In my post below Rob commented:
Surely the genetic evidence is pointing towards a single domestication event (see http://news.sciencemag.org/sciencenow/2011/11/new-data-fuels-dogfight-over-the.html?ref=hp)
My general response is not to accept the latest press release about the genetic origin of dogs. I keep track of the literature and it's rather fluid. For example, I woke up this morning, and this is what showed up in my RSS, Modern dogs are more Asian fusions than Euro pups, study finds:
Results from the study, which examined the DNA of 642 dogs, suggest that European and American canine breeds were much more influenced by dogs from Southeast Asia than by ancient Western dogs or by dogs from the Middle East, as was previously thought. Findings from the study by collaborators in California, Iran, Taiwan and Israel appear online in the journal Public Library of Science (PLoS) One. “The two most hotly debated theories propose that dogs originated in Southeast Asia or the Middle East,” said study co-author Ben Sacks, director of the Canid Diversity and Conservation Group in the Veterinary Genetics Laboratory in the UC Davis School of Veterinary Medicine. The laboratory is an international leader in animal genetics research and provides DNA testing and forensic analysis for numerous wildlife, companion animal and livestock species. “In contrast to those theories, our findings suggest that modern European and American dogs are overwhelmingly derived from dogs that were imported from Asia since the silk trade, rather than having descended directly from ancient dogs native to Europe,” Sacks said. “Therefore, previous arguments against Europe as a potential site of dog origins, based on modern European dog DNA, must be reconsidered, and our high-resolution Y-chromosome data from indigenous dogs of the Middle East and Southeast Asia now provide the means to test this hypothesis using ancient European dog DNA.”
I assume that as man's best friend dog genetics is going to be where human genetics is in a few years. I'm not well aware of how good the dog reference genome is, though I hear the cat genome isn't very good. After whole genome analysis gets going with humans I assume people will start looking at domesticates, companion animals as well as those with more direct economic productivity implications.