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Inbreeding
Inbreeding is when organisms mate with individuals of similar, closely related individuals producing a possibility of more homozygosity in the population. When this inbreeding causes a considerable amount of reduction in fitness, it can be referred to as inbreeding depression. The detrimental effects of inbreeding are especially prevalent in smaller populations and are therefore extensive in captive populations. Often the motive of captive breeding is to reduce the effects of deleterious allele expression caused by inbreeding and to restore genetic diversity. Comparing inbred populations against non-inbred or less-inbred populations can help determine the extent of detrimental effects if any are present. Then captive breeding select individuals can help restore heterozygosity and therefore a move towards better fitness in the population. Through the captive breeding experiments of endangered species such as the Speke's gazelle, it has been found that inbreeding depression is influenced more by environmental influences than selection. Inbreeding depression can also lead to the extinction of species so regulating it through captive breeding can help viability in all populations including endangered populations.

Closely monitoring the possibility of inbreeding within the captive bred population is also key to the success of reintroduction into the species' native habitat. Measuring the effects of other factors such as bottlenecks and initial population size are important to determining the effect of inbreeding and therefore the outcome of the reintroduction.

Methods Used in Captive Breeding
To overcome the challenges of captive breeding such as adaptive differences, loss of genetic diversity, inbreeding depression, and outbreeding depression and get desired results, captive breeding programs use many different monitoring methods. Artificial insemination is used to produce the desired offspring from individuals who don't mate naturally to reduce effects of mating closely related individuals such as inbreeding. Methods as seen in panda pornography allow programs to mate chosen individuals by encouraging mating behavior. As a concern in captive breeding is to minimize the effects of breeding closely related individuals, microsatellite regions from an organisms genome can be used to determine amounts of kinship among founders to minimize relatedness and pick the most distant individuals to breed. This method has successfully been used in the captive breeding of the California condor and the Guam rail. The maximum avoidance of inbreeding (MAI) scheme allows control at a group level rather than an individual level by rotating individuals between groups to avoid inbreeding. Maximizing genetic diversity is also a goal of captive breeding programs and this can be done in plants through ex-situ conservation which is the process in which seeds are stored and occasionally bred from the parent stock in captivity to help seed regeneration and the maximize genetic diversity in the population by collecting germplasm.

History
Captive breeding techniques can be traced back to the first human domestication of animals such as the goat and plants like wheat around 10,000 years ago. These practices were then expanded with the rise of the first zoo which started off as royal menageries in Egypt and its popularity which led to the increase in zoos world wide. The first actual captive breeding programs were only started in the 1960s. These programs, such as the Arabian Oryx breeding program from The Phoenix Zoo in 1962, were aimed at the reintroduction of these species into the wild. These programs were then expanded under The Endangered Species Act in 1973 of the Nixon Administration which was focused on protecting endangered species and their habitats to preserve biodiversity.