Captive breeding programs are powerful tools for the conservation of our natural resources. Both animal and plant biodiversity are in global decline (International Union for Conservation of Nature [IUCN] 2008), and the trend is for levels and rates of endangerment to continue increasing (Butchart et al. 2005; see also Chapter 1 by Honeycutt and colleagues). When in-situ conservation efforts are insufficient at stopping or reversing the decline of a species, captive populations often represent the only alternative for forestalling extinction. For example, it is currently estimated that hundreds of amphibian species will soon be extinct if emergency measures are not taken to protect populations in captivity until the threats to wild populations can be halted or overcome (Gascon et al. 2007). The success of numerous captive breeding programs has been well documented. As just a few of many examples, captive breeding programs have saved the black-footed ferret (Mustela nigripes), Przewalski's horse (Equus caballus przewalskii), and the California condor (Gymnogyps californianus) from final extinction (after the last wild populations were extirpated) and new wild populations of the golden lion tamarin (Leontopithecus rosalia), Arabian oryx (Oryx leucoryx), and whooping crane (Grus americana) have been successfully re-established from captive stocks.

Conservation breeding programs aim to maintain populations that are representative of their wild counterparts, to provide a reservoir for future reintroductions and recovery efforts (see Chapter 12 by Rhodes and Latch). Thus, the genetic goals of captive population management are to minimize genetic drift, retain genetic diversity, restrict inbreeding, and limit adaptation to captivity (Lacy 1994). The foundations of most captive breeding programs are pedigree analyses, which are used to manage both the demography and genetics of captive populations (Ballou & Foose 1996).