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In
genetics Genetics is a branch of biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, ...

genetics
, the phenotype () is the set of observable characteristics or
traits Trait may refer to: * Phenotypic trait in biology, which involve genes and characteristics of organisms * Trait (computer programming), a model for structuring object-oriented programs (a template class in the C++ programming language) * Trait the ...
of an
organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological me ...

organism
. The term covers the organism's morphology or physical form and structure, its developmental processes, its biochemical and physiological properties, its
behavior Behavior (American English American English (AmE, AE, AmEng, USEng, en-US), sometimes called United States English or U.S. English, is the set of varieties of the English language native to the United States. Currently, American English ...
, and the products of behavior. An organism's phenotype results from two basic factors: the
expression
 expression
of an organism's genetic code, or its
genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a specific ...
, and the influence of environmental factors. Both factors may interact, further affecting phenotype. When two or more clearly different phenotypes exist in the same population of a species, the species is called polymorphic. A well-documented example of polymorphism is Labrador Retriever coloring; while the coat color depends on many genes, it is clearly seen in the environment as yellow, black, and brown.
Richard Dawkins Richard Dawkins (born 26 March 1941) is a British evolutionary biologist Evolutionary biology is the subfield of biology that studies the evolutionary processes ( natural selection, common descent, speciation) that produced the Biodiver ...

Richard Dawkins
in 1978 and then again in his 1982 book ''
The Extended Phenotype ''The Extended Phenotype'' is a 1982 book by the evolutionary biologist Richard Dawkins Richard Dawkins (born 26 March 1941) is a British evolutionary biologist Evolutionary biology is the subfield of biology that studies the evoluti ...
'' suggested that one can regard bird nests and other built structures such as caddis-fly larva cases and
beaver dam Beaver dams or beaver impoundments are dam A dam is a barrier that stops or restricts the flow of surface water An example of surface water is Lake Kinney. Surface water is water Water is an Inorganic compound, inorganic, T ...

beaver dam
s as "extended phenotypes".
Wilhelm Johannsen Wilhelm Johannsen (3 February 1857 – 11 November 1927) was a Danish pharmacist, botanist Botany, also called , plant biology or phytology, is the science of plant life and a branch of biology. A botanist, plant scientist or phytologist i ...
proposed the
genotype–phenotype distinctionImage:PAX6 Phenotypes Washington etal PLoSBiol e1000247.png, 400px, Similar genotypic changes may result in similar phenotypic alterations, even across a wide range of species. The genotype–phenotype distinction is drawn in genetics. "Genotype" is ...
in 1911 to make clear the difference between an organism's
heredity Heredity, also called inheritance or biological inheritance, is the passing on of traits Trait may refer to: * Phenotypic trait in biology, which involve genes and characteristics of organisms * Trait (computer programming), a model for str ...

heredity
and what that heredity produces. The distinction resembles that proposed by
August Weismann Prof August Friedrich Leopold Weismann FRS (For), HonFRSE, LLD (17 January 18345 November 1914) was a German evolutionary biologist. Ernst Mayr Ernst Walter Mayr (; 5 July 1904 – 3 February 2005) was one of the 20th century's leading ...

August Weismann
(1834–1914), who distinguished between
germ plasm upAugust Weismann proposed the germ plasm theory in the 19th century, before the foundation of modern genetics. Germ plasm () is a biological concept developed in the 19th century by the German biologist August Weismann. It states that heritable ...
(heredity) and
somatic cell A somatic cell (from Ancient Greek Ancient Greek includes the forms of the Greek language used in ancient Greece and the classical antiquity, ancient world from around 1500 BC to 300 BC. It is often roughly divided into the following period ...
s (the body). The genotype–phenotype distinction should not be confused with
Francis Crick Francis Harry Compton Crick (8 June 1916 – 28 July 2004) was a British molecular biologist, biophysicist, and neuroscientist A neuroscientist (or neurobiologist) is a scientist A scientist is a person who conducts Scientific method, scie ...

Francis Crick
's
central dogma of molecular biology The central dogma of molecular biology is an explanation of the flow of genetic information within a biological system. It is often stated as "DNA makes RNA, and RNA makes protein", although this is not its original meaning. It was first stated by ...

central dogma of molecular biology
, a statement about the directionality of molecular sequential information flowing from
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
to protein, and not the reverse.


Difficulties in definition

Despite its seemingly straightforward definition, the concept of the phenotype has hidden subtleties. It may seem that anything dependent on the
genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a specific ...
is a phenotype, including
molecule A molecule is an electrically Electricity is the set of physical phenomena associated with the presence and motion Image:Leaving Yongsan Station.jpg, 300px, Motion involves a change in position In physics, motion is the phenomenon ...

molecule
s 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 The western blot (sometimes called the protein immunoblot), or western blotting, is a widely used analytical technique in molecular biology and immunogenetics to detect specific proteins in a sample of tissue homogenate or extract. Western blot ...
ting) and are thus part of the phenotype; human
blood groups The term human blood group systems is defined by International Society of Blood Transfusion as systems in the human species where cell-surface antigen In immunology, an antigen (Ag) is a molecule or molecular structure, such as may be present ...
are an example. It may seem that this goes beyond the original intentions of the concept with its focus on the (living) organism in itself. Either way, the term phenotype includes inherent traits or characteristics that are observable or traits 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. The term "phenotype" has sometimes been incorrectly used as a shorthand for phenotypic difference from
wild type Unlike culinary bananas, wild-type bananas have numerous large, hard seeds. The wild type (WT) is the phenotype right , Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of petal col ...
, yielding the statement that a "mutation has no phenotype". Another extension adds behavior to the phenotype, since behaviors are observable characteristics. Behavioral phenotypes include cognitive, personality, and behavioral patterns. Some behavioral phenotypes may characterize psychiatric disorders or syndromes.


Phenotypic variation

Phenotypic variation (due to underlying heritable
genetic variation thumb File:Genetic Variation and Inheritance.svg, Parents have similar gene coding in this specific situation where they reproduce and variation in the offspring is seen. Offspring containing the variation also reproduce and passes down traits t ...
) is a fundamental prerequisite for
evolution Evolution is change in the heritable Heredity, also called inheritance or biological inheritance, is the passing on of Phenotypic trait, traits from parents to their offspring; either through asexual reproduction or sexual reproduction, ...

evolution
by
natural selection Natural selection is the differential survival and reproduction of individuals due to differences in phenotype right , Here the relation between genotype and phenotype is illustrated, using a Punnett square, for the character of peta ...
. 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. 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
habitat Ibex in an alpine habitat In ecology Ecology (from el, οἶκος, "house" and el, -λογία, label=none, "study of") is the study of the relationships between living organisms, including humans, and their physical environment. ...

habitat
s in Sweden. One habitat is rocky, sea-side
cliff In geography and geology, a cliff is an area of rock Rock most often refers to: * Rock (geology) A rock is any naturally occurring solid mass or aggregate of minerals or mineraloid matter. It is categorized by the minerals included ...

cliff
s, where the plants are bushy with broad leaves and expanded
inflorescence An inflorescence is a group or cluster of flower A flower, sometimes known as a bloom or blossom Cherry blossoms in Paris in full bloom. In botany, blossoms are the flowers of stone fruit fruit tree, trees (genus ''Prunus'') and of some ...
s; the other is among
sand dunes A dune is a landform A landform is a natural or artificial feature of the solid surface of the Earth or other planetary body A planet is an astronomical body Astronomy (from el, ἀστρονομία, literally meaning the sc ...

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. An example of random variation in ''
Drosophila ''Drosophila'' () is a genus of fly, flies, belonging to the family (biology), family Drosophilidae, whose members are often called "small fruit flies" or (less frequently) pomace flies, vinegar flies, or wine flies, a reference to the character ...

Drosophila
'' flies is the number of
ommatidia thumbnail, Ommatidia of a krill. The compound eyes of arthropods An arthropod (, (gen. ποδός)) is an invertebrate Invertebrates are animals that neither possess nor develop a vertebral column (commonly known as a ''backbone'' or ''spin ...

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 Clone or Clones or Cloning or The Clone may refer to: Places * Clones, County Fermanagh * Clones, County Monaghan, a town in Ireland Biology * Clone (B-cell), a lymphocyte clone, the massive presence of which may indicate a pathological conditio ...

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 Silent mutations are mutation Image:Darwin Hybrid Tulip Mutation 2014-05-01.jpg, A tulip flower exhibiting a partially yellow petal due to a mutation in its genes In biology, a mutation is an alteration in the base sequence, nucleotide sequence ...
that do not change the corresponding amino acid sequence of a gene may change the frequency of
guanine Guanine () (symbol A symbol is a mark, sign, or word In linguistics, a word of a spoken language can be defined as the smallest sequence of phonemes that can be uttered in isolation with semantic, objective or pragmatics, practical me ...

guanine
-
cytosine Cytosine () (symbol A symbol is a mark, sign, or that indicates, signifies, or is understood as representing an , , or . Symbols allow people to go beyond what is n or seen by creating linkages between otherwise very different s and s. Al ...

cytosine
base pairs (
GC content GC may stand for: Computing * Garbage collection (computer science) File:Structure and Interpretation of Computer Programs p.764b.gif, 400px, ... After that, the working memory contents is discarded in favor of the compressed copy, and the rol ...
). These base pairs have a higher thermal stability (''melting point'') than
adenine Adenine (A, Ade) is a nucleobase 230px, Pyrimidine nucleobases are simple ring molecules. Nucleobases, also known as ''nitrogenous bases'' or often simply ''bases'', are nitrogen-containing biological compounds that form nucleosides Nucleos ...

adenine
-
thymine Thymine () (symbol A symbol is a mark, sign, or word In linguistics, a word of a spoken language can be defined as the smallest sequence of phonemes that can be uttered in isolation with semantic, objective or pragmatics, practical m ...

thymine
, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.


The extended phenotype

Richard Dawkins Richard Dawkins (born 26 March 1941) is a British evolutionary biologist Evolutionary biology is the subfield of biology that studies the evolutionary processes ( natural selection, common descent, speciation) that produced the Biodiver ...

Richard Dawkins
described a phenotype that included all effects that a gene has on its surroundings, including other organisms, as an extended phenotype, arguing that "An animal's behavior tends to maximize the survival of the genes 'for' that behavior, whether or not those genes happen to be in the body of the particular animal performing it." For instance, an organism such as a
beaver Beavers are large, semiaquatic In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interaction ...

beaver
modifies its environment by building a
beaver dam Beaver dams or beaver impoundments are dam A dam is a barrier that stops or restricts the flow of surface water An example of surface water is Lake Kinney. Surface water is water Water is an Inorganic compound, inorganic, T ...

beaver dam
; this can be considered an expression of its
gene In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interactions, Physiology, physiological mecha ...

gene
s, just as its
incisor Incisors (from Latin ''incidere'', "to cut") are the front teeth present in most mammals. They are located in the premaxilla above and on the mandible below. Humans have a total of eight (two on each side, top and bottom). Opossums have 18, wherea ...
teeth are—which it uses to modify its environment. Similarly, when a bird feeds a
brood parasite Brood parasites are organism In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biology, molecular interact ...
such as a
cuckoo Cuckoos are s in the Cuculidae family, the sole in the order Cuculiformes . The cuckoo family includes the , , s, s, s, s and . The coucals and anis are sometimes separated as distinct families, the and respectively. The cuckoo order Cuculi ...

cuckoo
, it is unwittingly extending its phenotype; and when genes in an
orchid Orchidaceae ( ), commonly called the orchid family, is a diverse and widespread family In human society A society is a Social group, group of individuals involved in persistent Social relation, social interaction, or a large social ...

orchid
affect
orchid bee The tribe The term tribe is used in many different contexts to refer to a category of human social group. The predominant usage of the term is in the discipline of anthropology. The definition is contested, in part due to conflicting theoret ...
behavior to increase pollination, or when genes in a
peacock Peafowl is a common name for three bird species in the genera Genus /ˈdʒiː.nəs/ (plural genera /ˈdʒen.ər.ə/) is a taxonomic rank Taxonomy (general) is the practice and science of classification of things or concepts, including the ...

peacock
affect the copulatory decisions of peahens, again, the phenotype is being extended. Genes are, in Dawkins's view, selected by their phenotypic effects. Other biologists broadly agree that the extended phenotype concept is relevant, but consider that its role is largely explanatory, rather than assisting in the design of experimental tests.


Phenome and phenomics

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''. Phenomics is an important field of study because it can be used to figure out which genomic variants affect phenotypes which then can be used to explain things like health, disease, and evolutionary fitness. Phenomics forms a large part of the
Human Genome Project The Human Genome Project (''HGP'') was an international scientific research The scientific method is an Empirical evidence, empirical method of acquiring knowledge that has characterized the development of science since at least the 17th cen ...
Phenomics has applications in agriculture. For instance, genomic variations such as drought and heat resistance can be identified through phenomics to create more durable GMOs. Phenomics may be a stepping stone towards
personalized medicine Personalized medicine, also referred to as precision medicine, is a medical model Medical model is the term coined by psychiatrist R. D. Laing in his ''The Politics of the Family and Other Essays'' (1971), for the "set of procedures in which al ...
, particularly
drug therapy Pharmacotherapy is therapy A therapy or medical treatment (often abbreviated tx, Tx, or Tx) is the attempted remediation of a health Health is a state of physical, mental and social well-being Well-being, also known as ''wellness'', ''pru ...
. Once the phenomic database has acquired more data, a person's phenomic information can be used to select specific drugs tailored to an individual.


Large-scale phenotyping and genetic screens

Large-scale
genetic screens A genetic screen or mutagenesis screen is an experimental technique used to identify and select for individuals who possess a phenotype of interest in a mutagenized population. Hence a genetic screen is a type of phenotypic screen. Genetic screen ...
can identify the genes or
mutations Image:Darwin Hybrid Tulip Mutation 2014-05-01.jpg, A red tulip exhibiting a partially yellow petal due to a mutation in its genes In biology, a mutation is an alteration in the base sequence, nucleotide sequence of the genome of an organism, vi ...
that affect the phenotype of an organism. Analyzing the phenotypes of mutant genes can also aid in determining gene function. For example, a large-scale
phenotypic screen Phenotypic screening is a type of screening used in biological research and drug discovery In the fields of medicine, biotechnology and pharmacology, drug discovery is the process by which new candidate pharmaceutical drug, medications are disc ...
has been used to study lesser understood phenotypes such as
behavior Behavior (American English American English (AmE, AE, AmEng, USEng, en-US), sometimes called United States English or U.S. English, is the set of variety (linguistics), varieties of the English language native to the United States. Cur ...
. In this screen, the role of mutations in mice were studied in areas such as learning and
memory Memory is the faculty of the brain A brain is an organ Organ may refer to: Biology * Organ (anatomy) An organ is a group of Tissue (biology), tissues with similar functions. Plant life and animal life rely on many organs that co-exis ...

memory
, , vision, responses to stress and response to
psychostimulants Stimulants (also often referred to as psychostimulants or colloquially as uppers) is an overarching term that covers many drugs including those that increase activity of the central nervous system and the body, drugs that are pleasurable and invi ...
(see table for details). This experiment involved the progeny of mice treated with
ENU ENU ENU ENU, also known as ''N''-ethyl-''N''- nitrosourea Urea, also known as carbamide, is an organic compound , CH4; is among the simplest organic compounds. In chemistry, organic compounds are generally any chemical compounds that conta ...

ENU
, or N-ethyl-N-nitrosourea, which is a potent mutagen that causes
point mutations A point mutation or substitution is a genetic mutation In biology Biology is the natural science that studies life and living organisms, including their anatomy, physical structure, Biochemistry, chemical processes, Molecular biolog ...

point mutations
. The mice were phenotypically screened for alterations in the different behavioral domains in order to find the number of putative mutants (see table for details). Putative mutants are then tested for heritability in order to help determine the inheritance pattern as well as map out the mutations. Once they have been mapped out, cloned, and identified, it can be determined whether a mutation represents a new gene or not. These experiments showed that mutations in the
rhodopsin Rhodopsin (also known as visual purple) is a light Light or visible light is electromagnetic radiation within the portion of the electromagnetic spectrum that is visual perception, perceived by the human eye. Visible light is usually def ...

rhodopsin
gene affected vision and can even cause retinal degeneration in mice. The same
amino acid Amino acids are organic compound In , organic compounds are generally any s that contain - . Due to carbon's ability to (form chains with other carbon s), millions of organic compounds are known. The study of the properties, reactions, a ...

amino acid
change causes human familial blindness, showing how phenotyping in animals can inform medical diagnostics and possibly therapy.


Evolutionary origin of phenotype

The
RNA world The RNA world is a hypothetical stage in the evolutionary history of life The history of life on Earth Earth is the third planet from the Sun and the only astronomical object known to harbour and support life. 29.2% of Earth's surfa ...
is the hypothesized pre-cellular stage in the evolutionary history of life on earth, in which self-replicating
RNA Ribonucleic acid (RNA) is a polymer A polymer (; Greek ''wikt:poly-, poly-'', "many" + ''wikt:-mer, -mer'', "part") is a Chemical substance, substance or material consisting of very large molecules, or macromolecules, composed of many Re ...

RNA
molecules proliferated prior to the evolution of
DNA Deoxyribonucleic acid (; DNA) is a molecule File:Pentacene on Ni(111) STM.jpg, A scanning tunneling microscopy image of pentacene molecules, which consist of linear chains of five carbon rings. A molecule is an electrically neutral gro ...

DNA
and
protein Proteins are large biomolecule , showing alpha helices, represented by ribbons. This poten was the first to have its suckture solved by X-ray crystallography by Max Perutz and Sir John Cowdery Kendrew in 1958, for which they received a No ...

protein
s.Michod R (1983) Population biology of the first replicators: On the origin of the genotype, phenotype and organism. Am Zool 23:5–14 The folded
three-dimensional Three-dimensional space (also: 3-space or, rarely, tri-dimensional space) is a geometric setting in which three values (called parameter A parameter (from the Ancient Greek language, Ancient Greek wikt:παρά#Ancient Greek, παρά, ''par ...
physical structure of the first RNA molecule that possessed ribozyme activity promoting replication while avoiding destruction would have been the first phenotype, and the
nucleotide sequence A nucleic acid sequence is a succession of bases signified by a series of a set of five different letters that indicate the order of nucleotides Nucleotides are organic molecules consisting of a nucleoside and a phosphate. They serve as monom ...
of the first self-replicating RNA molecule would have been the original genotype.


See also

*
Ecotype Image:Ecotypes of Physcomitrella patens.JPG, 224x224px, Four different ecotypes of ''Physcomitrella patens'', stored at the International Moss Stock Center In evolutionary ecology, an ecotype,Greek: ''οίκος'' = home and ''τύπος'' = type ...
* Endophenotype *
Genotype The genotype of an organism is its complete set of genetic material. Genotype can also be used to refer to the or variants an individual carries in a particular gene or genetic location. The number of alleles an individual can have in a specific ...
* Genotype-phenotype distinction * Molecular phenotyping *
Race and genetics Researchers have investigated the relationship between race and genetics as part of efforts to understand how biology may or may not contribute to human racial categorization. Many constructions of race are associated with phenotypical traits an ...


References


External links


Mouse Phenome Database

Human Phenotype Ontology

Europhenome: Access to raw and annotated mouse phenotype data

"Wilhelm Johannsen's Genotype-Phenotype Distinction" by E. Peirson at the Embryo Project Encyclopedia
{{Authority control Classical genetics Polymorphism (biology)