Little is known regarding the rates at which natural selection can modify or retain antigen presenting alleles at the major histocompatibility complex (MHC). Discovery of identical [1101 base pairs (bp)] coding regions at the MHC class I C locus in Pan troglodytes and Pan paniscus, chimpanzee species that diverged approximately 2.3 million years ago, now indicates that a class I allotype can survive for at least this period. Remarkable conservation was also reflected in the (1799 bp) introns where a maximum of only six substitutions distinguished five alleles (three from P. troglodytes and two from P. paniscus) that encoded the identical heavy chain allotype. Analysis of a more distantly related human allele, HLA-Cw*0702, corroborated that intron variation was non-uniform along the gene. Thus we provide a clear reference frame for the lifetime of an MHC class I allotype, a direct estimate of allelic substitution rates, and evidence for an unusual evolution of MHC class I introns.

Three new linkage groups of enzyme loci are described using Poeciliopsis monacha x P. viriosa-derived interspecific backcross hybrids. Comparison to known linkage groups of the confamilial genus Xiphophorus shows homology between Xiphophorus linkage group I and Poeciliopsis linkage group III, Xiphophorus linkage group II and Poeciliopsis linkage group I, and Xiphophorus linkage group IV and Poeciliopsis linkage group IV. Comparison of the gene content of other fish, amphibians, and mammal syntenic groups suggests retention of plesiomorphic vertebrate gene arrangements in at least two poeciliid linkage groups. Expansion of the Poeciliopsis gene map should be of utility in the identification of tumor regulatory genes through demonstration of linkage to biochemical markers.

The evolution of monomorphic proteins among closely related species has not been examined in detail. To investigate this phenomenon, the glycerol-3-phosphate dehydrogenase (Gpdh) locus was sequence in a broad range of Drosophila species. Although purifying selection to remove amino acid variation is the dominant force in the evolution of Gpdh, some replacements have occurred. The sequences were compared in the context of the phylogeny of the genus, revealing a high proportion of amino acid parallelism and reversal (homoplasy) at four sites. The level of homoplasy is significantly greater than that seen in other proteins for which multiple sequences are available, showing that Gpdh is strongly constrained by both the number of amino acid differences and the types of changes allowed. These four sites evolve at a much higher rate than do the other variable positions in the protein, accounting for half of the interspecific amino acid replacements. However, unlike typical hypervariable sites, where multiple changes to several different amino acids are seen, evolutionary 'flip-flopping' between two amino acid states defines this new class of hypervariable site.

The Gpdh locus was sequenced in a broad range of Drosophila species. In contrast to the extreme evolutionary constraint seen at the amino acid level, the synonymous sites evolve at rates comparable to those of other genes. Gpdh nucleotide sequences were used to infer a phylogenetic tree, and the relationships among the species of the obscura group were examined in detail. A survey of nucleotide polymorphism within D. pseudoobscura revealed no amino acid variation in this species. Applying a modified McDonald-Kreitman test, the amino acid divergence between species in the obscura group does not appear to be excessive, implying that drift is adequate to explain the patterns of amino acid change at this locus. In addition, the level of polymorphism at the Gpdh locus in D. pseudoobscura is comparable to that found at other loci, as determined by a Hudson-Kreitman-Aguadé test. Thus, the pattern of nucleotide variation within and between species at the Gpdh locus is consistent with a neutral model.