Background and aims – Formal inferences of the diatom phylogeny have largely depended on the nuclear-encoded small subunit of the rDNA gene (SSU). Large parts of the tree remain unresolved, suggesting that new sources of data need to be applied to this question. The next largest dataset consists of the large subunit of the ribulose-bisphosphate carboxylase gene (rbc L). The photosystem II gene psb C has also been applied to problems at higher levels of the diatom phylogeny. Thus, we sequenced each of these three genes for 136 diatoms in an attempt to determine their applicability to inferring the diatom phylogeny. Methods – We attempted to obtain a more or less even sampling across the diatom tree. In particular, we increased sampling among the radial and polar centrics and among taxa that morphologically appear to be transitional between polar centrics and araphid pennates. Normal sequencing methods were used. Data were analyzed under maximum likelihood. Key results – Analysis of SSU and chloroplast data returned many of the same clades and the same general structure of the tree. Combined, the data weakly reject monophyly of the radial centrics. The chloroplast data weakly support monophyly of the polar centrics but SSU and combined data weakly reject polar centric monophyly. There may be an hitherto unrecognized clade of araphid pennates sister to the remaining pennates. Conclusion – While it is obvious that more genetic data need to be collected, perhaps the greatest obstacle to inferring an accurate, or at least global and robust, diatom phylogeny is the fact that the parts of the diatom tree that appear to be the most intractable to date (relationships among centric groups and between centrics and pennates) are also the most undersampled. This is in part due to major extinctions in the radial and polar centrics. We believe diatomists need to support more effort in both the molecular and morphological studies of these diatoms, and in the search for more information about the first half of the diatom stratigraphic record.

DIATOMS; PHYLOGENY; PSBC; RBCL; SSU; STRATIGRAPHY