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Captive breeding is the process of breeding animals in controlled environments within well-defined settings, such as wildlife reserves, zoos and other commercial and noncommercial conservation facilities. Sometimes the process includes the 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. Release programs have the potential for diluting genetic diversity and species fitness.
The oldest known instances of captive breeding is attributed to the menageries or collections of European and Asian rulers.
Captive breeding has been successful in the past. The Pere David's Deer was successfully saved through captive breeding programs after almost being hunted to extinction in China. Captive-breeding was employed by modern conservationists. Peter Scott and Gerald Durrell, founders of the Wildfowl and Wetlands Trust and Jersey Zoo, in the 1950s and 1960s. They demonstrated success with a wide variety of species 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 efforts were successful in reintroducing the Arabian oryx (under the auspices of the Fauna and Flora Preservation Society), in 1963. The Przewalski's horse has recently been re-introduced to the wild in [Mongolia].
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 (Zoo and Aquarium Association ZAA)
- 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
Conservation efforts are directed toward eliminating threats from human activities. Threats can include: habitat loss and fragmentation, hunting, fishing, pollution, predation, disease, and parasitism. Conservation biologists are concerned with biodiversity, species diversity, and ecosystems.
Recall that endangered species are those on the verge of extinction and so are more than a very small population. A risk of captive breeding includes inbreeding, that is, mating between two closely related individuals as a result of a small gene pool. Some problems associated with inbreeding include a decrease in immunity to disease and phenotypic abnormalities. With the possibility of inbreeding, populations may under go genetic drift where genes have the potential to disappear completely not only reducing genetic variation but creating detrimental effects on natural selection by putting pressures on the remaining population and the species that prey on them.
Over a sufficient number of generations, inbred populations can regain "normal" genetic diversity.
It is important to note that some animals such as the cheetah have undergone genetic drift in the form of bottlenecks in the wild thousands of years ago, yet seem to experience little detrimental effects of inbreeding. 
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.
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.
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.
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.
- 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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- Smithsonian Conservation Biology Institute
- Article: How well can captive breeding programs conserve biodiversity? A review of salmonids