When whole length sequences are compared, class Ib molecules cluster by function within taxa. A) A schematic representation of the divergence of the eight species studied here. The divergence times, indicated in millions of years, are those estimated from the fossil record. B) A comparison of the whole length of the aligned protein sequences shown in Fig. 2 (270 aa). Percentage bootstrapping support values are indicated of the branches (values above 60% are generally considered as highly significant). Class Ia molecules appear in red. SLA is a pig class Ia molecule chosen as an outlier, since the split with the ancestor of pigs occurred much earlier than that between primates and rodents . CD94L molecules are shown in blue, and M3 molecules in green.