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|Darwin’s clear elucidation of natural selection launched a revolutionary new paradigm in biology wherein organismal traits could be studied and interpreted as products of natural (rather than supernatural) forces amenable to rational scientific inquiry. <ref name=nas3evolite>John C. Avise and Francisco J. Ayala, Editors. (2009) [http://www.nap.edu/openbook.php?record_id=12692&page=1 In the Light of Evolution III - Two Centuries of Darwin (2009), National Academy of Sciences (NAS)]. p1.</ref>
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In [[Biology|biology]], '''natural selection''' is the process by which changes in the [[Natural environment|natural environment]] favor, for survival and reproductive success, individual organisms who possess traits that best allow them to resist the adverse effects of the changes, or to best exploit the opportunities the changes present. Those lacking those traits have a lesser chance of surviving and reproducing, a process of 'natural elimination' that accompanies natural selection. Thus environmental changes tend to 'select' individuals whose physical and mental traits give them a reproductive advantage over their less so-endowed conspecifics in the particular environment they live in.<ref>'''<u>Note:</u>''' 'conspecifics' refers to members of the same species.</ref> For example, when there is not enough food for all to flourish, only those whose traits give them competitive advantage in securing food may so flourish. When advantageous traits can be inherited, those traits will tend to become more common in the subsequent generation. If the changed  environment persists, further selection may continue for many generations, increasing what biologists call the 'fit' between the species and environment. Thus biologists characterize natural selection as increasing the 'fitness' of the species, meaning its better 'adaptation' to its environment.


'''Natural selection''' is the process by which individual [[organism]]s with favorable [[trait (biological)|trait]]s are more likely to survive and [[Biological reproduction|reproduce]] than those with unfavorable traits. Natural selection works on the whole individual, but only the [[Heritability|heritable]] component of a [[trait (biological)|trait]] will be passed on to the offspring, with the result that favorable, heritable traits become more common in the next [[generation]]. Given enough time, this passive process can result in [[adaptation]]s and [[speciation]] (see [[evolution]]).
{{Image|Bence-Mate-HidePhotography-com-Bothriechis-schlegelii-Eyelash-Viper-Vipera1.jpg|left|350px|Natural selection at work: An Eyelash Viper ([[Bothriechis schlegelii]]) in [[eye contact]] with a [[kolibri]].}}
Natural selection depends on the fact that, in any species, individuals will all be slightly different from one other; they all have slightly different features or abilities - we call these different ''traits''. Many of these differences will be accidents of the environment - some individuals will be stronger than others because they were better fed when young for example, but some differences will be heritable - they can be passed on to the offspring. Any offspring that [[inheritance|inherit]] useful characteristics for the prevailing environment will more likely survive and reproduce, and so will tend pass on those traits to ''their'' offspring. Thus, over many generations, species can become increasingly adapted to their habitats. Subgroups of a species that live in different habitats will diverge over time, as each becomes adapted to their own niche; such divergence, given enough time, can lead to subpopulations becoming distinct species unable to interbreed.  


Natural selection is one of the cornerstones of modern biology. The term was introduced by [[Charles Darwin]] in his 1859 book ''[[The Origin of Species]]'' <ref name=origin> Darwin C (1859) ''[[The Origin of Species|On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life]]'' John Murray, London; modern reprint {{cite book|author = Charles Darwin, Julian Huxley|year = 2003|title = The Origin of Species| publisher = Signet Classics|id = ISBN 0-451-52906-5}}</ref>, by [[analogy]] with ''[[artificial selection]]'', by which a farmer selects his breeding stock.
This process of natural selection is a long series of events that accounts for the 'fit' between living creatures and their habitat, explaining the presence of drought tolerant plants in the desert and moisture-loving plants in the rain forest, heavily furred mammals in the colder climates and lightly furred mammals in the warmer climes. Across generations, natural selection ''results'' in change in the characteristics of species of plants, animals, and other [[organism]]s, so that some features become emphasized and others diminished. These changes, called adaptations, lead to particular strains or "natural breeds" within a species and can account for the creation of new species ([[speciation]]), and their further evolution over time.  


== An example: antibiotic resistance==
The theory of evolution by natural selection, like all theories, makes certain assumptions. It presumes some variety among the individual entities of any particular kind of living thing. Second, it presumes that offspring can inherit some of those variations. Third, it assumes that in any given situation, some characteristics make reproductive success of individuals more likely, whereas other characteristics make it less likely. Those characteristics often consist simply of the ability to survive. The theory of evolution by natural selection predicts that living things that inherit features that bestow ''survival advantages'' for an individual, or otherwise increase the the ability of the individual that has them to reproduce offspring that can mature and reproduce, will tend to ''multiply'' in frequency among members of the species over generations.  
[[Image:Antibiotic_resistance.gif|thumb|size=180px|right|'''Figure 1''': Schematic representation of how antibiotic resistance is enhanced by natural selection. The top section represents a population of bacteria before exposure to an antibiotic. The middle section shows the population directly after exposure, the phase in which selection took place. The last section shows the distribution of resistance in a new generation of bacteria. The legend indicates the resistance levels of individuals.]]


A well-known example of natural selection in action is the development of [[antibiotic resistance]] in [[microorganism]]s. [[Antibiotic]]s have been used to fight [[bacteria]]l diseases since the discovery of [[penicillin]] in 1928 by [[Alexander Fleming]]. However, the widespread use and especially misuse of antibiotics has led to increased microbial resistance against antibiotics, to the point that the [[Methicillin-resistant Staphylococcus aureus|methicillin-resistant ''Staphylococcus aureus'']] (MRSA) has been described as a '[[superbug]]' because of the threat it poses to health and its relative invulnerability to existing drugs. <ref>[http://www.inboxrobot.com/news/MRSASuperbug MRSA Superbug News] (accessed May 6, 2006)</ref>
The theory of evolution by natural selection is one of the cornerstones of modern [[biology]]. [[Charles Darwin]], introduced the term "natural selection" in his 1859 book ''[[The Origin of Species]]'' <ref name=origin> Darwin C (1859) ''[[The Origin of Species|On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life]]'' John Murray, London; modern reprint {{cite book|author = Charles Darwin, Julian Huxley|year = 2003|title = The Origin of Species| publisher = Signet Classics|id = ISBN 0-451-52906-5}}</ref>, through [[analogy]] with ''[[artificial selection]]'', by which farmers select breeding stock. Given time, a passive process of natural selection can result in [[adaptation]]s and [[speciation]]s (see [[evolution]]). Less dramatically, natural selection accounts for the differing strains and breeds of plants and animals of the same species that are found in varying habitats and geographic regions. The independent discoverer of the process of natural selection, [[Alfred Russel Wallace|Alfred Russel Wallace]], preferred the term 'survival of the fittest', in part because he saw some different consequences, and thus a poor analogy, between artificial and natural selection.


Natural populations of bacteria contain, among their vast numbers of individual members, considerable variation in their genetic material, primarily as the result of [[mutation]]s. When exposed to antibiotics, most bacteria die quickly, but some may have mutations that make them a little less susceptible. If the exposure to antibiotics is short, these individuals will survive the treatment. This selective elimination of ''maladapted'' individuals from a population is ''natural selection in action''.
==General principles, remarks and concepts==


These surviving bacteria will then reproduce again, producing the next generation. Due to the elimination of the maladapted individuals in the past generation, this population contains more bacteria that have some resistance against the antibiotic. At the same time, new mutations occur, contributing new genetic variation to the existing genetic variation. Spontaneous mutations are very rare, very few have any effect at all, and usually any effect is deleterious. However, populations of bacteria are enormous, and so a few individuals will have beneficial mutations. If a new mutation reduces their susceptibility to an antibiotic, these individuals are more likely to survive when next confronted with that antibiotic. Given enough time, and repeated exposure to the antibiotic, a population of antibiotic-resistant bacteria will emerge.  
===Basic principles===
Evolution by means of natural selection changes a population's so-called [[gene frequency]], or [[allele frequency]], the relative frequency of [[allele]]s for particular gene loci in the evolving population, measured for a gene locus as the number of a given allele relative to the number of all alleles at that gene locus. Allele frequencies give a measure of the degree of genetic diversity in a population, and changes in allele frequencies in the gene pool give objective evidence that evolution has occurred.<ref name=mader10th>Mader S. (2010) ''Biology''. 10th edition. New York: McGraw Hill. ISBN 9780073525433.</ref>
Darwin called it descent with modification which a rather wrong definition.


Recently, several new strains of MRSA have emerged that are resistant to [[vancomycin]] and [[teicoplanin]] <ref name=Schito_2006>{{cite journal | author=Schito GC | title=The importance of the development of antibiotic resistance in ''Staphylococcus aureus'' | journal=Clin Microbiol Infect | year=2006 | pages=3-8 | volume=12 Suppl 1|id={{PMID|16445718}} }} [http://www.blackwell-synergy.com/doi/abs/10.1111/j.1469-0691.2006.01343.x]</ref>. This is an example of what is sometimes called an '[[arms race]]', in which bacteria continue to develop strains that are less susceptible to antibiotics, while medical researchers continue to develop new antibiotics that can kill them. A similar situation occurs with [[Pesticide#Dangers of pesticides|pesticide resistance]] in plants and insects.
Darwin made four basic principles to make a evolution theory by means of natural selection:


==Background and context==
'''1. Variation'''
[[History of evolutionary thought|In the early 19th century]], growing awareness of the fossil record led to the recognition that species that lived in the distant past were often very different from those that exist today. Naturalists of the time tried to reconcile this with the emerging ideas of [[uniformitarianism (science)|uniformitarianism]] in [[geology]] - the notion that simple, weak forces, acting continuously over very long periods of time could have radical consequences, shaping the landscape as we know it today. Most importantly perhaps, these notions led to the awareness of the immensity of geological time, which makes it possible for slight causes to produce dramatic consequences. This opened the door to the notion that species might have arisen by descent with modification from ancestor species.  


Radical [[evolutionism|evolutionists]] such as [[Jean Baptiste Lamarck]] proposed that characteristics (adaptations) acquired by individuals might be inherited by their progeny, causing, in enough time, [[transmutation of species]]. By contrast, Darwin postulated that adaptation is a passive process in which the selective culling by nature of maladapted individuals results in an increase of the fittest individuals (see '''[[survival of the fittest]]'''). In other words, Darwin suggested that adaptation may be an unintended effect, rather than an intended cause. He realised that this simple and apparently inevitable process might be powerful enough to explain the evolution of the astounding ways in which organisms are adapted to their environments and the origins of the millions of species that exist.
Individuals within a certain population of a species are not identical. They are different in size, weight. They are different in [[phenotype]].


Evolutionary change can also happen without any selection, as a result of [[genetic drift]] or [[gene flow]]. However, ''adaptive'' change needs more than this, because it is very unlikely that favorable characteristics will consistently become more common in successive generations simply as a result of random fluctuations in occurrence. Favorable characteristics that can be attributed to genes that become more common through evolution by natural selection are called ''[[Adaptation (biology)|adaptations]]''.
'''2. Heritability'''


For Darwin, ''natural selection'' was synonymous with ''[[Evolution|evolution by natural selection]]''; other mechanisms of evolution such as '[[Genetic drift|evolution by genetic drift]]' were not explicitly formulated at that time, and Darwin realised that: ''"I am convinced that [it] has been the main, but not exclusive means of modification."''<ref>[[The Origin of Species]], page 6</ref> Now, scientists use ''natural selection'' mainly to describe the ''mechanism''. In this sense, natural selection includes ''any'' selection by a natural agent, including [[sexual selection]] and [[kin selection]]. Sometimes, sexual selection is distinguished from natural selection, but a more useful distinction is between sexual selection and [[ecological selection]].
There are two causes of these variations:


== Definitions of natural selection ==
*''1. Environment''
Scientists use several, slightly different definitions of natural selection. This section explains the different uses.


In each generation, only some individuals will produce offspring themselves, and of those that reproduce, some will leave more offspring than others. We can think of this as the "natural” process of selection of individuals to reproduce. Individuals with beneficial traits are more likely to be 'selected' than individuals with other traits. When those traits have a heritable component, they tend to become more common in the next generation. The mechanism of selection of individuals in a population does not "know" which traits are heritable; in this sense, the mechanisms of selection are "blind".
**Because of better available food animals can become bigger or plants grow faster in sunlight. The environment is really a vague thing. It is everything except the genetic variation in most contexts
   
*''2. Genetic''


However, the term ''natural selection'' is often used to encompass the consequence of blind selection as well as the mechanisms to describe the complete process that leads to the enrichment of the beneficial characteristics in the next generation. <ref name=origin/><ref name=fisher>Fisher RA (1930) ''[[The Genetical Theory of Natural Selection]]''  Clarendon Press, Oxford</ref><ref>{{cite book| author=Endler JA | year=1986| title=Natural Selection in the Wild| publisher=[[Princeton University Press]]| location=[[Princeton, New Jersey|Princeton]], [[New Jersey]]| id=ISBN 0-691-00057-3}}</ref><ref>{{cite book| author=Williams GC| year=1966| title=[[Adaptation and Natural Selection]]| publisher=Oxford University Press}}</ref>
**It is also called '''heritability''' which means that the variation is passed also from parent to offspring.
                   
'''3. Demographic abundance or variation in the success to survive'''


Nevertheless, it is sometimes helpful to distinguish clearly between the mechanisms of selection and the effects of selection. When this distinction is important, scientists define "natural selection" specifically as "those mechanisms that contribute to the selection of individuals that reproduce", without regard to whether the basis of the selection is heritable. This is sometimes referred to as 'phenotypic natural selection.' <ref>Lande R & Arnold SJ (1983) The measurement of selection on correlated characters. [[Evolution (journal)|''Evolution'']] 37:1210-26</ref><ref>[[Douglas J. Futuyma|Futuyma DJ]] (2005) ''Evolution''. Sinauer Associates, Inc., [[Sunderland, Massachusetts|Sunderland]], [[Massachusetts]]. ISBN 0-87893-187-2</ref><ref>Haldane, J.B.S. 1953. The measurement of natural selection. Proceedings of the 9th International Congress of Genetics. 1: 480-487</ref>
Populations are able to grow incredibly. But a great part of the offspring will die during development or before adulthood.  


This article discusses natural selection in this sense of being the mechanisms of selection of individuals to reproduce. Of particular importance is selection according to traits by which individuals differ from each other. It discusses the effects of this selection on the genetic characteristics of a population when some components of beneficial traits are heritable. Finally, the article ventures into the consequences of these effects for evolution.
Darwin himself made a calculation. Elephants were known to be the slowest breeder in Darwin's time. He calculated what would happen with an elephant population if none of the offspring would die in development or childhood. In 750 years one elephant couple would give rise to 19 million descendants.  
It is even more spectacular with the starfish. One pair can have 10<sup>79</sup> descendants in one year!


==Overview==
'''4. Non-random selection and selective pressure'''
Natural selection acts on the [[phenotype]]. The phenotype is the overall result of an individual's genetic make-up ([[genotype]]), the [[ecosystem|environment]], and the [[Epistasis|interactions between genes]] and between [[Gene-environment interaction|genes and the environment]]. Often, natural selection acts on specific traits of an individual, and the terms [[Genotype-phenotype distinction|phenotype and genotype]] are sometimes used narrowly to indicate these specific traits.


Some traits are determined by just a [[Mendelian inheritance|single gene]], but most are affected by many different genes. Variation in most of these genes has only a small effect on the phenotypic value of a trait, and the study of the genetics of these quantitative traits is called [[quantitative genetics]].<ref>Falconer DS & Mackay TFC (1996) ''Introduction to Quantitative Genetics'' Addison Wesley Longman, Harlow, Essex, UK ISBN 0-582-24302-5</ref>  
Different parents have a different amount of offspring, which is a result of a difference in the ability to survive and reproduce but also a result of the ability of the offspring to survive and reproduce. The amount of offspring is determined by the interaction between the phenotype of an individual and its environment (or nature as Darwin said ; hence natural selection). See how the parent's and offspring's survival is important.
Selection leads to a different success of individuals in reproduction and the survival of their offspring. See also the remarks about the non-random character of selection.<br /><br />
Another important thing is '''selective pressure'''. By selective pressure we mean the force or cause that selects the individuals. If there is no selective pressure there is no selection.


The key element in understanding natural selection is the concept of '''[[Fitness (biology)|fitness]]'''. Natural selection acts on individuals, but its ''average'' effect on all individuals with a particular genotype is the fitness of that genotype. Fitness is measured as the proportion of progeny that survives, multiplied by the average [[fecundity]], and it is equivalent to the ''[[reproductive success]]'' of a genotype. A fitness value of greater than one indicates that the frequency of that genotype in the population increases, while a value of less than one indicates that it decreases. The relative fitness of a genotype is estimated as the proportion of the fitness of a reference genotype. Related to relative fitness is the [[selection coefficient]], which is the difference between the relative fitness of two genotypes. The larger the selection coefficient, the stronger natural selection will act against the genotype with the lowest fitness.  
===Fitness and evolution===
The extent to which the variation of phenotype has a genetic base leads to a change in gene frequency. Remind that this is the definition of evolution. The variation in success in a certain environment is the driving force of evolution.


Natural selection can act on any phenotypic trait, and any aspect of the environment, including [[Sexual selection|mates]] and [[Competition#Competition in biology and ecology|conspecifics]], can produce selective pressure. However, this does not imply that natural selection is always [[directional selection|directional]] and results in adaptive evolution; natural selection often results in the maintenance of the ''status quo'' through [[purifying selection]]. The ''[[unit of selection]]'' is not limited to the level of individuals, but includes other levels within the hierarchy of biological organisation, such as [[intragenomic conflict|genes]], cells and [[kin selection|relatives]]. There is still debate, however, about whether natural selection acts at the level of [[group selection|groups or species]], (i.e. selection for adaptations that benefit the group or species, rather than the individual). Selection at a different level than the individual, for example the gene, can result in an increase in fitness for that gene, while at the same time reducing the fitness of the individuals carrying that gene (see [[intragenomic conflict]] for more details). Overall, the combined effect of all selection pressures at various levels determines the overall fitness of an individual, and hence the outcome of natural selection.
The success of a genotype or individual is called the fitness. It is defined as the '''relative''' contribution of a genotype in the next generation. As mentioned this is a very important concept in evolution and can be quantified.


[[Image:Selection_forces.gif|thumb|280px|right|'''Figure 2''': The life cycle of a sexually reproducing organism. Various components of natural selection are indicated for each life stage. <ref>Modified from Christiansen FB (1984) The definition and measurement of fitness. In: ''[[Evolutionary ecology]]'' (ed. Shorrocks B) pp65-79. [[Blackwell Publishing|Blackwell Scientific]], [[Oxford]] by adding survival selection in the reproductive phase</ref>]]
===Remarks===
Natural selection occurs at every life stage of an individual (see Figure 2), and selection at any of these stages can affect the likelihood that an individual will survive and reproduce. After an individual is born, it has to survive until adulthood before it can reproduce, and selection of those that reach this stage is called ''viability selection''. In many species, adults must compete with each other for mates (''[[sexual selection]]''), and success in this competition determines who will parent the next generation. When species reproduce more than once, a longer survival in the reproductive phase increases the number of offspring (''[[survival]] selection''). The fecundity of both females (e.g. how many eggs a female bird produces) and males (e.g. giant [[sperm]] in certain species of ''[[Drosophila]]''<ref>Pitnick S & Markow TA (1994) Large-male advantage associated with the costs of sperm production in ''Drosophila hydei'', a species with giant sperm. [[PNAS|''Proc Natl Acad Sci USA'']] 91:9277-81; Pitnick S (1996) Investment in testes and the cost of making long sperm in ''Drosophila''. [[American Naturalist|''Am Nat'']] 148:57-80</ref>) can be limited (''[[fecundity]] selection''). The viability of produced [[gamete]]s can differ, while [[intragenomic conflict]] (meiotic drive) between the [[haploid]] gametes can result in ''gametic'' or ''genic selection''. Finally, the union of some combinations of eggs and sperm might be more compatible that others (''compatibility selection'').
#Selection is not a process which leads to the perfect genotype, it rather selects for the genotype with the highest fitness from the available ''genotypes''<br /><br />
#Evolution by means of natural selection is only possible if there is heritable variation in '''fitness-related''' properties.<br /><br />
# One of the most confusing things in the selection concept is that selection is non-random, but there is no progression in it.
 
** Mutations and recombination, which are the input processes for variation, are indeed random. More specific they are random in the changes in phenotype they make.
 
** Selection is not random. It is a certain variation which is better then another. Selection increases the adaptation. So it's non-random.
:::Selection is not any predetermined plan. It means it is not leading to anything specific.
 
** Selection leads only to a better adaptation of the species to its environment
 
===Micro- and macro-evolution===
There is an certain difference between micro- and macro-evolution, though these things are essentially the same:<br /><br />
*Micro-evolution are processes that are driving evolution within a species<br /><br />
*Macro-evolution is about speciation and diversity.
 
Micro-evolution is the driving evolution and macro-evolution is rather a consequence of it.
 
==Examples==
 
===A simple example===
The most simple example is the lion-antelopes example. I will make the parallel between the first section and this section. Note that this example is rather hypothetical and is only to illustrate the concept of natural selection.
 
#'''Variation'''<br /><br /> There is an Antelope population in which the length of legs in varying. Some antelopes haves short legs and others have long legs. The antelopes with short legs are slower then the antelopes with long legs.<br /><br />
#'''Heritability'''<br /><br /> There are two causes of this variation<br /><br />
##Environment: Because of a dryer season plant grow slower and young antelopes eat bad food to grow and get long legs.<br /><br />
##Genetic: Some variation is passed from parent to offspring. This means that antelopes with a long-leg-gene will have longer legs then antelopes with a short-leg-gene if the environment were the same. <!--I'd like to write something about quantification of heritability and things like that later --><br /><br />
#'''Variation in success and selection''': Lions will hunt to get some juice piece of meat. They will catch mostly the slow and short-legged offspring. If the second principle is true, then in the next generation there will be relatively more long-legged genes.<br /><br />
#'''additionally''' you can say that the fitness of the long-legged animals is bigger.
 
===A more complex example===
<!-- I will add figures later on when i am sure i can publish them -->
====Introduction====
<!-- Source is Evolutionary analysis ,fourth edition, Pearson Education , Scott Freeman and Jon Herrron,2007 -->
This is the example of the so called Darwin's finches on the Galapagos Islands(see figure 1).<!-- I will give the sources later on but it is the Grant research -->
It is a great prove that micro- and macro-evolution are essentially the same. The Darwin's finches vary in a lot of aspects going from weight, length and more important for us the beak shape. <br />
Now let's compare the beak shape the 14 species (this is macro-evolution; see figure 2). Some beaks are small and pointy to get small and soft insects others have bigger beaks and can open seeds. It is even noticeable if we compare two species ''Geospiza fortis'' and ''G. magnirostris''.
The ''G. magnirostris'' has a large and big beak and he uses it to crack big seeds. The ''G. fortis'' though has a smaller beak and can crack smaller seeds.
 
====The research====
First of all we are not going to give much detail about the research itself, but if you are interested we'd recommend to read the Grants research.
Peter and Rosemary Grant were able to observe these finches in a field-experiment. They observed only one species (so micro-evolution), namely the ''G. fortis''. A great advantage is that the species doesn't leave the island and it's rather easy to interpret data.<br /><br />
We are going to try to prove evolution and one can ask if selection and evolution can be present if there no selective pressure. As said before the answer is no!!. Even more convenient would be a great selective pressure. In the case of Darwin's finches it was an El nino phenomenon. The consequence is a dry period during 1977 and 1978. During this period seeds become bigger and harder. What we would expect is an increase in beak shape and a decrease in the size of the population. '''Now the central question is if this is really (micro-)evolution.''' We are going to verify the basic principles
 
:'''1. Variation<br /><br />
:By marking the finches leg with an iron band with a number on the band, the Grants could trace the birds and measure the beak size. It is measured from the lowest base of the beak to the highest base of the beak. When the Grants measured the beak size of course they measured a variation. It sounds stupid, but look at the graph on figure 3. You can see that some birds have a beak that is twice as bid as others. So the variation is indeed enormous.
 
:'''2. Is the variation heritable?'''<br /><br />
:''Is it heritable?''<br /><br />To determine the amount of heritability we'd recommend the reader to read something about quantifying or estimating heritability. We can prove it by plotting the average value of parents versus the offspring value. It is called a midparent value-offspring plot (see figure 4)
:We can see here that parents with a big beak tend to have offspring with a big beak (figure 4) and parents with small beaks tend to have offspring with small beaks. The story is more complex because normally you should exclude maternal effects, which we don't explain now.<br /><br />
:''Genes that determine beak size '' <br /><br />
:One can wonder what gene responsible is. Luckily Abzhanov et. Al (2004) discovered an important gene. It is the gene that gives rise to the growfactor bonemorphogenic protein  4 (BMP4). They found that birds with a bigger beak made earlier in the development the BMP4 and also is larger quantities.
 
:'''3. Variation in success to survive'''<br /><br />
:As expected, many finches died due to the drought. So it seems the selective pressure is indeed big, so the selection is big.
 
:'''4. Is there selection?'''<br /><br />
:Yes, because the researchers saw the to distributions before and after the drought (figure 5). The mean before the drought is almost 1mm lower then after. This may not seem a lot, but you have to see this relatively. In one year, the beaks with a mean size of 9,4mm were 1mm enlarged to 10,2. This an enlargement of approximately 10 percent in one year!!!. It is as if you would be 160 cm and the next year you would be 176cm!!!.<br /> It can also be expressed like this: the average survivor had a bigger beak than the average non-surviving bird.<br /><br />
:'''5. Is there evolution?'''<br /><br />
:Yes and we can confirm it by comparing the offspring from bird before the drought and after the drought. And indeed the offspring after the drought have a bigger beak.
 
===Viral and bacterial example===
With viruses and bacteria one can witness evolution in real time. One of the selective forces that viruses such as influenza face is antibody in the bloodstream of influenza patients that neutralise the virus and prevent further infections, bringing epidemic spread to a halt. Similarly, bacteria that infect and colonise humans and domestic animals have been faced with widespread massive use of antibiotics since the discovery of penicillin and other new medicines in the 1940s. The natural selection of antigenic variants of influenza virus, and shifts in the major components of the virus caused by re-assortment and recombination of influenza virus genes, and the selection of multiple-drug resistant variants of bacteria are examples of natural selection occurring over the last half-century or so that are extensively documented in the medical literature.
<!--This is a holding example. I will look out for some non-microbiological example that is well documented  David Tribe.-->
<!-- I will leave it here , but can you add some more structure Joris?-->
 
===Other examples===
<!-- I can describe these if you like -->
 
There exists a wealth of other examples. The best researches are the ones of:<br /><br /> 1. Reznick et Al.in Nature 346, pages 357 - 359 (26 July 1990)<br /><br />2. Hanks, L. M. & R. F. Denno. 1994. Local adaptation in the armored scale insect Pseudaulacaspis pentagona (Targioni-Tozzetti) (Homoptera: Diaspididae). Ecology 75: 2301-2310.<br /><br />3. Raineny and Travisano, 1998, Adaptive radiation in a heterogeneous environment ,Nature 394, 69-72
 
==The creative power of natural selection==
While it is easy to see how natural selection can act as a force that refines pre-existing attributes, it is less easy to see how it can work to build wholly new functions. Today, molecular biologists can in part reconstruct how new functions might have arisen through evolution by natural selection.
 
To take just one example, [[oxytocin]] and [[vasopressin]] are two closely related molecules - they differ by just one amino acid. They come from two separate but very similar genes, genes so similar that we think they must have arisen by an initial step of gene duplication. Oxytocin and vasopressin are peptide hormones that exert their quite different physiological actions by acting on specific receptors, expressed in different target tissues. The genes for the receptors are also very similar to each other, so the receptor genes also arose by gene duplication, probably at the same time as the gene for the peptides was duplicated<ref>van Kesteren R ''et al.'' (1996) Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides. J Biol Chem 271:3619-3626</ref> So the initial mutation was a large scale gene duplication - such changes are generally neutral mutations, with no consequences for the organism. Almost all vertebrates that have been studied have genes for two peptides closely related to oxytocin and vasopressin, and virtually all invertebrates that have been studied have just one such gene. Among vertebrates, only Cyclostomata (lampreys and hagfishes) are known to have only one gene related to vasopressin and oxytocin, so the initial duplication probably occurred about 400 million years ago, before the evolution of the fishes <ref>Acher R ''et al.'' (1997) Molecular evolution of neurohypophysial hormones in relation to osmoregulation: the two fish options. ''Fish Physiol Biochem'' 17:325-32</ref>. When a gene is duplicated, one copy is now redundant, and so is under no immediate selection pressure; accordingly it will accumulate further mutations, some of which may have incidental benefits to the organism unrelated to the function of the original gene. Over time, as natural selection works on these initially minor and incidental benefits, the two genes diverge in functionality. Now (400 million years later), in modern mammals, vasopressin mainly controls water loss from the [[kidney]]s while oxytocin mainly controls the let down of milk from the mammary gland in lactation. This function of oxytocin is quite clearly new in evolutionary terms (and specific to mammals), yet it arose from slight mutations of elements that had previously existed for a quite different purpose, refined by natural selection over millions of years.  


==="Ecological selection" and "sexual selection"===
==="Ecological selection" and "sexual selection"===
It is also useful to make a mechanistic distinction between [[ecological selection]] and [[sexual selection]]. ''Ecological selection'' covers any mechanism of selection as a result of the environment (including relatives (e.g. [[kin selection]]) and conspecifics (e.g. [[Competition#Competition in biology and ecology|competition]], [[infanticide]])), while ''sexual selection'' refers specifically to competition between conspecifics for mates <ref>{{cite book| author=Andersson, M| year=1995| title=Sexual Selection| publisher=Princeton University Press| location=Princeton, New Jersey| id=ISBN 0-691-00057-3}}</ref>. Sexual selection includes mechanisms such as ''mate choice'' and ''male-male competition'' although the two forms can act in combination in some species, when females choose the winners of the male-male competition. Mate choice, or ''intersexual selection'', typically involves ''female choice'', as it is usually the females who are most choosy, but in some sex-role reversed species it is the males that choose. Some features that are confined to one sex only of a particular species can be explained by selection exercised by the other sex in the choice of a mate, e.g. the extravagant plumage of some male birds. Aggression between members of the same sex (intrasexual selection) is typically referred to as ''male-male competition'', and is sometimes associated with very distinctive features, such as the antlers of stags, which are used in combat with other stags. More generally, intrasexual selection is often associated with [[sexual dimorphism]], including differences in body size between males and females of a species.
It is useful to distinguish between [[ecological selection]] and the narrower term, [[sexual selection]]. ''Ecological selection'' covers any mechanism of selection as a result of the environment (including relatives, e.g. [[kin selection]], and conspecifics, e.g. [[Competition#Competition in biology and ecology|competition]] or [[infanticide]]). ''Sexual selection'' refers specifically to competition between conspecifics for mates <ref>{{cite book| author=Andersson, M| year=1995| title=Sexual Selection| publisher=Princeton University Press| location=Princeton, New Jersey| id=ISBN 0-691-00057-3}}</ref>.  


==="Selection for" versus "selection of"===
Sexual selection includes mechanisms such as ''mate choice'' and ''male-male competition'' although the two forms can act in combination in some species, when females choose the winners of the male-male competition. Mate choice, or ''intersexual selection'', typically involves ''female choice'', as it is usually the females who are most choosy, but in some sex-role reversed species it is the males that choose. Some features that are confined to one sex only of a particular species can be explained by selection exercised by the other sex in the choice of a mate, e.g. the extravagant plumage of some male birds. Aggression between members of the same sex (intrasexual selection) is typically referred to as ''male-male competition'', and is sometimes associated with very distinctive features, such as the antlers of stags, which are used in combat with other stags. More generally, intrasexual selection is often associated with [[sexual dimorphism]], including differences in body size between males and females of a species.
Selection targets specific traits of an individual, and if such a trait has a heritable component, the trait will tend to become more common in the next generation. "Selection for"  refers to the traits targeted by selection, the causes of selection whereas "selection of" is used to describe its effects. ''Selection for'' a specific trait therefore results in the ''selection of'' certain individuals <ref>[[Elliott Sober|Sober E]] (1984; 1993) ''The Nature of Selection: Evolutionary Theory in Philosophical Focus'' [[University of Chicago Press]] ISBN 0-226-76748-5</ref>.
 
''Selection for'' a specific trait can also result in the indirect ''selection of'' other traits ("free riders"). This can happen when two or more traits are genetically linked through mechanisms such as [[pleiotropy]] (single gene that affects multiple traits) and [[linkage disequilibrium]] (non-random association of two genes).


==Genetical theory of natural selection==
==Genetical theory of natural selection==
Natural selection by itself is a simple concept, in which fitness differences between phenotype play a crucial role. However, the interplay of the actual selection mechanism with the underlying genetics is where the explanatory power of natural selection comes from.  
Natural selection by itself is a simple concept, in which fitness differences between phenotypes are crucial. However, its explanatory power comes from understanding the interplay of the selection mechanism with the underlying genetics.  


===Directionality of selection===
===Directionality of selection===
When some component of a trait is heritable, selection will alter the frequencies of the different [[allele]]s (variants of a gene) involved. Selection can be divided into three classes, on the basis of their effect on the allele frequencies.
When some component of a variable trait is heritable, selection can alter the frequencies of the different [[allele]]s (variants of a gene) that are responsible for that variability. Selection can be divided into three classes:


[[directional selection|Positive or directional selection]] occurs when a certain allele has a greater fitness than others, resulting in an increase in frequency of that allele until it is fixed and the entire population expresses the fitter phenotype.
[[directional selection|Positive or directional selection]] occurs when a certain allele is associated with a greater fitness than others, resulting in an increase in frequency of that allele until it is fixed and the entire population expresses the fitter phenotype.


Far more common is [[stabilizing selection|purifying or stabilizing selection]], which lowers the frequency of alleles which have a deleterious effect on the phenotype (that is, lower fitness), until they are eliminated from the population. Purifying selection results in functional genetic features (e.g. [[Protein biosynthesis|protein-coding sequences]] or [[regulatory sequence]]s) being [[conservation (genetics)|conserved]] over time because of selective pressure against deleterious variants.
Far more common is [[stabilizing selection|purifying or stabilizing selection]], which lowers the frequency of alleles which have a deleterious effect on the phenotype until they are eliminated from the population. Purifying selection results in functional genetic features (e.g. [[Protein biosynthesis|protein-coding sequences]] or [[regulatory sequence]]s) being [[conservation (genetics)|conserved]] over time because of selective pressure against deleterious variants.


Finally, a number of forms of [[balancing selection]] exist, which do not result in fixation, but maintain an allele at intermediate frequencies in a population. This can occur in [[diploid]] species (with two pair of [[chromosome]]s) when individuals with a combination of two different alleles at a single [[Locus (genetics)|position at the chomosome]] ([[heterozygote]]) have a higher fitness than individuals that have two of the same alleles ([[homozygote]]). This is called [[heterozygote advantage]] or overdominance. Maintenance of allelic variation can also occur through [[disruptive selection|disruptive or diversifying selection]], which favors genotypes that depart from the average in either direction (that is, the opposite of overdominance), and can result in a [[bimodal distribution]] of trait values. Finally, it can occur through [[frequency-dependent selection]], where the fitness of one particular phenotype depends on the distribution of other phenotypes in the population (see also [[Game theory]]).
Finally, many forms of [[balancing selection]] do not result in fixation, but maintain an allele at intermediate frequencies in a population. This can happen in [[diploid]] species (with two pair of [[chromosome]]s) when individuals with a combination of two different alleles at a single [[Locus (genetics)|position at the chromosome]] ([[heterozygote]]) have a higher fitness than individuals that have two copies of the same allele ([[homozygote]]). This is called [[heterozygote advantage]] or overdominance. Allelic variation can also be maintained through [[disruptive selection|disruptive or diversifying selection]], which favors genotypes that depart from the average in either direction (that is, the opposite of overdominance), and can result in a [[bimodal distribution]] of trait values. Finally, it can occur by [[frequency-dependent selection]], where the fitness of one particular phenotype depends on the prevalence of other phenotypes in the population (see also [[Game theory]]).


===Selection and genetic variation===
===Selection and genetic variation===
A portion of all [[genetic variation]] is functionally [[neutral theory of molecular evolution|neutral]]; i.e., it produces no phenotypic effect or significant differences in fitness. Previously, this was thought to encompass most of the genetic variation in non-coding DNA, but recent studies have shown that large parts of those sequences are highly conserved and under strong purifying selection; i.e. they do not vary as much from individual to individual, indicating that mutations in these regions have deleterious consequences)<ref name=NCFitnessEffects>Kryukov GV, Schmidt S & Sunyaev S (2005) Small fitness effect of mutations in highly conserved non-coding regions. ''Human Molecular Genetics'' 14:2221-9</ref><ref name=NCFitnessEffects2>Bejerano G, Pheasant M, Makunin I, Stephen S, Kent WJ, Mattick JS & Haussler D (2004) Ultraconserved elements in the human genome. [[Science (journal)|''Science'']] 304:1321-5</ref>. When genetic variation does not result in differences in fitness, selection cannot directly affect the frequency of such variation. As a result, the genetic variation at those sites will be higher than at sites where selection does have a result.  
Some [[genetic variation]] is functionally [[neutral theory of molecular evolution|neutral]]; i.e., it produces no phenotypic effect or significant differences in fitness. Previously, this was thought to encompass most of the genetic variation in non-coding DNA, but parts of those sequences are highly conserved, indicating that they are  under strong purifying selection, and suggesting that mutations in these regions have deleterious consequences<ref name=NCFitnessEffects>Kryukov GV ''et al'' (2005) Small fitness effect of mutations in highly conserved non-coding regions. ''Human Molecular Genetics'' 14:2221-9Bejerano G ''et al'' (2004) Ultraconserved elements in the human genome. ''Science'' 304:1321-5</ref>. When genetic variation does not result in differences in fitness, selection cannot directly affect the frequency of such variation. As a result, the genetic variation at those sites will be higher than at sites where selection does have a result.  


====Genetic linkage====
====Genetic linkage====
[[Genetic linkage]] occurs when two alleles are in close proximity to each other. During the formation of the [[gametes]], [[genetic recombination|recombination]] of the genetic material results in reshuffling of the alleles. However, the chance that such a reshuffle occurs between two alleles depends on the distance between those alleles; the closer the alleles are to each other, the less likely it is that such a reshuffle will occur. Consequently, when selection targets one allele, this automatically results in selection of the other allele as well; through this mechanism, selection can have a strong influence on patterns of variation in the genome.
[[Genetic linkage]] occurs when two alleles are close to each other. During the formation of the [[gametes]], [[genetic recombination|recombination]] of the genetic material results in a reshuffling of the alleles. However, the chance that such a reshuffle occurs between two alleles depends on the distance between those alleles; the closer the alleles are to each other, the less likely it is that such a reshuffle will occur. Consequently, when selection targets one allele, this automatically results in selection of the other allele as well; through this mechanism, selection can have a strong influence on patterns of variation in the genome.


====Mutation-selection balance====
====Mutation-selection balance====
Natural selection results in the reduction of genetic variation through the elimination of maladapted individuals and, through that, of the mutations that causes the maladaptation. At the same time, new mutations occur, resulting in a [[mutation-selection balance]]. The exact outcome of the two processes depends both on the rate at which new mutations occurs and on the strength of the natural selection. Consequently, changes in the mutation rate or the selection pressure will result in a different mutation-selection balance.
Natural selection results in less genetic variation by eliminating maladapted individuals and, through that, the mutations that causes the maladaptation. At the same time, new mutations arise spontaneously, resulting in a [[mutation-selection balance]]. The exact outcome depends both on the rate at which new mutations occur and on the strength of the natural selection.  


====Selective sweep====
====Selective sweep====
[[Selective sweep]]s occur when an allele becomes more common in a population as a result of positive selection. As the prevalence of one allele increases, linked alleles (those nearby on the chromosome) can also become more common, whether they are neutral or even slightly deleterious. This is called ''[[genetic hitchhiking]]''. A strong selective sweep results in a region of the genome where the positively selected [[haplotype]] (the allele and its neighbours) are essentially the only ones that exist in the population.
[[Selective sweep]]s occur when an allele becomes more common in a population as a result of positive selection. As the prevalence of one allele increases, linked alleles (those nearby on the chromosome) can also become more common, whether they are neutral or even slightly deleterious. This is called ''[[genetic hitchhiking]]''. A strong selective sweep results in a region of the genome where the positively selected [[haplotype]] (the allele and its neighbours) are essentially the only ones that exist in the population.


Whether a selective sweep has occurred or not can be investigated by measuring [[linkage disequilibrium]], i.e., whether a given haplotype is overrepresented in the population. Normally, [[genetic recombination]] results in a reshuffling of the different alleles within a haplotype, and none of the haplotypes will dominate the population. However, during a selective sweep, selection for a specific allele will also result in selection of neighbouring alleles. Therefore, the presence of strong linkage disequilibrium might indicate that there has been a 'recent' selective sweep, and this can be used to identify sites recently under selection.
Whether a selective sweep has occurred or not can be investigated by measuring [[linkage disequilibrium]], i.e., whether a given haplotype is overrepresented in the population. Normally, [[genetic recombination]] results in a 'reshuffle' of the alleles within a haplotype, and none of the haplotypes will dominate the population. However, during a selective sweep, selection for a specific allele will also result in selection of neighbouring alleles. Therefore, the presence of strong linkage disequilibrium might indicate that there has been a 'recent' selective sweep, and this can be used to identify sites recently under selection.


====Background selection====
====Background selection====
[[Background selection]] is the opposite of a selective sweep. If a specific site experiences strong and persistent purifying selection (perhaps as a result of mutation-selection balance), linked variation will tend to be weeded out along with it. Background selection, however, acts as a result of new mutations, which can occur randomly in any haplotype. It therefore produces no linkage disequilibrium, though it reduces the amount of variation in the region.
[[Background selection]] is the opposite of a selective sweep. If a specific site experiences strong and persistent purifying selection (perhaps as a result of mutation-selection balance), linked variation will tend to be weeded out along with it. However, background selection acts as a result of new mutations, which can occur randomly in any haplotype. It therefore produces no linkage disequilibrium, although it reduces the amount of variation in the region.


==Evolution by means of natural selection==
==Evolution by means of natural selection==
{{main|Evolution|Darwinism}}
{{main|Evolution|Darwinism}}
A prerequisite for natural selection to result in [[adaptation|adaptive evolution]], novel traits and [[speciation]], is the presence of heritable [[genetic variation]] that results in fitness differences. Genetic variation is the result of [[mutation]]s, [[genetic recombination|recombination]]s and alterations in the [[karyotype]] (the number, shape, size and internal arrangement of the [[chromosome]]s). Any of these changes might have an effect that is highly advantageous or highly disadvantageous, but large effects are very rare. In the past, most changes in the genetic material were considered neutral or close to neutral because they occurred in [[noncoding DNA]] or resulted in a [[synonymous substitution]]. However, recent research suggests that many mutations in non-coding DNA do have slight deleterious effects<ref name=NCFitnessEffects/><ref name=NCFitnessEffects2/>. Overall, of those mutations that do affect the fitness of the individual, most are slightly deleterious, some reduce the fitness dramatically and some increase the fitness.  
A prerequisite for natural selection to result in [[adaptation|adaptive evolution]], novel traits and speciation, is the presence of heritable [[genetic variation]] that results in fitness differences. Genetic variation is the result of [[mutation]]s, [[genetic recombination|recombination]]s and alterations in the [[karyotype]] (the number, shape, size and internal arrangement of the [[chromosome]]s). Any of these changes might have an effect that is highly advantageous or highly disadvantageous, but large effects are very rare. In the past, most changes in the genetic material were considered neutral or close to neutral because they occurred in [[noncoding DNA]] or resulted in a [[synonymous substitution]]. However, recent research suggests that many mutations in non-coding DNA do have slight deleterious effects<!-- <ref name=NCFitnessEffects/><ref name=NCFitnessEffects2/> -->. Overall, of those mutations that do affect the fitness of the individual, most are slightly deleterious, some reduce the fitness dramatically and some increase the fitness.  
 
[[Image:Pavo cristatus albino001xx.jpg|right|thumb|280px|The exuberant tail of the [[peacock]] is thought to be the result of sexual selection by females. This peacock is an [[albino]] - it carries a mutation that makes it unable to produce [[melanin]]. Selection against albinos in nature is intense because they are easily spotted by predators or are unsuccessful in competition for mates, and so these mutations are usually rapidly eliminated by natural selection]]


By the definition of fitness, individuals with greater fitness are more likely to contribute offspring to the next generation, while individuals with lesser fitness are more likely to die early or they fail to reproduce. As a result, alleles which on average result in greater fitness become more abundant in the next generation, while alleles which generally reduce fitness become rarer. If the selection forces remain the same for many generations, beneficial alleles become more and more abundant, until they dominate the population, while alleles with a lesser fitness disappear. In every generation, new mutations and recombinations arise spontaneously, producing a new spectrum of phenotypes. Therefore, each new generation will be enriched by the increasing abundance of alleles that contribute to those traits that were favored by selection, enhancing these traits over successive generations.
By the definition of fitness, individuals with greater fitness are more likely to contribute offspring to the next generation, while individuals with lesser fitness are more likely to die early or they fail to reproduce. As a result, alleles which on average result in greater fitness become more abundant in the next generation, while alleles which generally reduce fitness become rarer. If the selection forces remain the same for many generations, beneficial alleles become more and more abundant, until they dominate the population, while alleles with a lesser fitness disappear. According to evolutionary biologists, in every generation, new mutations and recombinations arise spontaneously, producing a new spectrum of phenotypes (new physical characteristics: eye color, skin color, etc). However, this idea is disputed amongst biologists of different backgrounds, with other biologists saying that each new generation will be preserved by the selection of ''previously existing'' traits that were favored by the species, but not brand new characteristics.
[[Image:Polydactyly 01 Lhand AP.jpg|left|thumb|150px|X-ray of the left hand of a ten year old boy with [[polydactyly]]]]


Some mutations occur in so-called [[regulatory sequence|regulatory genes]]. Changes in these can have large effects on the phenotype of the individual because they regulate the function of many other genes. Most, but not all, mutations in regulatory genes result in non-viable [[zygote]]s. For example, mutations in some [[Homeobox|HOX genes]] in humans result in [[polydactyly|an increase in the number of fingers or toes]]<ref>Zakany J, FromentalRamain C, Warot X & Duboule D (1997) Regulation of number and size of digits by posterior Hox genes: a dose-dependent mechanism with potential evolutionary implications. [[PNAS|''Proc Natl Acad Sci USA'']] 94:13695-700</ref> or a [[cervical rib]]<ref>Galis F (1999) Why do almost all mammals have seven cervical [[vertebrae]]? developmental constraints, Hox genes, and cancer. ''J Exp Zool'' 285:19-26</ref>. When such mutations result in a higher fitness, natural selection will favor these phenotypes and the novel trait will spread in the population.  
Some mutations occur in so-called [[regulatory sequence|regulatory genes]]. Changes in these can have large effects on the phenotype of the individual because they regulate the function of many other genes. Most, but not all, mutations in regulatory genes result in non-viable [[zygote]]s. For example, mutations in some [[Homeobox|HOX genes]] in humans result in [[polydactyly|an increase in the number of fingers or toes]]<ref>Zakany J ''et al.'' (1997) Regulation of number and size of digits by posterior Hox genes: a dose-dependent mechanism with potential evolutionary implications. [[PNAS|''Proc Natl Acad Sci USA'']] 94:13695-700</ref> or a [[cervical rib]]<ref>Galis F (1999) Why do almost all mammals have seven cervical [[vertebrae]]? developmental constraints, Hox genes, and cancer. ''J Exp Zool'' 285:19-26</ref>. When such mutations result in a higher fitness, natural selection will favor these phenotypes and the novel trait will spread in the population.  


Established traits are not immutable: an established trait may lose its fitness if environmental conditions change. In these circumstances, in the absence of natural selection to preserve the trait, the trait will become more variable and will deteriorate over time. The power of natural selection will also inevitably depend upon prevailing environmental factors; in general, the number of offspring is (far) greater than the number of individuals that can survive to the next generation, and there will be intense selection of the best adapted individuals for the next generation.  
Established traits are not immutable: an established trait may lose its fitness if environmental conditions change. In these circumstances, in the absence of natural selection to preserve the trait, the trait will become more variable and will deteriorate over time. The power of natural selection will also inevitably depend upon prevailing environmental factors; in general, the number of offspring is (far) greater than the number of individuals that can survive to the next generation, and there will be intense selection of the best adapted individuals for the next generation.  
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[[Speciation]] requires selective mating, which result in a reduced [[gene flow]]. Selective mating can be the result of, for example, a change in the physical environment (physical isolation by an extrinsic barrier), or by sexual selection resulting in [[assortative mating]]. Over time, these subgroups might diverge radically to become different species, either because of differences in selection pressures on the different subgroups, or because different mutations arise spontaneously in the different populations, or because of [[founder effect]]s - some potentially beneficial alleles may, by chance, be present in only one or other of two subgroups when they first become separated. When the genetic changes result in increasing incompatibility between the genotypes of the two subgroups, gene flow between the groups will be reduced even more, and will stop altogether as soon as the mutations become fixed in the respective subgroups. As few as two mutations can result in speciation: if each mutation has a neutral or positive effect on fitness when they occur separately, but a negative effect when they occur together, then fixation of these genes in the respective subgroups will lead to two reproductively isolated populations. According to the biological species concept, these will be two different species.
[[Speciation]] requires selective mating, which result in a reduced [[gene flow]]. Selective mating can be the result of, for example, a change in the physical environment (physical isolation by an extrinsic barrier), or by sexual selection resulting in [[assortative mating]]. Over time, these subgroups might diverge radically to become different species, either because of differences in selection pressures on the different subgroups, or because different mutations arise spontaneously in the different populations, or because of [[founder effect]]s - some potentially beneficial alleles may, by chance, be present in only one or other of two subgroups when they first become separated. When the genetic changes result in increasing incompatibility between the genotypes of the two subgroups, gene flow between the groups will be reduced even more, and will stop altogether as soon as the mutations become fixed in the respective subgroups. As few as two mutations can result in speciation: if each mutation has a neutral or positive effect on fitness when they occur separately, but a negative effect when they occur together, then fixation of these genes in the respective subgroups will lead to two reproductively isolated populations. According to the biological species concept, these will be two different species.


==History of the principle==
==Historical context==
{{main|History of evolutionary thought|Inception of Darwin's theory|Development of Darwin's theory}}
[[History of evolutionary thought|Until the early 19th century]], the established view in Western societies was that differences between individuals of a species were uninteresting departures from their [[Platonic idealism|Platonic ideal (or typus)]] of created kinds. However, growing awareness of the fossil record led to the recognition that species that lived in the distant past were often very different from those that exist today. In the early 19th century, [[radical]] [[evolutionism|evolutionists]] such as [[Jean Baptiste Lamarck]] had proposed that characteristics (adaptations) acquired by individuals might be inherited by their progeny, causing, in enough time, [[transmutation of species]] (see [[Lamarckism]]).<ref>[[Jean-Baptiste Lamarck|Chevalier de Lamarck J-B, de Monet PA]] (1809) ''Philosophie Zoologique''</ref>
===Pre-Darwinian theories===  
Between 1842 and 1844, Charles Darwin outlined his theory of evolution by natural selection as an explanation for adaptation and speciation. He defined natural selection as the "principle by which each slight variation [of a trait], if useful, is preserved". The concept was simple but powerful: individuals best adapted to their environments are more likely to survive and reproduce. As long as there is some variation between them, there will be an inevitable selection of individuals with the most advantageous variations. If the variations are inherited, then differential reproductive success will lead to a progressive evolution of particular populations of a species, and populations that evolve to be sufficiently different might eventually become different species.
General concepts of biological evolution and species change date to ancient times; the [[Ionia]]n physician [[Empedocles]] said that many races ''"must have been unable to beget and continue their kind. For in the case of every species that exists, either craft or courage or speed has from the beginning of its existence protected and preserved it".''Several eighteenth-century thinkers wrote about similar theories, including [[Pierre Louis Moreau de Maupertuis]] in 1745, [[Lord Monboddo]] in his theories of species alteration, and Darwin's grandfather [[Erasmus Darwin]] in 1794–1796. However, these 'precursors' had little influence on evolutionary thought after Darwin.
 
[[History of evolutionary thought|Until the early 19th century]], the [[History of creationism#Renaissance to Darwin|established view]] in Western societies was that differences between individuals of a species were uninteresting departures from their [[Platonic idealism|Platonic ideal (or typus)]] of [[created kind]]s. However, growing awareness of the fossil record led to the recognition that species that lived in the distant past were often very different from those that exist today. In the early years of the 19th century, [[radical]] [[evolutionism|evolutionists]] such as [[Jean Baptiste Lamarck]] had proposed that characteristics (adaptations) acquired by individuals might be inherited by their progeny, causing, in enough time, [[transmutation of species]] (see [[Lamarckism]]).<ref>[[Jean-Baptiste Lamarck|Chevalier de Lamarck J-B, de Monet PA]] (1809) ''Philosophie Zoologique''</ref>[[Image:Charles Darwin aged 51.jpg|right|thumb|250px|The modern theory of natural selection derives from the work of [[Charles Darwin]] in the nineteenth century.]]
Between 1842 and 1844, [[Charles Darwin]] outlined his theory of evolution by natural selection as an explanation for adaptation and speciation. He defined natural selection as the "principle by which each slight variation [of a trait], if useful, is preserved". The concept was simple but powerful: individuals best adapted to their environments are more likely to survive and reproduce. As long as there is some variation between them, there will be an inevitable selection of individuals with the most advantageous variations. If the variations are inherited, then differential reproductive success will lead to a progressive evolution of particular populations of a species, and populations that evolve to be sufficiently different might eventually become different species.


Darwin thought of natural selection by [[analogy]] to how farmers select crops or livestock for breeding ([[artificial selection]]); in his early manuscripts he referred to a 'Nature' which would do the selection. In the next twenty years, he shared these theories with just a few friends, while gathering evidence and trying to address all possible objections. In 1858, [[Alfred Russel Wallace]]<ref>[[Alfred Russel Wallace|Wallace, Alfred Russel]] (1870) ''Contributions to the Theory of Natural Selection'' New York: Macmillan & Co. [http://www.hti.umich.edu/cgi/t/text/text-idx?c=moa&idno=AJP5195.0001.001&view=toc]</ref>, a young naturalist, independently conceived the principle and described it in a letter to Darwin. Not wanting to be scooped, Darwin contacted scientific friends to find an honorable way to handle this potentially embarrassing situation, and two short papers by the two were read at the [[Linnean Society]] announcing co-discovery of the principle. The following year, Darwin published ''[[The Origin of Species]]'', along with his evidence and detailed discussion. This became a topic of great dispute; evolutionary theories became the primary way of talking about speciation, but natural selection did not predominate as the mechanism by which it happened. What made natural selection controversial was doubt about whether it was powerful enough to result in speciation, and that it was 'unguided' rather than 'progressive', something that even Darwin's supporters balked at.
Darwin thought of natural selection by [[analogy]] to how farmers select crops or livestock for breeding ([[artificial selection]]); in his early manuscripts he referred to a 'Nature' which would do the selection. In the next twenty years, he shared these theories with just a few friends, while gathering evidence and trying to address all possible objections. In 1858, [[Alfred Russel Wallace]]<ref>[[Alfred Russel Wallace|Wallace, Alfred Russel]] (1870) ''Contributions to the Theory of Natural Selection'' New York: Macmillan & Co. [http://www.hti.umich.edu/cgi/t/text/text-idx?c=moa&idno=AJP5195.0001.001&view=toc]</ref>, a young naturalist, independently conceived the principle and described it in a letter to Darwin. Not wanting to be scooped, Darwin contacted scientific friends to find an honorable way to handle this potentially embarrassing situation, and two short papers by the two were read at the [[Linnean Society]] announcing co-discovery of the principle. The following year, Darwin published ''[[The Origin of Species]]'', along with his evidence and detailed discussion. This became a topic of great dispute; evolutionary theories became the primary way of talking about speciation, but natural selection did not predominate as the mechanism by which it happened. What made natural selection controversial was doubt about whether it was powerful enough to result in speciation, and that it was 'unguided' rather than 'progressive', something that even Darwin's supporters balked at.


Darwin's ideas were inspired by the observations that he had made on [[the Voyage of the Beagle]], and by the economic theories of [[Thomas Malthus]], who noted that population (if unchecked) increases exponentially whereas the food supply grows only arithmetically; thus limitations of resources would inevitably lead to a "struggle for existence", in which only the ''fittest'' would survive. Similar ideas go back to ancient times; the [[Ionia]]n physician [[Empedocles]] said that many races ''"must have been unable to beget and continue their kind. For in the case of every species that exists, either craft or courage or speed has from the beginning of its existence protected and preserved it".'' Several eighteenth-century thinkers wrote about similar theories, including [[Pierre Louis Moreau de Maupertuis]] in 1745, [[Lord Monboddo]] in his theories of species alteration, and Darwin's grandfather [[Erasmus Darwin]] in 1794–1796. In the 6th edition of ''The Origin of Species'' Darwin acknowledged that others &mdash; notably [[William Charles Wells]] in 1813, and [[Patrick Matthew]] in 1831 &mdash; had proposed similar theories, but had not presented them fully or in notable scientific publications. Wells presented his hypothesis to explain the origin of human races in person at the [[Royal Society]], and Matthew published his as an appendix to his book on [[arboriculture]]<ref>Dempster WJ (1996) ''Evolutionary concepts in the nineteeth century, natural selection and [[Patrick Matthew]]''. Durham: The Pentland Press. ISBN 185213568 {{Please check ISBN|185213568}}</ref>. [[Edward Blyth]] had also proposed a method of natural selection as a mechanism of keeping species constant. However, these 'precursors' had little influence on [[history of evolutionary thought|evolutionary thought]].  
Darwin's ideas were inspired by the observations that he had made on [[the Voyage of the Beagle]], and by the economic theories of [[Thomas Malthus]], who noted that population (if unchecked) increases exponentially whereas the food supply grows only arithmetically; thus limitations of resources would inevitably lead to a "struggle for existence", in which only the ''fittest'' would survive. Similar ideas go back to ancient times; the [[Ionia]]n physician [[Empedocles]] said that many races ''"must have been unable to beget and continue their kind. For in the case of every species that exists, either craft or courage or speed has from the beginning of its existence protected and preserved it".'' Several 18th-century thinkers wrote about similar theories, including [[Pierre Louis Moreau de Maupertuis]] in 1745, [[Lord Monboddo]] in his theories of species alteration, and Darwin's grandfather [[Erasmus Darwin]] in 1794–1796. In the 6th edition of ''The Origin of Species'' Darwin acknowledged that others &mdash; notably [[William Charles Wells]] in 1813, and [[Patrick Matthew]] in 1831 &mdash; had proposed similar theories, but had not presented them fully or in notable scientific publications. Wells presented his hypothesis to explain the origin of human races in person at the [[Royal Society]], and Matthew published his as an appendix to his book on [[arboriculture]]<ref>Dempster WJ (1996) ''Evolutionary concepts in the nineteenth century, natural selection and [[Patrick Matthew]]''. Durham: The Pentland Press. ISBN 185213568 </ref>. [[Edward Blyth]] had also proposed a method of natural selection as a mechanism of keeping species constant. However, these 'precursors' had little influence on [[history of evolutionary thought|evolutionary thought]].  


Within a decade of ''The Origin of Species'', most educated people had begun to accept that evolution had occurred in some form or another. However, of the many ideas of evolution that emerged, only [[August Weismann]]'s saw natural selection as the main evolutionary force. Even [[Thomas Henry Huxley|T.H. Huxley]] believed that there was more "purpose" in evolution than natural selection afforded, and neo-[[Jean-Baptiste Lamarck|Lamarckism]] was also popular. After reading Darwin, [[Herbert Spencer]] introduced the term ''[[survival of the fittest]]''; this became popular, and Wallace marked up an entire edition of ''The Origin of Species'', replacing every instance of ''natural selection'' with Spencer's phrase. Although the phrase is still often used by non-biologists, modern biologists avoid it because it is [[tautology|tautological]] if ''fittest'' is read to mean ''functionally superior''.
Concurrent with the publication of ''The Origin of Species'', many of Darwin's contemporaries advanced hypotheses regarding evolution. However, of the many ideas of evolution that emerged, only [[August Weismann]]'s saw natural selection as the main evolutionary force. [[Thomas Henry Huxley|T.H. Huxley]], for example, believed that there was more "purpose" in evolution than natural selection afforded.  A revised version of [[Jean-Baptiste Lamarck|Lamarckism]] also enjoyed some popularity.


===Modern evolutionary synthesis===
===Modern evolutionary synthesis===
{{main|Modern evolutionary synthesis}}
{{main|Modern evolutionary synthesis}}
Only after the integration of a theory of evolution with a complex statistical appreciation of [[Gregor Mendel|Mendel]]'s 're-discovered' laws of [[inheritance]] did natural selection become generally accepted by scientists. The work of [[Ronald Fisher]], who first tried to explain natural selection by the underlying [[The Genetical Theory of Natural Selection|genetic processes]]<ref name=fisher/>); [[J.B.S. Haldane]], who introduced the concept of the 'cost' of natural selection <ref>Haldane JBS (1932) ''[[The Causes of Evolution]]''; Haldane JBS (1957) The cost of natural selection. ''J Genet'' 55:511-24([http://www.blackwellpublishing.com/ridley/classictexts/haldane2.pdf]</ref>; [[Sewall Wright]], one of the founders of population genetics <ref>Wright S (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution] ''Proc 6th Int Cong Genet'' [http://www.blackwellpublishing.com/ridley/classictexts/wright.asp 1:356–66]</ref>; [[Theodosius Dobzhansky]], who established the idea that mutation, by creating [[Genetics and the Origin of Species|genetic diversity]], supplied the raw material for natural selection<ref>Dobzhansky Th (1937) ''[[Genetics and the Origin of Species]]'' Columbia University Press, New York. (2nd ed. 1941; 3rd edn. 1951)</ref>), [[William Hamilton]], who conceived of kin selection; [[Ernst Mayr]], who recognised the importance of [[Systematics and the Origin of Species|reproductive isolation ]]for speciation<ref>Mayr E (1942) ''[[Systematics and the Origin of Species]]'' Columbia University Press, New York. ISBN 0-674-86250-3</ref> and many others formed the [[modern evolutionary synthesis]]. This propelled natural selection to the forefront of evolutionary theories, where it remains today.
Only after the integration of a theory of evolution with a complex statistical appreciation of [[Gregor Mendel|Mendel]]'s 're-discovered' laws of [[inheritance]] did natural selection become generally accepted by scientists. The work of [[Ronald Fisher]], who first tried to explain natural selection by the underlying [[The Genetical Theory of Natural Selection|genetic processes]]<!-- <ref name=fisher/> -->); [[J. B. S. Haldane]], who introduced the concept of the 'cost' of natural selection <ref>Haldane JBS (1932) ''[[The Causes of Evolution]]''; Haldane JBS (1957) The cost of natural selection. ''J Genet'' 55:511-24([http://www.blackwellpublishing.com/ridley/classictexts/haldane2.pdf]</ref>; [[Sewall Wright]], one of the founders of population genetics <ref>Wright S (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution] ''Proc 6th Int Cong Genet'' [http://www.blackwellpublishing.com/ridley/classictexts/wright.asp 1:356–66]</ref>; [[Theodosius Dobzhansky]], who established the idea that mutation, by creating [[Genetics and the Origin of Species|genetic diversity]], supplied the raw material for natural selection<ref>Dobzhansky Th (1937) ''[[Genetics and the Origin of Species]]'' Columbia University Press, New York. (2nd ed. 1941; 3rd edn. 1951)</ref>), [[William Hamilton]], who conceived of kin selection; [[Ernst Mayr]], who recognised the importance of [[Systematics and the Origin of Species|reproductive isolation ]]for speciation<ref>Mayr E (1942) ''[[Systematics and the Origin of Species]]''. Columbia University Press, New York. ISBN 0-674-86250-3 | [http://books.google.com/books?id=mAIjnLp6r_MC&dq=Mayr+systematics&source=gbs_navlinks_s Google Books preview].</ref> and many others formed the [[modern evolutionary synthesis]]. This propelled natural selection to the forefront of evolutionary theories, where it remains today. The modern evolutionary synthesis continues to undergo extension and revision <ref>Francisco J. Ayala, Walter M. Fitch, and Michael T. Clegg, Editors, (2000) [http://books.nap.edu/openbook.php?record_id=9766&page=R1 ''Variation and Evolution in Plants and Microorganisms, Towards a New Synthesis 50 years after Stebbing.''] National Academy of Sciences, Washington DC.</ref>


==Impact of the idea==
==Impact of the idea==
Darwin's ideas, along with those of [[Adam Smith]] and [[Karl Marx]], had a profound influence on [[19th-century]] thought. Perhaps the most radical claim of the theory of evolution through natural selection is that "elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner" evolved from the simplest forms of life by a few simple principles. This claim inspired some of Darwin's most ardent supporters&mdash;and provoked the most profound opposition. The radicalism of natural selection, according to [[Stephen Jay Gould]] <ref>[http://www.nybooks.com/articles/1151 The New York Review of Books: Darwinian Fundamentalism] (accessed May 6, 2006)</ref>, lay in its power to "dethrone some of the deepest and most traditional comforts of Western thought". In particular, it challenged beliefs in nature's benevolence, order, and good design, the belief that humans occupy a summit of power and excellence, belief in an omnipotent, benevolent creator, and belief that nature has any meaningful direction, or that humans fit into any ''sensible'' pattern.
Darwin's ideas, along with those of [[Adam Smith]] and [[Karl Marx]], had a profound influence on 19th-century thought. Perhaps the most radical claim of Darwin's theory of evolution through natural selection is that "elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner"<ref name=origin/> evolved from the simplest forms of life by a few simple principles expressed in natural processes. This claim inspired some of Darwin's most ardent supporters<ref name=huxleyessays2>Huxley TH. (1896) ''Darwiniana: Essays by Thoms H. Huxley''. Vol. 2. D. Appleton and Co. | [http://books.google.com/books?id=WSILAQAAIAAJ&dq=inauthor:Thomas+inauthor:Huxley&source=gbs_navlinks_s Google Books Full-Text].
 
*"<font face="Gill Sans MT">That this most ingenious hypothesis enables us to give a reason for many apparent anomalies in the distribution of living beings in time and space, and that it is not contradicted by the main phenomena of life and organisation appear to us to be unquestionable; and, so far, it must be admitted to have an immense advantage over any of its predecessors.</font>"</ref>&nbsp;<ref name=bowlerchap6>Bowler PJ. (2003) Reception of Darwin's Theory. Chapter 6. In: Bowler PJ. (2003) ''Evolution: The History of an Idea.'' Third Edition, Completely Revised and Expanded. Berkeley: University of California Press. ISBN 0520236939. | [http://books.google.com/books?id=e2b5B0po8fwC&dq=editions:ISBN0520063864&source=gbs_navlinks_s Google Books Full View 1989 Edition].</ref>&mdash;and provoked the most profound opposition.<ref name=bowlerchap6/> The radicalism of natural selection, according to [[Stephen Jay Gould]] <ref>[http://www.nybooks.com/articles/1151 The New York Review of Books: Darwinian Fundamentalism] (accessed May 6, 2006)</ref>, lay in its power to "dethrone some of the deepest and most traditional comforts of Western thought". In particular, it challenged beliefs in nature's benevolence, order, and good design, the belief that humans occupy a summit of power and excellence, belief in an omnipotent, benevolent creator, and belief that nature has any meaningful direction, or that humans fit into any ''sensible'' pattern.
===Social Theory===
The social implications of the theory of evolution by natural selection also became the source of continuing controversy. [[Friedrich Engels|Engels]] in 1872 wrote that "Darwin did not know what a bitter satire he wrote on mankind when he showed that free competition, the struggle for existence, which the economists celebrate as the highest historical achievement, is the normal state of the animal kingdom".<ref>[[Engels]] F (1873-86) ''Dialectics of Nature''  3d ed. Moscow: Progress, 1964[http://www.marxists.org/archive/marx/works/1883/don/index.htm]</ref>. That natural selection had apparently led to 'advancement' in intelligence and civilisation also became used as a justification for [[colonialism]] and policies of [[eugenics]] &mdash;see [[Social Darwinism]]. [[Konrad Lorenz]] won the [[Nobel Prize]] in 1973 for his analysis of animal behavior in terms of the role of natural selection (particularly group selection). However, in Germany in 1940, in writings that he subsequently disowned, he used the theory as a justification for policies of the [[Nazi]] state. He wrote "... selection for toughness, heroism, and social utility...must be accomplished by some human institution, if mankind, in default of selective factors, is not to be ruined by domestication-induced degeneracy. The racial idea as the basis of our state has already accomplished much in this respect." <ref> Quoted in translation in Eisenberg L (2005) Which image for Lorenz? ''Am J Psychiatry'' 162:1760 [http://ajp.psychiatryonline.org/cgi/content/full/162/9/1760]</ref>. Others have developed ideas that human societies and culture [[evolution of societies|evolve]] by mechanisms that are analogous to those that apply to evolution of species <ref>e.g. Wilson, DS (2002) ''Darwin's Cathedral: Evolution, Religion, and the Nature of Society''. University of Chicago Press, ISBN 0-226-90134-3 </ref>. (see article on [[Sociocultural evolution]]).


===Energetic theory===
The concept of natural selection has had an influence on philosophical and ethical reflection. [[Francis Galton]], [[Thomas Malthus]] and other [[Social Darwinism|Social Darwinists]] used the principle of natural selection to justify social policies that gave no help or assistance to the poor and needy on the basis that one is then preventing the advancement of the species. Rather the poor and needy should die off to promote genetic fitness. This went much further in [[eugenics]] movements which moved to simply omitting to help those in need to actively sterilising people who fail to meet the relevant criteria for genetic health. Even today, some groups like [[Project Prevention]] – a U.S. charity that pays drug addicts $300 to be sterilised voluntarily – are considered by many to be advocating a form of eugenics. In contemporary Western societies, mainstream opinion generally regards the practice of eugenics and social Darwinism as barbaric and scientists condemn it as not just being ethically problematic but actually scientifically implausible too.
In 1922, [[Alfred J. Lotka|Alfred Lotka]] proposed that natural selection might be understood as a physical principle which can be energetically quantified.<ref>Lotka AJ (1922a) [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1085052&blobtype=pdf Contribution to the energetics of evolution] [PDF] ''Proc Natl Acad Sci USA'' 8:147–51</ref><ref>
Lotka AJ (1922b) [http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=1085053&blobtype=pdf Natural selection as a physical principle] [PDF] ''Proc Natl Acad Sci USA'' 8:151–4</ref>
Through the work of [[Howard T. Odum]] this became known as the [[maximum power principle]] whereby evolutionary systems with selective advantage maximise the rate of useful energy transformation.


===Information theory===
Eugenic and social Darwinist theories have had an especially horrendous role regarding race with nineteenth century scientists and social Darwinists producing elaborate descriptions of racial difference and grounding said differences in claims of biological difference, sometimes wrapped with natural selection: often suggesting that white Europeans were selected by evolution to be more intelligent – [[Peter Bowker]] lists a number of these including [[Petrus Camper]]'s physiological study of skulls, where he argued that the facial angle of black races was between that of ape ancestors and European races as well as pre-genetic classifications by [[Carl Linnaeus]] and others.<ref>[[Peter Bowker]], ''Evolution: The History of an Idea'', p. 52, diagram on p. 53.</ref> The development of [[genetics]] as a science has allowed many of these to be dismissed as myths. Some creationists use these unfortunate developments as a reason to dismiss evolutionary theory<ref>Richard Weikart's ''From Darwin to Hitler'', for instance.</ref> although such claims tend to get short shrift from mainstream historians.
Natural selection need not apply only to biological organisms. In computer-based systems (e.g., [[artificial life]]), simulating natural selection can be very effective in 'adapting' entities to their environments <ref> [[Stuart Kauffman|Kauffman SA]] (1993) ''The Origin of order. Self-organization and selection in evolution.'' New York: Oxford University Press ISBN 0-19-507951-5 </ref>. By combining this with simulated reproduction and random variation it is possible for instance to 'evolve' problem-solving abilities of computer-based systems. However, whether such systems show that evolution by means of natural selection ''per se'' can generate complexity is contested<ref>For an example confirming the possibility, see Bridgham JT, Carroll SM & Thornton JW (2006) Evolution of hormone-receptor complexity by molecular exploitation. [[Science (journal)|''Science'']] 312:97-101
PMID 16601189</ref>. The mathematician and [[science fiction]] writer [[Rudy Rucker]] explored the use of natural selection to create [[artificial intelligence]] in his best-known work, ''The [[Ware Tetralogy]]'', and in his novel ''The Hacker and the Ants''.


==Trivia==
The linking of natural selection as an account of how things ''are'' to how things ''ought'' to be is dismissed early on in [[Richard Dawkins]]' ''The Selfish Gene'', one of the more popular books in the English-speaking world on evolutionary theory for a general audience. While he is a Darwinian in terms of believing that the relevant facts in biology are best explained through evolution, he argues he is strongly anti-Darwinian in a normative sense:
* In a letter to [[Charles Lyell]] in September 1860, Darwin regrets the use of the term 'Natural Selection', preferring the term 'Natural Preservation'. <ref>{{cite web | url=http://darwin.lib.cam.ac.uk/perl/nav?pclass=calent;pkey=2931 | title=Darwin Correspondence Online Database: Darwin, C. R. to Lyell, Charles, 28 Sept 1860 | accessdate=2006-05-10}}</ref>


==References==
<blockquote>I am not advocating a morality of evolution. I am saying how things have evolved. I am not saying how we humans morally ought to behave. I stress this, because I know I am in danger of being misunderstood by those people, all too numerous, who cannot distingush a statement of belief in what is the case from an advocacy of what ought to be the case. My own feeling is that a human society based simply on the gene's law of universal ruthless selfishness would be a very nasty society in which to live. But unfortunately, however much we may deplore something, it does not stop it being true. This book is mainly intended to be interesting, but if you would extract a moral from it, read it as a warning. Be warned that if you wish, as I do, to build a society in which individuals cooperate generously and unselfishly towards a common good, you can expect little help from biological nature. Let us try to ''teach'' generosity and altruism, because we are born selfish. Let us understand what our own selfish genes are up to, because we may then at least have the chance to upset their designs, something that no other species has ever aspired to.<ref>[[Richard Dawkins]], ''[[The Selfish Gene]]'', p. 2-3.</ref></blockquote>
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==Further reading==
Darwinian thinking and the idea of natural selection has had an effect on other areas outside of the biological sciences. Philosophers including Daniel Dennett and [[Michael Ruse]] have argued that evolution and natural selection provide a new lens by which one can approach a variety of philosophical problems, with Dennett going so far as to argue that evolution is a "universal acid".<ref>In ''Darwin's Dangerous Idea''.</ref>
* For technical audiences
** {{cite book| author=[[Stephen Jay Gould|Gould SJ]]| year=2002|title=The Structure of Evolutionary Theory| publisher=Harvard University Press| id=ISBN 0-674-00613-5}}
** [[John Maynard Smith|Maynard Smith J]] (1993) ''The Theory of Evolution''  Cambridge University Press
** [[Karl Popper|Popper K]] (1978) Natural selection and the emergence of mind. ''Dialectica'' 32:339-55. See [http://www.geocities.com/criticalrationalist/popperevolution.htm]
** Sargent TD, Millar CD, Lambert DM (1998) The "classical" explanation of industrial melanism: Assessing the evidence. ''Evolutionary Biology'' 30:299-322.
** [[George C. Williams|Williams GC]] (1966) ''[[Adaptation and Natural Selection|Adaptation and Natural Selection: A Critique of Some Current Evolutionary Thought]]'' Oxford University Press.
** [[George C. Williams|Williams GC]] (1992) ''Natural Selection: Domains, Levels and Challenges'' Oxford University Press.


* For general audiences
Debates in [[epistemology]] have shifted to take on board that cognitive functions are evolved. Much epistemological work in justification is itself often based on a rejection of the Cartesian picture of the mind, and the purported compatibility of externalist accounts of justification (that is, accounts of justification that are based on the state of the world rather than the beliefs, mental states and conscious accessibility of ideas) with the actual history of our cognitive functions as produced by natural selection is argued to be a major point in their favour.
** [[Richard Dawkins|Dawkins R]], (1996) ''[[Climbing Mount Improbable]]'' Penguin Books, ISBN 0-670-85018-7
** [[Daniel Dennett|Dennett D]] (1995) ''[[Darwin's Dangerous Idea|Darwin's Dangerous Idea: Evolution and the Meanings of Life]]'' Simon & Schuster  ISBN 0-684-82471-X
** [[Stephen Jay Gould|Gould SJ]] (1997) ''Ever Since Darwin: Reflections in Natural History'' Norton, ISBN 0-393-06425-5
** [[Steve Jones|Jones S]] (2001) ''Darwin's Ghost: The Origin of Species Updated'' Ballantine Books ISBN 0-345-42277-5. Also published in Britain under the title ''Almost like a whale: the origin of species updated'' Doubleday. ISBN 1-86230-025-9
**[[Richard Lewontin|Lewontin RC]] (1978) Adaptation. ''Scientific American'' 239:212-30
**[[Jonathan Weiner|Weiner, J.]] (1994) [[The Beak of the Finch]]: A Story of Evolution in Our Time, Vintage Books, ISBN 0-679-73337-X


* Historical
Some 'causal history' accounts of various philosophical concepts now make reference to evolutionary history: for instance, to explain [[proper function]] (and to defend it from the competing supernaturalist account provided by the Christian philosopher [[Alvin Plantinga]]), so-called etiological accounts of proper function have been proposed by [[Ruth Millikan]] and [[Karen Neander]]. To say that a particular biological system is functioning properly in some instance is to say that it is functioning in the same way as it has in previous generations, and that function has been a result of natural selection.
** Kohm M (2004) ''A Reason for Everything: Natural Selection and the English Imagination'' London: Faber and Faber. ISBN 0-571-22392-3. For review, see [http://human-nature.com/nibbs/05/wyhe.html] van Wyhe J (2005) ''Human Nature Review'' 5:1-4


==External links==
In political philosophy, [[Peter Singer]] had advocated that left-wing political movements need to become "Darwinian" in the sense that they ought to accept the fact of natural selection and evolution and craft political views around the reality of an evolved human nature.
* [http://www.chains-of-reason.org/chains/evolution-by-natural-selection/introduction.htm Evolution by Natural Selection] - An introduction to the logic of the theory of natural selection
* [http://www.actionbioscience.org/evolution/futuyma.html#learnmore ''Natural selection: how evolution works''] Interview with [[Douglas J. Futuyma]]
* [http://www.literature.org/authors/darwin-charles/the-origin-of-species/chapter-04.html ''The Origin of Species'' by Charles Darwin] - Chapter 4,Natural Selection
* [http://www.wcer.wisc.edu/ncisla/muse/naturalselection/index.html Natural Selection]-  Modeling for Understanding in Science Education, University of Wisconsin
* [http://evolution.berkeley.edu/evolibrary/search/topicbrowse2.php?topic_id=53 natural selection] from University of Berkeley education website


==See also==
==References==
* [[Co-evolution]]
{{reflist|2}}[[Category:Suggestion Bot Tag]]
* [[Gene-centered view of evolution]]
* [[Genetic algorithm]]
* [[Negative selection]]
* [[Ring species]]
* [[Unit of selection]]
 
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{{popgen}}
 
[[Category:Selection]]
[[Category:Evolution]]
[[Category:Evolutionary biology]]
[[Category:Ecology]]
[[Category:CZ Live]]
 
{{CZ Live}}
[[Category:Biology Workgroup]]

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Darwin’s clear elucidation of natural selection launched a revolutionary new paradigm in biology wherein organismal traits could be studied and interpreted as products of natural (rather than supernatural) forces amenable to rational scientific inquiry. [1]

In biology, natural selection is the process by which changes in the natural environment favor, for survival and reproductive success, individual organisms who possess traits that best allow them to resist the adverse effects of the changes, or to best exploit the opportunities the changes present. Those lacking those traits have a lesser chance of surviving and reproducing, a process of 'natural elimination' that accompanies natural selection. Thus environmental changes tend to 'select' individuals whose physical and mental traits give them a reproductive advantage over their less so-endowed conspecifics in the particular environment they live in.[2] For example, when there is not enough food for all to flourish, only those whose traits give them competitive advantage in securing food may so flourish. When advantageous traits can be inherited, those traits will tend to become more common in the subsequent generation. If the changed environment persists, further selection may continue for many generations, increasing what biologists call the 'fit' between the species and environment. Thus biologists characterize natural selection as increasing the 'fitness' of the species, meaning its better 'adaptation' to its environment.

© Photo: Bence Máté
Natural selection at work: An Eyelash Viper (Bothriechis schlegelii) in eye contact with a kolibri.

Natural selection depends on the fact that, in any species, individuals will all be slightly different from one other; they all have slightly different features or abilities - we call these different traits. Many of these differences will be accidents of the environment - some individuals will be stronger than others because they were better fed when young for example, but some differences will be heritable - they can be passed on to the offspring. Any offspring that inherit useful characteristics for the prevailing environment will more likely survive and reproduce, and so will tend pass on those traits to their offspring. Thus, over many generations, species can become increasingly adapted to their habitats. Subgroups of a species that live in different habitats will diverge over time, as each becomes adapted to their own niche; such divergence, given enough time, can lead to subpopulations becoming distinct species unable to interbreed.

This process of natural selection is a long series of events that accounts for the 'fit' between living creatures and their habitat, explaining the presence of drought tolerant plants in the desert and moisture-loving plants in the rain forest, heavily furred mammals in the colder climates and lightly furred mammals in the warmer climes. Across generations, natural selection results in change in the characteristics of species of plants, animals, and other organisms, so that some features become emphasized and others diminished. These changes, called adaptations, lead to particular strains or "natural breeds" within a species and can account for the creation of new species (speciation), and their further evolution over time.

The theory of evolution by natural selection, like all theories, makes certain assumptions. It presumes some variety among the individual entities of any particular kind of living thing. Second, it presumes that offspring can inherit some of those variations. Third, it assumes that in any given situation, some characteristics make reproductive success of individuals more likely, whereas other characteristics make it less likely. Those characteristics often consist simply of the ability to survive. The theory of evolution by natural selection predicts that living things that inherit features that bestow survival advantages for an individual, or otherwise increase the the ability of the individual that has them to reproduce offspring that can mature and reproduce, will tend to multiply in frequency among members of the species over generations.

The theory of evolution by natural selection is one of the cornerstones of modern biology. Charles Darwin, introduced the term "natural selection" in his 1859 book The Origin of Species [3], through analogy with artificial selection, by which farmers select breeding stock. Given time, a passive process of natural selection can result in adaptations and speciations (see evolution). Less dramatically, natural selection accounts for the differing strains and breeds of plants and animals of the same species that are found in varying habitats and geographic regions. The independent discoverer of the process of natural selection, Alfred Russel Wallace, preferred the term 'survival of the fittest', in part because he saw some different consequences, and thus a poor analogy, between artificial and natural selection.

General principles, remarks and concepts

Basic principles

Evolution by means of natural selection changes a population's so-called gene frequency, or allele frequency, the relative frequency of alleles for particular gene loci in the evolving population, measured for a gene locus as the number of a given allele relative to the number of all alleles at that gene locus. Allele frequencies give a measure of the degree of genetic diversity in a population, and changes in allele frequencies in the gene pool give objective evidence that evolution has occurred.[4]

Darwin called it descent with modification which a rather wrong definition.

Darwin made four basic principles to make a evolution theory by means of natural selection:

1. Variation

Individuals within a certain population of a species are not identical. They are different in size, weight. They are different in phenotype.

2. Heritability

There are two causes of these variations:

  • 1. Environment
    • Because of better available food animals can become bigger or plants grow faster in sunlight. The environment is really a vague thing. It is everything except the genetic variation in most contexts
  • 2. Genetic
    • It is also called heritability which means that the variation is passed also from parent to offspring.

3. Demographic abundance or variation in the success to survive

Populations are able to grow incredibly. But a great part of the offspring will die during development or before adulthood.

Darwin himself made a calculation. Elephants were known to be the slowest breeder in Darwin's time. He calculated what would happen with an elephant population if none of the offspring would die in development or childhood. In 750 years one elephant couple would give rise to 19 million descendants. It is even more spectacular with the starfish. One pair can have 1079 descendants in one year!

4. Non-random selection and selective pressure

Different parents have a different amount of offspring, which is a result of a difference in the ability to survive and reproduce but also a result of the ability of the offspring to survive and reproduce. The amount of offspring is determined by the interaction between the phenotype of an individual and its environment (or nature as Darwin said ; hence natural selection). See how the parent's and offspring's survival is important. Selection leads to a different success of individuals in reproduction and the survival of their offspring. See also the remarks about the non-random character of selection.

Another important thing is selective pressure. By selective pressure we mean the force or cause that selects the individuals. If there is no selective pressure there is no selection.

Fitness and evolution

The extent to which the variation of phenotype has a genetic base leads to a change in gene frequency. Remind that this is the definition of evolution. The variation in success in a certain environment is the driving force of evolution.

The success of a genotype or individual is called the fitness. It is defined as the relative contribution of a genotype in the next generation. As mentioned this is a very important concept in evolution and can be quantified.

Remarks

  1. Selection is not a process which leads to the perfect genotype, it rather selects for the genotype with the highest fitness from the available genotypes

  2. Evolution by means of natural selection is only possible if there is heritable variation in fitness-related properties.

  3. One of the most confusing things in the selection concept is that selection is non-random, but there is no progression in it.
    • Mutations and recombination, which are the input processes for variation, are indeed random. More specific they are random in the changes in phenotype they make.
    • Selection is not random. It is a certain variation which is better then another. Selection increases the adaptation. So it's non-random.
Selection is not any predetermined plan. It means it is not leading to anything specific.
    • Selection leads only to a better adaptation of the species to its environment

Micro- and macro-evolution

There is an certain difference between micro- and macro-evolution, though these things are essentially the same:

  • Micro-evolution are processes that are driving evolution within a species

  • Macro-evolution is about speciation and diversity.

Micro-evolution is the driving evolution and macro-evolution is rather a consequence of it.

Examples

A simple example

The most simple example is the lion-antelopes example. I will make the parallel between the first section and this section. Note that this example is rather hypothetical and is only to illustrate the concept of natural selection.

  1. Variation

    There is an Antelope population in which the length of legs in varying. Some antelopes haves short legs and others have long legs. The antelopes with short legs are slower then the antelopes with long legs.

  2. Heritability

    There are two causes of this variation

    1. Environment: Because of a dryer season plant grow slower and young antelopes eat bad food to grow and get long legs.

    2. Genetic: Some variation is passed from parent to offspring. This means that antelopes with a long-leg-gene will have longer legs then antelopes with a short-leg-gene if the environment were the same.

  3. Variation in success and selection: Lions will hunt to get some juice piece of meat. They will catch mostly the slow and short-legged offspring. If the second principle is true, then in the next generation there will be relatively more long-legged genes.

  4. additionally you can say that the fitness of the long-legged animals is bigger.

A more complex example

Introduction

This is the example of the so called Darwin's finches on the Galapagos Islands(see figure 1). It is a great prove that micro- and macro-evolution are essentially the same. The Darwin's finches vary in a lot of aspects going from weight, length and more important for us the beak shape.
Now let's compare the beak shape the 14 species (this is macro-evolution; see figure 2). Some beaks are small and pointy to get small and soft insects others have bigger beaks and can open seeds. It is even noticeable if we compare two species Geospiza fortis and G. magnirostris. The G. magnirostris has a large and big beak and he uses it to crack big seeds. The G. fortis though has a smaller beak and can crack smaller seeds.

The research

First of all we are not going to give much detail about the research itself, but if you are interested we'd recommend to read the Grants research. Peter and Rosemary Grant were able to observe these finches in a field-experiment. They observed only one species (so micro-evolution), namely the G. fortis. A great advantage is that the species doesn't leave the island and it's rather easy to interpret data.

We are going to try to prove evolution and one can ask if selection and evolution can be present if there no selective pressure. As said before the answer is no!!. Even more convenient would be a great selective pressure. In the case of Darwin's finches it was an El nino phenomenon. The consequence is a dry period during 1977 and 1978. During this period seeds become bigger and harder. What we would expect is an increase in beak shape and a decrease in the size of the population. Now the central question is if this is really (micro-)evolution. We are going to verify the basic principles

1. Variation

By marking the finches leg with an iron band with a number on the band, the Grants could trace the birds and measure the beak size. It is measured from the lowest base of the beak to the highest base of the beak. When the Grants measured the beak size of course they measured a variation. It sounds stupid, but look at the graph on figure 3. You can see that some birds have a beak that is twice as bid as others. So the variation is indeed enormous.
2. Is the variation heritable?

Is it heritable?

To determine the amount of heritability we'd recommend the reader to read something about quantifying or estimating heritability. We can prove it by plotting the average value of parents versus the offspring value. It is called a midparent value-offspring plot (see figure 4)
We can see here that parents with a big beak tend to have offspring with a big beak (figure 4) and parents with small beaks tend to have offspring with small beaks. The story is more complex because normally you should exclude maternal effects, which we don't explain now.

Genes that determine beak size

One can wonder what gene responsible is. Luckily Abzhanov et. Al (2004) discovered an important gene. It is the gene that gives rise to the growfactor bonemorphogenic protein 4 (BMP4). They found that birds with a bigger beak made earlier in the development the BMP4 and also is larger quantities.
3. Variation in success to survive

As expected, many finches died due to the drought. So it seems the selective pressure is indeed big, so the selection is big.
4. Is there selection?

Yes, because the researchers saw the to distributions before and after the drought (figure 5). The mean before the drought is almost 1mm lower then after. This may not seem a lot, but you have to see this relatively. In one year, the beaks with a mean size of 9,4mm were 1mm enlarged to 10,2. This an enlargement of approximately 10 percent in one year!!!. It is as if you would be 160 cm and the next year you would be 176cm!!!.
It can also be expressed like this: the average survivor had a bigger beak than the average non-surviving bird.

5. Is there evolution?

Yes and we can confirm it by comparing the offspring from bird before the drought and after the drought. And indeed the offspring after the drought have a bigger beak.

Viral and bacterial example

With viruses and bacteria one can witness evolution in real time. One of the selective forces that viruses such as influenza face is antibody in the bloodstream of influenza patients that neutralise the virus and prevent further infections, bringing epidemic spread to a halt. Similarly, bacteria that infect and colonise humans and domestic animals have been faced with widespread massive use of antibiotics since the discovery of penicillin and other new medicines in the 1940s. The natural selection of antigenic variants of influenza virus, and shifts in the major components of the virus caused by re-assortment and recombination of influenza virus genes, and the selection of multiple-drug resistant variants of bacteria are examples of natural selection occurring over the last half-century or so that are extensively documented in the medical literature.

Other examples

There exists a wealth of other examples. The best researches are the ones of:

1. Reznick et Al.in Nature 346, pages 357 - 359 (26 July 1990)

2. Hanks, L. M. & R. F. Denno. 1994. Local adaptation in the armored scale insect Pseudaulacaspis pentagona (Targioni-Tozzetti) (Homoptera: Diaspididae). Ecology 75: 2301-2310.

3. Raineny and Travisano, 1998, Adaptive radiation in a heterogeneous environment ,Nature 394, 69-72

The creative power of natural selection

While it is easy to see how natural selection can act as a force that refines pre-existing attributes, it is less easy to see how it can work to build wholly new functions. Today, molecular biologists can in part reconstruct how new functions might have arisen through evolution by natural selection.

To take just one example, oxytocin and vasopressin are two closely related molecules - they differ by just one amino acid. They come from two separate but very similar genes, genes so similar that we think they must have arisen by an initial step of gene duplication. Oxytocin and vasopressin are peptide hormones that exert their quite different physiological actions by acting on specific receptors, expressed in different target tissues. The genes for the receptors are also very similar to each other, so the receptor genes also arose by gene duplication, probably at the same time as the gene for the peptides was duplicated[5] So the initial mutation was a large scale gene duplication - such changes are generally neutral mutations, with no consequences for the organism. Almost all vertebrates that have been studied have genes for two peptides closely related to oxytocin and vasopressin, and virtually all invertebrates that have been studied have just one such gene. Among vertebrates, only Cyclostomata (lampreys and hagfishes) are known to have only one gene related to vasopressin and oxytocin, so the initial duplication probably occurred about 400 million years ago, before the evolution of the fishes [6]. When a gene is duplicated, one copy is now redundant, and so is under no immediate selection pressure; accordingly it will accumulate further mutations, some of which may have incidental benefits to the organism unrelated to the function of the original gene. Over time, as natural selection works on these initially minor and incidental benefits, the two genes diverge in functionality. Now (400 million years later), in modern mammals, vasopressin mainly controls water loss from the kidneys while oxytocin mainly controls the let down of milk from the mammary gland in lactation. This function of oxytocin is quite clearly new in evolutionary terms (and specific to mammals), yet it arose from slight mutations of elements that had previously existed for a quite different purpose, refined by natural selection over millions of years.

"Ecological selection" and "sexual selection"

It is useful to distinguish between ecological selection and the narrower term, sexual selection. Ecological selection covers any mechanism of selection as a result of the environment (including relatives, e.g. kin selection, and conspecifics, e.g. competition or infanticide). Sexual selection refers specifically to competition between conspecifics for mates [7].

Sexual selection includes mechanisms such as mate choice and male-male competition although the two forms can act in combination in some species, when females choose the winners of the male-male competition. Mate choice, or intersexual selection, typically involves female choice, as it is usually the females who are most choosy, but in some sex-role reversed species it is the males that choose. Some features that are confined to one sex only of a particular species can be explained by selection exercised by the other sex in the choice of a mate, e.g. the extravagant plumage of some male birds. Aggression between members of the same sex (intrasexual selection) is typically referred to as male-male competition, and is sometimes associated with very distinctive features, such as the antlers of stags, which are used in combat with other stags. More generally, intrasexual selection is often associated with sexual dimorphism, including differences in body size between males and females of a species.

Genetical theory of natural selection

Natural selection by itself is a simple concept, in which fitness differences between phenotypes are crucial. However, its explanatory power comes from understanding the interplay of the selection mechanism with the underlying genetics.

Directionality of selection

When some component of a variable trait is heritable, selection can alter the frequencies of the different alleles (variants of a gene) that are responsible for that variability. Selection can be divided into three classes:

Positive or directional selection occurs when a certain allele is associated with a greater fitness than others, resulting in an increase in frequency of that allele until it is fixed and the entire population expresses the fitter phenotype.

Far more common is purifying or stabilizing selection, which lowers the frequency of alleles which have a deleterious effect on the phenotype until they are eliminated from the population. Purifying selection results in functional genetic features (e.g. protein-coding sequences or regulatory sequences) being conserved over time because of selective pressure against deleterious variants.

Finally, many forms of balancing selection do not result in fixation, but maintain an allele at intermediate frequencies in a population. This can happen in diploid species (with two pair of chromosomes) when individuals with a combination of two different alleles at a single position at the chromosome (heterozygote) have a higher fitness than individuals that have two copies of the same allele (homozygote). This is called heterozygote advantage or overdominance. Allelic variation can also be maintained through disruptive or diversifying selection, which favors genotypes that depart from the average in either direction (that is, the opposite of overdominance), and can result in a bimodal distribution of trait values. Finally, it can occur by frequency-dependent selection, where the fitness of one particular phenotype depends on the prevalence of other phenotypes in the population (see also Game theory).

Selection and genetic variation

Some genetic variation is functionally neutral; i.e., it produces no phenotypic effect or significant differences in fitness. Previously, this was thought to encompass most of the genetic variation in non-coding DNA, but parts of those sequences are highly conserved, indicating that they are under strong purifying selection, and suggesting that mutations in these regions have deleterious consequences[8]. When genetic variation does not result in differences in fitness, selection cannot directly affect the frequency of such variation. As a result, the genetic variation at those sites will be higher than at sites where selection does have a result.

Genetic linkage

Genetic linkage occurs when two alleles are close to each other. During the formation of the gametes, recombination of the genetic material results in a reshuffling of the alleles. However, the chance that such a reshuffle occurs between two alleles depends on the distance between those alleles; the closer the alleles are to each other, the less likely it is that such a reshuffle will occur. Consequently, when selection targets one allele, this automatically results in selection of the other allele as well; through this mechanism, selection can have a strong influence on patterns of variation in the genome.

Mutation-selection balance

Natural selection results in less genetic variation by eliminating maladapted individuals and, through that, the mutations that causes the maladaptation. At the same time, new mutations arise spontaneously, resulting in a mutation-selection balance. The exact outcome depends both on the rate at which new mutations occur and on the strength of the natural selection.

Selective sweep

Selective sweeps occur when an allele becomes more common in a population as a result of positive selection. As the prevalence of one allele increases, linked alleles (those nearby on the chromosome) can also become more common, whether they are neutral or even slightly deleterious. This is called genetic hitchhiking. A strong selective sweep results in a region of the genome where the positively selected haplotype (the allele and its neighbours) are essentially the only ones that exist in the population.

Whether a selective sweep has occurred or not can be investigated by measuring linkage disequilibrium, i.e., whether a given haplotype is overrepresented in the population. Normally, genetic recombination results in a 'reshuffle' of the alleles within a haplotype, and none of the haplotypes will dominate the population. However, during a selective sweep, selection for a specific allele will also result in selection of neighbouring alleles. Therefore, the presence of strong linkage disequilibrium might indicate that there has been a 'recent' selective sweep, and this can be used to identify sites recently under selection.

Background selection

Background selection is the opposite of a selective sweep. If a specific site experiences strong and persistent purifying selection (perhaps as a result of mutation-selection balance), linked variation will tend to be weeded out along with it. However, background selection acts as a result of new mutations, which can occur randomly in any haplotype. It therefore produces no linkage disequilibrium, although it reduces the amount of variation in the region.

Evolution by means of natural selection

For more information, see: Evolution and Darwinism.

A prerequisite for natural selection to result in adaptive evolution, novel traits and speciation, is the presence of heritable genetic variation that results in fitness differences. Genetic variation is the result of mutations, recombinations and alterations in the karyotype (the number, shape, size and internal arrangement of the chromosomes). Any of these changes might have an effect that is highly advantageous or highly disadvantageous, but large effects are very rare. In the past, most changes in the genetic material were considered neutral or close to neutral because they occurred in noncoding DNA or resulted in a synonymous substitution. However, recent research suggests that many mutations in non-coding DNA do have slight deleterious effects. Overall, of those mutations that do affect the fitness of the individual, most are slightly deleterious, some reduce the fitness dramatically and some increase the fitness.

By the definition of fitness, individuals with greater fitness are more likely to contribute offspring to the next generation, while individuals with lesser fitness are more likely to die early or they fail to reproduce. As a result, alleles which on average result in greater fitness become more abundant in the next generation, while alleles which generally reduce fitness become rarer. If the selection forces remain the same for many generations, beneficial alleles become more and more abundant, until they dominate the population, while alleles with a lesser fitness disappear. According to evolutionary biologists, in every generation, new mutations and recombinations arise spontaneously, producing a new spectrum of phenotypes (new physical characteristics: eye color, skin color, etc). However, this idea is disputed amongst biologists of different backgrounds, with other biologists saying that each new generation will be preserved by the selection of previously existing traits that were favored by the species, but not brand new characteristics.

Some mutations occur in so-called regulatory genes. Changes in these can have large effects on the phenotype of the individual because they regulate the function of many other genes. Most, but not all, mutations in regulatory genes result in non-viable zygotes. For example, mutations in some HOX genes in humans result in an increase in the number of fingers or toes[9] or a cervical rib[10]. When such mutations result in a higher fitness, natural selection will favor these phenotypes and the novel trait will spread in the population.

Established traits are not immutable: an established trait may lose its fitness if environmental conditions change. In these circumstances, in the absence of natural selection to preserve the trait, the trait will become more variable and will deteriorate over time. The power of natural selection will also inevitably depend upon prevailing environmental factors; in general, the number of offspring is (far) greater than the number of individuals that can survive to the next generation, and there will be intense selection of the best adapted individuals for the next generation.

Speciation

Speciation requires selective mating, which result in a reduced gene flow. Selective mating can be the result of, for example, a change in the physical environment (physical isolation by an extrinsic barrier), or by sexual selection resulting in assortative mating. Over time, these subgroups might diverge radically to become different species, either because of differences in selection pressures on the different subgroups, or because different mutations arise spontaneously in the different populations, or because of founder effects - some potentially beneficial alleles may, by chance, be present in only one or other of two subgroups when they first become separated. When the genetic changes result in increasing incompatibility between the genotypes of the two subgroups, gene flow between the groups will be reduced even more, and will stop altogether as soon as the mutations become fixed in the respective subgroups. As few as two mutations can result in speciation: if each mutation has a neutral or positive effect on fitness when they occur separately, but a negative effect when they occur together, then fixation of these genes in the respective subgroups will lead to two reproductively isolated populations. According to the biological species concept, these will be two different species.

Historical context

Until the early 19th century, the established view in Western societies was that differences between individuals of a species were uninteresting departures from their Platonic ideal (or typus) of created kinds. However, growing awareness of the fossil record led to the recognition that species that lived in the distant past were often very different from those that exist today. In the early 19th century, radical evolutionists such as Jean Baptiste Lamarck had proposed that characteristics (adaptations) acquired by individuals might be inherited by their progeny, causing, in enough time, transmutation of species (see Lamarckism).[11] Between 1842 and 1844, Charles Darwin outlined his theory of evolution by natural selection as an explanation for adaptation and speciation. He defined natural selection as the "principle by which each slight variation [of a trait], if useful, is preserved". The concept was simple but powerful: individuals best adapted to their environments are more likely to survive and reproduce. As long as there is some variation between them, there will be an inevitable selection of individuals with the most advantageous variations. If the variations are inherited, then differential reproductive success will lead to a progressive evolution of particular populations of a species, and populations that evolve to be sufficiently different might eventually become different species.

Darwin thought of natural selection by analogy to how farmers select crops or livestock for breeding (artificial selection); in his early manuscripts he referred to a 'Nature' which would do the selection. In the next twenty years, he shared these theories with just a few friends, while gathering evidence and trying to address all possible objections. In 1858, Alfred Russel Wallace[12], a young naturalist, independently conceived the principle and described it in a letter to Darwin. Not wanting to be scooped, Darwin contacted scientific friends to find an honorable way to handle this potentially embarrassing situation, and two short papers by the two were read at the Linnean Society announcing co-discovery of the principle. The following year, Darwin published The Origin of Species, along with his evidence and detailed discussion. This became a topic of great dispute; evolutionary theories became the primary way of talking about speciation, but natural selection did not predominate as the mechanism by which it happened. What made natural selection controversial was doubt about whether it was powerful enough to result in speciation, and that it was 'unguided' rather than 'progressive', something that even Darwin's supporters balked at.

Darwin's ideas were inspired by the observations that he had made on the Voyage of the Beagle, and by the economic theories of Thomas Malthus, who noted that population (if unchecked) increases exponentially whereas the food supply grows only arithmetically; thus limitations of resources would inevitably lead to a "struggle for existence", in which only the fittest would survive. Similar ideas go back to ancient times; the Ionian physician Empedocles said that many races "must have been unable to beget and continue their kind. For in the case of every species that exists, either craft or courage or speed has from the beginning of its existence protected and preserved it". Several 18th-century thinkers wrote about similar theories, including Pierre Louis Moreau de Maupertuis in 1745, Lord Monboddo in his theories of species alteration, and Darwin's grandfather Erasmus Darwin in 1794–1796. In the 6th edition of The Origin of Species Darwin acknowledged that others — notably William Charles Wells in 1813, and Patrick Matthew in 1831 — had proposed similar theories, but had not presented them fully or in notable scientific publications. Wells presented his hypothesis to explain the origin of human races in person at the Royal Society, and Matthew published his as an appendix to his book on arboriculture[13]. Edward Blyth had also proposed a method of natural selection as a mechanism of keeping species constant. However, these 'precursors' had little influence on evolutionary thought.

Concurrent with the publication of The Origin of Species, many of Darwin's contemporaries advanced hypotheses regarding evolution. However, of the many ideas of evolution that emerged, only August Weismann's saw natural selection as the main evolutionary force. T.H. Huxley, for example, believed that there was more "purpose" in evolution than natural selection afforded. A revised version of Lamarckism also enjoyed some popularity.

Modern evolutionary synthesis

For more information, see: Modern evolutionary synthesis.

Only after the integration of a theory of evolution with a complex statistical appreciation of Mendel's 're-discovered' laws of inheritance did natural selection become generally accepted by scientists. The work of Ronald Fisher, who first tried to explain natural selection by the underlying genetic processes); J. B. S. Haldane, who introduced the concept of the 'cost' of natural selection [14]; Sewall Wright, one of the founders of population genetics [15]; Theodosius Dobzhansky, who established the idea that mutation, by creating genetic diversity, supplied the raw material for natural selection[16]), William Hamilton, who conceived of kin selection; Ernst Mayr, who recognised the importance of reproductive isolation for speciation[17] and many others formed the modern evolutionary synthesis. This propelled natural selection to the forefront of evolutionary theories, where it remains today. The modern evolutionary synthesis continues to undergo extension and revision [18]

Impact of the idea

Darwin's ideas, along with those of Adam Smith and Karl Marx, had a profound influence on 19th-century thought. Perhaps the most radical claim of Darwin's theory of evolution through natural selection is that "elaborately constructed forms, so different from each other, and dependent on each other in so complex a manner"[3] evolved from the simplest forms of life by a few simple principles expressed in natural processes. This claim inspired some of Darwin's most ardent supporters[19] [20]—and provoked the most profound opposition.[20] The radicalism of natural selection, according to Stephen Jay Gould [21], lay in its power to "dethrone some of the deepest and most traditional comforts of Western thought". In particular, it challenged beliefs in nature's benevolence, order, and good design, the belief that humans occupy a summit of power and excellence, belief in an omnipotent, benevolent creator, and belief that nature has any meaningful direction, or that humans fit into any sensible pattern.

The concept of natural selection has had an influence on philosophical and ethical reflection. Francis Galton, Thomas Malthus and other Social Darwinists used the principle of natural selection to justify social policies that gave no help or assistance to the poor and needy on the basis that one is then preventing the advancement of the species. Rather the poor and needy should die off to promote genetic fitness. This went much further in eugenics movements which moved to simply omitting to help those in need to actively sterilising people who fail to meet the relevant criteria for genetic health. Even today, some groups like Project Prevention – a U.S. charity that pays drug addicts $300 to be sterilised voluntarily – are considered by many to be advocating a form of eugenics. In contemporary Western societies, mainstream opinion generally regards the practice of eugenics and social Darwinism as barbaric and scientists condemn it as not just being ethically problematic but actually scientifically implausible too.

Eugenic and social Darwinist theories have had an especially horrendous role regarding race with nineteenth century scientists and social Darwinists producing elaborate descriptions of racial difference and grounding said differences in claims of biological difference, sometimes wrapped with natural selection: often suggesting that white Europeans were selected by evolution to be more intelligent – Peter Bowker lists a number of these including Petrus Camper's physiological study of skulls, where he argued that the facial angle of black races was between that of ape ancestors and European races as well as pre-genetic classifications by Carl Linnaeus and others.[22] The development of genetics as a science has allowed many of these to be dismissed as myths. Some creationists use these unfortunate developments as a reason to dismiss evolutionary theory[23] although such claims tend to get short shrift from mainstream historians.

The linking of natural selection as an account of how things are to how things ought to be is dismissed early on in Richard Dawkins' The Selfish Gene, one of the more popular books in the English-speaking world on evolutionary theory for a general audience. While he is a Darwinian in terms of believing that the relevant facts in biology are best explained through evolution, he argues he is strongly anti-Darwinian in a normative sense:

I am not advocating a morality of evolution. I am saying how things have evolved. I am not saying how we humans morally ought to behave. I stress this, because I know I am in danger of being misunderstood by those people, all too numerous, who cannot distingush a statement of belief in what is the case from an advocacy of what ought to be the case. My own feeling is that a human society based simply on the gene's law of universal ruthless selfishness would be a very nasty society in which to live. But unfortunately, however much we may deplore something, it does not stop it being true. This book is mainly intended to be interesting, but if you would extract a moral from it, read it as a warning. Be warned that if you wish, as I do, to build a society in which individuals cooperate generously and unselfishly towards a common good, you can expect little help from biological nature. Let us try to teach generosity and altruism, because we are born selfish. Let us understand what our own selfish genes are up to, because we may then at least have the chance to upset their designs, something that no other species has ever aspired to.[24]

Darwinian thinking and the idea of natural selection has had an effect on other areas outside of the biological sciences. Philosophers including Daniel Dennett and Michael Ruse have argued that evolution and natural selection provide a new lens by which one can approach a variety of philosophical problems, with Dennett going so far as to argue that evolution is a "universal acid".[25]

Debates in epistemology have shifted to take on board that cognitive functions are evolved. Much epistemological work in justification is itself often based on a rejection of the Cartesian picture of the mind, and the purported compatibility of externalist accounts of justification (that is, accounts of justification that are based on the state of the world rather than the beliefs, mental states and conscious accessibility of ideas) with the actual history of our cognitive functions as produced by natural selection is argued to be a major point in their favour.

Some 'causal history' accounts of various philosophical concepts now make reference to evolutionary history: for instance, to explain proper function (and to defend it from the competing supernaturalist account provided by the Christian philosopher Alvin Plantinga), so-called etiological accounts of proper function have been proposed by Ruth Millikan and Karen Neander. To say that a particular biological system is functioning properly in some instance is to say that it is functioning in the same way as it has in previous generations, and that function has been a result of natural selection.

In political philosophy, Peter Singer had advocated that left-wing political movements need to become "Darwinian" in the sense that they ought to accept the fact of natural selection and evolution and craft political views around the reality of an evolved human nature.

References

  1. John C. Avise and Francisco J. Ayala, Editors. (2009) In the Light of Evolution III - Two Centuries of Darwin (2009), National Academy of Sciences (NAS). p1.
  2. Note: 'conspecifics' refers to members of the same species.
  3. 3.0 3.1 Darwin C (1859) On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life John Murray, London; modern reprint Charles Darwin, Julian Huxley (2003). The Origin of Species. Signet Classics. ISBN 0-451-52906-5. 
  4. Mader S. (2010) Biology. 10th edition. New York: McGraw Hill. ISBN 9780073525433.
  5. van Kesteren R et al. (1996) Co-evolution of ligand-receptor pairs in the vasopressin/oxytocin superfamily of bioactive peptides. J Biol Chem 271:3619-3626
  6. Acher R et al. (1997) Molecular evolution of neurohypophysial hormones in relation to osmoregulation: the two fish options. Fish Physiol Biochem 17:325-32
  7. Andersson, M (1995). Sexual Selection. Princeton, New Jersey: Princeton University Press. ISBN 0-691-00057-3. 
  8. Kryukov GV et al (2005) Small fitness effect of mutations in highly conserved non-coding regions. Human Molecular Genetics 14:2221-9; Bejerano G et al (2004) Ultraconserved elements in the human genome. Science 304:1321-5
  9. Zakany J et al. (1997) Regulation of number and size of digits by posterior Hox genes: a dose-dependent mechanism with potential evolutionary implications. Proc Natl Acad Sci USA 94:13695-700
  10. Galis F (1999) Why do almost all mammals have seven cervical vertebrae? developmental constraints, Hox genes, and cancer. J Exp Zool 285:19-26
  11. Chevalier de Lamarck J-B, de Monet PA (1809) Philosophie Zoologique
  12. Wallace, Alfred Russel (1870) Contributions to the Theory of Natural Selection New York: Macmillan & Co. [1]
  13. Dempster WJ (1996) Evolutionary concepts in the nineteenth century, natural selection and Patrick Matthew. Durham: The Pentland Press. ISBN 185213568
  14. Haldane JBS (1932) The Causes of Evolution; Haldane JBS (1957) The cost of natural selection. J Genet 55:511-24([2]
  15. Wright S (1932) The roles of mutation, inbreeding, crossbreeding and selection in evolution] Proc 6th Int Cong Genet 1:356–66
  16. Dobzhansky Th (1937) Genetics and the Origin of Species Columbia University Press, New York. (2nd ed. 1941; 3rd edn. 1951)
  17. Mayr E (1942) Systematics and the Origin of Species. Columbia University Press, New York. ISBN 0-674-86250-3 | Google Books preview.
  18. Francisco J. Ayala, Walter M. Fitch, and Michael T. Clegg, Editors, (2000) Variation and Evolution in Plants and Microorganisms, Towards a New Synthesis 50 years after Stebbing. National Academy of Sciences, Washington DC.
  19. Huxley TH. (1896) Darwiniana: Essays by Thoms H. Huxley. Vol. 2. D. Appleton and Co. | Google Books Full-Text.
    • "That this most ingenious hypothesis enables us to give a reason for many apparent anomalies in the distribution of living beings in time and space, and that it is not contradicted by the main phenomena of life and organisation appear to us to be unquestionable; and, so far, it must be admitted to have an immense advantage over any of its predecessors."
  20. 20.0 20.1 Bowler PJ. (2003) Reception of Darwin's Theory. Chapter 6. In: Bowler PJ. (2003) Evolution: The History of an Idea. Third Edition, Completely Revised and Expanded. Berkeley: University of California Press. ISBN 0520236939. | Google Books Full View 1989 Edition.
  21. The New York Review of Books: Darwinian Fundamentalism (accessed May 6, 2006)
  22. Peter Bowker, Evolution: The History of an Idea, p. 52, diagram on p. 53.
  23. Richard Weikart's From Darwin to Hitler, for instance.
  24. Richard Dawkins, The Selfish Gene, p. 2-3.
  25. In Darwin's Dangerous Idea.