Retro-genocide

It was believed that before the War broke out, the interventionist elite of the Homeworld committed multiple retro-genocides on members of the lesser species, erasing them from history altogether, in secret. (PROSE: The Book of the War)

The Charons, a species with the ability to warp the fabric of the universe, were erased before they existed in the Time Wars by the Time Lords as they feared that no other life in the universe could co-exist with them. (PROSE: Sky Pirates!)

The Last Great Time War between the Time Lords and the Daleks erased numerous species including the Malfinions, Hederons, Scarbians, who were so completely removed from time that, after the war ended, their names only survived as footnotes in old Time Lord records, later being mentioned in a historical chronicle as well. In fact, no one in the universe even remembered these races existed. (PROSE: The Whoniverse) Several races which were erased from existence during the war persisted as echoes displaced from time on a plane of non-reality, banding together to become the Bygone Horde. The Ninth Doctor thwarted their plan to return to existence, as it would have entailed the sacrifice of the human race. (AUDIO: The Other Side)