Nobody knows for certain how long ago we started to domesticate dogs, although it is estimated to around 15,000 years ago. Obviously it was a slow process and began with small things like giving food to the wolves who chased predators away (and didn't eat us). The wolves less aggressive towards humans were more likely to survive due to our help, thus contributing to natural selection and eventually evolving some of the wolves into dogs.
So by the time the Chee arrived, the domestication of dogs was already well under way. So either they merged the Pemalite essence with ancient dogs, or they did it with wolves as they said, which would support the theory that some dogs don't have the Pemalite essence. However, dogs have been cross bred so many times in the last few thousand years that it would be impossible to even guess which dog breeds might not have the Pemalite essence.