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Bottlenecks, Cheetahs, and Right Whales. In small populations, inbreeding depression may be more common because random mating is less likely and breeding among related animals may have a greater cumulative effect. Low genetic diversity and inbreeding is not always deleterious, and some small populations may be stable while permanently maintaining low levels of genetic diversity. In general, however, avoidance of inbreeding is a major goal in the management of small populations, since it has been shown to cause a reduction in fitness in captive populations of endangered species.

Perhaps the most famous case of a putative bottleneck being examined in conservation genetics is the cheetah, as examined by Stephen J. O'Brien, a molecular geneticist at the National Cancer Institute. In this 1980s study, cheetahs were shown to have extremely low levels of genetic diversity, which the researchers attributed to a bottleneck that happened less than ten thousand years ago and that may have left only a few females alive. The bottleneck was so extreme that even the usually highly diverse genes of our immune system, genes of the major histocompatibility complex, showed amazingly low levels of diversity. The extreme loss of genetic diversity was attributed to difficulties associated with the species' breeding in captivity and in the wild, abnormal sperm counts, and susceptibility to disease. While it remains controversial whether cheetah populations went through a bottleneck and the extent to which reproductive issues can be attributed to reduced genetic variation, the example remains one of the most prominent in the field of conservation.

Other species, such as the North Atlantic right whale, have faced demographic decline and extremely low levels of genetic diversity since the end of legal commercial hunting for whales at the beginning of the twentieth century. The North Atlantic right whale has maintained a low level of genetic diversity since the 1930s, but recent studies suggest that some additional genetic variation may eventually be lost.

Units of Conservation and DNA Sequences. Using genetic data to evaluate or define species and/or units of conservation can also lead to novel findings and enhance conservation management. Right whales are found in the North Atlantic, North Pacific, and southern oceans. For over a hundred years, they have been considered as two species—one in the north (in the Pacific and Atlantic Oceans) and one in the south. DNA diagnosis methods have corroborated that the southern right whales are distinct from all the others. However, the DNA data also clearly demonstrate that the North Pacific and North Atlantic whales are distinct from each other and warrant distinct species status. The ramifications for the conservation plan of these whales have been taken into consideration by the appropriate management authorities, who have developed a revised plan for naming and protecting three distinct species of right whales.

DNA Detectives and Endangered Species. As discussed above, conservation genetics can aid in the identification of endangered and threatened animals that are traded illegally as commercial products. Researchers at the Wildlife Conservation Society used species-identification methods to detect caiman crocodile tissue in leather products and thus thwart their illegal importation into the United States. Other scientists have used species identification methods to detect whale meat in Japanese fish markets and thus have had an impact on the policing of whale hunting.

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