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{{BioPsy}}
 
{{BioPsy}}
   
[[Image:Coquina variation3.jpg|thumb|right|260px|Individuals in the [[mollusk]] species [[Donax|''Donax variabilis'']] show diverse coloration and patterning in their phenotypes.]]
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{{for|a non-technical introduction to the topic|Introduction to genetics}}
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[[Image:Coquina variation3.jpg|thumb|right|250px|The [[mollusc shell|shells]] of individuals within the [[bivalve]] [[Mollusca|mollusk]] species ''[[Donax variabilis]]'' show diverse coloration and patterning in their phenotypes]]
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[[Image:Punnett square mendel flowers.svg|thumb|right|Here the relation between genotype and phenotype is illustrated, using a [[Punnett square]], for the character of petal colour in pea. The letters B and b represent genes for colour and the pictures show the resultant flowers.]]
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A '''phenotype''' (from Greek ''phainein'', 'to show' + ''typos'', 'type') is the composite of an [[organism]]'s observable characteristics or [[trait (biology)|traits]], such as its [[morphology (biology)|morphology]], [[Developmental biology|development]], biochemical or physiological properties, [[phenology]], [[behavior]], and products of behavior (such as a bird's nest). Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two. When two or more clearly different phenotypes exist in the same population of a species, it is called [[Polymorphism (biology)|polymorph]].
   
The '''phenotype''' of an individual [[organism]] is either its total physical appearance and constitution or a specific manifestation of a [[Trait (biological)|trait]], such as size, eye color, or [[behavior]] that varies between individuals. Phenotype is determined to some extent by [[genotype]], or by the identity of the [[allele]]s that an individual carries at one or more positions on the [[chromosome]]s. Many phenotypes are determined by multiple [[gene]]s and influenced by [[natural environment|environment]]al factors. Thus, the identity of one or a few known alleles does not always enable prediction of the phenotype.
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The [[genotype]] of an organism is the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and developmental conditions. Likewise, not all organisms that look alike necessarily have the same genotype.
   
Nevertheless, because phenotypes are much easier to observe than genotypes (it doesn't take chemistry or [[sequencing]] to determine a person's eye color), [[classical genetics]] uses phenotypes to deduce the functions of genes. Breeding experiments can then check these inferences. In this way, early [[geneticists]] were able to trace inheritance patterns without any knowledge of [[molecular biology]].
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This [[genotype-phenotype distinction]] was proposed by [[Wilhelm Johannsen]] in 1911 to make clear the difference between an organism's [[heredity]] and what that heredity produces.<ref>{{cite journal | last1 = Churchill | first1 = F.B. | year = 1974 | title = William Johannsen and the genotype concept | url = | journal = [[Journal of the History of Biology]] | volume = 7 | issue = | pages = 5–30 | doi = 10.1007/BF00179291 }}</ref><ref>{{cite journal | last1 = Johannsen | first1 = W. | year = 1911 | title = The genotype conception of heredity | url = | journal = [[American Naturalist]] | volume = 45 | issue = | pages = 129–159 }}</ref> The distinction is similar to that proposed by [[August Weismann]], who distinguished between [[germ plasm]] (heredity) and [[somatic cells]] (the body). The Genotype-Phenotype concept should not be confused with [[Francis Crick]]'s [[central dogma of molecular biology]], which is a statement about the directionality of molecular sequential information flowing from DNA to protein, and not the reverse.
   
Phenotypic variation (due to underlying heritable [[genetic variation]]) is a fundamental prerequisite for [[evolution]] by [[natural selection]]. The [[fitness (biology) | fitness]] of an organism is a high-level phenotype determined by the contributions of thousands of more specific phenotypes. Without phenotypic variation, individual organisms would all have the same fitness, and changes in phenotypic frequency would proceed without any selection (randomly).
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==Difficulties in definition==
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Despite its seemingly straightforward definition, the concept of the phenotype has hidden subtleties. It may seem that anything dependent on the [[genotype]] is a phenotype, including molecules such as RNA and proteins. Most [[molecules]] and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example by [[Western blot]]ting) and are thus part of the phenotype. Human [[Human blood group systems|blood groups]] are an example. It may also seem that this goes beyond the original intentions of the concept with its focus on the (living) organism in itself, meaning that the lowest level of biological organization compatible with the phenotype concept is at the cellular level. Either way, the term phenotype includes traits or characteristics that can be made visible by some technical procedure. A notable extension to this idea is the presence of "organic molecules" or metabolites that are generated by organisms from chemical reactions of enzymes, e.g. vitamins, that can be scored as phenotype. Another extension adds behavior to the phenotype, since behaviors are also observable characteristics. Indeed there is research into the clinical relevance of behavioral phenotypes as they pertain to a range of syndromes.<ref name=O'Brien&Yule1995>{{Cite book |year=1995 |editor1-last=O'Brien |editor1-first=Gregory |editor2-last=Yule |editor2-first=William |title=Behavioural Phenotypes |series=Clinics in Developmental Medicine No.138 |place=London |publisher=Mac Keith Press |isbn=1-898683-06-9 |postscript=<!-- Bot inserted parameter. Either remove it; or change its value to "." for the cite to end in a ".", as necessary. -->{{inconsistent citations}}}}</ref><ref name=O'Brien2002>{{Cite book |year=2002 |editor=O'Brien, Gregory |title=Behavioural Phenotypes in Clinical Practice |place=London |publisher=Mac Keith Press |isbn=1-898683-27-1 |url=http://books.google.com/?id=flz27_U0AhgC&printsec=frontcover&dq=%22behavioural+phenotypes+in+clinical+practice%22#v=onepage&q&f=false |accessdate=27 September 2010 |postscript=<!-- Bot inserted parameter. Either remove it; or change its value to "." for the cite to end in a ".", as necessary. -->{{inconsistent citations}}}}</ref> Often, the term "phenotype" is incorrectly used as a shorthand to indicate ''phenotypical changes'' observed in mutated organisms (most often in connection with [[knockout mouse|knockout mice]]).<ref name=pmid12884976>{{cite journal |author=Crusio WE |authorlink=Wim Crusio |title='My mouse has no phenotype' |journal=[[Genes, Brain and Behavior]] |volume=1 |issue=2 |pages=71 |year=2002 |month=May |pmid=12884976 |doi= 10.1034/j.1601-183X.2002.10201.x|url=http://www3.interscience.wiley.com/resolve/openurl?genre=article&sid=nlm:pubmed&issn=1601-1848&date=2002&volume=1&issue=2&spage=71 |accessdate=2009-12-29}}</ref>
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[[File:Biston.betularia.7200.jpg|thumb|250px|''Biston betularia'' morpha ''typica'', the standard light-colored Peppered Moth.]]
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[[File:Biston.betularia.f.carbonaria.7209.jpg|thumb|250px|''Biston betularia'' morpha ''carbonaria'', the melanic Peppered Moth, illustrating discontinuous variation.]]
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==Phenotypic variation==
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Phenotypic variation (due to underlying heritable [[genetic diversity|genetic variation]]) is a fundamental prerequisite for [[evolution]] by [[natural selection]]. It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection.{{citation needed|date=November 2011}}
   
 
The interaction between genotype and phenotype has often been conceptualized by the following relationship:
 
The interaction between genotype and phenotype has often been conceptualized by the following relationship:
   
:'''genotype + environment → phenotype'''
+
:'''genotype (G) + environment (E) → phenotype (P)'''
  +
  +
A more nuanced version of the relationship is:
  +
  +
:'''genotype (G) + environment (E) + genotype & environment interactions (GE) → phenotype (P)'''
  +
  +
Genotypes often have much flexibility in the modification and expression of phenotypes; in many organisms these phenotypes are very different under varying environmental conditions (see [[ecophenotypic variation]]). The plant ''[[Hieracium umbellatum]]'' is found growing in two different [[habitat]]s in [[Sweden]]. One habitat is rocky, sea-side [[cliff]]s, where the plants are bushy with broad leaves and expanded [[inflorescence]]s; the other is among [[dune|sand dunes]] where the plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate along the coast of Sweden and the habitat that the seeds of ''Hieracium umbellatum'' land in, determine the phenotype that grows.<ref name=Botanyonline>{{cite web |url=http://www.biologie.uni-hamburg.de/b-online/e37/37b.htm |title=Botany online: Evolution: The Modern Synthesis - Phenotypic and Genetic Variation; Ecotypes |work= |accessdate=2009-12-29}}</ref>
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An example of random variation in ''[[Drosophila]]'' flies is the number of [[ommatidia]], which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or between [[cloning|clones]] raised in different environments.
   
A slightly more nuanced version of the relationships is:
+
The concept of phenotype can be extended to variations below the level of the gene that affect an organism's fitness. For example, [[silent mutations]] that do not change the corresponding amino acid sequence of a gene may change the frequency of [[guanine]]-[[cytosine]] base pairs ([[GC content]]). These base pairs have a higher thermal stability (''melting point'', see also [[DNA-DNA hybridization]]) than [[adenine]]-[[thymine]], a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.
   
:'''genotype + environment + random-variation → phenotype'''
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===The Extended Phenotype===
  +
{{main|The Extended Phenotype}}
   
An example of the importance of random variation in phenotypic expression is [[Drosophila]] flies in which number of eyes may vary (randomly) between left and right sides in a single individual as much as they do between different genotypes overall, or between clones raised in different environments.
+
The idea of the phenotype has been generalized by [[Richard Dawkins]] in ''[[The Extended Phenotype]]'' to mean all the effects a gene has on the outside world that may influence its chances of being replicated. These can be effects on the organism in which the gene resides, the environment, or other organisms.
   
A phenotype is any detectable characteristic of an [[organism]] (i.e., structural, biochemical, physiological and behavioral) determined by an interaction between its [[genotype]] and environment (see [[genotype-phenotype distinction]] and [[phenotypic plasticity]] for a further elaboration of this distinction).
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For instance, a [[Beaver#Dams|beaver dam]] might be considered a phenotype of [[beaver]] [[gene]]s, the same way beavers' powerful [[incisor]] teeth are phenotype expressions of their genes. Dawkins also cites the effect of an organism on the behaviour of another organism (such as the devoted nurturing of a cuckoo by a parent of a different species) as an example of the extended phenotype.
   
According to the [[autopoiesis|autopoietic]] notion of living systems by [[Humberto Maturana]], the phenotype is epigenetically being constructed throughout [[ontogeny]], and we as observers do the distinctions that define any particular trait at any particular state of the organism's life cycle.
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The smallest unit of replicators is the gene. Replicators cannot be directly selected upon, but they are selected on by their phenotypic effects. These effects are packaged together in organisms. We should think of the replicator as having extended phenotypic effects. These are all of the ways it affects the world, not just the effects the replicators have on the body in which they reside.<ref>{{Cite book | last = Dawkins | first = Richard | title = The Extended Phenotype | publisher = Oxford University | year = 1982 | pages = 4 | url = http://www.amazon.com/Extended-Phenotype-Reach-Popular-Science/dp/0192880519#reader_0192880519 | isbn = 0-19-288051-9}}</ref>
   
The idea of the phenotype has been also generalized by [[Richard Dawkins]] to include effects on other organisms or the environment in ''[[The Extended Phenotype]]''.
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== Phenome and phenomics ==
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Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word ''phenome'' is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to as ''[[phenomics]]''.<ref>{{Cite journal | doi = 10.1006/jtbi.1996.0335 | author = Mahner, M. & Kary, M. | year = 1997 | title = What exactly are genomes, genotypes and phenotypes? And what about phenomes? | url = | journal = [[Journal of Theoretical Biology]] | volume = 186 | issue = | pages = 55–63 }}</ref><ref>{{Cite journal | first1 = A | last1 = Varki | year = 1998 | title = Great Ape Phenome Project? | url = | journal = [[Science (journal)|Science]] | volume = 282 | issue = 5387| pages = 239–240 |pmid = 9841385 | last2 = Wills | first2 = C | last3 = Perlmutter | first3 = D | last4 = Woodruff | first4 = D | last5 = Gage | first5 = F | last6 = Moore | first6 = J | last7 = Semendeferi | first7 = K | last8 = Bernirschke | first8 = K | last9 = Katzman | first9 = R | doi = 10.1126/science.282.5387.239d }}</ref>
   
 
==See also==
 
==See also==
 
*[[Assortative mating]]
 
*[[Assortative mating]]
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*[[Ecotype]]
 
*[[Emergenesis]]
 
*[[Emergenesis]]
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*[[Endophenotype]]
 
*[[Genetics]]
 
*[[Genetics]]
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*[[Phenocopy]]
 
*[[Polymorphism]]
 
*[[Polymorphism]]
  +
*[[Potentiality and actuality]]
   
 
==References==
 
==References==

Latest revision as of 13:50, October 10, 2013

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For a non-technical introduction to the topic, see Introduction to genetics.
Coquina variation3

The shells of individuals within the bivalve mollusk species Donax variabilis show diverse coloration and patterning in their phenotypes

File:Punnett square mendel flowers.svg

A phenotype (from Greek phainein, 'to show' + typos, 'type') is the composite of an organism's observable characteristics or traits, such as its morphology, development, biochemical or physiological properties, phenology, behavior, and products of behavior (such as a bird's nest). Phenotypes result from the expression of an organism's genes as well as the influence of environmental factors and the interactions between the two. When two or more clearly different phenotypes exist in the same population of a species, it is called polymorph.

The genotype of an organism is the inherited instructions it carries within its genetic code. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and developmental conditions. Likewise, not all organisms that look alike necessarily have the same genotype.

This genotype-phenotype distinction was proposed by Wilhelm Johannsen in 1911 to make clear the difference between an organism's heredity and what that heredity produces.[1][2] The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body). The Genotype-Phenotype concept should not be confused with Francis Crick's central dogma of molecular biology, which is a statement about the directionality of molecular sequential information flowing from DNA to protein, and not the reverse.

Difficulties in definitionEdit

Despite its seemingly straightforward definition, the concept of the phenotype has hidden subtleties. It may seem that anything dependent on the genotype is a phenotype, including molecules such as RNA and proteins. Most molecules and structures coded by the genetic material are not visible in the appearance of an organism, yet they are observable (for example by Western blotting) and are thus part of the phenotype. Human blood groups are an example. It may also seem that this goes beyond the original intentions of the concept with its focus on the (living) organism in itself, meaning that the lowest level of biological organization compatible with the phenotype concept is at the cellular level. Either way, the term phenotype includes traits or characteristics that can be made visible by some technical procedure. A notable extension to this idea is the presence of "organic molecules" or metabolites that are generated by organisms from chemical reactions of enzymes, e.g. vitamins, that can be scored as phenotype. Another extension adds behavior to the phenotype, since behaviors are also observable characteristics. Indeed there is research into the clinical relevance of behavioral phenotypes as they pertain to a range of syndromes.[3][4] Often, the term "phenotype" is incorrectly used as a shorthand to indicate phenotypical changes observed in mutated organisms (most often in connection with knockout mice).[5]

File:Biston.betularia.7200.jpg
File:Biston.betularia.f.carbonaria.7209.jpg

Phenotypic variationEdit

Phenotypic variation (due to underlying heritable genetic variation) is a fundamental prerequisite for evolution by natural selection. It is the living organism as a whole that contributes (or not) to the next generation, so natural selection affects the genetic structure of a population indirectly via the contribution of phenotypes. Without phenotypic variation, there would be no evolution by natural selection.[citation needed]

The interaction between genotype and phenotype has often been conceptualized by the following relationship:

genotype (G) + environment (E) → phenotype (P)

A more nuanced version of the relationship is:

genotype (G) + environment (E) + genotype & environment interactions (GE) → phenotype (P)

Genotypes often have much flexibility in the modification and expression of phenotypes; in many organisms these phenotypes are very different under varying environmental conditions (see ecophenotypic variation). The plant Hieracium umbellatum is found growing in two different habitats in Sweden. One habitat is rocky, sea-side cliffs, where the plants are bushy with broad leaves and expanded inflorescences; the other is among sand dunes where the plants grow prostrate with narrow leaves and compact inflorescences. These habitats alternate along the coast of Sweden and the habitat that the seeds of Hieracium umbellatum land in, determine the phenotype that grows.[6]

An example of random variation in Drosophila flies is the number of ommatidia, which may vary (randomly) between left and right eyes in a single individual as much as they do between different genotypes overall, or between clones raised in different environments.

The concept of phenotype can be extended to variations below the level of the gene that affect an organism's fitness. For example, silent mutations that do not change the corresponding amino acid sequence of a gene may change the frequency of guanine-cytosine base pairs (GC content). These base pairs have a higher thermal stability (melting point, see also DNA-DNA hybridization) than adenine-thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.

The Extended PhenotypeEdit

Main article: The Extended Phenotype

The idea of the phenotype has been generalized by Richard Dawkins in The Extended Phenotype to mean all the effects a gene has on the outside world that may influence its chances of being replicated. These can be effects on the organism in which the gene resides, the environment, or other organisms.

For instance, a beaver dam might be considered a phenotype of beaver genes, the same way beavers' powerful incisor teeth are phenotype expressions of their genes. Dawkins also cites the effect of an organism on the behaviour of another organism (such as the devoted nurturing of a cuckoo by a parent of a different species) as an example of the extended phenotype.

The smallest unit of replicators is the gene. Replicators cannot be directly selected upon, but they are selected on by their phenotypic effects. These effects are packaged together in organisms. We should think of the replicator as having extended phenotypic effects. These are all of the ways it affects the world, not just the effects the replicators have on the body in which they reside.[7]

Phenome and phenomics Edit

Although a phenotype is the ensemble of observable characteristics displayed by an organism, the word phenome is sometimes used to refer to a collection of traits, while the simultaneous study of such a collection is referred to as phenomics.[8][9]

See alsoEdit

ReferencesEdit

  1. (1974). William Johannsen and the genotype concept. Journal of the History of Biology 7: 5–30.
  2. (1911). The genotype conception of heredity. American Naturalist 45: 129–159.
  3. (1995) Behavioural Phenotypes, Mac Keith Press.
  4. (2002) O'Brien, Gregory Behavioural Phenotypes in Clinical Practice, Mac Keith Press. URL accessed 27 September 2010.
  5. Crusio WE (May 2002). 'My mouse has no phenotype'. Genes, Brain and Behavior 1 (2): 71.
  6. Botany online: Evolution: The Modern Synthesis - Phenotypic and Genetic Variation; Ecotypes. URL accessed on 2009-12-29.
  7. Dawkins, Richard (1982). The Extended Phenotype, 4, Oxford University.
  8. Mahner, M. & Kary, M. (1997). What exactly are genomes, genotypes and phenotypes? And what about phenomes?. Journal of Theoretical Biology 186: 55–63.
  9. (1998). Great Ape Phenome Project?. Science 282 (5387): 239–240.
The development of phenotype
Key concepts: Genotype-phenotype distinction | Norms of reaction | Gene-environment interaction | Heritability | Quantitative genetics
Genetic architecture: Dominance relationship | Epistasis | Polygenic inheritance | Pleiotropy | Plasticity | Canalisation | Fitness landscape
Non-genetic influences: Epigenetic inheritance | Epigenetics | Maternal effect | dual inheritance theory
Developmental architecture: Segmentation | Modularity
Evolution of genetic systems: Evolvability | Mutational robustness | Evolution of sex
Influential figures: C. H. Waddington | Richard Lewontin
Debates: Nature versus nurture
List of evolutionary biology topics
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