dividuals differ in their heritable viability, minimizing reproductive skew and thereby maximizing Ne might not be the best conservation strategy, since it disrupts the correlation between viability traits and reproductive success. Resistance to a virulent egg parasite is influence by both maternal and paternal effects. Random breeding and equalization would reduce reproductive skew, increasing genetic variation in freshly fertilized eggs, but both this genetic variation and egg number may later be reduced by directed selection from the egg pathogens. Alternatively, allowing preferential breeding by preferred males would decrease genetic variation in freshly fertilized eggs but increase mean survival of offspring. In some cases, preferential breeding would sufficiently reduce the effects of selection by pathogens and result in higher overall Ne. Random breeding and equalization could even increase the size of the pathogen population, further threatening population viability. This suggests that the supportive breeding program needs to find a breeding protocol that incorporates the heritable fitness benefits that come with natural mate choice.
Another example of the importance of incorporating natural breeding systems is seen in the life history decisions of precocious maturity in male salmon (Gross 1985). There is good theoretical reason to believe that precocious males (“jacks” or “precociously mature parr”) are those that have the best quality genes in the population and thus derive the highest fitness (Gross and Repka 1998a,b). This increased fitness results in the spread and maintenance of the high quality genes in the population. In current conservation genetics breeding protocols, these males would receive no more breeding advantage than the less fit delayed-maturity males (“hooknose” or “adult” males). This stalls the movement of high-quality genes into the population by unfairly increasing the relative fitness of poorquality genes.
In summary, supportive breeding programs that focus on maximizing genetic diversity are unlikely to maintain long-term genetic quality in wild populations. Studies of natural breeding systems reveal that genetic quality consists of good genes, compatible genes, and appropriate rather than random genetic diversity. The domestication of wildlife for agricultural consumption by human breeding protocols has only demonstrated that we can produce organisms with high fitness in artificial environments. We do not have equivalent evidence for the capacity of conservation breeding programs to produce organisms that are adapted for their natural environments. Until evolutionary and conservation genetics has matured in its understanding of genetic quality, the use of supplementation and the potential for genetic interactions between hatchery and wild fish should be viewed as further threats to population viability.