SILVA (from Latin silva, forest, http://www.arb-silva.de) is a comprehensive resource for up-to-date quality-controlled databases of aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains and supplementary online services. SILVA provides a manually curated taxonomy for all three domains of life, based on representative phylogenetic trees for the small- and large-subunit rRNA genes. This article describes the improvements the SILVA taxonomy has undergone in the last 3 years. Specifically we are focusing on the curation process, the various resources used for curation and the comparison of the SILVA taxonomy with Greengenes and RDP-II taxonomies. Our comparisons not only revealed a reasonable overlap between the taxa names, but also points to significant differences in both names and numbers of taxa between the three resources.

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The SILVA and "All-species Living Tree Project (LTP)" taxonomic frameworks.

A catalogue record for this book is available from the British Library ISBN 0 521 82347 1 hardback ISBN 0 521 53032 6 paperback Contents List of tables page vii Preface to the second edition ix Preface to the first edition xii 1 Why a global language? 1 What is a global language? 3 What makes a global language? 7 Why do we need a global language? 11 What are the dangers of a global language? 14 Could anything stop a global language? 25 A critical era 27 2 Why English? The historical context 29 Origins 30 America 31 Canada 36 The Caribbean 39 Australia and New Zealand 40 South Africa 43 South Asia 46 Former colonial Africa 49 Southeast Asia and the South Pacific 54 A world view 59 v Contents

English as a global language

Changes in the global production of major crops are important drivers of food prices, food security and land use decisions. Average global yields for these commodities are determined by the performance of crops in millions of fields distributed across a range of management, soil and climate regimes. Despite the complexity of global food supply, here we show that simple measures of growing season temperatures and precipitation—spatial averages based on the locations of each crop—explain ∼30% or more of year-to-year variations in global average yields for the world’s six most widely grown crops. For wheat, maize and barley, there is a clearly negative response of global yields to increased temperatures. Based on these sensitivities and observed climate trends, we estimate that warming since 1981 has resulted in annual combined losses of these three crops representing roughly 40 Mt or $5 billion per year, as of 2002. While these impacts are small relative to the technological yield gains over the same period, the results demonstrate already occurring negative impacts of climate trends on crop yields at the global scale.

https://iopscience.iop.org/article/10.1088/1748-9326/2/1/014002/pdf

Global Scale Climate-Crop Yield Relationships and the Impacts of Recent Warming

This revision of the classification of unicellular eukaryotes updates that of Levine et al. (1980) for the protozoa and expands it to include other protists. Whereas the previous revision was primarily to incorporate the results of ultrastructural studies, this revision incorporates results from both ultrastructural research since 1980 and molecular phylogenetic studies. We propose a scheme that is based on nameless ranked systematics. The vocabulary of the taxonomy is updated, particularly to clarify the naming of groups that have been repositioned. We recognize six clusters of eukaryotes that may represent the basic groupings similar to traditional ''kingdoms.'' The multicellular lineages emerged from within monophyletic protist lineages: animals and fungi from Opisthokonta, plants from Archaeplastida, and brown algae from Stramenopiles.

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The new higher level classification of eukaryotes with emphasis on the taxonomy of protists

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.

https://onlinelibrary.wiley.com/doi/pdf/10.1111/j.1550-7408.2012.00644.x

The revised classification of eukaryotes

David J. Patterson & Jacob Larsen: General introduction Tom Fenchel: Flagellate design and function Robert W. Sanders: Trophic strategies among heterotrophic flagellates Ulrike-G. Berninger, David A. Caron, Robert W. Saunders, & Bland J. Finlay: Heterotrophic flagellates of planktonic communities: their characteristics and methods of study Daniel M. Alongi: Flagellates of benthic communities: characteristics and methods of study David A. Caron: Heterotrophic flagellates associated with sedimenting detritus Wilhelm Foissner: Diversity and ecology of soil flagellates T. Cavalier-Smith: Cell diversification in heterotrophic flagellates G. Brugerolle: Cell organization in amitochondrial free-living heterotrophic flagellates A.P. Mylnikov: Diversity of flagellates without mitochondria Keith Vickerman: Organization of the bodonid flagellates B.F. Zhukov: The diversity of bodonids Richard E. Triemer & Mark A. Farmer: Ultrastructural organization of the heterotrophic euglenids and its evolutionary implications Jacob Larsen & David J. Patterson: The diversity of heterotrophic euglenids Paul Krugens & Robert E. Lee: Organization of cryptomonads David R.A. Hill: Diversity of heterotrophic cryptomonads Barry S.C. Leadbeater: Choanoflagellate organization with special reference to loricate taxa Helge A. Thomsen & Kurt R. Buck: Choanoflagellate diversity with particular emphasis on the Acanthoecidae Keith R. Roberts: The flagellar apparatus and cytoskeleton of dinoflagellates: organization and use in systematics Malte Elbrachter: Food uptake mechanisms in phagotrophic dinoflagellates and classification Jacob Larsen & Alain Sournia: The diversity of heterotrophic dinoflagellates Ojvind Moestrup & Robert A. Andersen: Organization of heterotrophic heterokonts H.R. Preisig, N. Vors & G. Hallfors: Diversity of heterotrophic heterokont flagellates J.C. Green: Phagotrophy in prymnesiophyte flagellates Stephen T. Moss: Thraustochytrids and other zoosporic marine fungi David J. Patterson & Michael Zolffel: Heterotrophic flagellates of uncertain taxonomic position Andrew J. Cowling: Free-living heterotrophic flagellates: methods of isolation and maintenance, including sources of strains in culture Index.

The Biology of free-living heterotrophic flagellates

The discipline of evolutionary protistology has emerged in the past 30 yr. There is as yet no agreed view of how protists are interrelated or how they should be classified. The foundations of a stable taxonomic superstructure for the protists and other eukaryotes lie in cataloging the diversity of the major monophyletic lineages of these organisms. The use of common patterns of cell organization (ultrastructural identity) seems to provide us with the most robust hypotheses of such lineages. These lineages are placed in 71 groups without identifiable sister taxa. These groups are here referred to as “major building blocks.” For the first time, the compositions, ultrastructural identities, synapomorphies (where available), and subgroups of the major building blocks are summarized. More than 200 further lineages without clear identities are listed. This catalog includes all known major elements of the comprehensive evolutionary tree of protists and eukaryotes. Different approaches among protistolog...

https://www.jstor.org/stable/10.1086/303287

The diversity of eukaryotes

An account is given of 114 new or otherwise interesting species of benthic marine flagellates from Fiji, Northern Australia (Queensland), Hawaii, Panama and Brazil. Most species are heterotrophs drawn from the euglendis, dinoflagellates, kinetoplastids, bicosoecids, heteroloboseids, and a variety of taxa of uncertain affinities. The work emphasizes the rich variety of protist taxa in marine benthic sites. New names are Amphidinium corrugatum, Anisonema glaciale, Bodo cephalophorus, B. platyrhynchus, B. saliens, Bordnamonas tropicana, Cafeteria ligulifera, C. marsupialis, C. minuta (Ruinen, 1938) nov. comb., Cryptaulax elegans, Dinematomonas inaequalis = Dinema inaequale, Dinematomonas maculata (= Dinema maculatum), Dinematononas valida (= Dinema validum), Diplonema ambulator, Diplonema metabolicum, Discocelis punctata, Dolium sedentarium, Goniomonas amphinema, Goniomonas pacifica, Gyrodinium oblongum, Heteronema exaratum, H. splendens, H. vittatum, Mastigamoeba psammobis, M. skujae nom. nov., Massisteria ...

Some flagellates (Protista) from tropical marine sediments

This chapter deals with sensitivities, adaptive capacity and vulnerability of agriculture to climate change. It covers: the direct and indirect effects of changes in climate and atmospheric constituents on crop yield, soils, agricultural pests, and livestock; estimates of yield and production changes for specific localities, countries, and the world; the conditions that determine vulnerability; and adaptation potential.

Agriculture in a changing climate: impacts and adaptation

An accurate reconstruction of the eukaryotic tree of life is essential to identify the innovations underlying the diversity of microbial and macroscopic (e.g., plants and animals) eukaryotes. Previous work has divided eukaryotic diversity into a small number of high-level “supergroups,” many of which receive strong support in phylogenomic analyses. However, the abundance of data in phylogenomic analyses can lead to highly supported but incorrect relationships due to systematic phylogenetic error. Furthermore, the paucity of major eukaryotic lineages (19 or fewer) included in these genomic studies may exaggerate systematic error and reduce power to evaluate hypotheses. Here, we use a taxon-rich strategy to assess eukaryotic relationships. We show that analyses emphasizing broad taxonomic sampling (up to 451 taxa representing 72 major lineages) combined with a moderate number of genes yield a well-resolved eukaryotic tree of life. The consistency across analyses with varying numbers of taxa (88–451) and levels of missing data (17–69%) supports the accuracy of the resulting topologies. The resulting stable topology emerges without the removal of rapidly evolving genes or taxa, a practice common to phylogenomic analyses. Several major groups are stable and strongly supported in these analyses (e.g., SAR, Rhizaria, Excavata), whereas the proposed supergroup “Chromalveolata” is rejected. Furthermore, extensive instability among photosynthetic lineages suggests the presence of systematic biases including endosymbiotic gene transfer from symbiont (nucleus or plastid) to host. Our analyses demonstrate that stable topologies of ancient evolutionary relationships can be achieved with broad taxonomic sampling and a moderate number of genes. Finally, taxon-rich analyses such as presented here provide a method for testing the accuracy of relationships that receive high bootstrap support (BS) in phylogenomic analyses and enable placement of the multitude of lineages that lack genome scale data.

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David J. Patterson

Papers

The Biology of free-living heterotrophic flagellates

The diversity of eukaryotes

Some flagellates (Protista) from tropical marine sediments

Agriculture in a changing climate: impacts and adaptation

Broadly Sampled Multigene Analyses Yield a Well-Resolved Eukaryotic Tree of Life