A distinctive feature of essential major histocompatibility complex (Mhc) loci is their
polymorphism characterized by large genetic distances between alleles and long persistence
times of allelic lineages. Since the lineages often span several successive speciations,
we investigated the behavior of the Mhc alleles during or close to the speciation phase.
We sequenced exon 2 of the class II B locus 4 from 232 East African cichlid fishes representing
32 related species. The divergence times of the (sub)species ranged from 6000 to 8.4 million
years. Two types of evolutionary analysis were used to elucidate the pattern of exon 2 sequence
divergence. First, phylogenetic methods were applied to reconstruct the most likely evolutionary
pathways leading from the last common ancestor of the set to the extant sequences, and to assess
the probable mechanisms involved in allelic diversification. Second, pairwise comparisons of
sequences were carried out to detect differences seemingly incompatible with origin by
nonparallel point mutations. The analysis revealed point mutations to be the most important
mechanism behind allelic divergences, with recombination playing only an auxiliary part.
Comparison of sequences from related species revealed evidence of random allelic (lineage)
losses apparently associated with speciation. Sharing of identical alleles could be
demonstrated between species that diverged 2 million years ago. The phylogeny of the exon
was incongruent with that of the flanking introns, indicating either a high degree of
convergent evolution at the peptide-binding region-encoding sites, or intron homogenization.