If you read February's issue of National Geographic, they go into this issue, showing that physical differences between breeds of dogs are regulated by a surprisingly low number of genes. In general, all breeds of dogs have incredibly similar genes, moreso than any other species. This is due to the 10,000 years of domestication, not because of 200 years of selective breeding.
Simply put, a pure bred dog and a mutt only differ on the tiniest number of activated genes. Selective breeding and natural breeding for dogs leads to essentially the same genetic problems, because all dogs come from an incredibly small gene pool
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