As Dr. Larson notes, “There has been so much admixture since dog domestication began, and especially in the last few hundred years, that looking at modern dogs is always going to be problematic. There may be modern populations that are less ‘corrupted’ or admixed, but even they will possess a legacy of several thousand years of crosses with large numbers of populations, and even wolves.” He adds, “The only way forward is to focus on other methods, including, but not limited to, ancient DNA from archaeological dog and wolf remains. And of course, there is the wider interpretation and understanding from lots of other fi elds to put it all in context.”

In the paper, researchers discussed an interesting pattern that emerges when sites with archaeological dog and wolf remains are overlaid onto maps showing the historical distribution of wolves. First, the archaeological remains are not found in the places where ancient breeds are believed to have been developed, intimating that dogs may have been domesticated multiple times from local wolf populations. Second, most of the ancient breeds come from areas where wolves never ranged, suggesting that humans had dogs as they migrated around the globe. Furthermore, dogs only appeared in these locations after agriculture was introduced.

The canine genome’s full story continues to evade scientists, but as DNA technology advances and analysis becomes cheaper and faster, researchers are optimistic that the answers they seek are right around the corner.

Will I continue to test my future shelter rescue mutts to find out who they are, even though I know that the answers will be the same — all modern dogs are so closely related that it’s almost impossible to discriminate ancestry? Probably. Other mysteries lie hidden in our dogs’ DNA. The idea that an animal can be morphed into so many extreme shapes and behaviors yet remain a simple combination of only a few stem parents is one of them.

We like to believe that scientific discovery advances tidily, fact by fact, to prove an irrefutable truth. But science is a messy business. And there is hardly a better example of just how messy than the search to tease out the mysteries hidden in the canine genome.