Patterns of reticulate evolution for the classical class I and II HLA loci

Some alleles of the major histocompatibility complex (MHC) genes have a reticulate pattern of evolution, probably resulting from the exchange of segments by gene conversion or recombination. Here we compare the extent and patterns of reticulate evolution among the classical class I and class II loci of the human MHC using the recently developed compatibility and partition matrix methods. A complex pattern is revealed with substantial differences among loci in the extent and pattern of reticulation. Extremely high levels of reticulation are observed at HLA-B and HLA-DPB1, high levels at HLA-A and HLA-DRB1, moderate levels at HLA-C and HLA-DQB1, and low levels at HLA-DQA1. The reticulate events are concentrated in the exons encoding the highly variable, peptide-binding domains, suggesting that the sequence combinations produced by these events are maintained by natural selection.