Imagine that dogs became extinct and all knowledge of their existence disappeared. If experts 1,000 years in the future unearthed dog fossils of various breeds, would they know a pug is the same animal as a Great Dane?
If found in isolation, based on anatomy they would likely determine they were closely related, but probably initially still classify them as different species.
If they were part of an archaeological find that associated them with human households, the surmise that they were descended from a deliberate breeding program would be strong - they might then speculate that they were breeds rather than species.
But of course ancient DNA analysis would soon discover they were essentially the same critter and would almost absolutely confirm that they were purpose bred ( though what purpose the pug served other than perhaps making odd snuffling noises would probably elude them 
). I’m sure 1,000 years from now the $12.99 Ronco Ancient DNA Analyzer and Pocket Fisherman from Walgreens would spit out that result after 5 seconds of testing.