In what appears to have been an unplanned quip, Wilberforce asked Huxley if he thought he was descended from an ape on his father's or mother's side. Huxley retorted that he would rather have simian relatives than claim kinship with a man who used his charisma and authority to quash free debate.
The point I want to make about methanogens is that they were the losers in the race through a bottleneck, yet nonetheless survived in niche environments. Similarly, on a larger scale, it is rare for the loser to disappear completely, or for the latecomers never to gain at least a precarious foothold. The fact that flight had already evolved among birds did not preclude its later evolution in bats, which became the most numerous mammalian species. The evolution of plants did not lead to the disappearance of algae, or indeed the evolution of vascular plants to the disappearance of mosses.