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      Establishing macroecological trait datasets: digitalization, extrapolation, and validation of diet preferences in terrestrial mammals worldwide

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          Abstract

          Ecological trait data are essential for understanding the broad-scale distribution of biodiversity and its response to global change. For animals, diet represents a fundamental aspect of species’ evolutionary adaptations, ecological and functional roles, and trophic interactions. However, the importance of diet for macroevolutionary and macroecological dynamics remains little explored, partly because of the lack of comprehensive trait datasets. We compiled and evaluated a comprehensive global dataset of diet preferences of mammals (“MammalDIET”). Diet information was digitized from two global and cladewide data sources and errors of data entry by multiple data recorders were assessed. We then developed a hierarchical extrapolation procedure to fill-in diet information for species with missing information. Missing data were extrapolated with information from other taxonomic levels (genus, other species within the same genus, or family) and this extrapolation was subsequently validated both internally (with a jack-knife approach applied to the compiled species-level diet data) and externally (using independent species-level diet information from a comprehensive continentwide data source). Finally, we grouped mammal species into trophic levels and dietary guilds, and their species richness as well as their proportion of total richness were mapped at a global scale for those diet categories with good validation results. The success rate of correctly digitizing data was 94%, indicating that the consistency in data entry among multiple recorders was high. Data sources provided species-level diet information for a total of 2033 species (38% of all 5364 terrestrial mammal species, based on the IUCN taxonomy). For the remaining 3331 species, diet information was mostly extrapolated from genus-level diet information (48% of all terrestrial mammal species), and only rarely from other species within the same genus (6%) or from family level (8%). Internal and external validation showed that: (1) extrapolations were most reliable for primary food items; (2) several diet categories (“Animal”, “Mammal”, “Invertebrate”, “Plant”, “Seed”, “Fruit”, and “Leaf”) had high proportions of correctly predicted diet ranks; and (3) the potential of correctly extrapolating specific diet categories varied both within and among clades. Global maps of species richness and proportion showed congruence among trophic levels, but also substantial discrepancies between dietary guilds. MammalDIET provides a comprehensive, unique and freely available dataset on diet preferences for all terrestrial mammals worldwide. It enables broad-scale analyses for specific trophic levels and dietary guilds, and a first assessment of trait conservatism in mammalian diet preferences at a global scale. The digitalization, extrapolation and validation procedures could be transferable to other trait data and taxa.

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          Rebuilding community ecology from functional traits.

          There is considerable debate about whether community ecology will ever produce general principles. We suggest here that this can be achieved but that community ecology has lost its way by focusing on pairwise species interactions independent of the environment. We assert that community ecology should return to an emphasis on four themes that are tied together by a two-step process: how the fundamental niche is governed by functional traits within the context of abiotic environmental gradients; and how the interaction between traits and fundamental niches maps onto the realized niche in the context of a biotic interaction milieu. We suggest this approach can create a more quantitative and predictive science that can more readily address issues of global change.
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            Multiple causes of high extinction risk in large mammal species.

            Many large animal species have a high risk of extinction. This is usually thought to result simply from the way that species traits associated with vulnerability, such as low reproductive rates, scale with body size. In a broad-scale analysis of extinction risk in mammals, we find two additional patterns in the size selectivity of extinction risk. First, impacts of both intrinsic and environmental factors increase sharply above a threshold body mass around 3 kilograms. Second, whereas extinction risk in smaller species is driven by environmental factors, in larger species it is driven by a combination of environmental factors and intrinsic traits. Thus, the disadvantages of large size are greater than generally recognized, and future loss of large mammal biodiversity could be far more rapid than expected.
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              Lymphoid tissue genesis induced by commensals through NOD1 regulates intestinal homeostasis.

              Intestinal homeostasis is critical for efficient energy extraction from food and protection from pathogens. Its disruption can lead to an array of severe illnesses with major impacts on public health, such as inflammatory bowel disease characterized by self-destructive intestinal immunity. However, the mechanisms regulating the equilibrium between the large bacterial flora and the immune system remain unclear. Intestinal lymphoid tissues generate flora-reactive IgA-producing B cells, and include Peyer's patches and mesenteric lymph nodes, as well as numerous isolated lymphoid follicles (ILFs). Here we show that peptidoglycan from Gram-negative bacteria is necessary and sufficient to induce the genesis of ILFs in mice through recognition by the NOD1 (nucleotide-binding oligomerization domain containing 1) innate receptor in epithelial cells, and beta-defensin 3- and CCL20-mediated signalling through the chemokine receptor CCR6. Maturation of ILFs into large B-cell clusters requires subsequent detection of bacteria by toll-like receptors. In the absence of ILFs, the composition of the intestinal bacterial community is profoundly altered. Our results demonstrate that intestinal bacterial commensals and the immune system communicate through an innate detection system to generate adaptive lymphoid tissues and maintain intestinal homeostasis.
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                Author and article information

                Journal
                Ecol Evol
                Ecol Evol
                ece3
                Ecology and Evolution
                Blackwell Publishing Ltd (Oxford, UK )
                2045-7758
                2045-7758
                July 2014
                16 June 2014
                : 4
                : 14
                : 2913-2930
                Affiliations
                [1 ]Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam P.O. Box 94248, 1090 GE, Amsterdam, The Netherlands
                [2 ]Section for Wildlife Ecology and Section for Biodiversity, Department of Bioscience, Aarhus University Grenåvej 14, DK-8410, Rønde, Denmark
                [3 ]Unité de Recherche Ecologie et Dynamique des Systèmes Anthropisés (EDYSAN, FRE 3498 CNRS-UPJV), Université de Picardie Jules Verne 1 Rue des Louvels, F-80037, Amiens Cedex, France
                [4 ]Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University Ny Munkegade 114, DK-08000, Aarhus C, Denmark
                [5 ]Department of Zoology, University of Oxford, Wildlife Conservation Research Unit, The Recanati-Kaplan Centre Tubney House, Abingdon Road, Tubney, Abingdon, OX13 5QL, U.K
                [6 ]Section for Genetics, Ecology and Evolution, Department of Bioscience, Aarhus University Ny Munkegade 114, DK-8000, Aarhus C, Denmark
                Author notes
                Wilm Daniel Kissling; Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, P.O. Box 94248, 1090 GE Amsterdam, The Netherlands. Tel: +31 (0)20 525 8423; Fax: +31 (0)20 525 7832; E-mail: danielkissling@ 123456web.de

                Funding Information This study was supported by the Villum Kann Rasmussen Foundation, the Danish Council for Independent Research | Natural Sciences, MADALGO – Center for Massive Data Algorithmics, the Center for Interdisciplinary Geospatial Informatics Research (CIGIR), the 15. Juni Fonden, Aarhus University, the University of Amsterdam (UvA), and the European Research Council.

                Article
                10.1002/ece3.1136
                4130448
                25165528
                1abd4599-b83e-4779-a835-2847c3e67342
                © 2014 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.

                This is an open access article under the terms of the Creative Commons Attribution License, which permits use, distribution and reproduction in any medium, provided the original work is properly cited.

                History
                : 07 February 2014
                : 08 May 2014
                : 13 May 2014
                Categories
                Original Research

                Evolutionary Biology
                diet ecology,ecological trait data,feeding guild,mammalia,phylogenetic conservatism,trophic structure

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