A molecular phylogeny of the bivalve genus Quadrula (Unionidae) was constructed based on nucleotide sequences of the mitochondrial ND1 gene. Phylogenetic analysis of 66 specimens representing 17 of the 20 currently recognized taxa within Quadrula, three closely allied species, and 16 outgroup taxa reveals a non-monophyletic Quadrula due to the placement of Tritogonia verrucosa,'Fusconaia' succissa, and 'Quincuncina' infucata. We suggest that the taxonomic description of the genus Quadrula be expanded to include these species. Within the genus, we continue to recognize three monophyletic species groups (the quadrula, metanvera, and pustulosa species groups), as historically described; however, the pustulosa species group must include 'F.' succissa and 'Quincuncina' infucata. Finally, while our findings place the monotypic genus Tritogonia within Quadrula, its relationship to members within the genus Quadrula remains unresolved.

Vesicomyid clams depend entirely on sulfur-oxidizing endosymbiotic bacteria for their nutriment. Endosymbionts that are transmitted cytoplasmically through eggs, such as these, should exhibit a phylogenetic pattern that closely parallels the phylogeny of host mitochondrial genes. Such parallel patterns are rarely observed, however, because they are obscured easily by small amounts of horizontal symbiont transmission or occasional host switching. The present symbiont genealogy, based on bacterial small subunit (16S) rDNA sequences, was closely congruent with the host genealogy, based on clam mitochondrial cytochrome oxidase subunit I and large subunit (16S) rDNA sequences. This phylogenetic evidence supports the hypothesis of cospeciation and a long term association between the participants in this symbiosis.

PCR-RFLP analysis has been applied to the identification of three clam species: Ruditapes decussatus (grooved carpet shell), Venerupis pullastra (pullet carpet shell), and Ruditapes philippinarum (Japanese carpet shell). PCR amplification was carried out using a set of primers designed from the DNA nucleotide sequences reported for alpha-actins from humans and various animals. Restriction endonuclease analysis based on sequence data of the PCR products of each clam species revealed the presence of species-specific polymorphic sites for MaeIII and RsaI endonucleases. Electrophoretic analysis of the amplicons digested with MaeIII and RsaI produced species-specific profiles that allowed the genetic identification of the three clam species.

Sequences of the internal transcribed spacer (ITS-1) ribosomal DNA region were compared among 88 soft-shell clams (Mya arenaria) from 12 sites (within three general areas) along the New England coast to determine whether populations were genetically heterogeneous. Two sequence variants were observed, with type 1 having a 3-nucleotide insertion and one point mutation relative to type 2. Allele-specific polymerase chain reaction (PCR); using primers specific to each sequence type, was performed to determine the distribution of individuals who had both allelic forms. DNA from soft-shell clams collected from three areas (Cobscook Bay, Maine; Gulf of Maine; and southern New England) were compared chi 2 analyses of allele-specific PCR results revealed no significant heterogeneity among the three population distributions.

Northeastern Pacific populations of the intertidal marine clam Lasaea are exclusively composed of polyploid asexual clones that lack pelagic larval development. We investigated the phylogeographic structure of this clonal assemblage by assaying genetic divergence in 4 populations along 2000 km of the west coast of North America. In each population a 462-nt portion of the mitochondrial Cytochrome Oxidase III gene was amplified and sequenced for 30 individuals. A total of 21 haplotypes were detected and phylogenetic analyses resolved this variation into 5 main branches that differ in sequence composition by 8.9-14.5%. Two of the branches each encompass a single haplotype, the other 3 terminate in clades containing 3-11 lineages and within clade divergence ranges from 0.4 to 2.3%. Obvious geographic structuring was evident in that 19 of the 21 lineages were restricted in their distributions to single populations and 3 of the main phylogenetic branches were limited to specific marine biogeographic provinces. Two of the clades were encountered in multiple, geographically distant populations; however, the absence of shared haplotypes indicates that long distance gene flow is rare among these direct-developing populations. Northeastern Pacific Lasaea clones form a robust monophyletic grouping relative to other studied populations of the cosmopolitan genus. We estimate divergence times among northeastern Pacific clones to range from 3 to 6 myr. If the latest common ancestor of these exclusively asexual, genetically diverse, regionally monophyletic Lasaea lineages was also asexual, this represents a minimal age estimate for asexuality in the genus. The most plausible alternate hypothesis requires that at least 5 northeastern Pacific sexual parental species have recently become extinct.