Prokaryotic evolution and the tree of life are two different things.

Bapteste E, O’Malley M A, Beiko R G, Ereshefsky M, Gogarten J P, Franklin-Hall L, Lapointe F J, Dupré J, Dagan T, Boucher Y, Martin W (2009); Biol Direct, 4:34. doi: 10.1186/1745-6150-4-34