Lakewood Fellow,
Ironically, in my post about understanding terms in discussions of evolution you misunderstood me. Your example of the genetic similarities between a wolf and shi-tzu is evidence of common descent. It is not evidence of the neo-Darwinian mechanism for evolution.
However, I don’t think it is actually evidence of either. I don’t think wolves are objectively a different species from dogs. If you define species objectively, meaning animals are of different species if they cannot produce viable fertile offspring, then they are of the same species. Variations within species can be emphasized and maintained (like skin colour) with extreme isolation to prevent regression but no one yet has managed to change an animal from one species to another (in the objective sense described above).
Obviously a neo-Darwinian mechanism would have much more time to work with. But it would have the disadvantage of using the much less efficient natural selection and ordinary course mutations. Remember, it is not the number of years that is important but the number of generations.
As I said above, however, there is plenty of evidence for common descent, the issue is the mechanism by which it was achieved.