Mutation in the context of Mosaic (genetics)

Evolutionary biology is a subfield of biology that analyzes the four mechanisms of evolution: natural selection, mutation, genetic drift, and gene flow. The purpose of evolutionary biology is to observe the diversity of life on Earth. The idea of natural selection was first researched by Charles Darwin as he studied bird beaks. The discipline of evolutionary biology emerged through what Julian Huxley called the modern synthesis of understanding, from previously unrelated fields of biological research, such as genetics and ecology, systematics, and paleontology. Huxley was able to take what Charles Darwin discovered and elaborate to build on his understandings.

The investigational range of current research has widened to encompass the genetic architecture of adaptation, molecular evolution, and the different forces that contribute to evolution, such as sexual selection, genetic drift, and biogeography. The newer field of evolutionary developmental biology ("evo-devo") investigates how embryogenesis is controlled, thus yielding a wider synthesis that integrates developmental biology with the fields of study covered by the earlier evolutionary synthesis.

Natural selection is the differential survival and reproduction of individuals due to differences in the relative fitness endowed on them by their own particular complement of observable characteristics. It is a key law or mechanism of evolution which changes the heritable traits characteristic of a population or species over generations. Charles Darwin popularised the term "natural selection", contrasting it with artificial selection, which is intentional, whereas natural selection is not.

For Darwin natural selection was a law or principle which resulted from three different kinds of process: inheritance, including the transmission of heritable material from parent to offspring and its development (ontogeny) in the offspring; variation, which partly resulted from an organism's own agency (see phenotype; Baldwin effect); and the struggle for existence, which included both competition between organisms and cooperation or 'mutual aid' (particularly in 'social' plants and social animals).

Allopatric speciation (from Ancient Greek ἄλλος (állos) 'other' and πατρίς (patrís) 'fatherland') – also called geographic speciation, vicariant speciation, or its earlier name the dumbbell model – is a mode of speciation that occurs when biological populations become geographically isolated from each other to an extent that prevents or interferes with gene flow.

Various geographic changes can arise such as the movement of continents, and the formation of mountains, islands, bodies of water, or glaciers. Human activity such as agriculture or developments can also change the distribution of species populations. These factors can substantially alter a region's geography, resulting in the separation of a species population into isolated subpopulations. The vicariant populations then undergo genetic changes as they become subjected to different selective pressures, experience genetic drift, and accumulate different mutations in the separated populations' gene pools. The barriers prevent the exchange of genetic information between the two populations leading to reproductive isolation. If the two populations come into contact they will be unable to reproduce—effectively speciating. Other isolating factors such as population dispersal leading to emigration can cause speciation (for instance, the dispersal and isolation of a species on an oceanic island) and is considered a special case of allopatric speciation called peripatric speciation.

Selective breeding (also called artificial selection) is the process by which humans use animal breeding and plant breeding to selectively develop particular phenotypic traits (characteristics) by choosing which typically animal or plant males and females will sexually reproduce and have offspring together. Domesticated animals are known as breeds, normally bred by a professional breeder, while domesticated plants are known as varieties, cultigens, cultivars, or breeds. Two purebred animals of different breeds produce a crossbreed, and crossbred plants are called hybrids. Flowers, vegetables and fruit-trees may be bred by amateurs and commercial or non-commercial professionals: major crops are usually the provenance of the professionals.

In animal breeding artificial selection is often combined with techniques such as inbreeding, linebreeding, and outcrossing. In plant breeding, similar methods are used. Charles Darwin discussed how selective breeding had been successful in producing change over time in his 1859 book, On the Origin of Species. Its first chapter discusses selective breeding and domestication of such animals as pigeons, cats, cattle, and dogs. Darwin used artificial selection as an analogy to propose and explain the theory of natural selection but distinguished the latter from the former as a separate process that is non-directed.

Cone cells or cones are photoreceptor cells in the retina of the vertebrate eye. Cones are active in daylight conditions and enable photopic vision, as opposed to rod cells, which are active in dim light and enable scotopic vision. Most vertebrates (including humans) have several classes of cones, each sensitive to a different part of the visible spectrum of light. The comparison of the responses of different cone cell classes enables color vision. There are about six to seven million cones in a human eye (vs ~92 million rods), with the highest concentration occurring towards the macula and most densely packed in the fovea centralis, a 0.3 mm diameter rod-free area with very thin, densely packed cones. Conversely, like rods, they are absent from the optic disc, contributing to the blind spot.

Cones are less sensitive to light than the rod cells in the retina (which support vision at low light levels), but allow the perception of color. They are also able to perceive finer detail and more rapid changes in images because their response times to stimuli are faster than those of rods. In humans, cones are normally one of three types: S-cones, M-cones and L-cones, with each type bearing a different opsin: OPN1SW, OPN1MW, and OPN1LW respectively. These cones are sensitive to visible wavelengths of light that correspond to short-wavelength, medium-wavelength and longer-wavelength light respectively. Because humans usually have three kinds of cones with different photopsins, which have different response curves and thus respond to variation in color in different ways, humans have trichromatic vision. Being color blind can change this, and there have been some verified reports of people with four types of cones, giving them tetrachromatic vision.The three pigments responsible for detecting light have been shown to vary in their exact chemical composition due to genetic mutation; different individuals will have cones with different color sensitivity.

Variegation is the appearance of differently coloured zones in the foliage, flowers, and sometimes the stems and fruit of plants, granting a speckled, striped, or patchy appearance. The colors of the patches themselves vary from a slightly lighter shade of the natural coloration to yellow, to white, or other colors entirely such as red and pink. This is caused by varying levels and types of pigment, such as chlorophyll in leaves. Variegation can be caused by genetic mutations affecting pigment production, or by viral infections such as those resulting from mosaic viruses. Many plants are also naturally variegated, such as Goeppertia insignis. Most of these are herbaceous or climbing plants, and are most often species native to tropical rainforests.

Many species which are normally non-variegated are known to display variegation. Their appearance is desirable to enthusiasts, and many such plants are propagated and sold as unique cultivars. However, in individuals where the variegation occurs in normally-photosynthetic cells, the lack of functioning chloroplasts can slow growth rate. Conversely, naturally-variegated plants derive benefits from their appearance, such as improved photosynthetic efficiency in low-light conditions and herbivore deterrence.

Self-replication is any behavior of a dynamical system that yields construction of an identical or similar copy of itself. Biological cells, given suitable environments, reproduce by cell division. During cell division, DNA is replicated and can be transmitted to offspring during reproduction. Biological viruses can replicate, but only by commandeering the reproductive machinery of cells through a process of infection. Harmful prion proteins can replicate by converting normal proteins into rogue forms. Computer viruses reproduce using the hardware and software already present on computers. Self-replication in robotics has been an area of research and a subject of interest in science fiction. Any self-replicating mechanism which does not make a perfect copy (mutation) will experience genetic variation and will create variants of itself. These variants will be subject to natural selection, since some will be better at surviving in their current environment than others and will out-breed them.

In biology, a mechanism is a system of causally interacting parts and processes that produce one or more effects. Phenomena can be explained by describing their mechanisms. For example, natural selection is a mechanism of evolution; other mechanisms of evolution include genetic drift, mutation, and gene flow. In ecology, mechanisms such as predation and host-parasite interactions produce change in ecological systems. In practice, no description of a mechanism is ever complete because not all details of the parts and processes of a mechanism are fully known. For example, natural selection is a mechanism of evolution that includes countless, inter-individual interactions with other individuals, components, and processes of the environment in which natural selection operates.

Budding or blastogenesis is a type of asexual reproduction in which a new organism develops from an outgrowth or bud due to cell division at one particular site. For example, the small bulb-like projection coming out from the yeast cell is known as a bud. Since the reproduction is asexual, the newly created organism is a clone and, excepting mutations, is genetically identical to the parent organism. Organisms such as hydra use regenerative cells for reproduction in the process of budding.

In hydra, a bud develops as an outgrowth due to repeated cell division of the parent body at one specific site. These buds develop into tiny individuals and, when fully mature, detach from the parent body and become new independent individuals.

In population genetics, fixation is the change in a gene pool from a situation where there exists at least two variants of a particular gene (allele) in a given population to a situation where only one of the alleles remains. That is, the allele becomes fixed. In the absence of mutation or heterozygote advantage, any allele must eventually either be lost completely from the population, or fixed, i.e. permanently established at 100% frequency in the population. Whether a gene will ultimately be lost or fixed is dependent on selection coefficients and chance fluctuations in allelic proportions. Fixation can refer to a gene in general or particular nucleotide position in the DNA chain (locus).

In the process of substitution, a previously non-existent allele arises by mutation and undergoes fixation by spreading through the population by random genetic drift or positive selection. Once the frequency of the allele is at 100%, i.e. being the only gene variant present in any member, it is said to be "fixed" in the population.

In biology, and especially in 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. It is a characteristic that would not be observed naturally in a specimen. The term mutant is also applied to a virus with an alteration in its nucleotide sequence whose genome is 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.

A genetic disorder is a health problem caused by one or more abnormalities in the genome. It can be caused by a mutation in a single gene (monogenic) or multiple genes (polygenic) or by a chromosome abnormality. Although polygenic disorders are the most common, the term is mostly used when discussing disorders with a single genetic cause, either in a gene or chromosome. The mutation responsible can occur spontaneously before embryonic development (a de novo mutation), or it can be inherited from two parents who are carriers of a faulty gene (autosomal recessive inheritance) or from a parent with the disorder (autosomal dominant inheritance). When the genetic disorder is inherited from one or both parents, it is also classified as a hereditary disease. Some disorders are caused by a mutation on the X chromosome and have X-linked inheritance. Very few disorders are inherited on the Y chromosome or mitochondrial DNA (due to their size).

There are well over 6,000 known genetic disorders, and new genetic disorders are constantly being described in medical literature. More than 600 genetic disorders are treatable. Around 1 in 50 people are affected by a known single-gene disorder, while around 1 in 263 are affected by a chromosomal disorder. Around 65% of people have some kind of health problem as a result of congenital genetic mutations. Due to the significantly large number of genetic disorders, approximately 1 in 21 people are affected by a genetic disorder classified as "rare" (usually defined as affecting less than 1 in 2,000 people). Most genetic disorders are rare in themselves.

In genetics, dominance is the phenomenon of one variant (allele) of a gene on a chromosome masking or overriding the effect of a different variant of the same gene on the other copy of the chromosome. The first variant is termed dominant and the second is called recessive. This state of having two different variants of the same gene on each chromosome is originally caused by a mutation in one of the genes, either new (de novo) or inherited. The terms autosomal dominant or autosomal recessive are used to describe gene variants on non-sex chromosomes (autosomes) and their associated traits, while those on sex chromosomes (allosomes) are termed X-linked dominant, X-linked recessive or Y-linked; these have an inheritance and presentation pattern that depends on the sex of both the parent and the child (see Sex linkage). Since there is only one Y chromosome, Y-linked traits cannot be dominant or recessive. Additionally, there are other forms of dominance, such as incomplete dominance, in which a gene variant has a partial effect compared to when it is present on both chromosomes, and co-dominance, in which different variants on each chromosome both show their associated traits.

Dominance is a key concept in Mendelian inheritance and classical genetics. Letters and Punnett squares are used to demonstrate the principles of dominance in teaching, and the upper-case letters are used to denote dominant alleles and lower-case letters are used for recessive alleles. An often quoted 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 (homozygous) individuals have round peas, and the rr (homozygous) individuals have wrinkled peas. In Rr (heterozygous) individuals, the R allele masks the presence of the r allele, so these individuals also have round peas. Thus, allele R is dominant over allele r, and allele r is recessive to allele R.

Natural Selection is the manuscript in which Charles Darwin drafted his planned species book to publish his theory of natural selection. He had noted his concepts in an 1842 Pencil Sketch and an 1844 Essay. In September 1854 he "began sorting notes for species Theory" in preparation for publication, and in May 1856 began writing his Natural Selection "big book". He was on track to publish sometime between 1859 and 1861, but was interrupted by Wallace sending him a similar concept in 1858, so their essays were read together as papers "On the Tendency of Species to form Varieties; and on the Perpetuation of Varieties and Species by Natural Means of Selection". Darwin then wrote an abstract, titled On the Origin of Species by Means of Natural Selection, or the Preservation of Favoured Races in the Struggle for Life, which he published in 1859.

The first two chapters were published in 1868 as The Variation of Animals and Plants Under Domestication.The unpublished eight and a half chapters of Natural Selection were among the manuscripts collated after Darwin's death, and were first transcribed and published in 1975, by Robert C. Stauffer.

Evolutionary thought, the recognition that species change over time and the perceived understanding of how such processes work, has roots in antiquity. With the beginnings of modern biological taxonomy in the late 17th century, two opposed ideas influenced Western biological thinking: essentialism, the belief that every species has essential characteristics that are unalterable, a concept which had developed from medieval Aristotelian metaphysics, and that fit well with natural theology; and the development of the new anti-Aristotelian approach to science. Naturalists began to focus on the variability of species; the emergence of palaeontology with the concept of extinction further undermined static views of nature. In the early 19th century prior to Darwinism, Jean-Baptiste Lamarck proposed his theory of the transmutation of species, the first fully formed theory of evolution.

In 1858 Charles Darwin and Alfred Russel Wallace published a new evolutionary theory, explained in detail in Darwin's On the Origin of Species (1859). Darwin's theory, originally called descent with modification, is known contemporarily as Darwinism or Darwinian theory. Unlike Lamarck, Darwin proposed common descent and a branching tree of life, meaning that two very different species could share a common ancestor. Darwin based his theory on the idea of natural selection: it synthesized a broad range of evidence from animal husbandry, biogeography, geology, morphology, and embryology. Debate over Darwin's work led to the rapid acceptance of the general concept of evolution, but the specific mechanism he proposed, natural selection, was not widely accepted until it was revived by developments in biology that occurred during the 1920s through the 1940s. Before that time most biologists regarded other factors as responsible for evolution. Alternatives to natural selection suggested during "the eclipse of Darwinism" (c. 1880 to 1920) included inheritance of acquired characteristics (neo-Lamarckism), an innate drive for change (orthogenesis), and sudden large mutations (saltationism). Mendelian genetics, a series of 19th-century experiments with pea plant variations rediscovered in 1900, was integrated with natural selection by Ronald Fisher, J. B. S. Haldane, and Sewall Wright during the 1910s to 1930s, and resulted in the founding of the new discipline of population genetics. During the 1930s and 1940s population genetics became integrated with other biological fields, resulting in a widely applicable theory of evolution that encompassed much of biology—the modern synthesis.

Immunization, or immunisation, is the process by which an individual's immune system becomes fortified against an infectious agent (known as the immunogen). When this system is exposed to molecules that are foreign to the body, called non-self, it will orchestrate an immune response, and it will also develop the ability to quickly respond to a subsequent encounter because of immunological memory. This is a function of the adaptive immune system. Therefore, by exposing a human, or an animal, to an immunogen in a controlled way, its body can learn to protect itself: this is called active immunization. The most important elements of the immune system that are improved by immunization are the T cells, B cells, and the antibodies B cells produce. Memory B cells and memory T cells are responsible for a swift response to a second encounter with a foreign molecule. Passive immunization is direct introduction of these elements into the body, instead of production of these elements by the body itself.

Immunization happens in various ways, both in the wild and as done by human efforts in health care. Natural immunity is gained by those organisms whose immune systems succeed in fighting off a previous infection, if the relevant pathogen is one for which immunization is even possible. Natural immunity can have degrees of effectiveness (partial rather than absolute) and may fade over time (within months, years, or decades, depending on the pathogen). In health care, the main technique of artificial induction of immunity is vaccination, which is a major form of prevention of disease, whether by prevention of infection (pathogen fails to mount sufficient reproduction in the host), prevention of severe disease (infection still happens but is not severe), or both. Vaccination against vaccine-preventable diseases is a major relief of disease burden even though it usually cannot eradicate a disease. Vaccines against microorganisms that cause diseases can prepare the body's immune system, thus helping to fight or prevent an infection. The fact that mutations can cause cancer cells to produce proteins or other molecules that are known to the body forms the theoretical basis for therapeutic cancer vaccines. Other molecules can be used for immunization as well, for example in experimental vaccines against nicotine (NicVAX) or the hormone ghrelin in experiments to create an obesity vaccine.