As requested by Evlyn M.
Galactic ecology is akin to a hive city: layers built upon layers built upon layers that have collapsed and fused together so that it has become more or less impossible to separate them, but not so fused that one cannot scrape aside the current state of affairs to see what lies beneath.
Each civilization follows the same pattern. They spread out from their homeworld, bringing with them all manner of pets, pests and other animals with them. Alien ecologies are either wiped out or integrated upon contact; those brought along for the ride spread further afield, and through intent, chaos incursion, or the typical turns of nature, drift from their original forms.
Transplantation is the name of the game.
Then that civilization collapses, and the biosphere stops spreading, and changes become more pronounced. The same animal brought to two different Necrontyr worlds could result in hundreds of different descendant species each, given enough time.
Then a new civilization comes along, and the cycle repeats. They introduce their own local life forms, alien life is further transplanted between the worlds of the new civilization, and this continues until that civilization also collapses.
Repeat cycle, add chaos to taste.
In terms of where this leaves us practically regarding the dark and grim ecology of the 41st millennium, it's a clusterfuck.
The Eldar, Slann, Necrontyr, C'Tan, and Old Ones all came before and all left behind vast swathes of their own biomes, all of which have shifted over time. For several of them, their cast-off pets have evolved into sapient species of their own right, with their own growing civilizations. The Imperium itself comes and goes in great waves, so many of its worlds have had mass introductions and transplantations multiple times over. Then there are the Tau, who integrate everyone they come in contact with (and thus spread a huge hybrid biosphere among their controlled territories) Orks and Tyranids just make more of themselves ad infinitum.
In short, it's likely that only obscure worlds of the galaxy have a native biosphere. Everyone else is using some gigantic chimeric clusterfuck, as it right and proper for the setting.