This example is flawed, and here is why:
Dogs did not exist more than 2000 years ago. They were selectively bread from wolves over that time-frame to select for certain genes.
Technically speaking, they are still essentially the SAME genome (same EXACT number of genes, and use of those genes, just different phenotypic variants and expression).
Wolves and dogs can interbreed because they are genetically the same species (even if man feels like he must sub-divide them into 50 million named "breeds")
BTW, the logistics of a Chiwawa and something the size of a wolf breeding are mind boggling.
