The Genotype/Phenotype Distinction

First published Fri Jan 23, 2004; substantive revision Tue Apr 26, 2011

The distinction between phenotype and genotype is fundamental to the understanding of heredity and development of organisms. The genotype of an organism is the class to which that organism belongs as determined by the description of the actual physical material made up of DNA that was passed to the organism by its parents at the organism's conception. For sexually reproducing organisms that physical material consists of the DNA contributed to the fertilized egg by the sperm and egg of its two parents. For asexually reproducing organisms, for example bacteria, the inherited material is a direct copy of the DNA of its parent. The phenotype of an organism is the class to which that organism belongs as determined by the description of the physical and behavioral characteristics of the organism, for example its size and shape, its metabolic activities and its pattern of movement. It is essential to distinguish the descriptors of the organism, its genotype and phenotype, from the material objects that are being described. The genotype is the descriptor of the genomewhich is the set of physical DNA molecules inherited from the organism's parents. The phenotype is the descriptor of the phenome, the manifest physical properties of the organism, its physiology, morphology and behavior. The concepts of phenotype and genotype also demand the distinction between types and tokens. As the words “genotype” and “phenotype” suggest, these are types, sets of which any given organism and its genome are members, sets defined by their physical description. Any individual organism and its genome are members of those sets, tokens of those types.
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1. Heredity and Development 2. Partial Genotype and Partial Phenotype 3. Mapping Genotype Into Phenotype o 3.1 DNA-protein relations o 3.2 Relations between genes o 3.3 Genes and environment o 3.4 Stochastic effects 4. Conclusion Bibliography Academic Tools Other Internet Resources Related Entries

there could be no inheritance of acquired characteristics. This can be represented schematically as: generation 1 heredity ↓ genome development ↓ phenome → generation 2 heredity ↓ genome development ↓ phenome → generation n heredity ↓ genome development ↓ phenome The distinction between genotype and phenotype was introduced by Wilhelm Johannsen in 1908 as a consequence of the realization that the hereditary and developmental pathways were causally separate. According to Weismann the somatoplasm developed and was influenced by the environment. on the other. whereas the germplasm was segregated early in development and was not susceptible to environmental influences. not by Weismannism. While the genome is an element in the causal pathway leading from the first stage in the life of the organism to the final individual. was however. and. . and the somatoplasm. who differentiated between the germplasm of an organism. Thus. the tissues of the rest of the body. This claim had already been made explicitly by August Weismann at the end of the nineteenth century. Heredity and Development The distinction that is made between genotype and phenotype is made necessary by the separation of causal pathways that lead on the one hand to the passage of information about organisms between successive generations. induced. to the growth and development of an organism within a generation from conception to death.1. The mechanism of inheritance is such that the causal pathway of inheritance is from genomes in one generation to genomes in the next without any influence on the genome of the events that occur in the development of the phenome during the life history of the organism. Johannsen's distinction between genotype and phenotype. there is no reciprocal effect of the phenome of the developed organism on the genome passed between generations. the tissue that forms the gametes to produce the next generation. The mechanism of development of the phenome within a generation from the genome is such that the outcome of development is terminated at the death of the organism.

while red-flowered plants had two red factors. The outward appearance of the plant provides the description of its phenotype. one contributed by its maternal parent and one by its paternal parent. but maintained their discrete individuality. in no way affected the nature of the factors themselves. “factors”. they did not physically blend or contaminate each other. the Law of Independent Assortment asserts that when there are factor pairs for different characteristics. these red-flowered hybrids were crossed with each other. The critical feature of Mendel's result was the result he obtained in the first and second generations of crosses between pea plants with clear-cut phenotypic differences. This scheme of Mendelian explanation makes a clear distinction between what we now call the “genome” and the “phenome”. As a consequence. In order to explain this extraordinary reappearance of white-flowered plants in the second generation despite the fact that the first generation cross produced only red-flowered plants. both red-flowered and white-flowered plants appeared in the progeny. Mendel's Third Law. when two hybrid plants were crossed. when the hybrid plants produced pollen and ovules. Most important. Mendel distinguished between the internal state of the plants and their outward appearance. Mendel's Second Law. all the offspring in the first generation were redflowered. however. He postulated the presence of internal discrete elements. will separate again. When. That dominance in physiological action. the formal description of the properties of causal pathways. however. The red flowers of this hybrid were a consequence of the “dominance” of red factors over white factors in their causal interaction in producing flower color. that the segregation of the flower color factors when gametes are formed is causally independent of the segregation of the factor pair .but by the rediscovery in 1900 of Mendel's work on inheritance in the garden pea. the Law of Segregation. encapsulated in Mendel's Laws make a clear separation between the hereditary and the developmental pathways. say a factor pair for flower color and a factor pair for plant height. which separated again. When a pure breeding red-flowered variety was crossed to a pure breeding white-flowered form. Thus a pure bred white-flowered plant had two white factors. The hybrid between these two pure bred varieties would then have one white factor and one red factor. uncontaminated. some of the offspring would have received a white factor from both pollen and ovules and would have white flowers. asserts that the factors that come together when an egg is fertilized. that were contributed by the parents to the offspring. While these factors interacted in some way to produce the external appearance of the plants. unaffected by their mixture in the developed organism and unaffected by their physiological interaction that produces the phenotype of the adult. The Mendelian factors are part of the genome and a description of their state is a genotypic description.

Alterations in the observable physical form of specific places on chromosomes could be associated with specific alterations in phenotype and heritable alterations in phenotype could be produced by bombarding organisms with high energy radiation ionizing radiation. The chief advance was the demonstration that the different factors. On the other hand. That is. RNA. The Second and Third Laws are then descriptions of regularities in inheritance.for plant height. The differences among genes are differences in the number and particular order of the four nucleotide types in a gene string. The development of molecular biology began with the definitive identification of DNA as the material basis of genes in the late 1940s and early 1950s. It is the transcription of the genomic DNA into a special separate molecule. genotypes had to be inferred from their phenotypic effects. For the first half of the twentieth century very little progress was made in identifying the physical basis of Mendel's factors. The behavior of the chromosomes in the process of gamete formation was what was predicted from the formal hereditary properties of genes. But genes remained abstract entities whose existence as the elements of heredity and the causes of development depended entirely on inferences from the phenotypes of organisms involved in various breeding experiments. All of these molecular details confirmed the causal independence of the hereditary behavior of the genome from its developmental functions. and the different RNA molecules transcribed from the different genes carry the information that specifies the chemical structure of the various proteins from which cells are built. The DNA is replicated by the cells by directly copying the DNA strings into progeny DNA molecules. at which times in development and in what amounts is also contained in stretches of DNA called controlling or regulatory elements. asserting that when the two factors of a factor pair in an individual organism differ in their physiological effect. one will dominate the other in the final result of development. Information about which genes are to be transcribed in which cells. and a detailed molecular description of the way in which cells converted the information in the DNA of genes into the molecules of physiological and developmental function. which. now renamed “genes” were linearly arranged along bodies in the nucleus of cells. . the chromosomes. The DNA of various genes is first transcribed into a related molecule. Mendel's First Law. the reading of the genotypic information by the cells and the use of that information to produce molecules that underlie development of the characteristics of the phenotype is carried out by a different pathway. RNA. The DNA of the genome consists of long strings made up of a succession of nucleotides of which there are only four kinds. the Law of Dominance. in contrast is a developmental law. the molecular mechanism of its reproduction in heredity. This was then followed by the elucidation of the chemical and physical structure of DNA.

Even very closely related individuals have many genetic differences. individual members of any species differ in very large numbers of nucleotides that make up their DNA. It is the mechanism which allows the genome to be a cause of the phenotype but which. First. insulates the genome from the reverse influence of the phenome. no two organisms have identical genomes. Second. carries the genotypic information into the metabolic apparatus of the cell that is the critical element in the separation of the hereditary and the developmental functions of the turn. Partial Genotype and Partial Phenotype Real organisms are characterized by great variation one from another. a particular aspect of the total phenotype is chosen for description. 2. say the rate of production of melanin pigment from the biochemical processing of small molecules by enzymes. Taken literally. In humans there are 3 million nucleotide differences on the average between any two people taken at random. although identical in genotype. preventing the inheritance of acquired characteristics. restricted to some subset of the characteristics of the organism that is regarded as relevant for a particular explanatory or experimental purpose. the distinction between genetic or phenotypic types and tokens. Thus. because many mutations occur in cells during the process of growth and development so that all the cells in the body do not contain identical genomes. Even asexually single-celled organisms like bacteria that are reproduced by the division of the parental cell differ in their genomes because mutations of DNA are sufficiently common that at least one of the nucleotides that constitute their DNA will have undergone a spontaneous change during cell division. In practice genotypic and phenotypic descriptions are not total but partial. a decision must be made about what set of phenotypes and genotypes are to be regarded as indistinguishable and so are to be included in the definitions of the partial genotypic and phenotypic classes. With the exception of twins or individuals cloned from the same parent. even cloned individuals or identical twins . would seem to be of no practical import. Typically. In the delimitation of partial phenotypic and genotypic descriptions two decisions must be made. at the same time. while logically correct. phenotypes are also classes with only a single member. Moreover. Moreover there is some ambiguity in assignment of an individual to a genotype. will differ from each other in phenotype because of variations in their developmental environments. Thus genotypes are classes with only a single member. which then dictates that the genes that code for the enzyme proteins involved in the reaction are part of the partial genotype of interest. In the case of melanin pigmentation there is a continuous distribution of the trait from very light to very dark color because of environmental variations and because of small variations .

The problem of what parts of the genome and phenome are to be included in the partial genotypic and phenotypic descriptions of the organism in particular cases is one of the most problematic in biology. It is also unclear what sets of genotypes are to be included within a particular partial genotypic class for three reasons. So the problem of phenotypic class boundaries must be addressed. such third position variation can affect the rate at which the cell reads the DNA code and so such variation may indeed delineate effectively different genotypes. it is simply impossible to consider all pathways of connection. in turn. the result of genetic variations in the genes that code for them. although pigment intensity is a continuous variable. Sometimes biologists choose a partial genotype and partial phenotype because of practical limitations on how much can be done experimentally and simply pretend for the sake of convenience that the rest of the organism really is constant. While it is undoubtedly true that every part of the genome is connected causally with the phenome by some pathway. because the proteins coded for by the “secondary” genes are. there are variations in the DNA of the genome outside the coding regions of genes that do not affect the chemical structure of enzyme proteins but affect the rate of their synthesis. Small variations in phenotype arise in part because the interconnections of metabolic pathways in the organism are so complex that variation in proteins that are not directly part of the melanin production pathway may nevertheless have an effect on the rate of melanin formation. On the other hand.from individual to individual in the actual rates of enzymatic activity. the relation between DNA sequence and the amino acid content of proteins is many-to-one. Second. These are variations in the DNA of the so-called “controlling elements” that are part of each gene and which influence rate at which the cell will read the gene in making proteins. The DNA code is redundant so that triplets that differ only in their third position do not affect which amino acid is specified. so from this perspective all the redundant variations are included in the same partial genotypic class. But these variations in such peripheral proteins are. discrete classes. Should the genes that code for those proteins be included in the definition of the partial genotype. by their nature. in which case the number of genotypic classes in the partial genotype becomes very large? But the problem is recursive. affected in their rates of activity by yet other proteins and so on until all the genes in the genome become included in the “partial” genotypic description. genotypes are. in turn. What range of melanin deposition will be regarded as belonging to the same phenotypic class? The necessity of establishing boundaries for phenotypic classes arises because. Sometimes they explicitly recognize the heterogeneity of the rest of the genome and phenome but claim that it is effectively causally irrelevant to the phenomena . Finally.

of the production machinery and of the order in which the materials pass through that machinery. but treat it as background experimental “noise” that can be averaged out in sufficiently large set of observations. that organisms can be understood by cutting them up into intuitively reasonable small parts whose separate study will be sufficient to lead to an understanding of the whole. the different partial genotypes and phenotypes that are the subject of the analysis and experiment are not differentially affected by the variation in the rest of the genome and phenome. The current state of the study of organismic development ignores this . However. movement across an uneven surface depends on coordination of the contraction of the leg muscles with predictive visual cues so the problem of locomotion makes these two developmentally independent subsystems part of the same functional unit. a description of the materials used. The claim for the validity of this assumption is part of a commitment to the reductionism of analytic biology. and developmental traumas can make an animal blind without making it lame. That is. 3. Mapping Genotype Into Phenotype If the mechanisms of development were such that every change in genotype resulted in a different phenotype and every different phenotype was the consequence of a difference in genotype. The difficulty is that the boundaries of these subsystems are not fixed. There is no question that organisms are a collection of effective subsystems within which causal interactions are strong and between which they are weak. The claim that the rest of the genomic and phenomic effects can be ignored or averaged out depends on the assumption that these pathways are causally orthogonal to the pathways that are being analyzed in the observations. the underlying causal genotype could be unambiguously inferred and vice versa. However. much like the production of an automobile can be completely reconstructed from the blueprints. beginning with the reading of the genome by the cell and ending with the final state. The problem of understanding the manifest variation among organisms would then be reduced to providing a mechanical story of a chain of biochemical reactions. Given a knowledge of the phenotype. Eyes and legs are developmentally independent. Genetic variation exists that affects the size and shape of one without any impact on the size and shape of the other. and sometimes they explicitly recognize the causal relevance of the rest of the genome and phenome. the study of the origin of organic variation would be greatly simplified.under investigation. but change from function to function so they must be determined from observations on an ad hoc basis from case to case. the actual correspondence between genotype and phenotype is a manymany relation in which any given genotype corresponds to many different phenotypes and there are different genotypes corresponding to a given phenotype.

It is not that developmental biologists are unaware of the manymany relationship between genotype and phenotype. a change any part of the gene that causes a replacement of any one of these amino acids will prevent the physiological activity of the protein. Thus. create and reinforce an overly simple view of the relationship between genes and characters. He observed similar dominance of one gene form and recessiveness of the alternative gene form in other characters as well leading him to generalize the phenomenon as a law. 3. the Law of Dominance. (4) stochastic variations of molecular processes within cells. He observed that plants that carried one member of a gene pair specifying red flowers and one member specifying white flowers were indistinguishable from plants carrying two copies of the red form of the gene. The many-many mapping between genotype and phenotype arises from four sources: (1) the relation between the DNA sequence and the chemical structure of proteins. each one of which is coded for by a triplet of nucleic acids in the string of DNA constituting a gene. Rather.1 DNA-protein relations A protein consists of a string of amino acids.many-many relationship and is structured on the model of the automobile assembly plant. (3) the dependence of development and physiology on both the genotype of the organism and the temporal sequence of environments in which the organism develops and functions. An unintended side product of this strategic decision is that the language used to describe the problematic. This is the most common form of many-to-one mappings of genotype onto phenotype. It is impossible to say from observing the phenotype. what change in the genotype has occurred. lack of physiological activity of the protein. leaving for the future the issues posed by the many-many relation. (2)relations between the products of the transcription and translation of the information coded in the genome.2 Relations between genes Mendel's observations provide the classic example of an ambiguity in the relation between genotype and phenotype. For the protein to have physiological activity the identity of many of these amino acids is essential. While subsequent research has shown that dominance of one copy of a gene over another is far from universal. and the results of the research. it is sufficiently common that a large fraction of genetic variation present in populations of organisms is hidden at the level of phenotype and requires special . pragmatic considerations dictate that the understanding of the mechanisms of development will best be achieved by first concentrating on those developmental outcomes that have an unambiguous relationship between genotype and phenotype. 3.

Haldane 1939. Wright 1934). This is especially true when one copy of the gene is defective so that protein with less than normal activity is produced from that copy. Such interactions occur when the physiological effect is the outcome of a chain of chemical steps. For example all individuals of all species of the fruit-fly genus Drosophila have exactly three simple light receptors. If the products of reading the different genes are all necessary to produce a physiological effect. some flies with two or fewer ocelli are observed. and another determines whether the color of the pigment is black or brown. There are many phenotypic features of organisms that show no variation between individuals belonging to the same species or are even constant among many related species. in which there is buffering of development against perturbing forces. while the alternate normal copy codes for protein that is physiologically active enough to produce the normal phenotype (Fisher 1931. each step being mediated by a product of a different gene. There is genetic variation among individuals for genes that affect ocellus number. arranged in a symmetrical triangle on the midline of the top of their heads. but that all the different genotypes mapped onto the same phenotype. but the . If this gene is defective the coat will be white. then alterations in any one of the genes will block the effect. If those with fewer than three ocelli are used as parents for the next generation they produced more abnormal flies than the parental generation. When the process of selective breeding from abnormal flies is continued over many generations a line of flies is produced that consistently has two ocelli. there is a third gene that codes for an enzyme that is necessary for any color at all to be expressed. One determines the distribution of pigment in the hair. This is the phenomenon of developmental canalization. However.experimental techniques to reveal it. Various combinations of different genotypes of these genes correspond to different coat colors. coat color in mammals is the result of the action of the products of three different genes. however. The success of such a selection experiment proves that there was genotypic variation for ocellus number and arrangement in the original population of normal flies. A third source of a many-to-one relation between genotype and phenotype is the phenomenon of developmental buffering whose mechanism is poorly understood. A second form of interaction that is extremely common is that which occurs between the products read from different genes in the genome. irrespective of the genotype of the other genes (Wright 1925). even in the absence of any external disturbance of development and these ocelli can be symmetrically or asymmetrically arranged (Maynard Smith and Sondhi 1960). ocelli. For example. The simplest assumption is that there is no genetic variation for this trait and that its development is resistant to normal environmental disturbance. If the development of the fly is sufficiently disturbed.

so that phenotypic uniformity cannot be taken as a demonstration of relevant genotypic uniformity (Rendel 1967. DeVisser et al. 1957). Thus. no correlation among the plants in their growth in the different environments. in fact. One piece of each plant was grown at low elevation in the Sierra Range. If the phenotype of the organism of a given genotype is plotted against an environmental variable the function that is produced is called the norm of reaction of the genotype (Schmalhausen 1949). while other genotypes flowered at that elevation but not at high elevation. The classic demonstration of the complexities of this mapping is the experiment on clones of the plant Achillea (Clausen. 3. Many experiments on many different organisms where it has been possible to produce multiple individuals of the same genotype show this same result (Lewontin and Goss 2004).3 Genes and environment The complete DNA sequence of an organism does not contain the information necessary to specify the organism. Moreover. the mapping of different genotypes into phenotypes in one environment is often completely unpredictable from their mapping in another environment. the developmental buffering capacity is overcome and the genetic variation for ocellus number is revealed. 1993). For example. Individual immature plants were collected from nature and from each plant three clones were produced by the simple method of cutting them into three pieces. it is not possible to predict the phenotypes of different .developmental effects of that variation are prevented by the system of buffering (Waddington 1953. There was. It is the common experience that norms of reaction of different genotypes are curves of irregular shape that cross each other. the genotype that grew tallest at low elevation was the shortest at medium elevation and the second tallest at high elevation. where as this genotype flowered at low and high elevation it failed to flower at medium elevation. It is then possible to select genotypes that are so extreme in their effect on development that they are beyond the buffering capacity of the normal developing system and produce unusual phenotypes even under normal circumstances. The result of the growth at the three elevations was that the relative heights of the various plants was unpredictable from one environment to another. Moreover. The outcome of developmental processes depends both on the genotype and on the temporal sequence of environments in which the organism develops. one at medium elevation and one at high elevation. Experiments with various other constant features of various animals have shown that developmental canalization is a common feature. It is the mapping function of environment into phenotype for that genotype. Keck and Hiesey 1958). If a sufficiently large perturbation is introduced.

So. in general. The Law of Mass Action of chemistry which is based on statistical averaging over very large numbers of molecules does not apply when there only three of one molecule and seven of another. On the average over many individuals the number is the same on both sides but there is fluctuating asymmetry from fly to fly. but each a few minutes earlier or later than others and so on until the population of cells is growing continuously in time with no synchronization of division. But these are not typical of natural variation among organisms. Yet the genes of the left and right sides are the same and no usual meaning of environment will allow that the left and right hands of a foetus in its mother's womb have different developmental environments. but not simultaneously. nor is there any possibility of different environments in the constantly stirred culture. If the left and right sides of a bilaterally “symmetrical” organism are examined it will be discovered that.4 Stochastic effects Even a complete specification of both the genotype and the temporal order of the developmental environment is insufficient to predict the phenotype. One individual will have. But that is precisely the situation of molecular numbers within cells. but that the direction and amount of asymmetry varies from individual to individual with no average difference between sides. in the early stages of the development of the culture there have not been enough generations to accumulate mutations. Those two cells will then each divide about an hour later. some genotypes that are so defective that they will not survive in any natural environment. six bristles on the right and eight on the left. Their daughter cells will again divide. Yet.genotypes in new environments. The source of these asymmetries and asynchronies is the very low numbers of copies of biologically important large molecules in each cell. do not have the same fingerprints on their left and right hands and the differences in pattern can be so great that no similarity at all can be detected. 3. The same asynchrony of divisions occur at all stages in the division of cells from the fertilized egg in embryos. Another important phenomenon of random variation is the asynchrony of cell divisions. while another will five on the right and seven on the left. There are. Each kind of molecule is in low numbers and they are distributed over . flies have small sensory bristles on their left and right sides. of course. Humans. so the cells are genetically identical. A single bacterial cell innoculated in a large flask of constantly stirred medium will divide into two cells after about an hour. that it is asymmetrical. say . It may be taken as a general rule that the outcome of development of any genotype is a unique consequence of the interaction between genome and environment.

McAdams and Arkin 1997). 1974. 1958. “Experimental Studies in the Nature of Species. 4. If there are seven molecules of a certain type present at the time of cell division. . “Naturalists and Experimentalists: The Genotype and the Phenotype. there is considerable random variation from cell to cell in the timing of cell division and in its outcome. Unlike atoms or planets they are intermediate in size and internally functionally heterogeneous.” Studies in History of Biology. so that it will require different amounts of time for these cells to synthesize enough copies of the molecules for the next division (Goss and Peccoud 1998.” Journal of the History of Biology. Conclusion The complex contingency of the relations between genotype and phenotype arise from the nature of organisms as physical systems. and W. Even Mendel's Laws have many exceptions and the Biogenetic Law of all life from life cannot always have been true or there would be no organisms. They differ from the physical systems that have been the objects of study of most physics and chemistry in two respects.B. in within the cell. ultimately as a consequence of quantum uncertainty. spatial location and reactivity of each kind of molecule. The consequence for the understanding of the structure and function of organisms. Environmental Responses of Climatic Races of Achillea. Hiesey. As is true for living systems in general. Lewontin and Goss 2004.” Carnegie Institution of Washington Publication 581: 1–129.. Churchill. varying from case to case. including their individual and social behavior. Clausen. As a consequence of the stochastic variation in number. III. relations between genotype and phenotype are contingent. Bibliography    Allen. K. is that there is not some small set of universals like Newton's Laws. G. 3: 179–210. Keck. “William Johannsen and the Genotype Concept. one daughter cell may receive three copies and one four copies. fluctuating for each molecule.. 1979. Vibrational states are. D. For a reaction to occur between molecules they must be in proximity and each molecule in the reaction must be in the right vibrational state for interaction. F. 7: 5–30. Extensive measurements of fluctuating asymmetry and of asynchrony have demonstrated that these stochastic effects are important sources of phenotypic variation. As a consequence they are the nexus of a very large number of weakly determining interacting causal chains and subject to the effect of random noise at all levels.

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. > Copyright © 2011 by . Enhanced bibliography for this entry at PhilPapers. 1925. Preview the PDF version of this entry at the Friends of the SEP Society. Academic Tools How to cite this entry. S. S. “The Factors of the Albino Series of Guinea-pigs and their Effects on Black and yellow Pigment. Wright.harvard. Other Internet Resources  Can Nonlinear Epigenetic Interactions Obscure Causal Relations Between Genotype and Phenotype? by Andreas Wagner (Yale University) in Nonlinearity Related Entries biology: philosophy of | character/trait | Darwinism | developmental biology | evolution | gene | genetics: and genomics | information: biological | innate/acquired distinction | molecular biology | natural selection | natural selection: units and levels of | types and tokens Richard Lewontin <lewontin@oeb. 1934. 68: 25–53.” Genetics.. “Physiological and Evolutionary Theories of Dominance. Look up this entry topic at the Indiana Philosophy Ontology Project (InPhO). 10: 223–260.” American Naturalist. with links to its database.

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