The phenotype (from Greek, Modern phainein, meaning 'to show', and typos, meaning 'type') of an organism is the composite of the organism's observable characteristics or traits, including its morphology or physical form and structure; its developmental processes; its biochemical and physiological properties; its behavior, and the products of behavior, for example, a bird's nest. An organism's phenotype results from two basic factors: the expression of an organism's genetic code, or its genotype, and the influence of environmental factors, which 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 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 in 1978 and then again in his 1982 book The Extended Phenotype suggested that bird nests and other built structures such as caddis fly larvae cases and beaver dams can be considered as "extended phenotypes".
The 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. The distinction is similar to that proposed by August Weismann, who distinguished between germ plasm (heredity) and somatic cells (the body).
The genotype-phenotype distinction 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.
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 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.
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 (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.
The interaction between genotype and phenotype has often been conceptualized by the following relationship:
A more nuanced version of the relationship is:
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.
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) than adenine-thymine, a property that might convey, among organisms living in high-temperature environments, a selective advantage on variants enriched in GC content.
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 modifies its environment by building a beaver dam; this can be considered an expression of its genes, just as its incisor teeth are—which it uses to modify its environment. Similarly, when a bird feeds a brood parasite such as a cuckoo, it is unwittingly extending its phenotype; and when genes in an orchid affect orchid bee behavior to increase pollination, or when genes in a 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.
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
Phenomics has widespread applications in the agricultural industry. With an exponentially growing population and inconsistent weather patterns due to global warming, it has become increasingly difficult to cultivate enough crops to support the world’s population. Advantageous genomic variations, like drought and heat resistance, can be identified through the use of phenomics to create more durable GMOs.
Phenomics is also a crucial stepping stone towards personalized medicine, particularly drug therapy. This application of phenomics has the greatest potential to avoid testing drug therapies that will prove to be ineffective or unsafe. Once the phenomic database has acquired more data, patient phenomic information can be used to select specific drugs tailored to the patient. As the regulation of phenomics develops there is a potential that new knowledge bases will help achieve the promise of personalized medicine and treatment of neuropsychiatric syndromes.
Adrenoleukodystrophy (ALD) is a disease linked to the X chromosome. It is a result of fatty acid buildup caused by the relevant enzymes not functioning properly, which then causes damage to the myelin sheath of the nerves, resulting in seizures and hyperactivity. Other symptoms include problems with speaking, listening, and understanding verbal instructions.
In more detail, it is a disorder of peroxisomal fatty acid beta oxidation which results in the accumulation of very long chain fatty acids in tissues throughout the body. The most severely affected tissues are the myelin in the central nervous system, the adrenal cortex, and the Leydig cells in the testes. Clinically, ALD is a heterogeneous disorder, presenting with several distinct phenotypes, and no clear pattern of genotype-phenotype correlation. As an X-linked disorder, ALD presents most commonly in males, however approximately 50% of heterozygote females show some symptoms later in life. Approximately two-thirds of ALD patients will present with the childhood cerebral form of the disease, which is the most severe form. It is characterized by normal development in early childhood, followed by rapid degeneration to a vegetative state. The other forms of ALD vary in terms of onset and clinical severity, ranging from adrenal insufficiency to progressive paraparesis in early adulthood (this form of the disease is typically known as adrenomyeloneuropathy).
ALD is caused by mutations in ABCD1, a gene located on the X chromosome that codes for ALD, a peroxisomal membrane transporter protein. The exact mechanism of the pathogenesis of the various forms of ALD is not known. Biochemically, individuals with ALD show very high levels of unbranched, saturated, very long chain fatty acids, particularly cerotic acid (26:0). The level of cerotic acid in plasma does not correlate with clinical presentation. Treatment options for ALD are limited. Dietary treatment is with Lorenzo's oil. For the childhood cerebral form, stem cell transplant and gene therapy are options if the disease is detected early in the clinical course. Adrenal insufficiency in ALD patients can be successfully treated. ALD is the most common peroxisomal inborn error of metabolism, with an incidence estimated between 1:18,000 and 1:50,000. It does not have a significantly higher incidence in any specific ethnic groups.Canalisation (genetics)
Canalisation is a measure of the ability of a population to produce the same phenotype regardless of variability of its environment or genotype. It is a form of evolutionary robustness. The term was coined in 1942 by C. H. Waddington to capture the fact that "developmental reactions, as they occur in organisms submitted to natural selection...are adjusted so as to bring about one definite end-result regardless of minor variations in conditions during the course of the reaction". He used this word rather than robustness to take into account that biological systems are not robust in quite the same way as, for example, engineered systems.
Biological robustness or canalisation comes about when developmental pathways are shaped by evolution. Waddington introduced the concept of the epigenetic landscape, in which the state of an organism rolls "downhill" during development. In this metaphor, a canalised trait is illustrated as a valley (which he called a creode) enclosed by high ridges, safely guiding the phenotype to its "fate". Waddington claimed that canals form in the epigenetic landscape during evolution, and that this heuristic is useful for understanding the unique qualities of biological robustness.Directional selection
In population genetics, directional selection, or positive selection is a mode of natural selection in which an extreme phenotype is favored over other phenotypes, causing the allele frequency to shift over time in the direction of that phenotype. Under directional selection, the advantageous allele increases as a consequence of differences in survival and reproduction among different phenotypes. The increases are independent of the dominance of the allele, and even if the allele is recessive, it will eventually become fixed.Directional selection was first described by Charles Darwin in the book On the Origin of Species as a form of natural selection. Other types of natural selection include stabilizing and disruptive selection. Each type of selection contains the same principles, but is slightly different. Disruptive selection favors both extreme phenotypes, different from one extreme in directional selection. Stabilizing selection favors the middle phenotype, causing the decline in variation in a population over time.Dominance (genetics)
Dominance in genetics is a relationship between alleles of one gene, in which the effect on phenotype of one allele masks the contribution of a second allele at the same locus. The first allele is dominant and the second allele is recessive. For genes on an autosome (any chromosome other than a sex chromosome), the alleles and their associated traits are autosomal dominant or autosomal recessive. Dominance is a key concept in Mendelian inheritance and classical genetics. Often the dominant allele codes for a functional protein whereas the recessive allele does not.
A classic example of dominance is the inheritance of seed shape in peas. Peas may be round, associated with allele R, or wrinkled, associated with allele r. In this case, three combinations of alleles (genotypes) are possible: RR, Rr, and rr. The RR individuals have round peas and the rr individuals have wrinkled peas. In Rr individuals the R allele masks the presence of the r allele, so these individuals also have round peas. Thus, allele R is dominant to allele r, and allele r is recessive to allele R. This use of upper case letters for dominant alleles and lower case ones for recessive alleles is a widely followed convention.
More generally, where a gene exists in two allelic versions (designated A and a), three combinations of alleles are possible: AA, Aa, and aa. If AA and aa individuals (homozygotes) show different forms of some trait (phenotypes), and Aa individuals (heterozygotes) show the same phenotype as AA individuals, then allele A is said to dominate, be dominant to or show dominance to allele a, and a is said to be recessive to A.
Dominance is not inherent to either an allele or its phenotype. It is a relationship between two alleles of a gene and their associated phenotypes; one allele can be dominant over a second allele, recessive to a third allele, and codominant to a fourth. Also, an allele may be dominant for a particular aspect of phenotype but not for other aspects influenced by the same gene. Dominance differs from epistasis, a relationship in which an allele of one gene affects the expression of another allele at a different gene.Fitness (biology)
Fitness (often denoted or ω in population genetics models) is the quantitative representation of natural and sexual selection within evolutionary biology. It can be defined either with respect to a genotype or to a phenotype in a given environment. In either case, it describes individual reproductive success and is equal to the average contribution to the gene pool of the next generation that is made by individuals of the specified genotype or phenotype. The fitness of a genotype is manifested through its phenotype, which is also affected by the developmental environment. The fitness of a given phenotype can also be different in different selective environments.
With asexual reproduction, it is sufficient to assign fitnesses to genotypes. With sexual reproduction, genotypes are scrambled every generation. In this case, fitness values can be assigned to alleles by averaging over possible genetic backgrounds. Natural selection tends to make alleles with higher fitness more common over time, resulting in Darwinian evolution.
The term "Darwinian fitness" can be used to make clear the distinction with physical fitness. Fitness does not include a measure of survival or life-span; Herbert Spencer's well-known phrase "survival of the fittest" should be interpreted as: "Survival of the form (phenotypic or genotypic) that will leave the most copies of itself in successive generations."
Inclusive fitness differs from individual fitness by including the ability of an allele in one individual to promote the survival and/or reproduction of other individuals that share that allele, in preference to individuals with a different allele. One mechanism of inclusive fitness is kin selection.Genotype
The genotype is the part of the genetic makeup of a cell, and therefore of any individual, which determines one of its characteristics (phenotype). The term was coined by the Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1903.Genotype is one of three factors that determine phenotype, along with inherited epigenetic factors and non-inherited environmental factors. Not all organisms with the same genotype look or act the same way because appearance and behavior are modified by environmental and growing conditions. Likewise, not all organisms that look alike necessarily have the same genotype.
One's genotype differs subtly his one's genomic sequence, because it refers to how an individual differs or is specialized within a group of individuals or a species. So, typically, one refers to an individual's genotype with regard to a particular gene of interest and the combination of alleles the individual carries (see homozygous, heterozygous). Genotypes are often denoted with letters, for example Bb, where B stands for one allele and b for another.
Somatic mutations which are acquired rather than inherited, such as those in cancers, are not part of the individual's genotype. Hence, scientists and physicians sometimes talk about the genotype of a particular cancer, that is, of the disease as distinct from the diseased.
An example of a characteristic determined by a genotype is the petal color in a pea plant. The collection of all genetic possibilities for a single trait are called alleles; two alleles for petal color are purple and white.Genotype–phenotype distinction
The genotype–phenotype distinction is drawn in genetics. "Genotype" is an organism's full hereditary information. "Phenotype" is an organism's actual observed properties, such as morphology, development, or behavior. This distinction is fundamental in the study of inheritance of traits and their evolution.
It is the organism's physical properties which directly determine its chances of survival and reproductive output, but the inheritance of physical properties is dependent on the inheritance of genes. Therefore, understanding the theory of evolution via natural selection, requires understanding the genotype–phenotype distinction. The genes contribute to a trait, and the phenotype is the observable expression of the genes (and therefore the genotype that affects the trait). If a white mouse had recessive genes that caused the genes responsible for color to be inactive, its genotype would be responsible for its phenotype (the white color).
The mapping of a set of genotypes to a set of phenotypes is sometimes referred to as the genotype–phenotype map.
An organism's genotype is a major (the largest by far for morphology) influencing factor in the development of its phenotype, but it is not the only one. Even two organisms with identical genotypes normally differ in their phenotypes. One experiences this in everyday life with monozygous (i.e. identical) twins. Identical twins share the same genotype, since their genomes are identical; but they never have the same phenotype, although their phenotypes may be very similar. This is apparent in the fact that their mothers and close friends can always tell them apart, even though others might not be able to see the subtle differences. Further, identical twins can be distinguished by their fingerprints, which are never completely identical.
The concept of phenotypic plasticity defines the degree to which an organism's phenotype is determined by its genotype. A high level of plasticity means that environmental factors have a strong influence on the particular phenotype that develops. If there is little plasticity, the phenotype of an organism can be reliably predicted from knowledge of the genotype, regardless of environmental peculiarities during development. An example of high plasticity can be observed in larval newts1: when these larvae sense the presence of predators such as dragonflies, they develop larger heads and tails relative to their body size and display darker pigmentation. Larvae with these traits have a higher chance of survival when exposed to the predators, but grow more slowly than other phenotypes.
In contrast to phenotypic plasticity, the concept of genetic canalization addresses the extent to which an organism's phenotype allows conclusions about its genotype. A phenotype is said to be canalized if mutations (changes in the genome) do not noticeably affect the physical properties of the organism. This means that a canalized phenotype may form from a large variety of different genotypes, in which case it is not possible to exactly predict the genotype from knowledge of the phenotype (i.e. the genotype–phenotype map is not invertible). If canalization is not present, small changes in the genome have an immediate effect on the phenotype that develops.
The terms "genotype" and "phenotype" were created by Wilhelm Johannsen in 1911, although the meaning of the terms and the significance of the distinction have evolved since they were introduced.Hh blood group
The h/h blood group, also known as Oh or the Bombay blood group, is a rare blood type. This blood phenotype was first discovered in Bombay, now known as Mumbai, in India, by Dr. Y. M. Bhende in 1952. It is mostly found in India, Bangladesh, Pakistan, and Iran.Human physical appearance
Human physical appearance is the outward phenotype or look of human beings.
There are infinite variations in human phenotypes, though society reduces the variability to distinct categories. Physical appearance of humans, in particular those attributes which are regarded as important for physical attractiveness, are believed by anthropologists to significantly affect the development of personality and social relations. Humans are acutely sensitive to their physical appearance. Some differences in human appearance are genetic, others are the result of age, lifestyle or disease, and many are the result of personal adornment.
Some people have linked some differences, with ethnicity, such as skeletal shape, prognathism or elongated stride. Different cultures place different degrees of emphasis on physical appearance and its importance to social status and other phenomena.Kell antigen system
The Kell antigen system (also known as Kell–Cellano system) is a group of antigens on the human red blood cell surface which are important determinants of blood type and are targets for autoimmune or alloimmune diseases which destroy red blood cells. Kell can be noted as K, k, or Kp. The Kell antigens are peptides found within the Kell protein, a 93-kilodalton transmembrane zinc-dependent endopeptidase which is responsible for cleaving endothelin-3.McLeod syndrome
McLeod syndrome (pronounced ) is an X-linked recessive genetic disorder that may affect the blood, brain, peripheral nerves, muscle, and heart. It is caused by a variety of recessively inherited mutations in the XK gene on the X chromosome. The gene is responsible for producing the Kx protein, a secondary supportive protein for the Kell antigen on the red blood cell surface.Mutant
In biology and especially genetics, a mutant is an organism or a new genetic character arising or resulting from an instance of mutation, which is generally an alteration of the DNA sequence of the genome or chromosome of an organism. The term mutant is also applied to a virus with an alteration in its nucleotide sequence whose genome is RNA, rather than DNA. In multicellular eukaryotes, a DNA sequence may be altered in an individual somatic cell that then gives rise to a mutant somatic cell lineage as happens in cancer progression. Also in eukaryotes, alteration of a mitochondrial or plastid DNA sequence may give rise to a mutant lineage that is inherited separately from mutant genotypes in the nuclear genome. The natural occurrence of genetic mutations is integral to the process of evolution. The study of mutants is an integral part of biology; by understanding the effect that a mutation in a gene has, it is possible to establish the normal function of that gene.N-acetyltransferase 2
N-acetyltransferase 2 (arylamine N-acetyltransferase), also known as NAT2, is an enzyme which in humans is encoded by the NAT2 gene.Natural selection
Natural selection is the differential survival and reproduction of individuals due to differences in phenotype. It is a key mechanism of evolution, the change in the heritable traits characteristic of a population over generations. Charles Darwin popularised the term "natural selection", contrasting it with artificial selection, which in his view is intentional, whereas natural selection is not.
Variation exists within all populations of organisms. This occurs partly because random mutations arise in the genome of an individual organism, and offspring can inherit such mutations. Throughout the lives of the individuals, their genomes interact with their environments to cause variations in traits. The environment of a genome includes the molecular biology in the cell, other cells, other individuals, populations, species, as well as the abiotic environment. Because individuals with certain variants of the trait tend to survive and reproduce more than individuals with other, less successful variants, the population evolves. Other factors affecting reproductive success include sexual selection (now often included in natural selection) and fecundity selection.
Natural selection acts on the phenotype, the characteristics of the organism which actually interact with the environment, but the genetic
(heritable) basis of any phenotype that gives that phenotype a reproductive advantage may become more common in a population. Over time, this process can result in populations that specialise for particular ecological niches (microevolution) and may eventually result in speciation (the emergence of new species, macroevolution). In other words, natural selection is a key process in the evolution of a population.
Natural selection is a cornerstone of modern biology. The concept, published by Darwin and Alfred Russel Wallace in a joint presentation of papers in 1858, was elaborated in Darwin's influential 1859 book On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life. He described natural selection as analogous to artificial selection, a process by which animals and plants with traits considered desirable by human breeders are systematically favoured for reproduction. The concept of natural selection originally developed in the absence of a valid theory of heredity; at the time of Darwin's writing, science had yet to develop modern theories of genetics. The union of traditional Darwinian evolution with subsequent discoveries in classical genetics formed the modern synthesis of the mid-20th century. The addition of molecular genetics has led to evolutionary developmental biology, which explains evolution at the molecular level. While genotypes can slowly change by random genetic drift, natural selection remains the primary explanation for adaptive evolution.Online Mendelian Inheritance in Man
Online Mendelian Inheritance in Man (OMIM) is a continuously updated catalog of human genes and genetic disorders and traits, with a particular focus on the gene-phenotype relationship. As of 12 February 2017, approximately 8,425 of the over 23,000 entries in OMIM represented phenotypes; the rest represented genes, many of which were related to known phenotypes.The Extended Phenotype
The Extended Phenotype is a 1982 book by Richard Dawkins, in which the author introduced a biological concept of the same name. The main idea is that phenotype should not be limited to biological processes such as protein biosynthesis or tissue growth, but extended to include all effects that a gene has on its environment, inside or outside the body of the individual organism.
Dawkins considers The Extended Phenotype to be a sequel to The Selfish Gene (1976) aimed at professional biologists, and as his principal contribution to evolutionary theory.UCSC Genome Browser
The UCSC Genome Browser is an on-line, and downloadable, genome browser hosted by the University of California, Santa Cruz (UCSC). It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations. The Browser is a graphical viewer optimized to support fast interactive performance and is an open-source, web-based tool suite built on top of a MySQL database for rapid visualization, examination, and querying of the data at many levels. The Genome Browser Database, browsing tools, downloadable data files, and documentation can all be found on the UCSC Genome Bioinformatics website.Wild type
Wild type (WT) refers to the phenotype of the typical form of a species as it occurs in nature. Originally, the wild type was conceptualized as a product of the standard "normal" allele at a locus, in contrast to that produced by a non-standard, "mutant" allele. "Mutant" alleles can vary to a great extent, and even become the wild type if a genetic shift occurs within the population. Continued advancements in genetic mapping technologies have created a better understanding of how mutations occur and interact with other genes to alter phenotype. It is now appreciated that most or all gene loci exist in a variety of allelic forms, which vary in frequency throughout the geographic range of a species, and that a uniform wild type does not exist. In general, however, the most prevalent allele – i.e., the one with the highest gene frequency – is the one deemed wild type.The concept of wild type is useful in some experimental organisms such as fruit flies Drosophila melanogaster, in which the standard phenotypes for features such as eye color or wing shape are known to be altered by particular mutations that produce distinctive phenotypes, such as "white eyes" or "vestigial wings". Wild-type alleles are indicated with a "+" superscript, for example w+ and vg+ for red eyes and full-size wings, respectively. Manipulation of the genes behind these traits led to the current understanding of how organisms form and how traits mutate within a population. Research involving the manipulation of wild-type alleles has application in many fields, including fighting disease and commercial food production.X-linked recessive inheritance
X-linked recessive inheritance is a mode of inheritance in which a mutation in a gene on the X chromosome causes the phenotype to be expressed in males (who are necessarily hemizygous for the gene mutation because they have one X and one Y chromosome) and in females who are homozygous for the gene mutation, see zygosity.
X-linked inheritance means that the gene causing the trait or the disorder is located on the X chromosome. Females have two X chromosomes, while males have one X and one Y chromosome. Carrier females who have only one copy of the mutation do not usually express the phenotype, although differences in X chromosome inactivation can lead to varying degrees of clinical expression in carrier females since some cells will express one X allele and some will express the other. The current estimate of sequenced X-linked genes is 499 and the total including vaguely defined traits is 983.Some scholars have suggested discontinuing the terms dominant and recessive when referring to X-linked inheritance due to the multiple mechanisms that can result in the expression of X-linked traits in females, which include cell autonomous expression, skewed X-inactivation, clonal expansion, and somatic mosaicism.
The development of phenotype
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