Neutral and nonneutral mitochondrial genetic variation in deep-sea clams from the family Vesicomyidae

Nucleotide sequences at two mitochondrial genes from 57 individuals represe nting eight species of deep-sea clams (Vesicomyidae) were examined for vari ation consistent with the neutral model of molecular evolution. One gene, c ytochrome oxidase subunit I (COI), deviated from the expectations of neutra lity by containing an excess of intraspecific nonsynonymous polymorphism. A dditionally, one species, Calyptogena kilmeri, showed a significant excess of rare polymorphism specifically at the COI locus. In contrast, a second m itochondrial gene, the large-subunit 16S ribosomal RNA gene (16S), showed l ittle deviation from neutrality either between or within species. Together, COI and 16S show no deviation from neutral expectations by the HKA test, p roduce congruent phylogenetic relationships between species, and show corre lated numbers of fixed differences between species and polymorphism within species. These patterns of both neutral and nonneutral evolution within the mitochondrial genome are most consistent with a model where intraspecific nonsynonymous polymorphism at COI is near neutrality. In addition to examin ing the forces of molecular evolution, we extend hypotheses about interspec ific relationships within this family for geographical locations previously unexamined by molecular methods including habitats near the Middle Atlanti c, the Aleutian Trench, and Costa Rica,