Population bottleneck simply refers to a period when the population of a particular organism grows smaller. If, as the population decreases, it also loses genetic variation through genetic drift, it doesn't get that variation back right away when (or if) it gets bigger again.
For an example of a population bottleneck, consider the plight of the northern elephant seal. This seal was hunted almost to extinction in the late 1800s. On a couple of occasions, folks thought that the species had actually gone extinct, but a few seals occasionally turned up on an island off Baja California. Most of these seals were killed as well (sometimes by biologists collecting them for museum specimens!). Obviously, things weren't going well for the northern elephant seal; at the species' low point, the population was estimated to be between 20 and 100 individuals.
In the early 1900s, the Mexican government made the seals' last breeding ground a protected area, and the species began to rebound. Today, the species numbers over 100,000, and elephant seals appear to be out of immediate danger of extinction. This example is a nice success story of species conservation in a world that has too many unhappy endings.
Before you get out the party hats, however, remember that genetic variation is necessary for evolution by natural selection. If the species we humans conserve are going to respond to future environmental changes, those species require genetic variability. The world may have 30,000 elephant seals now, but those 30,000 seals are descended from the few that survived hunting. That means they're very closely related to one other and, as a result, are genetically very similar, so they are still at risk from events such as diseases. In a genetically uniform population, a disease that can attack one of the individuals is likely to attack them all.
The southern elephant seal was also extensively hunted, but its population was not driven as low at that of the northern elephant seal. As a result, the southern species has more genetic diversity than the northern species.
The genetic diversity of a species is a fundamental part of what is unique about that species. Yet the forces of genetic drift can eliminate genetic diversity in small populations, and small populations are often characteristic of species that humans are trying to prevent from going extinct. Therefore, counteracting the effects of genetic drift — and not inadvertently creating more population bottlenecks by using too few individuals for breeding in captive breeding programs — is important in species-conservation efforts. Genetic diversity (heritable variation) is what allows species to respond to selective events (such as novel diseases or environmental change). Conservationists want not just to conserve a few individuals of a species but also to conserve the genetic variation that will allow the species to survive events it may encounter in the future.
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