Showing papers by "Edward A. D. Mitchell published in 2012"
Dalhousie University1, University of Saskatchewan2, University of Rhode Island3, Sewanee: The University of the South4, Natural History Museum5, New York State Department of Health6, University of British Columbia7, Kaiserslautern University of Technology8, Charles University in Prague9, University of Guelph10, Le Moyne College11, Georgia College & State University12, University of Colorado Boulder13, University of Geneva14, Edinburgh Napier University15, University of Arkansas16, Saint Petersburg State University17
TL;DR: This revision of the classification of eukaryotes retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees.
Abstract: This revision of the classification of eukaryotes, which updates that of Adl et al. [J. Eukaryot. Microbiol. 52 (2005) 399], retains an emphasis on the protists and incorporates changes since 2005 that have resolved nodes and branches in phylogenetic trees. Whereas the previous revision was successful in re-introducing name stability to the classification, this revision provides a classification for lineages that were then still unresolved. The supergroups have withstood phylogenetic hypothesis testing with some modifications, but despite some progress, problematic nodes at the base of the eukaryotic tree still remain to be statistically resolved. Looking forward, subsequent transformations to our understanding of the diversity of life will be from the discovery of novel lineages in previously under-sampled areas and from environmental genomic information.
1,414 citations
University of Geneva1, Centre national de la recherche scientifique2, University of Saskatchewan3, Natural History Museum4, New York State Department of Health5, Charles University in Prague6, Kaiserslautern University of Technology7, University of Greifswald8, Dalhousie University9, Free University of Berlin10, Academy of Sciences of the Czech Republic11, University of British Columbia12, Sewanee: The University of the South13, Saint Petersburg State University14, Royal Botanic Garden Edinburgh15, University of Cologne16, Uppsala University17, University of New Brunswick18, Halifax19, National Institutes of Health20, University of Giessen21, National Museum of Natural History22
TL;DR: A group of protist experts proposes a two-step DNA barcoding approach, comprising a universal eukaryotic pre-barcode followed by group-specific barcodes, to unveil the hidden biodiversity of microbial Eukaryotes.
Abstract: Animals, plants, and fungi—the three traditional kingdoms of multicellular eukaryotic life—make up almost all of the visible biosphere, and they account for the majority of catalogued species on Earth [1]. The remaining eukaryotes have been assembled for convenience into the protists, a group composed of many diverse lineages, single-celled for the most part, that diverged after Archaea and Bacteria evolved but before plants, animals, or fungi appeared on Earth. Given their single-celled nature, discovering and describing new species has been difficult, and many protistan lineages contain a relatively small number of formally described species (Figure 1A), despite the critical importance of several groups as pathogens, environmental quality indicators, and markers of past environmental changes. It would seem natural to apply molecular techniques such as DNA barcoding to the taxonomy of protists to compensate for the lack of diagnostic morphological features, but this has been hampered by the extreme diversity within the group. The genetic divergence observed between and within major protistan groups greatly exceeds that found in each of the three multicellular kingdoms. No single set of molecular markers has been identified that will work in all lineages, but an international working group is now close to a solution. A universal DNA barcode for protists coupled with group-specific barcodes will enable an explosion of taxonomic research that will catalyze diverse applications.
458 citations
TL;DR: In this article, the authors investigate the effect of size on the probability of between-continent dispersal using virtual microorganisms in a global model of the Earths atmosphere, and they find that the small size of microbes allows most microbial species to colonize all suitable sites around the globe or whether their ranges are limited by opportunities for dispersal.
Abstract: Aim We investigate the long-standing question of whether the small size of microbes allows most microbial species to colonize all suitable sites around the globe or whether their ranges are limited by opportunities for dispersal. In this study we use a modelling approach to investigate the effect of size on the probability of between-continent dispersal using virtual microorganisms in a global model of the Earths atmosphere.
214 citations
TL;DR: The results show that the traditional morphology-based taxonomy underestimates the diversity within the Nebela group, and that phylogenetic relationships are best inferred from shell shape rather than from the material used to build the shell.
100 citations
TL;DR: The performance of most testate amoeba-hydrology transfer functions is worse than previously assumed and reconstructions are more uncertain, so leave-one-site-out cross-validation and the cluster bootstrap are described as appropriate methods for clustered training-sets.
Abstract: Transfer functions are widely used in palaeoecology to infer past environmental conditions from fossil remains of many groups of organisms. In contrast to traditional training-set design with one observation per site, some training-sets, including those for peatland testate amoeba-hydrology transfer functions, have a clustered structure with many observations from each site. Here we show that this clustered design causes standard performance statistics to be overly optimistic. Model performance when applied to independent data sets is considerably weaker than suggested by statistical cross-validation. We discuss the reasons for these problems and describe leave-one-site-out cross-validation and the cluster bootstrap as appropriate methods for clustered training-sets. Using these methods we show that the performance of most testate amoeba-hydrology transfer functions is worse than previously assumed and reconstructions are more uncertain.
55 citations
TL;DR: Functional traits offer a new framework to understand the ecology of organisms and overcome taxonomic difficulties that currently limit the study of minute soil taxa and promising candidates include the relationships between shell biovolume and vegetation structure and between shell compression and plant litter input variables.
54 citations
Wageningen University and Research Centre1, Uppsala University2, VU University Amsterdam3, University of Ferrara4, École Polytechnique Fédérale de Lausanne5, Swiss Federal Institute for Forest, Snow and Landscape Research6, Macaulay Institute7, Mount Holyoke College8, McGill University9, Laval University10, University of Franche-Comté11, Radboud University Nijmegen12, Centre national de la recherche scientifique13, Swedish University of Agricultural Sciences14, University of Alberta15, Norwegian Forest and Landscape Institute16, University of Giessen17, Tallinn University18, Southern Illinois University Carbondale19
TL;DR: Although glasshouse experiments are reliable proxies for field experiments for assessing interactions between N deposition and environment as controls on Sphagnum N concentration and production, field experiments are needed to properly quantify these effects.
Abstract: • Peat bogs have accumulated more atmospheric carbon (C) than any other terrestrial ecosystem today. Most of this C is associated with peat moss (Sphagnum) litter. Atmospheric nitrogen (N) deposition can decrease Sphagnum production, compromising the C sequestration capacity of peat bogs. The mechanisms underlying the reduced production are uncertain, necessitating multifactorial experiments. • We investigated whether glasshouse experiments are reliable proxies for field experiments for assessing interactions between N deposition and environment as controls on Sphagnum N concentration and production. We performed a meta-analysis over 115 glasshouse experiments and 107 field experiments. • We found that glasshouse and field experiments gave similar qualitative and quantitative estimates of changes in Sphagnum N concentration in response to N application. However, glasshouse-based estimates of changes in production – even qualitative assessments – diverged from field experiments owing to a stronger N effect on production response in absence of vascular plants in the glasshouse, and a weaker N effect on production response in presence of vascular plants compared to field experiments. • Thus, although we need glasshouse experiments to study how interacting environmental factors affect the response of Sphagnum to increased N deposition, we need field experiments to properly quantify these effects.
53 citations
TL;DR: Most arcellinids are divided into two major clades, the genus Difflugia is not monophyletic, and the genera Netzelia and Arcella are closely related, and CryptodifflUGia branches at the base of the Arcellinida clade.
51 citations
TL;DR: The results show that testate amoebae are widely encountered in Quaternary palynological studies, primarily in peatlands, but the information which they can provide is undermined by limited taxonomic knowledge.
44 citations
TL;DR: The data suggest that diatoms and testate amoebae are sensitive to farming systems, and molecular tools would be very useful for further development of the use of protists in bioindication.
39 citations
TL;DR: The distribution of earthworm traits varied among habitats in relation to changes in flooding frequency: poorly developed gravel bar soils most exposed to flooding were characterised by high abundance of small epigeic species and low abundance of large anecic species, which were identified as indicators of soil development in floodplains.
TL;DR: It is demonstrated that, by combining the foci of different nomenclature codes with the current knowledge of relationships, a large number of genera and species end up being regulated by two codes (Patterson's ambiregnal taxa) and, in some cases, may even be regulated by none.
Abstract: Nomenclature of microbial eukaryotes has been historically relegated to secondary importance. This is a legacy of the traditional classification of life into the most studied multicellular forms (plants, fungi, and animals). Despite the revolution in an understanding of eukaryotic diversity and relationships that has been achieved as a result of the use of molecular techniques, the description of microbial eukaryote genera and species is more difficult today than in the past. Researchers are at liberty to choose between the botanical (in the traditional sense) and zoological codes of nomenclature, although there is no obligation to comply with either. We demonstrate that, by combining the foci of different nomenclature codes with the current knowledge of relationships, a large number of genera and species end up being regulated by two codes (Patterson's ambiregnal taxa) and, in some cases, may even be regulated by none. We briefly present historically proposed types of solutions to this problem, and propose that an elaboration of authoritative guidelines to regulate the nomenclature of microbial eukaryotes by the community of researchers is most appropriate at this time. Most importantly, we plead to the community of researchers to resolve this centuries old outstanding issue. © 2012 The Linnean Society of London, Biological Journal of the Linnean Society, 2012, 107, 469–476.
TL;DR: In this article, the authors applied testate amoeba transfer functions to the results of experiments adding pollutants (N, P, S, Pb, O3) to peatlands and similar ecosystems.
Journal Article•
University of Geneva1, Centre national de la recherche scientifique2, University of Saskatchewan3, Natural History Museum4, New York State Department of Health5, Charles University in Prague6, Kaiserslautern University of Technology7, University of Greifswald8, Dalhousie University9, Free University of Berlin10, Academy of Sciences of the Czech Republic11, University of British Columbia12, Sewanee: The University of the South13, Royal Botanic Garden Edinburgh14, University of Cologne15, Uppsala University16, University of New Brunswick17, Halifax18, Saint Petersburg State University19, University of Giessen20, National Museum of Natural History21
01 Apr 2012
TL;DR: In this paper, the authors present an analysis of biogeography and palaeoecology at the Adam Mickiewicz University in Poznan, Poland, where the authors propose a method for the identification of the boundary between ecosystems and biogeographies.
Abstract: (1) Adam Mickiewicz University, Department of Biogeography and Palaeoecology, Poznan, Poland (mariuszl@amu.edu.pl), (2) Swiss Federal Research Institute WSL, Ecosystem Boundaries Research Unit, Wetlands Research Group, Station 2, CH–1015 Lausanne, Switzerland, (3) École Polytechnique Fédérale de Lausanne (EPFL), Laboratoire des Systèmes Écologiques, Station 2, CH–1015 Lausanne, Switzerland, (4) Laboratory of Soil Biology, Institute of Biology, University of Neuchâtel, CH–2000 Neuchâtel, Switzerland 5Department of Biology and Evolution, University of Ferrara, Ferrara, Italy, (5) Poznan University of Life Sciences, Department of Agrometeorology, Poznan Poland, (6) Institute of Technology and Life Sciences, Regional Research Division in Bydgoszcz, Glinki 60, 85-174 Bydgoszcz, Poland, (7) Department of Environmental Resources and Geohazard, Institute of Geography and Spatial Organization, Polish Academy of Sciences, Kopernika 19, 87-100 Toruń, Poland