[gene flow]]. Natural selection favors genes that improve capacity for survival and reproduction. Genetic drift is random change in the frequency of alleles, caused by the random sampling of a generation's genes during reproduction. Gene flow is the transfer of genes within and between populations. The relative importance of natural selection and genetic drift in a population varies depending on the strength of the selection and the [[effective population size]], which is the number of individuals capable of breeding.<ref name=Whitlock>{{cite journal |author=Whitlock M |title=Fixation probability and time in subdivided populations |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12807795 |journal=Genetics |volume=164 |issue=2 |pages=767–79 |year=2003 |pmid=12807795}}</ref> Natural selection usually predominates in large populations, while genetic drift dominates in small populations. The dominance of genetic drift in small populations can even lead to the fixation of slightly deleterious mutations.<ref name=Ohta>{{cite journal |author=Ohta T |title=Near-neutrality in evolution of genes and gene regulation |url=http://www.pnas.org/cgi/content/abstract/252626899v1 |journal=[[Proceedings of the National Academy of Sciences|PNAS]] |volume=99 |issue=25 |pages=16134–37 |year=2002 |doi=10.1073/pnas.252626899 |pmid=12461171}}</ref> As a result, changing population size can dramatically influence the course of evolution. [[Population bottleneck]]s, where the population shrinks temporarily and therefore loses genetic variation, result in a more uniform population.<ref name=Amos/> Bottlenecks also result from alterations in gene flow such as decreased migration, [[founder effect|expansions into new habitats]], or population subdivision.<ref name=Whitlock/>
=== Natural selection ===
{{details more|Natural selection|Fitness (biology)}}
[[किपा:Mutation and selection diagram.svg|thumb|right|300px|[[Natural selection]] of a population for dark coloration.]]
[[Natural selection]] is the process by which genetic mutations that enhance reproduction become, and remain, more common in successive generations of a population. It has often been called a "self-evident" mechanism because it necessarily follows from three simple facts:
* Heritable variation exists within populations of organisms.
* Organisms produce more offspring than can survive.
* These offspring vary in their ability to survive and reproduce.
These conditions produce competition between organisms for survival and reproduction. Consequently, organisms with traits that give them an advantage over their competitors pass these advantageous traits on, while traits that do not confer an advantage are not passed on to the next generation.<ref name=Hurst>{{cite journal |author=Hurst LD |title=Fundamental concepts in genetics: genetics and the understanding of selection |journal=Nat. Rev. Genet. |volume=10 |issue=2 |pages=83–93 |year=2009 |month=February |pmid=19119264 |doi=10.1038/nrg2506}}</ref>
The central concept of natural selection is the [[fitness (biology)|evolutionary fitness]] of an organism. This measures the organism's genetic contribution to the next generation. However, this is not the same as the total number of offspring: instead fitness measures the proportion of subsequent generations that carry an organism's genes.<ref name=Haldane>{{cite journal |author=Haldane J |title=The theory of natural selection today |journal=Nature |volume=183 |issue=4663 |pages=710–13 |year=1959 |pmid=13644170 | doi=10.1038/183710a0}}</ref> Consequently, if an allele increases fitness more than the other alleles of that gene, then with each generation this allele will become more common within the population. These traits are said to be "selected ''for''". Examples of traits that can increase fitness are enhanced survival, and increased [[fecundity]]. Conversely, the lower fitness caused by having a less beneficial or deleterious allele results in this allele becoming rarer — they are "selected ''against''".<ref name=Lande/> 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"/>
Natural selection within a population for a trait that can vary across a range of values, such as height, can be categorized 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 |author=Hoekstra H, Hoekstra J, Berrigan D, Vignieri S, Hoang A, Hill C, Beerli P, Kingsolver J |title=Strength and tempo of directional selection in the wild |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11470913 |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=98 |issue=16 |pages=9157–60 |year=2001 |pmid=11470913 |doi=10.1073/pnas.161281098}}</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 [[stabilizing 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>{{cite journal |author=Felsenstein |title=Excursions along the Interface between Disruptive and Stabilizing Selection |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17248980 |journal=Genetics |volume=93 |issue=3 |pages=773–95 |year=1979 |pmid=17248980}}</ref><ref name=Hurst/> This would, for example, cause organisms to slowly become all the same height.
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 |author=Andersson M, Simmons L |title=Sexual selection and mate choice |journal=Trends Ecol. Evol. (Amst.) |volume=21 |issue=6 |pages=296–302 |year=2006 |pmid=16769428 |doi=10.1016/j.tree.2006.03.015}}</ref> Traits that evolved through sexual selection are particularly prominent in males of some animal species, despite traits such as cumbersome antlers, mating calls or bright colors that attract predators, decreasing the survival of individual males.<ref>{{cite journal |author=Kokko H, Brooks R, McNamara J, Houston A |title=The sexual selection continuum |url=http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1691039&blobtype=pdf |journal=Proc. Biol. Sci. |volume=269 |issue=1498 |pages=1331–40 |year=2002 |pmid=12079655 |doi=10.1098/rspb.2002.2020}}</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 |author=Hunt J, Brooks R, Jennions M, Smith M, Bentsen C, Bussière L |title=High-quality male field crickets invest heavily in sexual display but die young |journal=Nature |volume=432 |issue=7020 |pages=1024–27 |year=2004 |pmid=15616562 | doi=10.1038/nature03084}}</ref>
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|physical]] as well as [[biotic|biological]], in their local [[environment (biophysical)|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 (ie: exchange of materials between living and nonliving parts) within the system."<ref name="Odum1971">Odum, EP (1971) Fundamentals of ecology, third edition, Saunders New York</ref> Each population within an ecosystem occupies a distinct [[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.
An active area of research is the [[unit of selection]], with natural selection being proposed to work at the level of genes, cells, individual organisms, groups of organisms and even species.<ref name=Gould>{{cite journal |author=Gould SJ |title=Gulliver's further travels: the necessity and difficulty of a hierarchical theory of selection |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533127 |journal=Philos. Trans. R. Soc. Lond., B, Biol. Sci. |volume=353 |issue=1366 |pages=307–14 |year=1998 |pmid=9533127 |doi=10.1098/rstb.1998.0211}}</ref><ref>{{cite journal |author=Mayr E |title=The objects of selection |doi= 10.1073/pnas.94.6.2091 |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=94 |issue=6 |pages=2091–94 |year=1997 |pmid=9122151}}</ref> None of these are mutually exclusive and selection may act on multiple levels simultaneously.<ref>{{cite journal |author=Maynard Smith J |title=The units of selection |journal=Novartis Found. Symp. |volume=213 |pages=203–11; discussion 211–17 |year=1998 |pmid=9653725}}</ref> An example of selection occurring below the level of the individual organism are genes called [[transposon]]s, which can replicate and spread throughout a [[genome]].<ref>{{cite journal |author=Hickey DA |title=Evolutionary dynamics of transposable elements in prokaryotes and eukaryotes |journal=Genetica |volume=86 |issue=1–3 |pages=269–74 |year=1992 |pmid=1334911 | doi=10.1007/BF00133725}}</ref> Selection at a level above the individual, such as [[group selection]], may allow the evolution of co-operation, as discussed below.<ref>{{cite journal |author=Gould SJ, Lloyd EA |title=Individuality and adaptation across levels of selection: how shall we name and generalize the unit of Darwinism? |doi= 10.1073/pnas.96.21.11904 |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=96 |issue=21 |pages=11904–09 |year=1999 |pmid=10518549}}</ref>
=== Genetic drift ===
{{details more|Genetic drift|Effective population size}}
[[किपा:Allele-frequency.png|thumb|right|250px| 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.]]
Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in offspring are a [[sampling (statistics)|random sample]] of those in the parents, as well as from the role that chance plays in determining whether a given individual will survive and reproduce.<ref name=Amos/> In mathematical terms, alleles are subject to [[sampling error]]. As a result, when selective forces are absent or relatively weak, allele frequencies tend to "drift" upward or downward randomly (in a [[random walk]]). This drift halts when an allele eventually becomes [[Fixation (population genetics)|fixed]], either by disappearing from the population, or 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 began with the same genetic structure to drift apart into two divergent populations with different sets of alleles.<ref>{{cite journal |author=Lande R |title=Fisherian and Wrightian theories of speciation |journal=Genome |volume=31 |issue=1 |pages=221–27 |year=1989 |pmid=2687093}}</ref>
The time for an allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations.<ref>{{cite journal |author=Otto S, Whitlock M |title=The probability of fixation in populations of changing size |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9178020 |journal=Genetics |volume=146 |issue=2 |pages=723–33 |year=1997 |pmid=9178020}}</ref> The precise measure of population that is important is called the [[effective population size]]. The effective population is always smaller than the total population since it takes into account factors such as the level of inbreeding, the number of animals that are too old or young to breed, and the lower probability of animals that live far apart managing to mate with each other.<ref>{{cite journal |author=Charlesworth B |title=Fundamental concepts in genetics: Effective population size and patterns of molecular evolution and variation |journal=Nat. Rev. Genet. |volume=10 |pages=195-205 |year=2009 |month=March |pmid=19204717 |doi=10.1038/nrg2526}}</ref>
Although natural selection is responsible for adaptation, the relative importance of the two forces of natural selection and genetic drift in driving evolutionary change in general is an area of current research in evolutionary biology.<ref>{{cite journal |author=Nei M |title=Selectionism and neutralism in molecular evolution |doi= 10.1093/molbev/msi242 |journal=Mol. Biol. Evol. |volume=22 |issue=12 |pages=2318–42 |year=2005 |pmid=16120807}}</ref> These investigations were prompted by the [[neutral theory of molecular evolution]], which proposed that most evolutionary changes are the result of the fixation of [[neutral mutation]]s that do not have any immediate effects on the fitness of an organism.<ref>{{cite journal |author=Kimura M |title=The neutral theory of molecular evolution: a review of recent evidence |url=http://www.jstage.jst.go.jp/article/jjg/66/4/66_367/_article |journal=Jpn. J. Genet. |volume=66 |issue=4 |pages=367–86 |year=1991 |pmid=1954033 |doi=10.1266/jjg.66.367}}</ref> Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift.<ref>{{cite journal |author=Kimura M |title=The neutral theory of molecular evolution and the world view of the neutralists |journal=Genome |volume=31 |issue=1 |pages=24–31 |year=1989 |pmid=2687096}}</ref> This form of the neutral theory is now largely abandoned, since it does not seem to fit the genetic variation seen in nature.<ref>{{cite journal |author=Kreitman M |title=The neutral theory is dead. Long live the neutral theory |journal=Bioessays |volume=18 |issue=8 |pages=678–83; discussion 683 |year=1996 |month=August |pmid=8760341 |doi=10.1002/bies.950180812 |url=http://www.cs.ucsb.edu/~ambuj/Courses/bioinformatics/neutral-theory}}</ref><ref>{{cite journal|author=Leigh E.G. (Jr) | year=2007| title=Neutral theory: a historical perspective.| journal=[[Journal of Evolutionary Biology]] |volume=20 |pages=2075–2091| doi=10.1111/j.1420-9101.2007.01410.x}}</ref> However, a more recent and better-supported version of this model is the [[nearly neutral theory of molecular evolution|nearly-neutral theory]], where most mutations only have small effects on fitness.<ref name=Hurst/>
=== Gene flow ===
{{details more|Gene flow|Hybrid (biology)|Horizontal gene transfer}}
[[किपा:Lion waiting in Namibia.jpg|250px|thumb|left|Male [[lion]]s leave the pride where they are born and take over a new pride to mate. This results in [[gene flow]] between prides.]]
[[Gene flow]] is the exchange of genes between populations, which are usually of the same species.<ref>{{cite journal |author=Morjan C, Rieseberg L |title=How species evolve collectively: implications of gene flow and selection for the spread of advantageous alleles |journal=Mol. Ecol. |volume=13 |issue=6 |pages=1341–56 |year=2004 |pmid=15140081 |doi=10.1111/j.1365-294X.2004.02164.x}}</ref> Examples of gene flow within a species include the migration and then breeding of organisms, or the exchange of [[pollen]]. Gene transfer between species includes the formation of [[Hybrid (biology)|hybrid]] organisms and [[horizontal gene transfer]].
Migration into or out of a population can change allele frequencies, as well as introducing genetic variation into a population. Immigration may add new genetic material to the established [[gene pool]] of a population. Conversely, emigration may remove genetic material. As [[reproductive isolation|barriers to reproduction]] between two diverging populations are required for the populations to [[speciation|become new species]], gene flow may slow this process by spreading genetic differences between the populations. Gene flow is hindered by mountain ranges, oceans and deserts or even man-made structures such as the [[Great Wall of China]], which has hindered the flow of plant genes.<ref>{{cite journal |author=Su H, Qu L, He K, Zhang Z, Wang J, Chen Z, Gu H |title=The Great Wall of China: a physical barrier to gene flow? |journal=Heredity |volume=90 |issue=3 |pages=212–19 |year=2003 |pmid=12634804 |doi=10.1038/sj.hdy.6800237}}</ref>
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 [[horse]]s and [[donkey]]s mating to produce [[mule]]s.<ref>{{cite journal |author=Short RV |title=The contribution of the mule to scientific thought |journal=J. Reprod. Fertil. Suppl. |issue=23 |pages=359–64 |year=1975 |pmid=1107543}}</ref> Such [[Hybrid (biology)|hybrids]] are generally [[infertility|infertile]], due to the two different sets of chromosomes being unable to pair up during [[meiosis]]. 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 |author=Gross B, Rieseberg L |title=The ecological genetics of homoploid hybrid speciation |doi= 10.1093/jhered/esi026 |journal=J. Hered. |volume=96 |issue=3 |pages=241–52 |year=2005 |pmid=15618301}}</ref> The importance of hybridization in creating [[hybrid speciation|new species]] of animals is unclear, although cases have been seen in many types of animals,<ref>{{cite journal |author=Burke JM, Arnold ML |title=Genetics and the fitness of hybrids |journal=Annu. Rev. Genet. |volume=35 |issue= |pages=31–52 |year=2001 |pmid=11700276 |doi=10.1146/annurev.genet.35.102401.085719 }}</ref> with the [[gray tree frog]] being a particularly well-studied example.<ref>{{cite journal |author=Vrijenhoek RC |title=Polyploid hybrids: multiple origins of a treefrog species |journal=Curr. Biol. |volume=16 |issue=7 | pages = R245 |year=2006 |pmid=16581499 |doi=10.1016/j.cub.2006.03.005 }}</ref>
Hybridization is, however, an important means of speciation in plants, since [[polyploidy]] (having more than two copies of each chromosome) is tolerated in plants more readily than in animals.<ref name=Wendel>{{cite journal |author=Wendel J |title=Genome evolution in polyploids |journal=Plant Mol. Biol. |volume=42 |issue=1 |pages=225–49 |year=2000 |pmid=10688139 |doi=10.1023/A:1006392424384 }}</ref><ref name=Semon>{{cite journal |author=Sémon M, Wolfe KH |title=Consequences of genome duplication |journal=Curr Opin Genet Dev |volume=17 |issue=6 |pages=505–12 |year=2007 |pmid=18006297 |doi=10.1016/j.gde.2007.09.007 }}</ref> Polyploidy is important in hybrids as it allows reproduction, with the two different sets of chromosomes each being able to pair with an identical partner during meiosis.<ref>{{cite journal |author=Comai L |title=The advantages and disadvantages of being polyploid |journal=Nat. Rev. Genet. |volume=6 |issue=11 |pages=836–46 |year=2005 |pmid=16304599 |doi=10.1038/nrg1711 }}</ref> Polyploids also have more genetic diversity, which allows them to avoid [[inbreeding depression]] in small populations.<ref>{{cite journal |author=Soltis P, Soltis D |title=The role of genetic and genomic attributes in the success of polyploids |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10860970 |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=97 |issue=13 |pages=7051–57 |year=2000 |pmid=10860970 |doi=10.1073/pnas.97.13.7051 }}</ref>
[[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 |author=Boucher Y, Douady CJ, Papke RT, Walsh DA, Boudreau ME, Nesbo CL, Case RJ, Doolittle WF |title=Lateral gene transfer and the origins of prokaryotic groups |doi=10.1146/annurev.genet.37.050503.084247 |journal=Annu Rev Genet |volume=37 |pages=283–328 |year=2003 |pmid=14616063}}</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>{{cite journal |author=Walsh T |title=Combinatorial genetic evolution of multiresistance |journal=Curr. Opin. Microbiol. |volume=9 |issue=5 |pages=476–82 |year=2006 |pmid=16942901 |doi=10.1016/j.mib.2006.08.009 }}</ref> Horizontal transfer of genes from bacteria to eukaryotes such as the yeast ''[[Saccharomyces cerevisiae]]'' and the adzuki bean beetle ''Callosobruchus chinensis'' may also have occurred.<ref>{{cite journal |author=Kondo N, Nikoh N, Ijichi N, Shimada M, Fukatsu T |title=Genome fragment of Wolbachia endosymbiont transferred to X chromosome of host insect |journal=Proc. Natl. Acad. Sci. U.S.A. |volume=99 |issue=22 |pages=14280–85 |year=2002 |pmid=12386340 |doi=10.1073/pnas.222228199 }}</ref><ref>{{cite journal |author=Sprague G |title=Genetic exchange between kingdoms |journal=Curr. Opin. Genet. Dev. |volume=1 |issue=4 |pages=530–33 |year=1991 |pmid=1822285 |doi=10.1016/S0959-437X(05)80203-5}}</ref> An example of larger-scale transfers are the eukaryotic [[Bdelloidea|bdelloid rotifers]], which appear to have received a range of genes from bacteria, fungi, and plants.<ref>{{cite journal |author=Gladyshev EA, Meselson M, Arkhipova IR |title=Massive horizontal gene transfer in bdelloid rotifers |journal=Science (journal) |volume=320 |issue=5880 |pages=1210–3 |year=2008 |month=May |pmid=18511688 |doi=10.1126/science.1156407}}</ref> [[Virus]]es can also carry DNA between organisms, allowing transfer of genes even across [[domain (biology)|biological domains]].<ref>{{cite journal |author=Baldo A, McClure M |title=Evolution and horizontal transfer of dUTPase-encoding genes in viruses and their hosts |url=http://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10438861 |journal=J. Virol. |volume=73 |issue=9 |pages=7710–21 |year=1999 |pmid=10438861}}</ref> Large-scale gene transfer has also occurred between the ancestors of [[eukaryote|eukaryotic cells]] and prokaryotes, during the acquisition of [[chloroplast]]s and [[Mitochondrion|mitochondria]].<ref name = "rgruqh">{{cite journal |author=Poole A, Penny D |title=Evaluating hypotheses for the origin of eukaryotes |journal=Bioessays |volume=29 |issue=1 |pages=74–84 |year=2007 |pmid=17187354 |doi=10.1002/bies.20516 }}</ref>
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