Potential examples occur in the homosporous pteridophytes. Data for the ferns Polystichum munitum (n = 41) and Ceratopteris richardii (n = 39) may address these alternatives. Pichersky et al. (1990) studied the genes for the chlorophyll a/b binding proteins in P. munitum. These proteins are important in photosynthesis and are encoded by a small multigene family (Pichersky et al., 1990). P. munitum exhibits diploid isozyme expression (Soltis and Soltis, 1987, 1990; Soltis et al., 1991). If this species is of ancient polyploid origin but has since undergone substantial gene silencing, then pseudogenes should be detectable in the genome. Five clones of the CAB genes were analyzed by Pichersky et al. Three of the five clones were structurally nonfunctional, a fourth clone had a structurally intact sequence but was nonfunctional at the sequence level, and a fifth clone was a functional sequence. Possible explanations for these results (Pichersky et al., 1971) are (i) amplification of nonfunctional sequences in the genome of P. munitum, regardless of the ploidy of P. munitum, (ii) P. munitum is diploid with a large number of mutant CAB genes, and (iii) P. munitum is polyploid, with silencing of multiple genes that are present because of ancient polyploidy. In C. richardii, cDNA clones hybridized to multiple fragments on genomic DNA blots, suggesting that 50% or more of these expressed sequences were present in multiple copies in this fern genome (McGrath et al., 1994). In contrast, a similar experiment with A. thaliana detected only 15% duplicated fragments (McGrath et al., 1993). Further characterization of the hybridizing fragments of the genome is necessary to document that they are in fact duplicated sequences. However, this evidence for multiple hybridizing fragments in C. richardii, along with the CAB gene data for P. munitum, suggests that the genomes of homosporous ferns may in fact be anciently polyploid.
Gene silencing remains an underinvestigated area of polyploid research. If it occurs as described in models of wholesale diploidization of the polyploid genome (Haufler, 1987), what are the mechanisms and at what rate does such silencing occur? Or does silencing occur gradually, essentially one locus at a time? Many unanswered questions remain.
Leitch and Bennett (1997) have suggested that the evolutionary potential of a polyploid depends on a number of factors associated with the formation of the polyploid and with genetic divergence between the parents; unfortunately, the factors involved in the origin and establishment of polyploids in nature are largely unknown (Ramsey and Schemske, 1998). The success of a polyploid may depend, in part, on the parental origin of particular DNA sequences—is the sequence maternal or paternal and does it interact favorably with the organellar genomes? The type