Tooth structure, count, position in the jaw, etc etc are all tied closely to species. For example, marsupials generally will have 3 premolars and 4 molars on each side of the upper and lower jaw while having more teeth overall than placental mammals, which have 4 premolars and 3 molars on each side of the upper and lower jaw.
Likewise it’s easy to tell the difference between canine teeth (dogs) and Equine teeth (horses). Additionally, all canines (and equines) will have unique tooth anatomy to each species. If you have a coyote and a domestic dog skull of approximately the same size, there will be marked differences in tooth layout and size, even if they are all canine teeth.
If they can extract good DNA it is relatively easy. DNA breaks down over time (relatively quickly relative to geological time) so the really old stuff won’t have usable DNA. If the bone shapes do not match the expected shape of an animal of a known species they may attribute the difference to being a new species. They have to try and rule out natural deformities and differences due to age. The more different the shape from the expected (after ruling out deformities or age related size issues) the more certain that it is from a different species.
There have been numerous cases where something originally classified as a different species was found to actually have been part of an existing species after later examination.
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