Lee and Ó Foighil 2002

Lee T, Ó Foighil D. 2002. 6-Phosphogluconate dehydrogenase (PGD) allele phylogeny is incongruent with a recent origin of polyploidization in some North American Sphaeriidae (Mollusca, Bivalvia). Molecular Phylogenetics and Evolution 25: 112-124.

These authors produced a phylogeny for seven species in three genera in the freshwater clam family Sphaeriidae. These clams have high and variable chromosome numbers, with previous studies suggesting a majority of species polyploid up to 13n (e.g. Lee, 1999). The earliest fossils from the family are found in Cretaceous freshwater deposits, with some genera appearing in the Miocene.

Allopolyploids, derived by hybridization between relatively interfertile (segmental allopolyploidy) or nearly intersterile (genomic allopolyploidy) cause reticulations in phylogenies. Phylogenies based on mtDNA (as exist for this family: Cooley and Ó Foighil, 2000) will not capture such reticulations because of the uniparental inheritance of mtDNA. Nuclear markers, on the other hand, may show a wide range of fates after a duplication event, including gene silencing, homogenization, or independent evolution and differentiation. This variation makes some nuclear markers difficult to analyze in the context of ancient polyploidy.

These authors chose to construct a phylogeny based on a single nuclear gene, using c-DNA to examine only expressed alleles. They found many alleles for this gene in two major clades in the three genera examined. Clade A was widespread and common, while Clade B was not found at all in several species and had fewer alleles in fewer individuals where it was found. Why this imbalance should appear is difficult to state with great certainty. The authors suggest the most likely explanation is that more Clade B alleles have been lost through psuedogenization and / or recombination, though they also acknowledge the possibility, considered by them less likely, that their primer set was biased towards amplification of Clade A alleles. This is considered less likely because some B alleles were detected, such that any bias must be considerably less than 100% effective.

Overall, while the family-level tree does provide evidence of an allopolyploidization event predating the divergence of the three genera, at least some of the more recently-derived lineages experienced duplication events not reflected in this phylogeny. Further examination of the alleles of this gene in more members of this ecologically important family are required to elucidate the history of genomic and genetic events.

One outgroup species came from Cuba, and was preserved and shipped in a solution containing “TRI Reagent (Molecular Research Center)”. This reagent was also used in RNA extraction procedures for all species. I am unfamiliar with this reagent, though its possible use as a tissue preservative that appears to preserve chromatin as well as RNA is very interesting.