Molecular phylogeny of the Cymbellales (Bacillariophyceae, Heterokontophyta) with a comparison of models for accommodating rate variation across sites

Abstract:

We reconstructed the phylogeny of representatives from nine genera and three families of the Cymbellales using two nuclear and three chloroplast genes. After rooting with Anomoeoneis, Placoneis was found as sister to a clade composed of Cymbella, Cymbopleura, Encyonema, Gomphonema, and Gomphoneis. The latter group was divided into lineages with mainly heteropolar and dorsiventral valve symmetry. The data and chloroplast morphology also supported a close relationship between Geissleria decussis and Placoneis. Expectedly, the sequenced genes exhibited substantial across-site rate variation (ASRV) that prompted us to assess the stability of the inferred relationships in the face of different approaches for modelling ASRV. While the overall topology remained stable across analyses, relationships between Cymbella and Cymbopleura and within one clade of Gomphonema varied dependent on the employed model. In some cases a strongly supported relationship in one analysis was not recovered by another that differed solely in how the data were partitioned. These topological fluctuations appeared in areas of the tree with the least balanced taxon sampling, and they altered the outcomes of phylogenetic hypotheses tests of monophyly. Assessing how different models for ASRV affect tree topology and clade support values, therefore, seems important in cases of sparse or unbalanced taxon sampling or when assessing the phylogenetic affinity of previously unsampled taxa when lineage-specific biases in base composition or evolutionary rate are more difficult to detect.

Key words::

• Across-site rate variation
• Alignment partitioning
• Cymbella
• Cymbopleura
• Diatoms
• Geissleria
• Gomphonema
• Phylogeny
• Placoneis

ACKNOWLEDGEMENTS

TN and ECT thank the members of the Department of Cell Ultrastructure at the Limnological Institute, Siberian Branch of the Russian Academy of Sciences (Irkutsk, Russia) for their warm welcome and invaluable assistance in the field and laboratory. TN and ECT are especially grateful to Drs Michael A. Grachev and Yelena Likhoshway for their logistic support of this study. Tanya and Sergey Shishlyannikov, Asya Kostykovskaya, and Volodya Bulatov offered companionship and field assistance around Lake Baikal. Matt Ashworth and Sandra Pelc helped with scanning electron microscopy and data collection, respectively. The authors acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing HPC resources that have contributed to the research results reported within this paper (http://www.tacc.utexas.edu). This study was partially funded by NSF ATOL AToL0629564 (ECT), Blumberg fellowship (ECT), and USGS/NPS NRPP 141338 (SAS). TN thanks the Plant Biology Graduate program (UT Austin) for student research scholarships.

SUPPLEMENTARY DATA

Supplementary data associated with this article can be found online at http://dx.doi.org/10.2216/14-002.1.s1.