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In [[biology]], '''evolution''' is the change in the [[heritability|inherited]] [[trait (biology)|traits]] of a [[population]] from generation to generation. These traits are the [[gene expression|expression]] of [[gene]]s that are copied and passed on to offspring during [[biological reproduction|reproduction]]. [[Mutation]]s in these genes can produce new or altered traits, resulting in heritable differences ([[genetic variation]]) between organisms. New traits can also come from transfer of genes between populations, as in [[migration]], or between species, in [[horizontal gene transfer]]. Evolution occurs when these heritable differences become more common or rare in a population, either non-randomly through [[natural selection]] or randomly through [[genetic drift]].

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Natural selection is a process that causes heritable traits that are helpful for survival and reproduction to become more common, and harmful traits to become rarer. This occurs because organisms with advantageous traits pass on more copies of these traits to the next generation. The measurement of selection on correlated characters (Evolution, volume 37 Over many generations, [[adaptation]]s occur through a combination of successive, small, random changes in traits, and natural selection of those variants best-suited for their environment.) [~~http~~://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_14] In contrast, [[genetic drift]] produces random changes in the frequency of traits in a population. Genetic drift arises from the element of chance involved in which individuals survive and reproduce.

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Natural selection is a process that causes heritable traits that are helpful for survival and reproduction to become more common, and harmful traits to become rarer. This occurs because organisms with advantageous traits pass on more copies of these traits to the next generation. The measurement of selection on correlated characters (Evolution, volume 37 Over many generations, [[adaptation]]s occur through a combination of successive, small, random changes in traits, and natural selection of those variants best-suited for their environment.) [https://evolution.berkeley.edu/evolibrary/article/0_0_0/evo_14] In contrast, [[genetic drift]] produces random changes in the frequency of traits in a population. Genetic drift arises from the element of chance involved in which individuals survive and reproduce.

<center>For lessons on the [[topic]] of '''''Evolution''''', follow [https://nordan.daynal.org/wiki/index.php?title=Category:Evolution this link].</center>

One definition of a [[species]] is a group of organisms that can reproduce with one another and produce fertile offspring. However, when a species is separated into populations that are [[reproductive isolation|prevented from interbreeding]], mutations, genetic drift, and the selection of novel traits cause the accumulation of differences over generations and the emergence of [[speciation|new species]]. Stephen Gould, The Structure of Evolutionary Theory, Belknap Press, ISBN 0-674-00613-5 . The similarities between organisms suggest that all known species are [[common descent|descended from a common ancestor]] (or ancestral gene pool) through this process of gradual divergence. {Douglas J. Futuyma, Evolution, Sinauer Associates, Sunderland, Massachusetts, ISBN 0-87893-187-2 )

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The [[Theory#Science|theory]] of evolution by natural selection was first proposed by [[Charles Darwin]] and [[Alfred Russel Wallace]] and set out in detail in Darwin's 1859 book [[On the Origin of Species]][~~http~~://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=16]. Related earlier ideas were acknowledged in [~~http~~://darwin-online.org.uk/content/frameset?itemID=F381&viewtype=text&pageseq=20] In the 1930s, Darwinian natural selection was combined with [[Gregor Mendel|Mendelian]] [[Mendelian inheritance|inheritance]] to form the [[modern evolutionary synthesis]], "understanding evolution" in which the connection between the ''units'' of evolution ([[gene]]s) and the ''mechanism'' of evolution (natural selection) was made. This powerful explanatory and [[predictive power|predictive]] theory has become the central organizing principle of modern biology, providing a unifying explanation for the [[biodiversity|diversity of life]] on Earth. [~~http~~://www.interacademies.net/Object.File/Master/6/150/Evolution%20statement.pdf] Statement on the Teaching of Evolution, The Interacademy Panel on International Issues, [~~http~~://www.aaas.org/news/releases/2006/pdf/0219boardstatement.pdf] Statement on the Teaching of Evolution, American Association for the Advancement of Science.

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The [[Theory#Science|theory]] of evolution by natural selection was first proposed by [[Charles Darwin]] and [[Alfred Russel Wallace]] and set out in detail in Darwin's 1859 book [[On the Origin of Species]][https://darwin-online.org.uk/content/frameset?itemID=F373&viewtype=text&pageseq=16]. Related earlier ideas were acknowledged in [https://darwin-online.org.uk/content/frameset?itemID=F381&viewtype=text&pageseq=20] In the 1930s, Darwinian natural selection was combined with [[Gregor Mendel|Mendelian]] [[Mendelian inheritance|inheritance]] to form the [[modern evolutionary synthesis]], "understanding evolution" in which the connection between the ''units'' of evolution ([[gene]]s) and the ''mechanism'' of evolution (natural selection) was made. This powerful explanatory and [[predictive power|predictive]] theory has become the central organizing principle of modern biology, providing a unifying explanation for the [[biodiversity|diversity of life]] on Earth. [https://www.interacademies.net/Object.File/Master/6/150/Evolution%20statement.pdf] Statement on the Teaching of Evolution, The Interacademy Panel on International Issues, [https://www.aaas.org/news/releases/2006/pdf/0219boardstatement.pdf] Statement on the Teaching of Evolution, American Association for the Advancement of Science.

==Heredity==

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==Variation==

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Because an individual's [[phenotype]] results from the interaction of their [[genotype]] with the environment, the variation in phenotypes in a population reflects the variation in these organisms' genotypes. The [[modern evolutionary synthesis]] defines evolution as the change over time in this genetic variation. (Stoltzfus A, Mutationism and the dual causation of evolutionary change, Evol. Dev., v. 8, 2006) The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of [[fixation (population genetics)|fixation]] when it either disappears from the population or replaces the ancestral allele entirely. (Harwood AJ , Factors affecting levels of genetic diversity in natural populations, Philos. Trans. R. Soc. Lond., B, Biol. Sci. v. 353, 1998 [~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533122]

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Because an individual's [[phenotype]] results from the interaction of their [[genotype]] with the environment, the variation in phenotypes in a population reflects the variation in these organisms' genotypes. The [[modern evolutionary synthesis]] defines evolution as the change over time in this genetic variation. (Stoltzfus A, Mutationism and the dual causation of evolutionary change, Evol. Dev., v. 8, 2006) The frequency of one particular allele will fluctuate, becoming more or less prevalent relative to other forms of that gene. Evolutionary forces act by driving these changes in allele frequency in one direction or another. Variation disappears when an allele reaches the point of [[fixation (population genetics)|fixation]] when it either disappears from the population or replaces the ancestral allele entirely. (Harwood AJ , Factors affecting levels of genetic diversity in natural populations, Philos. Trans. R. Soc. Lond., B, Biol. Sci. v. 353, 1998 [https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533122]

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Variation comes from [[mutation]]s in [[genetic material]], migration between populations ([[gene flow]]), and the reshuffling of genes through [[sexual reproduction]]. Variation also comes from exchanges of genes between different species, through [[horizontal gene transfer]] in [[bacteria]], and [[hybrid]]ization in plants. (Draghi J, Turner P, DNA secretion and gene-level selection in bacteria, Microbiology (Reading, Engl.) v.152 |issue=Pt 9, 2006) (Mallet J., Hybrid speciation, Nature, v. 446, 2007) Despite the constant introduction variation through these processes, most of the [[genome]] of a species is identical in all individuals of that species. Butlin RK, Tregenza T, Levels of genetic polymorphism: marker loci versus quantitative traits, Philos. Trans. R. Soc. Lond., B, Biol. Sci., v. 353, 1998) [~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533123] However, even relatively small changes in genotype can lead to dramatic changes in phenotype; for example, chimpanzees and humans differ in only about 5% of their genomes. (Wetterbom A, Sevov M, Cavelier L, Bergström TF, Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution, J. Mol. Evol., v. 63, 2006)

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Variation comes from [[mutation]]s in [[genetic material]], migration between populations ([[gene flow]]), and the reshuffling of genes through [[sexual reproduction]]. Variation also comes from exchanges of genes between different species, through [[horizontal gene transfer]] in [[bacteria]], and [[hybrid]]ization in plants. (Draghi J, Turner P, DNA secretion and gene-level selection in bacteria, Microbiology (Reading, Engl.) v.152 |issue=Pt 9, 2006) (Mallet J., Hybrid speciation, Nature, v. 446, 2007) Despite the constant introduction variation through these processes, most of the [[genome]] of a species is identical in all individuals of that species. Butlin RK, Tregenza T, Levels of genetic polymorphism: marker loci versus quantitative traits, Philos. Trans. R. Soc. Lond., B, Biol. Sci., v. 353, 1998) [https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533123] However, even relatively small changes in genotype can lead to dramatic changes in phenotype; for example, chimpanzees and humans differ in only about 5% of their genomes. (Wetterbom A, Sevov M, Cavelier L, Bergström TF, Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution, J. Mol. Evol., v. 63, 2006)

===Mutation===

Genetic variation comes from [[randomness|random]] mutations that occur in the genomes of organisms. Mutations are changes in the DNA sequence of a cell's genome and are caused by [[Radioactive decay|radiation]], [[virus]]es, [[transposon]]s and [[mutagen|mutagenic chemicals]], as well as errors that occur during [[meiosis]] or [[DNA replication]]. (Bertram, The molecular biology of cancer, Mol. Aspects Med., v. 21, 2000) (Aminetzach YT, Macpherson JM, Petrov DA, Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila, Science, v. 309 2005)

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These mutagens produce several different types of change in DNA sequences; these can either have no effect, alter the [[gene product|product of a gene]], or prevent the gene from functioning. Studies in the fly ''[[Drosophila melanogaster]]'' suggest that about 70 percent of mutations are deleterious, and the remainder are either neutral or have a weak beneficial effect. [~~http~~://www.pnas.org/cgi/content/full/104/16/6504] Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as [[DNA repair]] to remove mutations.

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These mutagens produce several different types of change in DNA sequences; these can either have no effect, alter the [[gene product|product of a gene]], or prevent the gene from functioning. Studies in the fly ''[[Drosophila melanogaster]]'' suggest that about 70 percent of mutations are deleterious, and the remainder are either neutral or have a weak beneficial effect. [https://www.pnas.org/cgi/content/full/104/16/6504] Due to the damaging effects that mutations can have on cells, organisms have evolved mechanisms such as [[DNA repair]] to remove mutations.

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Large sections of DNA can also be [[gene duplication|duplicated]], which is a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. ISBN 1-4051-1950-0. Most genes belong to larger [[gene family|families of genes]] of [[homology (biology)|shared ancestry]]. Novel genes are produced either through duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. For example, the human eye uses four genes to make structures that sense light: three for [[Cone cell|color vision]] and one for [[Rod cell|night vision]]; all four arose from a single ancestral gene. An advantage of duplicating a gene (or even an ([[polyploid|entire genome]]) is that overlapping or [[Redundancy (engineering)|redundant functions]] in multiple genes allows alleles to be retained that would otherwise be harmful, thus increasing genetic diversity. [~~http~~://www.genome.org/cgi/content/full/9/4/317]

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Large sections of DNA can also be [[gene duplication|duplicated]], which is a major source of raw material for evolving new genes, with tens to hundreds of genes duplicated in animal genomes every million years. ISBN 1-4051-1950-0. Most genes belong to larger [[gene family|families of genes]] of [[homology (biology)|shared ancestry]]. Novel genes are produced either through duplication and mutation of an ancestral gene, or by recombining parts of different genes to form new combinations with new functions. For example, the human eye uses four genes to make structures that sense light: three for [[Cone cell|color vision]] and one for [[Rod cell|night vision]]; all four arose from a single ancestral gene. An advantage of duplicating a gene (or even an ([[polyploid|entire genome]]) is that overlapping or [[Redundancy (engineering)|redundant functions]] in multiple genes allows alleles to be retained that would otherwise be harmful, thus increasing genetic diversity. [https://www.genome.org/cgi/content/full/9/4/317]

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Changes in chromosome number may also involve the breakage and rearrangement of DNA within chromosomes. For example, two chromosomes in the [[Homo (genus)|''Homo'']] genus fused to produce human chromosome 2; this fusion did not occur in the chimpanzee [[Lineage (evolution)|lineage]] and chimpanzees retain these separate chromosomes. [~~http~~://www.genome.org/cgi/content/full/14/5/845] In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by preserving genetic differences within populations.

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Changes in chromosome number may also involve the breakage and rearrangement of DNA within chromosomes. For example, two chromosomes in the [[Homo (genus)|''Homo'']] genus fused to produce human chromosome 2; this fusion did not occur in the chimpanzee [[Lineage (evolution)|lineage]] and chimpanzees retain these separate chromosomes. [https://www.genome.org/cgi/content/full/14/5/845] In evolution, the most important role of such chromosomal rearrangements may be to accelerate the divergence of a population into new species by preserving genetic differences within populations.

Sequences of DNA that can move about the genome, such as [[transposon]]s, make up a major fraction of the genetic material of plants and animals, and may have been important in the evolution of genomes. For example, more than a million copies of the [[Alu sequence]] are present in the [[human genome]], and these sequences have now been recruited to perform functions such as regulating [[gene expression]]. Another effect of these mobile DNA sequences is that when they move within a genome, they can mutate or delete existing genes and thereby produce genetic diversity.

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===Recombination===

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In asexual organisms, genes are inherited together, or ''linked'', as they cannot mix with genes in other organisms during reproduction. However, the offspring of [[sex]]ual organisms contain a random mixture of their parents' chromosomes that is produced through [[independent assortment]]. In the related process of [[genetic recombination]], sexual organisms can also exchange DNA between two matching chromosomes. These shuffling processes can allow even alleles that are close together in a strand of DNA to be [[Mendelian inheritance#Mendel.27s law of segregation|inherited independently]]. However, as only about one recombination event occurs per million [[base pair]]s in humans, genes close together on a chromosome may not be shuffled away from each other, and tend to be inherited together. [~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10677316] This tendency is measured by finding how often two alleles occur together, which is called their [[linkage disequilibrium]]. A set of alleles that is usually inherited in a group is called a [[haplotype]], and this co-inheritance can indicate that the locus is under positive selection. Recombination in sexual organisms helps to remove harmful mutations and retain beneficial mutations. Consequently, when alleles cannot be separated by recombination – such as in mammalian [[Y chromosome]]s, which pass intact from fathers to sons – harmful [[Muller's ratchet|mutations accumulate]].[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11127901] In addition, recombination can produce individuals with new and advantageous gene combinations. These positive effects of recombination are balanced by the fact that this process can cause mutations and separate beneficial combinations of genes. The optimal rate of recombination for a species is therefore a trade-off between conflicting factors.

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In asexual organisms, genes are inherited together, or ''linked'', as they cannot mix with genes in other organisms during reproduction. However, the offspring of [[sex]]ual organisms contain a random mixture of their parents' chromosomes that is produced through [[independent assortment]]. In the related process of [[genetic recombination]], sexual organisms can also exchange DNA between two matching chromosomes. These shuffling processes can allow even alleles that are close together in a strand of DNA to be [[Mendelian inheritance#Mendel.27s law of segregation|inherited independently]]. However, as only about one recombination event occurs per million [[base pair]]s in humans, genes close together on a chromosome may not be shuffled away from each other, and tend to be inherited together. [https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10677316] This tendency is measured by finding how often two alleles occur together, which is called their [[linkage disequilibrium]]. A set of alleles that is usually inherited in a group is called a [[haplotype]], and this co-inheritance can indicate that the locus is under positive selection. Recombination in sexual organisms helps to remove harmful mutations and retain beneficial mutations. Consequently, when alleles cannot be separated by recombination – such as in mammalian [[Y chromosome]]s, which pass intact from fathers to sons – harmful [[Muller's ratchet|mutations accumulate]].[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11127901] In addition, recombination can produce individuals with new and advantageous gene combinations. These positive effects of recombination are balanced by the fact that this process can cause mutations and separate beneficial combinations of genes. The optimal rate of recombination for a species is therefore a trade-off between conflicting factors.

==Mechanisms==

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There are three basic mechanisms of evolutionary change: [[natural selection]], [[genetic drift]], and [[gene flow]]. Natural selection favors genes that improve capacity for survival and reproduction. Genetic drift is the random sampling of a generation's genes during reproduction, causing random changes in the frequency of alleles, and 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.[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12807795] 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.[~~http~~://www.pnas.org/cgi/content/abstract/252626899v1] 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. Bottlenecks also result from alterations in gene flow such as decreased migration, [[founder effect|expansions into new habitats]], or population subdivision.

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There are three basic mechanisms of evolutionary change: [[natural selection]], [[genetic drift]], and [[gene flow]]. Natural selection favors genes that improve capacity for survival and reproduction. Genetic drift is the random sampling of a generation's genes during reproduction, causing random changes in the frequency of alleles, and 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.[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=12807795] 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.[https://www.pnas.org/cgi/content/abstract/252626899v1] 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. Bottlenecks also result from alterations in gene flow such as decreased migration, [[founder effect|expansions into new habitats]], or population subdivision.

===Natural selection===

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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. 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''". 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.

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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.[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11470913] 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.[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17248980] This would, for example, cause organisms to slowly become all the same height.

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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.[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=11470913] 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.[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=17248980] This would, for example, cause organisms to slowly become all the same height.

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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. 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.[~~http~~://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1691039&blobtype=pdf] This survival disadvantage is balanced by higher reproductive success in males that show these [[Handicap principle|hard to fake]], sexually selected traits.

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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. 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.[https://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1691039&blobtype=pdf] This survival disadvantage is balanced by higher reproductive success in males that show these [[Handicap principle|hard to fake]], sexually selected traits.

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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.[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533127] [~~http~~://www.pnas.org/cgi/content/full/94/6/2091] None of these models are mutually-exclusive and selection may act on multiple levels simultaneously. Below the level of the individual, genes called transposons try to copy themselves throughout the [[genome]]. Selection at a level above the individual, such as [[group selection]], may allow the evolution of co-operation, as discussed below. [~~http~~://www.pnas.org/cgi/content/full/96/21/11904] Drift is more rapid in the smaller population.]]

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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.[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9533127] [https://www.pnas.org/cgi/content/full/94/6/2091] None of these models are mutually-exclusive and selection may act on multiple levels simultaneously. Below the level of the individual, genes called transposons try to copy themselves throughout the [[genome]]. Selection at a level above the individual, such as [[group selection]], may allow the evolution of co-operation, as discussed below. [https://www.pnas.org/cgi/content/full/96/21/11904] Drift is more rapid in the smaller population.]]

===Genetic drift===

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Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in the offspring generation are a [[sampling (statistics)|random sample]] of those in the parent generation, and are thus subject to [[sampling error]]. As a result, when selective forces are absent or relatively weak, allele frequencies tend to "drift" upward or downward 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, and two separate populations that began with the same genetic structure can drift apart by random fluctuation into two divergent populations with different sets of alleles. The time for an allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations.[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9178020]

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Genetic drift is the change in allele frequency from one generation to the next that occurs because alleles in the offspring generation are a [[sampling (statistics)|random sample]] of those in the parent generation, and are thus subject to [[sampling error]]. As a result, when selective forces are absent or relatively weak, allele frequencies tend to "drift" upward or downward 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, and two separate populations that began with the same genetic structure can drift apart by random fluctuation into two divergent populations with different sets of alleles. The time for an allele to become fixed by genetic drift depends on population size, with fixation occurring more rapidly in smaller populations.[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=9178020]

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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.[~~http~~://mbe.oxfordjournals.org/cgi/content/full/22/12/2318] These investigations were prompted by the [[neutral theory of molecular evolution]], which proposed that most evolutionary changes are the result the fixation of [[neutral mutation]]s that do not have any immediate effects on the fitness of an organism. [~~http~~://www.jstage.jst.go.jp/article/jjg/66/4/66_367/_article] Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift.

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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.[https://mbe.oxfordjournals.org/cgi/content/full/22/12/2318] These investigations were prompted by the [[neutral theory of molecular evolution]], which proposed that most evolutionary changes are the result the fixation of [[neutral mutation]]s that do not have any immediate effects on the fitness of an organism. [https://www.jstage.jst.go.jp/article/jjg/66/4/66_367/_article] Hence, in this model, most genetic changes in a population are the result of constant mutation pressure and genetic drift.

===Gene flow===

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[[Migration]] into or out of a population can change allele frequencies. 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.

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Depending on how far two species have diverged since their [[last common ancestor]], it may still be possible for them to produce offspring, as with [[horse]]s and [[donkey]]s mating to produce [[mule]]s. Such [[hybrid]]s 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. [~~http~~://jhered.oxfordjournals.org/cgi/content/full/96/3/241] Hybridization rarely leads to [[hybrid speciation|new species]] in animals, although this has been seen in [[Gray tree frog]]. 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.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. Polyploids also have more genetic diversity, which allows them to avoid [[inbreeding depression]] in small populations. [~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10860970]

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Depending on how far two species have diverged since their [[last common ancestor]], it may still be possible for them to produce offspring, as with [[horse]]s and [[donkey]]s mating to produce [[mule]]s. Such [[hybrid]]s 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. [https://jhered.oxfordjournals.org/cgi/content/full/96/3/241] Hybridization rarely leads to [[hybrid speciation|new species]] in animals, although this has been seen in [[Gray tree frog]]. 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.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. Polyploids also have more genetic diversity, which allows them to avoid [[inbreeding depression]] in small populations. [https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10860970]

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[[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 [[bacterium|bacteria]]. [~~http~~://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.37.050503.084247] 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. 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. [[Virus]]es can also carry DNA between organisms, allowing transfer of genes even across [[domain (biology)|biological domains]]. Gene transfer has also occurred within [[eukaryote|eukaryotic cells]], from the [[chloroplast]] and [[mitochondria]]l genomes to [[cell nucleus|nuclear genomes]].

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[[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 [[bacterium|bacteria]]. [https://arjournals.annualreviews.org/doi/abs/10.1146/annurev.genet.37.050503.084247] 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. 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. [[Virus]]es can also carry DNA between organisms, allowing transfer of genes even across [[domain (biology)|biological domains]]. Gene transfer has also occurred within [[eukaryote|eukaryotic cells]], from the [[chloroplast]] and [[mitochondria]]l genomes to [[cell nucleus|nuclear genomes]].

==Outcomes==

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These outcomes of evolution are sometimes divided into [[macroevolution]], which is evolution that occurs at or above the level of species, such as [[speciation]], and [[microevolution]], which is smaller evolutionary changes, such as adaptations, within a species or population. In general, macroevolution is the outcome of long periods of microevolution.(Hendry AP, Kinnison MT, An introduction to microevolution: rate, pattern, process |journal=Genetica |volume=112–113) Thus, the distinction between micro- and macroevolution is not a fundamental one - the difference is simply the time involved. However, in macroevolution, the traits of the entire species are important. For instance, a large amount of variation among individuals allows a species to rapidly adapt to new habitats, 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 can sometimes be separate.

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A common misconception is that evolution is "progressive," but natural selection has no long-term goal and does not necessarily produce greater complexity.[~~http~~://www.sciam.com/askexpert_question.cfm?articleID=00071863-683B-1C72-9EB7809EC588F2D7 Scientific American; Biology: Is the human race evolving or devolving?], see also [[biological devolution]]. Although [[evolution of complexity|complex species]] have evolved, this occurs as a side effect of the overall number of organisms increasing, and simple forms of life remain more common. (Chance and necessity: the evolution of morphological complexity and diversity |journal=Nature |volume=409 |issue=6823 |pages=1102-09 |year=2001 |pmid=11234024) For example, the overwhelming majority of species are microscopic [[prokaryote]]s, which form about half the world's biomass despite their small size, (Whitman W, Coleman D, Wiebe W Prokaryotes: the unseen majority [~~http~~://www.pnas.org/cgi/content/full/95/12/6578] and constitute the vast majority of Earth's biodiversity.[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590780#r6] Simple organisms therefore remain the dominant form of life on Earth, and complex life appears more diverse only because it is [[biased sample|more noticeable]].

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A common misconception is that evolution is "progressive," but natural selection has no long-term goal and does not necessarily produce greater complexity.[https://www.sciam.com/askexpert_question.cfm?articleID=00071863-683B-1C72-9EB7809EC588F2D7 Scientific American; Biology: Is the human race evolving or devolving?], see also [[biological devolution]]. Although [[evolution of complexity|complex species]] have evolved, this occurs as a side effect of the overall number of organisms increasing, and simple forms of life remain more common. (Chance and necessity: the evolution of morphological complexity and diversity |journal=Nature |volume=409 |issue=6823 |pages=1102-09 |year=2001 |pmid=11234024) For example, the overwhelming majority of species are microscopic [[prokaryote]]s, which form about half the world's biomass despite their small size, (Whitman W, Coleman D, Wiebe W Prokaryotes: the unseen majority [https://www.pnas.org/cgi/content/full/95/12/6578] and constitute the vast majority of Earth's biodiversity.[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=15590780#r6] Simple organisms therefore remain the dominant form of life on Earth, and complex life appears more diverse only because it is [[biased sample|more noticeable]].

===Adaptation===

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Adaptations are structures or behaviors that enhance a specific function, causing organisms to become better at surviving and reproducing. They are produced by a combination of the continuous production of small, random changes in traits, followed by natural selection of the variants best-suited for their environment.(The genetic theory of adaptation: a brief history |journal=Nat. Rev. Genet. |volume=6 |issue=2 |pages=119–27 |year=2005 |pmid=15716908) This process can 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 mutations causing [[antibiotic resistance]] by either modifying the target of the drug, or removing the transporters that allow the drug into the cell.([~~http~~://www.jstage.jst.go.jp/article/mandi/46/6/46_391/_article/-char/en]) 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. One example is the African lizard ''Holapsis 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.

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Adaptations are structures or behaviors that enhance a specific function, causing organisms to become better at surviving and reproducing. They are produced by a combination of the continuous production of small, random changes in traits, followed by natural selection of the variants best-suited for their environment.(The genetic theory of adaptation: a brief history |journal=Nat. Rev. Genet. |volume=6 |issue=2 |pages=119–27 |year=2005 |pmid=15716908) This process can 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 mutations causing [[antibiotic resistance]] by either modifying the target of the drug, or removing the transporters that allow the drug into the cell.([https://www.jstage.jst.go.jp/article/mandi/46/6/46_391/_article/-char/en]) 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. One example is the African lizard ''Holapsis 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.

As adaptation occurs through the gradual modification of existing structures, structures with similar internal organization may have very different functions in related organisms. This is the result of a single [[homology (biology)|ancestral structure]] being adapted to function in different ways. The bones within bat wings, for example, are structurally similar to both human hands and seal flippers, due to the common descent of these structures from an ancestor that also had five digits at the end of each forelimb. Other idiosyncratic anatomical features, such as [[sesamoid bone|bones in the wrist]] of the [[panda]] being formed into a false "thumb," indicate that an organism's evolutionary lineage can limit what adaptations are possible.

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During adaption, some structures may lose their original function and become [[vestigial structure]]s. 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 the non-functional remains of eyes in blind cave-dwelling fish, [~~http~~://jhered.oxfordjournals.org/cgi/content/full/96/3/185] wings in flightless birds, and the presence of hip bones in whales and snakes. Examples of vestigial structures in humans include [[wisdom teeth]], the [[coccyx]], and the [[vermiform appendix]].

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During adaption, some structures may lose their original function and become [[vestigial structure]]s. 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 the non-functional remains of eyes in blind cave-dwelling fish, [https://jhered.oxfordjournals.org/cgi/content/full/96/3/185] wings in flightless birds, and the presence of hip bones in whales and snakes. Examples of vestigial structures in humans include [[wisdom teeth]], the [[coccyx]], and the [[vermiform appendix]].

An area of current investigation in [[evolutionary developmental biology]] is the [[Developmental biology|developmental]] basis of adaptations and exaptations. This research addresses the origin and evolution of [[Embryogenesis|embryonic development]] and how modifications of development and developmental processes produce novel features. These studies have shown that evolution can alter development to create new structures, such as embryonic bone structures that develop into the jaw in other animals instead forming part of the middle ear in mammals. 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 [[chicken]]s causing embryos to grow teeth similar to those of [[crocodile]]s.

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These examples of cooperation within species are thought to have evolved through the process of [[kin selection]], which is where one organism acts to help raise a relative's offspring. 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. Other processes that may promote cooperation include [[group selection]], where cooperation provides benefits to a group of organisms.

===Speciation===

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[[Speciation]] is the process where a species diverges into two or more descendant species. It has been observed multiple times under both controlled laboratory conditions and in nature.[~~http~~://www.talkorigins.org/faqs/faq-speciation.html]| In sexually-reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four mechanisms for speciation. The most common in animals is [[allopatric speciation]], which occurs in populations initially isolated geographically, such as by [[habitat fragmentation]] or migration. As selection and drift act independently in isolated populations, separation will eventually produce organisms that cannot interbreed.(Hoskin CJ, Higgle M, McDonald KR, Moritz C , Reinforcement drives rapid allopatric speciation, Nature)

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[[Speciation]] is the process where a species diverges into two or more descendant species. It has been observed multiple times under both controlled laboratory conditions and in nature.[https://www.talkorigins.org/faqs/faq-speciation.html]| In sexually-reproducing organisms, speciation results from reproductive isolation followed by genealogical divergence. There are four mechanisms for speciation. The most common in animals is [[allopatric speciation]], which occurs in populations initially isolated geographically, such as by [[habitat fragmentation]] or migration. As selection and drift act independently in isolated populations, separation will eventually produce organisms that cannot interbreed.(Hoskin CJ, Higgle M, McDonald KR, Moritz C , Reinforcement drives rapid allopatric speciation, Nature)

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The second mechanism 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 through both rapid genetic drift and selection on a small gene pool. (Templeton AR, The theory of speciation via the founder principle [~~http~~://www.genetics.org/cgi/reprint/94/4/1011] , Genetics)

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The second mechanism 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 through both rapid genetic drift and selection on a small gene pool. (Templeton AR, The theory of speciation via the founder principle [https://www.genetics.org/cgi/reprint/94/4/1011] , Genetics)

The third mechanism of speciation 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 localized metal pollution from mines. Here, plants evolve that have resistance to high levels of metals in the soil. Selection against interbreeding with the metal-sensitive parental population produces a change in flowering time of the metal-resistant plants, causing reproductive isolation. Selection against hybrids between the two populations may cause ''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.

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One type of sympatric speciation involves cross-breeding of two related species to produce a new [[hybrid]] species. This is not common in animals as animal hybrids are usually sterile, because during [[meiosis]] the [[homologous chromosome]]s from each parent, being from different species cannot successfully pair. It is more common in plants, however because plants often double their number of chromosomes, to form [[polyploidy|polyploids]]. This allows the chromosomes from each parental species to form a matching pair during meiosis, as each parent's chromosomes is represented by a pair already. An example of such a speciation event is when the plant species ''[[Arabidopsis thaliana]]'' and ''Arabidopsis arenosa'' cross-bred to give the new species ''Arabidopsis suecica'' and the speciation process has been repeated in the laboratory, which allows the study of the genetic mechanisms involved in this process. 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.

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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.[~~http~~://www.blackwellpublishing.com/ridley/classictexts/eldredge.asp "Punctuated equilibria: an alternative to phyletic gradualism"] In this theory, speciation and 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.

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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.[https://www.blackwellpublishing.com/ridley/classictexts/eldredge.asp "Punctuated equilibria: an alternative to phyletic gradualism"] In this theory, speciation and 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.

===Extinction===

[[Extinction]] is the disappearance of an entire species. Extinction is not an unusual event, as species regularly appear through speciation, and disappear through extinction. Indeed, virtually all animal and plant species that have lived on earth are now extinct. These extinctions have happened continuously throughout the history of life, although the rate of extinction spikes in occasional mass [[extinction event]]s. The [[Cretaceous–Tertiary extinction event]], during which the dinosaurs went extinct, is the most well-known, but the earlier [[Permian-Triassic extinction event]] was even more severe, with approximately 96 percent of species driven to extinction. 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 percent of species may be extinct by the mid 21st century. Human activities are now the primary cause of the ongoing extinction event; [[global warming]] may further accelerate it in the future.

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* Darwin's Dangerous Idea: Evolution and the Meanings of Life, ISBN 978-0684824710

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* History of Science: Origins of Evolutionary Theory [~~http~~://www.mala.bc.ca/~johnstoi/darwin/sect3.htm]

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* History of Science: Origins of Evolutionary Theory [https://www.mala.bc.ca/~johnstoi/darwin/sect3.htm]

* Evolution: The History of an Idea, Third Edition, ISBN 978-0520236936

* Intelligent design and biological complexity, Gene, volume 385

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Although many religions have reconciled their beliefs with evolution through various concepts of theistic evolution, there are many who believe that evolution is contradicted by the creation stories found in their respective religions.[~~http~~://www.answersingenesis.org/home/area/re1/chapter1.asp|title=Evolution & creation, science & religion, facts & bias] As Darwin recognized early on, the most controversial aspect of evolutionary thought is its implications for human origins. In some countries, notably the United States, these tensions between scientific and religious teachings have fueled the ongoing creation–evolution controversy, a religious conflict focusing on [[politics]] in public education. While other scientific fields such as [[cosmology]] and [[earth science]] also conflict with literal interpretations of many religious texts, evolutionary biology is strongly opposed by many religious believers.

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Although many religions have reconciled their beliefs with evolution through various concepts of theistic evolution, there are many who believe that evolution is contradicted by the creation stories found in their respective religions.[https://www.answersingenesis.org/home/area/re1/chapter1.asp|title=Evolution & creation, science & religion, facts & bias] As Darwin recognized early on, the most controversial aspect of evolutionary thought is its implications for human origins. In some countries, notably the United States, these tensions between scientific and religious teachings have fueled the ongoing creation–evolution controversy, a religious conflict focusing on [[politics]] in public education. While other scientific fields such as [[cosmology]] and [[earth science]] also conflict with literal interpretations of many religious texts, evolutionary biology is strongly opposed by many religious believers.

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Evolution has been used to support philosophical positions that promote discrimination and [[race|racism]]. For example, the [[eugenics]] of [[Francis Galton]] were developed to argue that the human gene pool should be improved by selective breeding policies, including incentives for those considered "good stock" to reproduce, and the compulsory sterilization, prenatal testing, birth control, and even killing, of those considered ''bad stock''.[~~http~~://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10445929] Another example of an extension of evolutionary theory that is now widely regarded as unwarranted is "[[Social Darwinism]]," a term given to the 19th century British Whig Party. [[Malthusian]] theory developed by [[Herbert Spencer]] into ideas about "[[survival of the fittest]]" in commerce and human societies as a whole, and by others into claims that social inequality, racism, and [[imperialism]] were justified. On the history of eugenics and evolution, see:

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Evolution has been used to support philosophical positions that promote discrimination and [[race|racism]]. For example, the [[eugenics]] of [[Francis Galton]] were developed to argue that the human gene pool should be improved by selective breeding policies, including incentives for those considered "good stock" to reproduce, and the compulsory sterilization, prenatal testing, birth control, and even killing, of those considered ''bad stock''.[https://www.pubmedcentral.nih.gov/articlerender.fcgi?tool=pubmed&pubmedid=10445929] Another example of an extension of evolutionary theory that is now widely regarded as unwarranted is "[[Social Darwinism]]," a term given to the 19th century British Whig Party. [[Malthusian]] theory developed by [[Herbert Spencer]] into ideas about "[[survival of the fittest]]" in commerce and human societies as a whole, and by others into claims that social inequality, racism, and [[imperialism]] were justified. On the history of eugenics and evolution, see:

*Name of Eugenics: Genetics and the Uses of Human Heredity ISBN 978-0674445574

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