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

REFERENCES

• Alverson A.J., Jansen R.K. & Theriot E.C. 2007. Bridging the Rubicon: phylogenetic analysis reveals repeated colonizations of marine and fresh waters by thalassiosiroid diatoms. Molecular Phylogenetics and Evolution 45: 193–210.
   PubMed Web of Science ®Google Scholar
• Brown J.M. & Lemmon A.R. 2007. The importance of data partitioning and the utility of Bayes factors in Bayesian phylogenetics. Systematic Biology 56: 643–655.
   PubMed Web of Science ®Google Scholar
• Brown J.M., Hedtke S.M., Lemmon A.R. & Lemmon E.M. 2010. When trees grow too long: investigating the causes of highly inaccurate Bayesian branch-length estimates. Systematic Biology 59: 145–161.
   PubMed Web of Science ®Google Scholar
• Bruder K. & Medlin L.K. 2007. Molecular assessment of phylogenetic relationships in selected species/genera in the naviculoid diatoms (Bacillariophyta). I. The genus Placoneis. Nova Hedwigia 85: 331–352.
   Web of Science ®Google Scholar
• Cannone J.J., Subramanian S., Schnare M.N., Collett J.R., D'souza L.M., Du Y., Feng B., Lin N., Madabusi L.V., Müller K.M., Pande N., Shang Z., Yu N. & Gutell R.R. 2002. The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3: 2.
   PubMed Web of Science ®Google Scholar
• Cox E.J. 1987. Placoneis Mereschkowsky: the re-evaluation of a diatom genus originally characterized by its chloroplast type. Diatom Research 2: 145–157.
   Google Scholar
• Cox E.J. & Williams D.M. 2006. Systematics of naviculoid diatoms (Bacillariophyta): a preliminary analysis of protoplast and frustule characters for family and order level classification. Systematics and Biodiversity 4: 385–399.
   Web of Science ®Google Scholar
• Cummins C.A. & McInerney J.O. 2011. A method for inferring the rate of evolution of homologous characters that can potentially improve phylogenetic inference, resolve deep divergence and correct systematic biases. Systematic Biology 60: 833–844.
   Web of Science ®Google Scholar
• Czarnecki D.B. 1987. Freshwater diatom culture collection at Loras College, Dubuque, Iowa. Notulae Naturae 465: 1–16.
   Google Scholar
• Guiry M.D. & Guiry G.M. 2013. AlgaeBase. World-wide electronic publication, National university of Ireland, Galway. http://www.algaebase.org; searched on 09 December 2013.
   Google Scholar
• Huelsenbeck J.P., Larget B. & Alfaro M.E. 2004. Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo. Molecular Biology and Evolution 21: 1123–1133.
   PubMed Web of Science ®Google Scholar
• Jones H.M., Simpson G.E., Stickle A.J. & Mann D.G. 2005. Life history and systematics of Petroneis (Bacillariophyta), with special reference to British waters. European Journal ofPhycology 40: 61–87.
   Web of Science ®Google Scholar
• Kermarrec L., Ector L., Bouchez A., Rimet F. & Hoffmann L. 2011. A preliminary phylogenetic analysis of the Cymbellales based on 18S rDNA gene sequencing. Diatom Research 26: 305–315.
   Web of Science ®Google Scholar
• Kilham S., Kreeger D. & Lynn S. 1998. COMBO: a defined freshwater culture medium for algae and zooplankton. Hydrobiologia 147–159.
   Google Scholar
• Kociolek J.P. & Stoermer E.F. 1986. Phylogenetic relationships and classification of monoraphid diatoms based on phenetic and cladistic methodologies. Phycologia 25: 297–303.
   Web of Science ®Google Scholar
• Kociolek J.P. & Stoermer E.F. 1988. A preliminary investigation of the phylogenetic relationships among the freshwater, apical pore field-bearing cymbelloid and gomphonemoid diatoms (Bacillariophyceae). Journal of Phycology 24: 377–385.
   Web of Science ®Google Scholar
• Kociolek J.P. & Stoermer E.F. 1989. Phylogenetic relationships and evolutionary history of the diatom genus Gomphoneis. Phycologia 28: 438–454.
   Web of Science ®Google Scholar
• Kociolek J.P. & Stoermer E.F. 1993. Freshwater gomphonemoid diatom phylogeny: preliminary results. In: Twelfth international diatom symposium (Ed. by H. Van Dam), pp. 31–38. Springer, Dordrecht, the Netherlands.
   Google Scholar
• Krammer K. 2003. Cymbopleura, Delicata, Navicymbula, Gomphocymbellopsis, Afrocymbella. In: Diatoms of Europe, vol. 4 (Ed. by H. Lange-Bertalot), pp. 529. ARG Gantner Verlag, Ruggel, Liechtenstein.
   Google Scholar
• Krammer K. & Lange-Bertalot H. 1986. Bacillariophyceae. Teil 1: Naviculaceae. In: Süwasserflora von Mitteleuropa (Ed. by H. Ettl, J. Gerloff, H. Heynig & D. Mollenhauer), pp. 879. Gustaf Fischer Verlag, Stuttgart, Germany.
   Google Scholar
• Lanfear R., Calcott B., Ho S.Y.W. & Guindon S. 2012. PartitionFinder: combined selection of partitioning schemes and substitution models for phylogenetic analyses. Molecular Biology and Evolution 29: 1695–1701.
   PubMed Web of Science ®Google Scholar
• Lange-Bertalot H. & Metzeltin D. 1996. Indicators of oligotrophy. In: Iconographia Diatomologica, vol. 2 (Ed. by H. Lange-Bertalot), pp. 390. ARG Gantner Verlag, Ruggel, Liechtenstein.
   Google Scholar
• Lartillot N. & Philippe H. 2004. A bayesian mixture model for across-site heterogeneities in the amino-acid replacement process. Molecular Biology and Evolution 21: 1095–1109.
   PubMed Web of Science ®Google Scholar
• Lartillot N., Brinkmann H. & Philippe H. 2007. Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model. BMC Evolutionary Biology 7: S4.
   PubMed Web of Science ®Google Scholar
• Lartillot N., Rodrigue N., Stubbs D. & Richer J.H. 2013. PhyloBayes MPI: phylogenetic reconstruction with infinite mixtures of profiles in a parallel environment. Systematic Biology 62: 611–615.
   PubMed Web of Science ®Google Scholar
• Mann D.G. & Stickle A.J. 1995. Sexual reproduction and systematics of Placoneis (Bacillariophyta). Phycologia 34: 74–86.
   Web of Science ®Google Scholar
• Nawrocki E.P. 2009. Structural RNA homology search and alignment using covariance models. Washington University, St. Louis, Missouri, USA. pp. 282.
   Google Scholar
• Nawrocki E.P., Kolbe D.L. & Eddy S.R. 2009. Infernal 1.0: inference of RNA alignments. Bioinformatics 25: 1335–1337.
   PubMed Web of Science ®Google Scholar
• Nylander J.A.A., Wilgenbusch J.C., Warren D.L. & Swofford D.L. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24: 581–583.
   PubMed Web of Science ®Google Scholar
• Rajan V. 2013. A method of alignment masking for refining the phylogenetic signal of multiple sequence alignments. Molecular Biology and Evolution 30: 689–712.
   Web of Science ®Google Scholar
• Richlen M.L. & Barber P.H. 2005. A technique for the rapid extraction of microalgal DNA from single live and preserved cells. Molecular Ecology Notes 5: 688–691.
   Web of Science ®Google Scholar
• Ronquist F., Teslenko M., Van Der Mark P., Ayres D.L., Darling A., Höhna S., Larget B., Liu L., Suchard M.A. & Huelsenbeck J.P. 2012. MrBayes 3.2: Efficient Bayesian phylogenetic inference and model choice across a large model space. Systematic Biology 61: 539–542.
   PubMed Web of Science ®Google Scholar
• Round F.E., Crawford R.M. & Mann D.G. 1990. The diatoms. Biology and morphology of the genera. Cambridge University Press, Cambridge, UK. 747 pp.
   Google Scholar
• Ruck E.C. & Theriot E.C. 2011. Origin and evolution of the canal raphe system in diatoms. Protist 162: 723–737.
   PubMed Web of Science ®Google Scholar
• Sperling E.A., Peterson K.J. & Pisani D. 2009. Phylogenetic-signal dissection of nuclear housekeeping genes supports the paraphyly of sponges and the monophyly of eumetazoa. Molecular Biology and Evolution 26: 2261–2274.
   Web of Science ®Google Scholar
• Stabelli O.R., Lartillot N., Philippe H. & Pisani D. 2013. Serine codon usage bias in deep phylogenomics: pancrustacean relationships as a case study. Systematic Biology 62: 121–133.
   Web of Science ®Google Scholar
• Sullivan J. & Swofford D.L. 1997. Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics. Journal of Mammalian Evolution 4: 77–86.
   Google Scholar
• Theriot E.C., Cannone J.J., Gutell R.R. & Alverson A.J. 2009. The limits of nuclear-encoded SSU rDNA for resolving the diatom phylogeny. European Journal of Phycology 44: 277–290.
   PubMed Web of Science ®Google Scholar
• Will S., Reiche K., Hofacker I.L., Stadler P.F. & Backofen R. 2007. Inferring noncoding RNA families and classes by means of genome-scale structure-based clustering. PLoS Computational Biology 3(4): e65. doi:10.1371/journal.pcbi.0030065
   Web of Science ®Google Scholar
• Yang Z. 1996. Among-site rate variation and its impact on phylogenetic analyses. Trends in Ecology and Evolution 11: 367–372.
   PubMed Web of Science ®Google Scholar