Neither the T-cell receptors nor the immunoglobulins have been found in any species evolutionarily earlier than the cartilaginous fishes, in which they have essentially the same form that we see in mammals. The identification of TCRβ-chain and δ-chain homologs from sharks, and of distinct TCRα, β, γ, and δ chains from a skate, show that even at the earliest time that these adaptive immune system receptors can be identified, they had already diversified into at least two recognition systems. Moreover, each lineage shows diversity resulting from combinatorial somatic rearrangement. The identification of many ligands recognized by γ:δ T cells has helped clarify their role in the immune response. Although a complete list is still lacking, the trend appears to be more similar to a kind of innate sensing rather than the fine peptide specificity of the α:β T cells. Ligands of γ:δ T cells include various lipids that may derive from microbes and nonclassical MHC class Ib molecules whose expression may be an indication of infection or cellular stress (see Section 6-17). Even certain α:βT cells appear to participate in a form of innate recognition, such as the mucosa-associated invariant T cells described in Section 4-18. This could indicate that early in the evolution of RAG-dependent adaptive immunity, the receptors generated by excision of the primordial retrotransposon were useful in innate sensing of infections, and this role has persisted in certain minor T-cell populations to this day. In any case, the very early divergence of these two classes of T-cell receptors and their conservation through subsequent evolution suggests an important early separation of functions.
5-22 MHC class I and class II molecules are also first found in the cartilaginous fishes.
One would expect to see the specific ligands of T-cell receptors, the MHC molecules, emerge at around the same time in evolution as the receptors. Indeed, MHC molecules are present in the cartilaginous fishes and in all higher vertebrates, but, like the T-cell receptors, they have not been found in agnathans or invertebrates. Both MHC class I and class II α-chain and β-chain genes are present in sharks, and their products seem to function in an identical way to mammalian MHC molecules. The key residues of the peptide-binding cleft that interact with the ends of the peptide in MHC class I molecules or with the central region of the peptide in MHC class II molecules are conserved in shark MHC molecules.
Moreover, the MHC genes are also polymorphic in sharks, with multiple alleles of class I and class II loci. In some species, more than 20 MHC class I alleles have been identified so far. For the shark MHC class II molecules, both the class II α and the class II β chains are polymorphic. Thus, not only has the function of the MHC molecules in selecting peptides for presentation evolved during the divergence of the agnathans and the cartilaginous fishes, but the continuous selection imposed by pathogens has also resulted in the polymorphism that is a characteristic feature of the MHC.
Section 4-20 introduced the division between classical MHC class I genes (sometimes called class Ia) and the nonclassical MHC class Ib genes, which will be discussed in Chapter 6. This division is also present in cartilaginous fishes, because the class I genes of sharks include some that resemble mammalian class Ib molecules. However, it is thought that the shark class Ib genes are not the direct ancestors of the mammalian class Ib genes. For the class I genes, it seems that within each of the five major vertebrate lineages studied (cartilaginous fishes, lobe-finned fishes, ray-finned fishes, amphibians, and mammals), these genes have independently separated into classical and nonclassical loci.