All breeders (whether they know it or not)who represent a continuum of emphasis from the supposed importance of maintaining purity of lines to the need to outcross to maintain health, at some point  must recognize the importance of population genetics. Different breeders, different philosophies regardless of how we would like to view the two extremes as polar opposites, it is not useful for understanding this topic.

Much depends on the breed, where you are in your breeding program, the structure of your breed, the number and type of genetic disorders that exist in your breed, the effective population size, how many dogs you produce as a breeder, the level of sophistication of the breeder, and other considerations that you can pick up on if you do further reading in this area.  When  examined  in the light of genetic diversity many find that they can no longer in good conscience use breeding modalities that are wasteful of the genetic resources of a breed, namely inbreeding or linebreeding.

Diversity advocates do favor assortative (not random) mating, "best to best" they just differ in the definition of of "the best" by putting much value on less related breedings. They still apply strict selection criteria, from my experience they are more stringent in their selection than formulaic high COI (Coefficient of Inbreeding) breeders.

Here is an educated laymans article outlining sound scientific reasons for doing so. (see below)
http://siriusdog.com/bragg.htm


Dr. Bragg is an individual who created a breed of sled dogs in Canada.

Many breeders would like to believe that population genetics is in its infancy and while it might have application to managing wild animal populations is not germane to dog breeding.  We could actually dismiss all of science as being "in its infancy". that does not mean that we do not use the technology available to us. Population genetics was founded at the beginning of the last century, it is established science and is widely used for the management of many species.   With few founders, closed stud books, the promotion of popular sires, inbreeding being widely used as a tool of selection, I would submit that many purebred dog breeds may fit that category.

If you want to describe effects in any breeding group, population genetics provides a framework for understanding them.
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As an aside: Cheetahs, Chillingham cattle, and naked mole rats are all highly inbred. Cheetahs are an endangered species (as we all know) it is not just the destruction of habitat that threatens them but the fact that their immune systems are so similar that if one cheetah is infected by a pathogen and kills the cheetah, and that pathogen if spread it will likely kill all cheetahs it contacts. Chillingham cattle and naked mole rats "never leave home" so it is of little importance if their immune systems can meet diverse challenges because are so restricted in their range. If you moved the Chillingham herd to Brazil I do not think it would last a day. If the novel diseases did not get them the jaguars would.  The more inbred an animal the less competent its immune system.

In this context let us consider dogs. Dogs are being dispersed to the four corners of the earth.  The closest model for the dog is the wolf. They are the same species. How do wolves breed?

http://www.npwrc.usgs.gov/resource/2000/wfincst/discuss.htm

As you can see from the above article, wolves constantly outcross to maintain genetic diversity.  They have an instinctual avoidance to inbreeding.  Breeders of the top Schutzhund 3 german shepherd dogs in Germany also use continual outcrosses to produce their dogs.  The result in both cases are animals that are more fit in a biological sense than are inbred canines.


David M. Iwinski B.S.M.S. Master of a Fila
www.webcanine.com