Nucleotide substitution at major histocompatibility complex class II loci: evidence for overdominant selection

Allelic genealogy under overdominant and frequency-dependent selection and polymorphism of major histocompatibility complex loci

To explain the long-term persistence of polymorphic alleles (trans-specific polymorphism) at the major histocompatibility complex (MHC) loci in rodents and primates, a computer simulation study was conducted about the coalescence time of different alleles sampled under various forms of selection. At the same time, average heterozygosity, the number of alleles in a sample, and the rate of codon substitution were examined to explain the mechanism of maintenance of polymorphism at the MHC loci. The results obtained are as follows. (1) The coalescence time for neutral alleles is too short to explain the trans-specific polymorphism at the MHC loci. (2) Under overdominant selection, the coalescence time can be tens of millions of years, depending on the parameter values used. The average heterozygosity and the number of alleles observed are also high enough to explain MHC polymorphism. (3) The pathogen adaptation model proposed by Snell is incapable of explaining MHC polymorphism, since the coalescence time for this model is too short and the expected heterozygosity and the expected number of alleles are too small. (4) From the mathematical point of view, the minority advantage model of frequency-dependent selection is capable of explaining a high degree of polymorphism and trans-specific polymorphism. (5) The molecular mimicry hypothesis also gives a sufficiently long coalescence time when the mutation rate is low in the host but very high in the parasite. However, the expected heterozygosity and the expected number of alleles tend to be too small. (6) Consideration of the molecular mechanism of the function of MHC molecules and other biological observations suggest that the most important factor for the maintenance of MHC polymorphism is overdominant selection. However, some experiments are necessary to distinguish between the overdominance and frequency-dependent selection hypotheses.

Allelic diversification at the class II DQB locus of the mammalian major histocompatibility complex

The allelic diversity at HLA class II loci either arose after the divergence of hominoid lineages or, alternatively, the polymorphism was present before speciation and has been maintained by selection. Here, we report the use of oligonucleotide primers to amplify, by the polymerase chain reaction, and sequence the polymorphic second exon of the DQB locus from 11 species, spanning more than 40 million years of mammalian evolution. Phylogenetic analysis reveals that of the four human DQB allelic types (DQB1-B4), three (DQB1-3) were found in chimpanzee and gorilla and two (DQB3 and -4) were identified in the rhesus monkey, suggesting that some of these types are 5-20 million years old. The ratio of replacement to silent substitutions was calculated between members of the same allelic type from different species. These results suggest that the evolution of the DQB3 allelic type is more constrained than that of the DQB1 allelic type; both evolve more slowly than the DXB locus, a linked but presumably nonexpressed locus. Further, the clustering of allelic subtypes by species in the phylogenetic tree indicates that allelic diversification has occurred subsequent to the divergence of hominoids. Finally, some haplotype combinations of DQA and DQB alleles are common to several hominoid species and may have been maintained for at least 5 million years.

The MHC molecules of nonmammalian vertebrates

There is very little known about the long-term evolution of the MHC and MHC-like molecules. This is because both the theory (the evolutionary questions and models) and the practice (the animals systems, functional assays and reagents to identify and characterize these molecules) have been difficult to develop. There is no molecular evidence yet to decide whether vertebrate immune systems (and particularly the MHC molecules) are evolutionarily related to invertebrate allorecognition systems, and the functional evidence can be interpreted either way. Even among the vertebrates, there is great heterogeneity in the quality and quantity of the immune response. The functional evidence for T-lymphocyte function in jawless and cartilagenous fish is poor, while the bony fish seem to have many characteristics of a mammalian immune system. The organization and sequence of fish Ig genes also indicate that important events in the evolution of the immune system and the MHC occurred in the fish, but thus far there is no molecular evidence for recognizable MHC-like molecules in any fish. There is clearly an MHC in amphibians and birds with many characteristics like the MHC of mammals (a single genetic region encoding polymorphic class I and class II molecules) and evidence for polymorphic class I and class II molecules in reptiles. However, many details differ from the mammals, and it is not clear whether these reflect historical accident or selection for different lifestyles or environment. For example, the adult frog Xenopus has a vigorous immune system with many similarities to mammals, a ubiquitous class I molecule, but a much wider class II tissue distribution than human, mouse and chicken. The Xenopus tadpole has a much more restricted immune response, no cell surface class I molecules and a mammalian class II distribution. The axolotl has a very poor immune response (as though there are no helper T cells), a wide class II distribution and, for most animals, no cell surface class I molecule. It would be enlightening to understand both the mechanisms for the regulation of the MHC molecules during ontogeny and the consequences for the immune system and survival of the animals. These animals also differ markedly in the level of MHC polymorphism. Another difference from mammals is the presence of previously uncharacterized molecules. In Xenopus and reptiles, there are two populations of class I alpha chain on the surface of erythrocytes, those in association with beta 2m and those in association with a disulfide-linked homodimer.(ABSTRACT TRUNCATED AT 400 WORDS)

Selection for polymorphism in the antigen recognition site of major histocompatibility complex class II molecules

The genetic basis for the extensive polymorphism of major histocompatibility complex (MHC) class II molecules was investigated by statistical analysis. Nucleotide sequences of human DQA1, DQB1, DRB1, and DRB3 genes and murine A alpha, A beta, and E beta genes were used. The results show that polymorphism is selected for in the antigen recognition site of class II molecules since replacement substitutions in this region were found to occur at a significantly higher frequency than expected in the absence of selection. In contrast, replacement substitutions are selected against in the remaining part of the first domain exon and in the second domain exon. Furthermore, comparing the sequence variability pattern among different class II alpha and beta sequences, using a variability index for each residue, showed that, with few exceptions, highly polymorphic residues occur in the antigen recognition site. There was a strong and highly significant correlation in the variability pattern in the homologous DRB/E beta sequences but not for DQB/A beta or DQA/A alpha sequences. This difference may be related to the fact that both alpha and beta chains of DQ/A molecules are polymorphic, while only beta chains of DR/E molecules vary.

Ancient interlocus exon exchange in the history of the HLA-A locus

The major histocompatibility complex (MHC) in humans and chimpanzees includes three classical class I loci, A, B and C, which encode glycoproteins expressed on the surface of all nucleated cells. There are also several nonclassical class I loci including E, which have more limited expression. By analyzing published sequences, we have shown that in exons 4 and 5, A locus alleles from both humans and chimpanzees are much more similar to E than to B or C alleles, whereas in exons 2 and 3 alleles from all three classical class I loci are much more similar to each other than any one is to E. We propose that some 20 million years ago, interlocus recombination led to the formation of a hybrid gene in which exons 2 and 3 were derived from the original A locus and exons 4 and 5 were derived from the E locus. The fact that such an ancient event can still be detected suggests that interlocus recombination is rare in the MHC and does not significantly contribute to MHC polymorphism, which is known to be extremely high. The present finding, however, supports Gilbert's idea that exons in a gene may occasionally be replaced by those from another gene in the evolutionary process.