Your sentences are both perfectly grammatical, but they don’t mean the same thing (and one of them is likely odd).
If you put back the “zero thats” (one from a that-clause and the other from a relative clause), I think you can see the difference in meaning:
It is dangerous for ecologists to assume [that] other species sense the environment [that] we do in the same manner.
It is dangerous for ecologists to assume [that] other species sense the environment in the same manner [that] we do.
Here’s a paraphrasing:
It is dangerous for ecologists to assume that other species sense the human environment in the same manner that humans do.
It is dangerous for ecologists to assume that other species sense the environment (that humans and other species share) in the same
manner that humans do.
I think sentence 2 reflects your intended communication.