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. While captive breeding programs may save species from extinction, release programs have the potential for diluting genetic diversity and fitness.
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 is employed by modern conservationists, and has saved a wide variety of species from extinction, ranging from birds (e.g., the pink pigeon), mammals (e.g., the pygmy hog), reptiles (e.g., the 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 was also successfully reintroduced in the wild after being bred in captivity.
The breeding of endangered species is coordinated by cooperative breeding programs containing international studbooks and coordinators, who evaluate the roles of individual animals and institutions from a global or regional perspective. These studbooks contain information on birth date, gender, location, and lineage (if known), which helps determine survival and reproduction rates, number of founders of the population, and inbreeding coefficients. A species coordinator reviews the information in studbooks and determines a breeding strategy that would produce most advantageous offspring.
If two compatible animals are found at different zoos, the animals may be transported for mating, but this is stressful, which could in turn make mating less likely. However, this is still a popular breeding method among European zoological organizations. Artificial fertilization (by shipping semen) is another option, but male animals can experience stress during semen collection, and the same goes for females during the artificial insemination procedure. Furthermore, this approach yields lower-quality semen, because shipping requires extending the life of the sperm for the transit time.
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
Conservationists can use captive breeding to help species that are being threatened by human activities such as habitat loss and fragmentation, hunting, fishing, pollution, predation, disease, and parasitism.
Endangered species are those on the verge of extinction and consequently are often very small populations. A risk of captive breeding includes inbreeding, i.e., mating between two closely related individuals, which can lead to offspring that are homozygous recessive for traits that may not have been visible in the parents. As a result, inbreeding may lead to decreased disease immunity and phenotypic abnormalities. This risk is heightened due to the small effective population size. Another consequence of small captive population size is the increased impact of genetic drift, where genes have the potential to fix or disappear completely, thereby reducing genetic diversity.
In the case of captive breeding prior to reintroduction into the wild, it's possible for species to evolve to adapt to the captive environment, rather than the environment that they will be reintroduced to. Selection intensity, initial genetic diversity, and effective population size can impact how much the species adapts to its captive environment. Modeling works indicate that the duration of programs (i.e., time from the foundation of the captive population to the last release event) is an important determinant of reintroduction success. Success is maximized for intermediate project duration allowing the release of a sufficient number of individuals, while minimizing the number of generations undergoing relaxed selection in captivity. 
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). TKSSP's annual breeding recommendations to preserve genetic diversity are based on mean kinship strategy (to retain adaptive potential and avoid inbreeding's disadvantages). To evaluate a how well a captive breeding program maintains genetic diversity, researchers compare the captive breeding population's genetic diversity to the wild population. According to 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.
When evaluating the extinction risk of a species, it is important to consider the species that it interacts with in its environment. Many population models only consider isolated single-species systems, but understanding the multi-species dynamics of each ecosystem can assist in creating more effective conservation efforts. An example of this involves the black-footed ferret, which preys on prairie dogs. When prairie dogs at Conata Basin were infected with sylvatic plague, Yersinia pestis, numbers were reduced, leaving the ferrets with a smaller food source. When attempting to release black-footed ferrets after breeding them in captivity, conservations performed multispecies ‘metamodeling’ techniques to minimize the risks of other species impacting the ferret population size.
Another example is the cheetah, the least genetically variable felid species. This makes it very difficult to increase genetic diversity while breeding in captivity because all cheetahs are essentially genetically identical. Interestingly, although the cheetah has undergone bottlenecks thousands of years ago, they seem to experience few of inbreeding's detrimental effects.
Captive breeding can contribute to behavioural problems in animals that are subsequently released because they are unable to hunt or forage for food, which leads to starvation, possibly because the young animals spent the critical learning period in captivity. Released animals often do not avoid predators and may die because of it. Golden lion tamarin mothers often die in the wild before having offspring because they cannot climb and forage. This leads to continuing population declines despite reintroduction as the species are unable to produce viable offspring. Training can improve anti-predator skills, but its effectiveness varies.
A study on mice has found that after captive breeding had been in place for multiple generations and these mice were "released" to breed with wild mice, that the captive-born mice bred amongst themselves instead of with the wild mice. This suggests that captive breeding may affect mating preferences, and has implications for the success of a reintroduction program.
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.
Climate change and invasive species are threatening an increasing number of species with extinction. A decrease in population size can reduce genetic diversity, which detracts from a population's ability to adapt in a changing environment. In this way extinction risk is related to loss of genetic polymorphism, which is a difference in DNA sequence among individuals, groups or populations. Conservation programs can now obtain measurements of genetic diversity at functionally important genes thanks to advances in technology.
The De Wildt Cheetah and Wildlife Centre, established in South Africa in 1971, has a cheetah captive breeding program. Between 1975 and 2005, 242 litters were born with a total of 785 cubs. The survival rate of cubs was 71.3% for the first twelve months and 66.2% for older cubs, validating the fact that cheetahs can be bred successfully (and their endangerment decreased). It also indicated that failure in other breeding habitats may be due to "poor" sperm morphology.
Wild Tasmanian devils have declined by 90% due to a transmissible cancer called 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. Keeley, Fanson, Masters, and McGreevy (2012) sought to "increase our understanding of the estrous cycle of the devil and elucidate potential causes of failed male-female pairings" by examining temporal patterns of fecal progestogen and corticosterone metabolite concentrations. They found that 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 (MHC) is a genome region that is emerging as an exciting research field. Researchers found that genes that code for MHC affect 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 serve as an indirect measure of a population's immunological fitness. Captive breeding programs that selectively breed for disease-resistant genes may facilitate successful reintroductions.
There have also been recent advances in captive breeding programs with the use of induced pluripotent stem cell (iPSC) technology, which has been tested on endangered species. Scientists hope that they can convert stem cells into germ cells, and use those to diversify the gene pools of threatened species. Healthy mice have been born with this technology. iPSC may one day be used to treat captive animals with diseases.
- Breeding in the wild
- European Endangered Species Programme (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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