As part of our studies of the class II genes of miniature swine, we have isolated and characterized cDNA clones corresponding to DRB genes from two major histocompatibility complex homozygous strains. Comparison of the sequences of these clones to those of human DRB genes revealed a striking amino acid homology between the hypervariable residues of SLA-DRBC and the human DRBI-0101 allele. The percentage of differences in these residues between the pig DRBC allele and the human DRBI-OlO allele was significantly lower (29%) than that between the DRBI-OO0 allele and all other human alleles (average, 66.2%). This similarity was not seen in a comparison of the number of silent substitutions, by which the swine DRBC and the human DRB-0101 differed. Since phenotypic selection operates at the level of protein products rather than nucleotide sequences, these data suggest the existence of selective mechanisms that have resulted in similar hypervariable regions in certain alleles even in these widely disparate species. Consistent with this hypothesis, an examination of available murine and bovine class II sequences revealed a homology in hypervariable residues between the human DRBI-1401 allele and the mouse Eps allele as well as a cow DRB allele. Consideration of these data along with intraspecies allelic sequence comparisons suggests that at least some of the interspecies similarities have emerged as the result of convergent evolution, possibly as the result of a need to react to common pathogens.The major histocompatibility complex (MHC) contains genes encoding cell-surface molecules playing a pivotal role in antigen presentation to T cells (1). The MHC of mammals is one of the most polymorphic genetic systems known, in terms of both number of alleles and structural differences between alleles. The MHC genes are divided into two classes, I and II, of which the class II genes encode two separate chains, a and A, forming a dimer on the cell surface.Almost all of the polymorphism in the class II A3 chains is concentrated in <20 amino acid residues, all of which have been hypothesized to be in direct contact with, or in close proximity to, the antigen and/or the T-cell receptor during antigen presentation (2).The MHC of swine, termed SLA (3), has been shown to exhibit extensive similarities to its human counterpart in both structure and function (4). As a large animal model for studies of transplantation biology, our laboratory has developed a herd of partially inbred miniature swine in which three independent MHC haplotypes (SLAa, SLAC, and SLAd) and three intra-SLA recombinant haplotypes (SLA, SLA", and SLAh) are maintained (5, 6). Studies of vascular grafts in these animals have shown that long-term tolerance can be obtained without exogenous immunosuppression by matching for SLA class II loci only, despite differences at class I and numerous minor loci (7). Because these results suggest the possibility of modifying transplantation immunity by genetic engineering of SLA class II genes, we have recently begun a de...