Figure 5

Intra-species concerted evolution is particularly prominent in the α3 domain. A) The tree was generated using the protein sequences of the α3 domain (last 90 aa of the aligned protein sequences shown in Fig. 2). B) The tree was generated using the protein sequences for the α1/α2 co-domain (first 180 aa of the aligned protein sequences shown in Fig. 2). Percentage bootstrapping support 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 [83]. CD94L molecules are shown in blue, and M3 molecules in green.