I'm reasonably sure it's the elephant uplifts that are completely extinct, which makes sense if you're dealing with a recent development that's solely on Earth. A lot of the uplift lines/species were developed in the outer system, but elephants are big land-dwelling air-breathing beasties. Elephants generally may have gone extinct, but if you can grow one of the bigger biomorphs you can grow a baby elephant, if someone took the time and effort to sequence them propperly. Given how close some varieties are to excinction in the wild even now, I'd be surprised if nobody did that. (On plot thoughts I had a character half-built for an abandoned fic who was the last of the mercenary commanders at the Kilamanjaro elevator during the fall, and whose increasingly brutal attempts to control the exodus included being the one to render the line extinct. How many viable human beings can you get to the orbital stations instead of these lab experiments, or more to the point how much life support equipment or consumables for the bastards already suffucating in tin cans?)