Inbreeding in the context of Purifying selection

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.

In population genetics, gene flow (also known as migration and allele flow) is the transfer of genetic material from one population to another. If the rate of gene flow is high enough, then two populations will have equivalent allele frequencies and therefore can be considered a single effective population. It has been shown that it takes only "one migrant per generation" to prevent populations from diverging due to drift. Populations can diverge due to selection even when they are exchanging alleles, if the selection pressure is strong enough. Gene flow is an important mechanism for transferring genetic diversity among populations. Migrants change the distribution of genetic diversity among populations, by modifying allele frequencies (the proportion of members carrying a particular variant of a gene). High rates of gene flow can reduce the genetic differentiation between the two groups, increasing homogeneity. Gene flow has been thought to constrain speciation and prevent range expansion by combining the gene pools of the groups, thus preventing the development of differences in genetic variation that would have led to differentiation and adaptation for this reason. In some cases dispersal resulting in gene flow may also result in the addition of novel genetic variants under positive selection to the gene pool of a species or population (adaptive introgression.)

There are a number of factors that affect the rate of gene flow between different populations. Gene flow is expected to be lower in species that have low dispersal or mobility, that occur in fragmented habitats, where there are long distances between populations, and when there are small population sizes. Mobility plays an important role in dispersal rate, as highly mobile individuals tend to have greater movement prospects. Although animals are thought to be more mobile than plants, pollen and seeds may be carried great distances by animals, water or wind. When gene flow is impeded, there can be an increase in inbreeding, measured by the inbreeding coefficient (F) within a population. For example, many island populations have low rates of gene flow due to geographic isolation and small population sizes. The Black Footed Rock Wallaby has several inbred populations that live on various islands off the coast of Australia. The population is so strongly isolated that lack of gene flow has led to high rates of inbreeding.

Inbreeding depression is the reduced biological fitness caused by loss of genetic diversity as a result of inbreeding, or mating between closely related individuals within a species. This reduction of fitness occurs because inbreeding increases genetic similarity, which can amplify harmful genes and overall decreases diversity. Inbreeding depression is often attributed to small population size, often stemming from a population bottleneck, where low genetic variation restricts a species’ ability to adapt.

Biological fitness refers to an organism’s capability to survive and transmit its genetic material to the next generation. Higher genetic variation within a breeding population increases the fitness and survivability of a species. Inbreeding depression appears to be present in most populations of organisms but varies across mating systems. In summary, inbreeding depression demonstrates the importance of genetic diversity within populations of species and how it contributes to natural selection.

The coefficient of relationship is a measure of the degree of consanguinity (or biological relationship) between two individuals. The term coefficient of relationship was defined by Sewall Wright in 1922, and was derived from his definition of the coefficient of inbreeding of 1921. The measure is most commonly used in genetics and genealogy. A coefficient of inbreeding can be calculated for an individual, and is typically one-half the coefficient of relationship between the parents.

In general, the higher the level of inbreeding the closer the coefficient of relationship between the parents approaches a value of 1, expressed as a percentage, and approaches a value of 0 for individuals with arbitrarily remote common ancestors.
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A cousin marriage is a marriage where the spouses are cousins (i.e. people with common grandparents or people who share other fairly recent ancestors). The practice was common in earlier times and continues to be common in some societies today. In some jurisdictions such marriages are prohibited due to concerns about inbreeding. Worldwide, more than 10% of marriages are between first or second cousins. Cousin marriage is an important topic in anthropology and alliance theory.

In some cultures and communities, cousin marriages are considered ideal and are actively encouraged and expected; in others, they are seen as incestuous and are subject to social stigma and taboo. Other societies may take a neutral view of the practice, neither encouraging nor condemning it, though it is usually not considered the norm. Cousin marriage was historically practiced by indigenous cultures in Australia, North America, South America, and Polynesia.

Philip III (Spanish: Felipe III, Portuguese: Filipe II; 14 April 1578 – 31 March 1621) was King of Spain and Portugal (as Philip II) during the period known as the Iberian Union, reigning from 1598 until his death in 1621. He was also King of Naples and Sicily, Duke of Milan, and Lord of the Seventeen Provinces. A member of the House of Habsburg, he was born in Madrid to King Philip II of Spain and his fourth wife, Anna of Austria. The family was heavily inbred; Philip II and Anna were uncle and niece, as well as cousins.

One year after inheriting the throne, he married his Habsburg cousin Margaret of Austria, the sister of Ferdinand II, Holy Roman Emperor. Philip quickly delegated most of his power and duties to his chief minister, the Duke of Lerma, whose influence shaped much of his reign. In the outskirts of his territories, military power was upheld by successful but capricious proconsuls, such as Ambrogio Spinola and the Duke of Osuna. Though Philip is associated with a period of relative peace in Western Europe, called the Pax Hispanica by some historians, his lack of focus contributed to the Spanish Empire's gradual decline.

Supernumerary body parts are most commonly a congenital disorder involving the growth of an additional part of the body and a deviation from the body plan. Body parts may be easily visible or hidden away, such as internal organs.

Many additional body parts form by the same process as conjoined twins: the zygote begins to split but fails to completely separate. This condition may also be a symptom of repeated occurrences of continuous inbreeding in a genetic line.

A crossbreed is an organism with purebred parents of two different breeds, varieties, or populations. A domestic animal of unknown ancestry, where the breed status of only one parent or grandparent is known, may also be called a crossbreed though the term "mixed breed" is technically more accurate. Outcrossing is a type of crossbreeding used within a purebred breed to increase the genetic diversity within the breed, particularly when there is a need to avoid inbreeding.

In animal breeding, crossbreeds are crosses within a single species, while hybrids are crosses between different species. In plant breeding terminology, the term crossbreed is uncommon, and no universal term is used to distinguish hybridization or crossing within a population from those between populations, or even those between species.

Self-incompatibility (SI) is a general name for several genetic mechanisms that prevent self-fertilization in sexually reproducing organisms, and thus encourage outcrossing and allogamy. It is contrasted with separation of sexes among individuals (dioecy), and their various modes of spatial (herkogamy) and temporal (dichogamy) separation.

SI is best-studied and particularly common in flowering plants, although it is present in other groups, including sea squirts and fungi. In plants with SI, when a pollen grain produced in a plant reaches a stigma of the same plant or another plant with a matching allele or genotype, the process of pollen germination, pollen-tube growth, ovule fertilization, or embryo development is inhibited, and consequently no seeds are produced. SI is one of the most important means of preventing inbreeding and promoting the generation of new genotypes in plants and it is considered one of the causes of the spread and success of angiosperms on Earth.

Ecosystem decay is a term coined by Thomas Lovejoy to define the process of which species become extinct locally based on habitat fragmentation. This process is what led to the extinction of several species, including the Irish Elk. Ecosystem decay can be mainly attributed to population isolation, leading to inbreeding, leading to a decrease in the population of local species. Another factor is the absence of competition, preventing the mechanisms of natural selection to benefit the population. This leads to a lack of a skill set for the animal to adjust and adapt to a new environment. Habitat fragmentation and loss lead to smaller habitat sizes, and ecosystem decay predicts ecological processes are changed so heavily in smaller habitats that the loss in diversity is more extreme than expected by fragmentation alone.

Although similar to forest fragmentation and island biogeography, ecosystem decay is what results in the event of forest fragmentation.

Sewall Green Wright ForMemRSHonFRSE (December 21, 1889 – March 3, 1988) was an American geneticist known for his influential work on evolutionary theory and also for his work on path analysis. He was a founder of population genetics alongside Ronald Fisher and J. B. S. Haldane, which was a major step in the development of the modern synthesis combining genetics with evolution. He discovered the inbreeding coefficient and methods of computing it in pedigree animals. He extended this work to populations, computing the amount of inbreeding between members of populations as a result of random genetic drift, and along with Fisher he pioneered methods for computing the distribution of gene frequencies among populations as a result of the interaction of natural selection, mutation, migration and genetic drift. Wright also made major contributions to mammalian and biochemical genetics.

A population bottleneck or genetic bottleneck is a sharp reduction in the size of a population due to environmental events such as famines, earthquakes, floods, fires, disease, and droughts; or human activities such as genocide, speciocide, widespread violence or intentional culling. Such events can reduce the variation in the gene pool of a population; thereafter, a smaller population, with a smaller genetic diversity, remains to pass on genes to future generations of offspring. Genetic diversity remains lower, increasing only when gene flow from another population occurs or very slowly increasing with time as random mutations occur. This results in a reduction in the robustness of the population and in its ability to adapt to and survive selecting environmental changes, such as climate change or a shift in available resources. Alternatively, if survivors of the bottleneck are the individuals with the greatest genetic fitness, the frequency of the fitter genes within the gene pool is increased, while the pool itself is reduced.

The genetic drift caused by a population bottleneck can change the proportional random distribution of alleles and even lead to loss of alleles. The chances of inbreeding and genetic homogeneity can increase, possibly leading to inbreeding depression. Smaller population size can also cause deleterious mutations to accumulate.

A wildlife corridor, also known as a habitat corridor, or green corridor, is a designated area that connects wildlife populations that have been separated by human activities or structures, such as development, roads, or land clearings. These corridors enable movement of individuals between populations, which helps to prevent negative effects of inbreeding and reduced genetic diversity, often caused by genetic drift, that can occur in isolated populations. Additionally, corridors support the re-establishment of populations that may have been reduced or wiped out due to random events like fires or disease. They can also mitigate some of the severe impacts of habitat fragmentation, a result of urbanization that divides habitat areas and restricts animal movement. Habitat fragmentation from human development poses an increasing threat to biodiversity, and habitat corridors help to reduce its harmful effects. Corridors aside from their benefit to vulnerable wildlife populations can conflict with communities surrounding them when human-wildlife conflicts are involved. In other communities the benefits of wildlife corridors to wildlife conservation are used and managed by indigenous communities.

The coefficient of inbreeding (COI) is a number measuring how inbred an individual is. Specifically, it is the probability that two alleles at any locus in an individual are identical by descent from a common ancestor of the two parents. A higher COI will make the traits of the offspring more predictable, but also increases the risk of health issues. In dog breeding, it is recommended to keep the COI less than 5%; however, in some breeds this may not be possible without outcrossing.