Mechanisms for evolving hypervariability: The case of conopeptides

Hypervariability is a prominent feature of large gene families that mediate interactions between organisms, such as venom-derived toxins or immunoglob ulins. In order to study mechanisms for evolution of hypervariability, we e xamined an EST-generated assemblage of 170 distinct conopeptide sequences f rom the venoms of five species of marine Conus snails. These sequences were assigned to eight gene families, defined by conserved elements in the sign al domain and untranslated regions. Order-of-magnitude differences were obs erved in the expression levels of individual conopeptides, with five to sev en transcripts typically comprising over 50% of the sequenced clones in a g iven species. The conopeptide precursor alignments revealed four striking f eatures peculiar to the mature peptide domain: (1) an accelerated rate of n ucleotide substitution, (2) a bias for transversions over transitions in nu cleotide substitutions, (3) a position-specific conservation of cysteine co dons within the hypervariable region, and (4) a preponderance of nonsynonym ous substitutions over synonymous substitutions. We propose that the first three observations argue for a mutator mechanism targeted to mature domains in conopeptide genes, combining a protective activity specific for cystein e codons and a mutagenic polymerase that exhibits transversion bias, such a s DNA polymerase V. The high D-n/D-s ratio is consistent with positive or d iversifying selection, and further analyses by intraspecific/interspecific gene tree contingency tests weakly support recent diversifying selection in the evolution of conopeptides. Since only the most highly expressed transc ripts segregate in gene trees according to the feeding specificity of the s pecies, diversifying selection might be acting primarily on these sequences . The combination of a targeted mutator mechanism to generate high variabil ity with the subsequent action of diversifying selection on highly expresse d variants might explain both the hypervariability of conopeptides and the large number of unique sequences per species.