A preliminary multigene phylogeny of the diatoms (Bacillariophyta): challenges for future research

Abstract

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 (rbcl). The photosystem II gene psbC 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.

A combined paleolimnological/genetic analysis of diatoms reveals divergent evolutionary lineages of Staurosira and Staurosirella (Bacillariophyta) in Siberian lake sediments along a latitudinal transect

“…This argument is supported by the fact that our haplotypes tend to mirror intraspecific rather than interspecific diversity (ESM Tables 6 and 7). The only other reference from the first group in the Staurosira/Staurosirella-like clade originates from Canadian freshwaters (S. construens HQ912451; Theriot et al 2010). This GenBank entry, however, is questionable, as it was obtained from an alga culture (UTEX, FD 323), which refers, according to the UTEX webpage, to Pseudostaurosira construens, but was named S. construens in Theriot et al (2010).…”

“…The only other reference from the first group in the Staurosira/Staurosirella-like clade originates from Canadian freshwaters (S. construens HQ912451; Theriot et al 2010). This GenBank entry, however, is questionable, as it was obtained from an alga culture (UTEX, FD 323), which refers, according to the UTEX webpage, to Pseudostaurosira construens, but was named S. construens in Theriot et al (2010). If we consider the HQ912451 entry to be Pseudostaurosira, the haplotype 6_577 that primarily assigns to this genus could be a representative for Pseudostaurosira pseudoconstruens.…”

“…The phylogenetic tree was calculated with MrBayes (Huelsenbeck and Ronquist 2001), using Plagiogramma sp. (JX413563), the sister group to pennates (Theriot et al 2010), as the outgroup. Two independent runs were performed for 1,000,000 generations.…”

Comparative analysis of the interaction between habitat and growth form in diatoms

“…New taxa were added to complement previous data sets in areas of limited taxon sampling (Theriot et al, 2010;Ashworth et al, 2013). A total of 35 nSSU, 37 rbcL and 34 psbC sequences were newly generated (GenBank accessions: KJ577839-KJ577944).…”

“…Recent efforts in reconstructing the diatom phylogeny are approaching nearly complete sampling of the major extant lineages of diatoms providing the opportunity to examine functional trait evolution in previously unattainable detail (Theriot et al, 2009(Theriot et al, , 2010Ashworth et al, 2013). Moreover, advances in the methodology for modeling discrete traits that relax the assumption of rate constancy across a phylogeny allow evaluation of more realistic evolutionary scenarios (Beaulieu et al, 2013).…”