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      18S rDNA Phylogeny of Lamproderma and Allied Genera (Stemonitales, Myxomycetes, Amoebozoa)

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          Abstract

          The phylogenetic position of the slime-mould genus Lamproderma (Myxomycetes, Amoebozoa) challenges traditional taxonomy: although it displays the typical characters of the order Stemonitales, it appears to be sister to Physarales. This study provides a small subunit (18S or SSU) ribosomal RNA gene-based phylogeny of Lamproderma and its allies, with new sequences from 49 specimens in 12 genera. We found that the order Stemonitales and Lamproderma were both ancestral to Physarales and that Lamproderma constitutes several clades intermingled with species of Diacheopsis, Colloderma and Elaeomyxa. We suggest that these genera may have evolved from Lamproderma by multiple losses of fruiting body stalks and that many taxonomic revisions are needed. We found such high genetic diversity within three Lamproderma species that they probably consist of clusters of sibling species. We discuss the contrasts between genetic and morphological divergence and implications for the morphospecies concept, highlighting the phylogenetically most reliable morphological characters and pointing to others that have been overestimated. In addition, we showed that the first part (∼600 bases) of the SSU rDNA gene is a valuable tool for phylogeny in Myxomycetes, since it displayed sufficient variability to distinguish closely related taxa and never failed to cluster together specimens considered of the same species.

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          Most cited references67

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          MRBAYES: Bayesian inference of phylogenetic trees.

          The program MRBAYES performs Bayesian inference of phylogeny using a variant of Markov chain Monte Carlo. MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html.
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            The general stochastic model of nucleotide substitution.

            DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases.
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              Simultaneous Assessment of Soil Microbial Community Structure and Function through Analysis of the Meta-Transcriptome

              Background Soil ecosystems harbor the most complex prokaryotic and eukaryotic microbial communities on Earth. Experimental approaches studying these systems usually focus on either the soil community's taxonomic structure or its functional characteristics. Many methods target DNA as marker molecule and use PCR for amplification. Methodology/Principal Findings Here we apply an RNA-centered meta-transcriptomic approach to simultaneously obtain information on both structure and function of a soil community. Total community RNA is random reversely transcribed into cDNA without any PCR or cloning step. Direct pyrosequencing produces large numbers of cDNA rRNA-tags; these are taxonomically profiled in a binning approach using the MEGAN software and two specifically compiled rRNA reference databases containing small and large subunit rRNA sequences. The pyrosequencing also produces mRNA-tags; these provide a sequence-based transcriptome of the community. One soil dataset of 258,411 RNA-tags of ∼98 bp length contained 193,219 rRNA-tags with valid taxonomic information, together with 21,133 mRNA-tags. Quantitative information about the relative abundance of organisms from all three domains of life and from different trophic levels was obtained in a single experiment. Less frequent taxa, such as soil Crenarchaeota, were well represented in the data set. These were identified by more than 2,000 rRNA-tags; furthermore, their activity in situ was revealed through the presence of mRNA-tags specific for enzymes involved in ammonia oxidation and CO2 fixation. Conclusions/Significance This approach could be widely applied in microbial ecology by efficiently linking community structure and function in a single experiment while avoiding biases inherent in other methods.
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                Author and article information

                Contributors
                Role: Editor
                Journal
                PLoS One
                PLoS ONE
                plos
                plosone
                PLoS ONE
                Public Library of Science (San Francisco, USA )
                1932-6203
                2012
                18 April 2012
                : 7
                : 4
                : e35359
                Affiliations
                [1 ]Institute of Botany and Landscape Ecology, University of Greifswald, Greifswald, Germany
                [2 ]The Institute of Low Temperature Science, Hokkaido University, Sapporo, Japan
                [3 ]Le Bayet, Rognaix, France
                [4 ]Zoology Department, University of Oxford, Oxford, United Kingdom
                University of Florida, United States of America
                Author notes

                Conceived and designed the experiments: AMF-D MM. Performed the experiments: AMF-D AK. Analyzed the data: AMF-D. Contributed reagents/materials/analysis tools: MS MF TC-S. Wrote the paper: AMF-D. Proofread the manuscript: AK MM MS MF TC-S.

                Article
                PONE-D-11-25444
                10.1371/journal.pone.0035359
                3329430
                22530009
                6b62a763-37d6-4143-a737-2459e3ba66e3
                Fiore-Donno et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
                History
                : 16 December 2011
                : 14 March 2012
                Page count
                Pages: 10
                Categories
                Research Article
                Biology
                Evolutionary Biology
                Evolutionary Systematics
                Molecular Systematics
                Phylogenetics
                Genetics
                Population Genetics
                Genetic Polymorphism
                Microbiology
                Protozoology
                Protozoan Classification
                Slime Molds
                Myxomycota

                Uncategorized
                Uncategorized

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