sPlot – the global vegetation-plot database

Vegetation-plot databases contain biodiversity data on presence and relative abundance of plants co- occurring in the same community. Compared to databases based on occurrence records of individual species aggregated at the level of grid cells, vegetation-plot databases have the advantage of providing information on species relative cover, co-occurrences, and to provide more reliable information on true absences. Although large collections of plant community data are now available at national to regional level, they are rarely accessible at continental or global extents, as their compilation is technically and conceptually challenging, due to different data formats and taxonomical nomenclatures used. Here we present the sPlot database, which merges and standardizes data contributed by more than 100 regional, national and continental databases, and contains records from 1,121,244 vegetation plots, for a total of 23,586,216 plant species entries with relative cover or abundance. All plots are georeferenced, although with varying precision, their size varies from less than 1 m 2 to 25 ha, and span from year 1885 to 2015. The vegetation-plot data are stored in a SQLite database, managed with TURBOVEG v3 software, and further processed in R for data integration and analysis. In order to make sPlot suitable for the exploration of global patterns in taxonomic, functional and phylogenetic diversity at the plant community level we performed three steps. 1) We standardized the species lists of the different databases in sPlot through the construction of a taxonomic backbone using existing databases on accepted plant species names. 2) We calculated functional attributes of each plot (community-weighted means and variances of traits) using gap-filled data from the global plant trait database TRY. 3) We generated a phylogeny for 50,167 out of the 54,519 vascular plant species occurring in sPlot. Finally, in addition to the information provided by the data owners, we retrieved for each plot information on environmental conditions (i.e. climate, soil) and the biogeographic context (i.e. biomes) from external sources. sPlot provides a unique, integrated global repository of data that would otherwise be fragmented in unconnected and structurally inconsistent databases at national or regional level. We believe that sPlot can be the basis for a new generation of studies, not only to address fundamental ecological questions related to plant diversity patterns or community assembly rules, but also to foster further development and testing of macroecological theories and as an information baseline for refining interdisciplinary conservation studies in a human-dominated, changing world. Further information: https://www.idiv.de/en/sdiv/working_groups/wg_pool/splot.htm

Grazers and fires: Their role in shaping the structure and functioning of the Río de la Plata Grasslands

Los Pastizales del Río de la Plata (PRP) son una de las áreas más extensas de ecosistemas abiertos (pastizales, arbustales y sabanas) del mundo. Históricamente, estos sistemas han experimentado, y lo siguen haciendo, una enorme pérdida de hábitats naturales. Más aun, en buena medida, su importancia ha sido invisibilizada frente a sistemas boscosos. El área remanente de ecosistemas abiertos (EA) varía según las fuentes del 38 al 58% del área original. Los EA son agroecosistemas particulares porque pueden combinar el suministro tanto de servicios ecosistémicos (SE) de provisión como de regulación y soporte. La maximización del suministro de SE en estos hábitats naturales depende, en parte, de comprender el papel de las dos principales perturbaciones que operan en ellos: el pastoreo y el fuego. Aunque estas dos perturbaciones son componentes naturales de los EA, son manipuladas por prácticas humanas. En este artículo revisamos el papel del pastoreo y el fuego en la estructura y el funcionamiento del PRP, partiendo de su papel durante el final del Pleistoceno y el Holoceno, y resumiendo evidencias de los efectos actuales del pastoreo y el fuego sobre la vegetación, la fauna y los procesos biogeoquímicos. Las evidencias muestran que los sistemas ganaderos en EA tienen, en dimensiones claves de la huella ambiental tales como la preservación de hábitats y la oferta de SE, el menor impacto entre las actividades agropecuarias. Los valores estimados de producción de carne equivalente en los EA representan una alta proporción de la producción total de la región, un volumen de producción capaz de cubrir el consumo de un 2.5% de la población mundial.The Río de la Plata Grasslands (RPG) are one of the largest areas of open ecosystems (grasslands, shrublands and savannas) in the world. Historically, these systems have experienced, and continue to experience, an enormous loss of natural habitats. Moreover, their importance has been largely invisible in comparison to forested systems. The remaining area of open ecosystems in the RPG region varies according to the source from 38 to 58% of the original area. Open Ecosystems (OE) are a special case of agroecosystems because they can combine the supply of both provisioning and regulating and supporting ecosystem services (ES). Preserving the provision of ES in these natural habitats depends, in part, on understanding the role of the two main disturbances operating in them: grazing and fire. Although these two disturbances are natural components of OE, both are manipulated by humans. In this paper we reviewed the role played by fire and grazing in the structure and functioning of the RPG starting from the late Pleistocene and Holocene, and summarizing current evidence on the effects of fire and grazing on vegetation, fauna and biogeochemical processes. The evidence indicates that among agricultural activities, direct grazing systems in OE have the lowest environmental footprint. At the same time are the key for habitat preservation and ES supply. Overall, the OE of the RPG still represent a high proportion of the area, are capable of covering 2.5% of the world’s population needs of high quality protein and, at the same time, guarding the regulation of key processes.Fil: Paruelo, José. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Oesterheld, Martin. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Altesor, Alice. Universidad de la Republica; UruguayFil: Piñeiro, Gervasio. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Rodríguez, Claudia. Universidad de la Republica; UruguayFil: Baldassini, Pablo. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: Irisarri, Jorge Gonzalo Nicolás. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: López Mársico, Luis. Universidad de la Republica; UruguayFil: Pillar, Valério D.. Universidad de la Republica; Urugua

Towards an applied metaecology

The complexity of ecological systems is a major challenge for practitioners and decision-makers who work to avoid, mitigate and manage environmental change. Here, we illustrate how metaecology – the study of spatial interdependencies among ecological systems through fluxes of organisms, energy, and matter – can enhance understanding and improve managing environmental change at multiple spatial scales. We present several case studies illustrating how the framework has leveraged decision-making in conservation, restoration and risk management. Nevertheless, an explicit incorporation of metaecology is still uncommon in the applied ecology literature, and in action guidelines addressing environmental change. This is unfortunate because the many facets of environmental change can be framed as modifying spatial context, connectedness and dominant regulating processes - the defining features of metaecological systems. Narrowing the gap between theory and practice will require incorporating system-specific realism in otherwise predominantly conceptual studies, as well as deliberately studying scenarios of environmental change.We thank FAPESP (grants 2014/10470-7 to AM, 2013/04585-3 to DL, 2013/50424-1 to TS and 2015/18790-3to LS), CNPq (Productivity Fellowships 301656/2011-8 to JAFDF,308205/2014-6 to RP, 306183/2014-5 to PIP and 307689/2014-0 to VDP), the National Science Foundation (DEB 1645137 toJGH), the Natural Sciences and Engineering Council of Canada (SJL,PPN), and the Academy of Finland (grants 257686 and 292765 toMC) for support. This work contributes to the Labex OT-Med (no.ANR-11-LABX-0061), funded by the French government throughthe A*MIDEX project (no. ANR-11-IDEX-0001-02)

Species niches, not traits, determine abundance and occupancy patterns: A multi‐site synthesis

International audienceAim: Locally abundant species are usually widespread, and this pattern has been related to properties of the niches and traits of species. However, such explanations fail to account for the potential of traits to determine species niches and often overlook statistical artefacts. Here, we examine how trait distinctiveness determines the abilities of species to exploit either common habitats (niche position) or a range of habitats (niche breadth) and how niche position and breadth, in turn, affect abundance and occupancy. We also examine how statistical artefacts moderate these relationships. Location: Sixteen sites in the Neotropics. Time period 1993–2014. Major taxa studied Aquatic invertebrates from tank bromeliads. Methods: We measured the environmental niche position and breadth of each species and calculated its trait distinctiveness as the average trait difference from all other species at each site. Then, we used a combination of structural equation models and a meta-analytical approach to test trait–niche relationships and a null model to control for statistical artefacts. Results: The trait distinctiveness of each species was unrelated to its niche properties, abundance and occupancy. In contrast, niche position was the main predictor of abundance and occupancy; species that used the most common environmental conditions found across bromeliads were locally abundant and widespread. Contributions of niche breadth to such patterns were attributable to statistical artefacts, indicating that effects of niche breadth might have been overestimated in previous studies. Main conclusions: Our study reveals the generality of niche position in explaining one of the most common ecological patterns. The robustness of this result is underscored by the geographical extent of our study and our control of statistical artefacts. We call for a similar examination across other systems, which is an essential task to understand the drivers of commonness across the tree of life

TRY plant trait database – enhanced coverage and open access

Plant traits - the morphological, anatomical, physiological, biochemical and phenological characteristics of plants - determine how plants respond to environmental factors, affect other trophic levels, and influence ecosystem properties and their benefits and detriments to people. Plant trait data thus represent the basis for a vast area of research spanning from evolutionary biology, community and functional ecology, to biodiversity conservation, ecosystem and landscape management, restoration, biogeography and earth system modelling. Since its foundation in 2007, the TRY database of plant traits has grown continuously. It now provides unprecedented data coverage under an open access data policy and is the main plant trait database used by the research community worldwide. Increasingly, the TRY database also supports new frontiers of trait‐based plant research, including the identification of data gaps and the subsequent mobilization or measurement of new data. To support this development, in this article we evaluate the extent of the trait data compiled in TRY and analyse emerging patterns of data coverage and representativeness. Best species coverage is achieved for categorical traits - almost complete coverage for ‘plant growth form’. However, most traits relevant for ecology and vegetation modelling are characterized by continuous intraspecific variation and trait–environmental relationships. These traits have to be measured on individual plants in their respective environment. Despite unprecedented data coverage, we observe a humbling lack of completeness and representativeness of these continuous traits in many aspects. We, therefore, conclude that reducing data gaps and biases in the TRY database remains a key challenge and requires a coordinated approach to data mobilization and trait measurements. This can only be achieved in collaboration with other initiatives

Identifying the Informational/Signal Dimension in Principal Component Analysis

The identification of a reduced dimensional representation of the data is among the main issues of exploratory multidimensional data analysis and several solutions had been proposed in the literature according to the method. Principal Component Analysis (PCA) is the method that has received the largest attention thus far and several identification methods—the so-called stopping rules—have been proposed, giving very different results in practice, and some comparative study has been carried out. Some inconsistencies in the previous studies led us to try to fix the distinction between signal from noise in PCA—and its limits—and propose a new testing method. This consists in the production of simulated data according to a predefined eigenvalues structure, including zero-eigenvalues. From random populations built according to several such structures, reduced-size samples were extracted and to them different levels of random normal noise were added. This controlled introduction of noise allows a clear distinction between expected signal and noise, the latter relegated to the non-zero eigenvalues in the samples corresponding to zero ones in the population. With this new method, we tested the performance of ten different stopping rules. Of every method, for every structure and every noise, both power (the ability to correctly identify the expected dimension) and type-I error (the detection of a dimension composed only by noise) have been measured, by counting the relative frequencies in which the smallest non-zero eigenvalue in the population was recognized as signal in the samples and that in which the largest zero-eigenvalue was recognized as noise, respectively. This way, the behaviour of the examined methods is clear and their comparison/evaluation is possible. The reported results show that both the generalization of the Bartlett’s test by Rencher and the Bootstrap method by Pillar result much better than all others: both are accounted for reasonable power, decreasing with noise, and very good type-I error. Thus, more than the others, these methods deserve being adopted