A series of devastating disasters completely wipes out humanity. How does the world look several thousand years later? What new species have evolved and what threatened or endangered species recover?
1) Any disasters that wipes out (not 'reduce to 18th century technology', not 'kill off a significant portion of', not even 'kill off most of', WIPE OUT) in any sort of recent time is going to leave the Earth in pretty bad shape, unless it wipes out humanity in the very early stage of development (say, 500,000 years ago). Your post was extremely unclear, we only know by default that this wipe out, was happening before 1900 (which rules out nuclear weapons), and what we can deduce by talks of 'endangered species'.
2) Several thousand years may be enough time for bacteria and algae to evolve. That's about it. Nothing else is going to change at all significantly. Try several million years, at LEAST. Again, how that changes entirely depends on the nature of the disaster. If it was a series of localised disasters in Africa, probably nothing much... if it was something like a Paleocene-Eocene extinction event, or, funner still, Cretaceous-Tertiary... then something else entirely.
3) Try to throw more than two-lines at a PoD of this complexity, this WI is so poorly designed so as to make it pointless.