[PapaBear]

In a sense that is what we do on our very small scale. Changing gene pools by manipulating breeding patterns to achieve our own ends. What is curious to me is the different results one gets in species by breeding back within a family line.
In the beef cattle industry (odd connection but bear with me) breeding back closely within a family tree is avoided to prevent deformities (father/daughter pairings) and sterility (grandfather/granddaughter pairings). At the same time their are a very few who intentionally breed Grandfather to granddaughter to produce sterile offspring called "prime martins". They have all of the best physical traits of the genetic line thereby producing superior beef quality and growth while sacrificing the ability to reproduce those traits in future generations. (This practice is generally limited to pen raised baby beef and milk fed veal)
Fortunately for us Koi sterility issues haven't come into play with linebreeding, but the deformity rate is rather high at culling time which reveals the genetic weakness our manipulations inevitably cause. These issues make it just that much more important to introduce outside lines from time to time to keep enough genetic variety to keep from further weakening the genepools of our favorite lines.