INTRAGENOMIC nrDNA POLYMORPHISM IN THE STEPHANODISCUS NIAGARAE COMPLEX (BACILLARIOPHYCEAE)

Goertzen, L. Green, R., Hartung, L. L. & Theriot, E. C. Section of Integrative Biology, The University of Texas at Austin, Austin, Texas 78712 USA Although concerted evolution generally acts to homogenize nuclear ribosomal DNA (rDNA) arrays, a certain amount of intragenomic variation is not uncommon. Despite its potential to seriously compromise phylogenetic reconstruction, this variation has largely been ignored by systematists. We examined levels of intragenomic ITS variation within the recently and rapidly derived Stephanodiscus niagarae complex, where speciation has almost certainly proceeded faster than concerted evolution. We examined multiple populations of Stephanodiscus niagarae and its closest relatives, included related species of Stephanodiscus, and sampled several species of Cyclostephanos and Cyclotella. PCR was performed on DNA extracted from monoclonal cultures, ITS fragments were cloned, and 6‐10 amplicons selected for each of 14 populations for a total of about 125 sequences. Every species examined contains some level of intragenomic ITS polymorphism, ranging from multiple haplotypes differing by a few basepairs to highly diverged paralogues that probably represent independent loci. Phylogenetic analyses indicate several haplotypes shared among S. niagarae and its derivatives that probably predate the origin of the species complex. Despite extensive variation within other species, there appears in some cases to have been sufficient homogenization (and unambiguous clustering) of ITS types to clearly resolve deeper nodes in the family. These results suggest caution concerning the use of ITS sequences, which, unless sampled and analyzed carefully, may actually obscure species relationships and provide misleading information about population structure. We discuss the phylogenetic implications of the preliminary ITS gene tree and consider the use of fossil data to calibrate ITS evolution in diatoms.