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Captive breeding is the process of breeding animals in human controlled environments with restricted settings, such as wildlife reserves, zoos and other conservation facilities; sometimes the process is construed to include release of individual organisms to the wild, when there is sufficient natural habitat to support new individuals or when the threat to the species in the wild is lessened. Captive breeding programs facilitate biodiversity and may save species from extinction. However, such programs may also reduce genetic diversity and species fitness.
Captive breeding has been used with success for some species for some time, with probably the oldest known instances of captive breeding being attributed to menageries of European and Asian rulers, a case in point being the Pere David's Deer. This species was successfully saved through captive breeding programs after almost being hunted to extinction in China. The idea was popularized among modern conservationists independently by Peter Scott and Gerald Durrell in the 1950s and 1960s, founders of the Wildfowl and Wetlands Trust and Jersey Zoo, who demonstrated success with a wide variety of life forms in the 1970s ranging from birds (e.g. Pink Pigeon), mammals (e.g. Pygmy Hog), reptiles (e.g. Round Island Boa) and amphibians (e.g. Poison arrow frogs). Their ideas were independently validated by the success of Operation Oryx (under the auspices of the Fauna and Flora Preservation Society), which captive bred the Arabian oryx starting in 1963 for eventual reintroduction to the wild. The Przewalski's horse has recently been re-introduced to the wild in Mongolia, its native habitat.
The breeding of endangered species is coordinated by cooperative breeding programmes containing international studbooks and coordinators, who evaluate the roles of individual animals and institutions from a global or regional perspective. There are regional programmes for the conservation of endangered species:
- Americas: Species Survival Plan SSP (Association of Zoos and Aquariums AZA, Canadian Association of Zoos and Aquariums CAZA)
- Europe: European Endangered Species Programme EEP (European Association of Zoos and Aquaria EAZA)
- Australasia: Australasian Species Management Program ASMP (Australasian Regional Association of Zoological Parks and Aquaria ARAZPA)
- Africa: African Preservation Program APP (African Association of Zoological Gardens and Aquaria PAAZAB)
- Japan: Conservation activities of Japanese Association of Zoos and Aquariums JAZA
- South Asia: Conservation activities of South Asian Zoo Association for Regional Cooperation SAZARC
- South East Asia: Conservation activities of South East Asian Zoos Association SEAZA
Captive breeding techniques are usually difficult to implement for highly mobile species like some migratory birds (e.g. cranes) and fishes (e.g. Hilsa). Species like large cetaceans (whales, dolphins, etc.) may also have some difficulties as it would be hard to meet their biological requirements in captivity, especially the vast amount of space required to keep large populations.
If the captive breeding population is too small, inbreeding may occur due to the reduced gene pool, which may lead to the population lacking immunity to diseases and other problems. Over a sufficient number of generations, inbred populations can regain "normal" genetic diversity.
For example, since the 1970s the Matschie's tree-kangaroo, an endangered species, has been bred in captivity. The Tree Kangaroo Species Survival Plan (TKSSP) was established in 1992 to help with the management of Association of Zoos and Aquariums (AZA). The mean kinship strategy (MK) is used by TKSSP to make annual breeding recommendations to preserve genetic diversity in small populations. This is done to retain their adaptive potential and avoid the negative consequences of inbreeding. Comparison of the genetic diversity of the captive breeding population to wild populations is done to evaluate how the captive breeding program is retaining the population’s genetic diversity over time. In a study done by McGreezy et al. (2010), "AZA Matschie tree kangaroo’s haplotype diversity was almost two times lower than wild Matschie tree kangaroos." This difference with allele frequencies shows the changes that can happen over time, like genetic drift and mutation, when a species is taken out of its natural habitat.
Behaviour changes 
Impacts of captive breeding include behavioural problems in released animals, which are not being able to hunt or forage for food leading to starvation. This could occur because when in captivity young animals miss critical learning periods. Released animals often do not avoid predators and are not able to find ample shelter for themselves and may die as a result. Golden Lion Tamarin mothers often die in the wild before having offspring because they do not have the climbing and foraging skills they need to survive. This results in populations continuing to decline despite reintroduction because the species does not produce viable offspring. Training can improve anti-predator skills, but the effectiveness of such interventions is influenced by a number of constraints.
Domestication is another challenge that captive breeding faces. In a study done by Belyaev (1979), silver foxes were bred in captivity over several decades and many generations to display behavioral and physiological characteristics of a domesticated dog. The study found that after several generations of breeding the domesticated silver foxes picked up behavioral traits seen in domesticated dogs, such as wagging their tails, and licking the hands and faces of humans. They also showed physiological changes such as drooping ears, erect tails and two breeding periods per year. All of these characteristics are not present in wild silver foxes. The experimenters also mentioned that the domesticated foxes "eagerly seek human contact", which could be detrimental as they are hunted for their fur and are viewed as pests by poultry farmers.
Loss of habitat 
Another challenge with captive breeding is the habitat loss that occurs while they are in captivity being bred (though it is occurring even before they are captured). This may make release of the species nonviable if there is no habitat left to support larger populations.
As climate change increases and more invasive species are introduced, more and more species become threatened with extinction. Just from a decrease in population size, reductions in genetic diversity occurs which leads to a decrease in the ability of populations to adapt to the changing environment. In this context, loss of genetic polymorphism, which is a difference in DNA sequence among individuals, groups or populations, is related to extinction risk. Conservation programs can now obtain measurements of genetic diversity at functionally important genes due to advances in technology.
In 1971 the de Wildt Cheetah and Wildlife Centre was established. Between 1975 and 2005, 242 litters were born with a total of 785 cubs. In a study done by Bertschinger, H. J., Meltzer, D. J. A., & Van Dyk, A. (2008), the survival rate of cubs was examined. "Mean cub survival from 1 to 12 months and greater than 12 months of age was 71.3 and 66.2%, respectively." This study shows that cheetahs can be bred successfully and that their endangerment can be decreased through these breeding programs. It also indicated that failure in other breeding habitats may be due to "poor" sperm morphology.
Recently, the number of wild Tasmanian devils is declining from transmissible Devil Facial Tumor Disease. A captive insurance population program has started, but the captive breeding rates at the moment are lower than they need to be. A study done by Keeley, T. J., O, J. K., Fanson, B. G., Masters, K., and McGreevy, P. D. (2012), had a goal to "increase our understanding of the estrous cycle of the devil and elucidate potential causes of failed male-female pairings." The temporal patterns of fecal progestogen and corticosterone metabolite concentrations were examined. The majority of unsuccessful females were captive-born, suggesting that if the species' survival depended solely on captive breeding, the population would probably disappear.
Recent advances 
The Major Histocompatibility Complex is a region of the genome that is being studied by researchers in the field. Scientists have found that genes that code for the major histocompatibility complex have an effect on the ability of certain species (such as Batrachochytrium dendrobatidis) to resist certain infections because the MHC has a mediating effect on the interaction between the body’s immune cells with other body cells. Measuring polymorphism at these genes can give an indirect measure of the immunological fitness of populations. It is suggested that captive breeding programs that place emphasis on selectively breeding those organisms that carry the disease resistant gene, can help in reintroducing endangered species with a better chance in the wild.
There have also been recent advances in captive breeding programs with the use of induced pluripotent stem cell (iPSC) technology. This technology has been tested on several endangered species. Scientists hope the stem cells could be used to be converted into germ cells in captive breeding programs to help diversify the gene pools of threatened species. Healthy mice have been born with this technology. It is suggested that induced pluripotent stem cells may one day be used in producing therapeutic solutions for captive animals suffering from diseases and increasing the size of endangered animal populations.
See also 
- Breeding in the wild
- European Endangered Species Programme or EEP
- Ex-situ conservation
- Panda pornography
- Species Survival Plan or SSP
- World Conference on Breeding Endangered Species in Captivity as an Aid to their Survival or WCBESCAS
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- McGreevy, T.J.; Dabek, L., & Husband, T. P. (2010). "Genetic evaluation of the association of zoos and aquariums matschie's tree kangaroo (dendrolagus matschiei) captive breeding program". Zoo Biology 30 (60): 636–646. doi:10.1002/zoo.20362.
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- Bertschinger, H.J.; Meltzer, D. J. A., & Van Dyk, A. (2008). "Captive breeding of cheetahs in South Africa – 30 years of data from the de Wildt Cheetah and Wildlife Centre". Reproduction in Domestic Animals 43 (16): 66–73. doi:10.1111/j.1439-0531.2008.01144.x. Retrieved April 13, 2012.
- Keeley, T.J.; O, J. K., Fanson, B. G., Masters, K., & McGreevy, P. D. (2012). "The reproductive cycle of the Tasmanian devil (sarcophilus harrisii) and factors associated with reproductive success in captivity". Elsevier Science. Retrieved April 13, 2012.
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- Smithsonian Conservation Biology Institute
- Article: How well can captive breeding programs conserve biodiversity? A review of salmonids