160 Works

Aboveground plant biomass and soil respiration for seven European shrublands under drought and warming manipulations (1998-2012)

S. Reinsch, E. Koller, A. Sowerby, G. De Dato, M. Estiarte, G. Guidolotti, E. Kovács-Láng, G Kröel-Dula, E. Lellei-Kovács, K.S. Larsen, D. Liberati, R Ogaya, J. Peñuelas, J. Ransijn, D.A. Robinson, I.K. Schmidt, A.R. Smith, A. Tietema, J.S. Dukes, C. Beier & B.A. Emmett
The data consists of annual measurements of standing aboveground plant biomass, annual aboveground net primary productivity and annual soil respiration between 1998 and 2012. Data were collected from seven European shrublands that were subject to the climate manipulations drought and warming. Sites were located in the United Kingdom (UK), the Netherlands (NL), Denmark ( two sites, DK-B and DK-M), Hungary (HU), Spain (SP) and Italy (IT). All field sites consisted of untreated control plots, plots...

2014 Machine Learning Data Set for NASA's Solar Dynamics Observatory - Atmospheric Imaging Assembly

David Fouhey, Meng Jin, Mark Cheung, Abndres Munoz-Jaramillo, Richard Galvez, Rajat Thomas, Paul Wright, Alexander Szenicer, Monica G. Bobra, Yang Liu & James Mason
We present a curated dataset from the NASA Solar Dynamics Observatory (SDO) mission in a format suitable for machine learning research. Beginning from level 1 scientific products we have processed various instrumental corrections, downsampled to manageable spatial and temporal resolutions, and synchronized observations spatially and temporally. We anticipate this curated dataset will facilitate machine learning research in heliophysics and the physical sciences generally, increasing the scientific return of the SDO mission. This work is a...

Data from: The trouble with isolation by distance

Patrick G. Meirmans
The genetic population structure of many species is characterised by a pattern of isolation by distance (IBD): due to limited dispersal, individuals that are geographically close tend to be genetically more similar than individuals that are far apart. Despite the ubiquity of IBD in nature, many commonly used statistical tests are based on a null model that is completely non-spatial, the Island model. Here, I argue that patterns of spatial autocorrelation deriving from IBD present...

Data from: Vegetation trends over eleven years on mountain summits in NW Argentina

Julieta Carilla, Stephan Halloy, Soledad Cuello, Alfredo Grau, Agustina Malizia & Francisco Cuesta
As global climate change leads to warmer and dryer conditions in the central Andes, alpine plant communities are forced to upward displacements following their climatic niche. Species range shifts are predicted to have major impacts on alpine communities by reshuffling species composition and abundances. Using a standardized protocol, we surveyed alpine plant communities in permanent plots on four high Andean summits in NW Argentina, which range from 4040 to 4740 m a.s.l. After a baseline...

Change in terrestrial human footprint drives continued loss of intact ecosystems

Brooke Williams, Oscar Venter, James Allan, Scott Atkinson, Jose Rehbein, Michelle Ward, Moreno Di Marco, Hedley Grantham, Jamison Ervin, Scott Goetz, Andrew Hansen, Patrick Jantz, Rajeev Pillay, Susana Rodríguez-Buriticá, Christina Supples, Anne Virnig & James Watson
Human pressure mapping is important for understanding humanity's role in shaping Earth’s patterns and processes. Our ability to map this influence has evolved, thanks to powerful computing, earth observing satellites, and new bottom-up census and crowd-sourced data. Here, we provide the latest temporally inter-comparable maps of the terrestrial human footprint, and assessment of change in human pressure at global, biome, and ecoregional scales. In 2013, 42% of terrestrial Earth could be considered relatively free of...

Data from: Deconstructing species richness–environment relationships in Neotropical lianas

Leila Meyer, W. Daniel Kissling, Lucia G. Lohmann, Joaquín Hortal & José A. F. Diniz-Filho
Abstract Aim: Studying species richness patterns by considering all species as equivalent units may prevent a deeper understanding of the origin and maintenance of biodiversity. Here, we deconstructed the species richness of Neotropical lianas by specific attributes of species to study richness–environment relationships. Location: Neotropics Taxon: Tribe Bignonieae (Bignoniaceae), the largest clade of Neotropical lianas Methods: We used five morphological, one geographical and two evolutionary attributes of species, each with 2–7 attribute states. We compared...

Single-cell visualization indicates direct role of sponge host in uptake of dissolved organic matter

Michelle Achlatis, Mathieu Pernice, Kathryn Green, Jasper De Goeij, Paul Guagliardo, Matt Kilburn, Ove Hoegh-Guldberg & Sophie Dove
Marine sponges are set to become more abundant in many near-future oligotrophic environments, where they play crucial roles in nutrient cycling. Of high importance is their mass turnover of dissolved organic matter (DOM), a heterogeneous mixture that constitutes the largest fraction of organic matter in the ocean and is recycled primarily by bacterial mediation. Little is known however about the mechanism that enables sponges to incorporate large quantities of DOM in their nutrition, unlike most...

Data from: Cascading effects of climate variability on the breeding success of an edge population of an apex predator

Laura Gangoso, Duarte Viana, Adriaan Dokter, Judy Shamoun-Baranes, Jordi Figuerola, Sergio Barbosa & Willem Bouten
1. Large-scale environmental forces can influence biodiversity at different levels of biological organization. Climate, in particular, is often associated to species distributions and diversity gradients. However, its mechanistic link to population dynamics is still poorly understood. 2. Here, we unraveled the full mechanistic path by which a climatic driver, the Atlantic trade winds, determines the viability of a bird population. 3. We monitored the breeding population of Eleonora’s falcons in the Canary Islands for over...

Scale-dependent drivers of the phylogenetic structure and similarity of tree communities in northwestern Amazonia

Sebastián González-Caro, Joost Duivenvoorden, Henrik Balslev, Jaime Cavelier, Carlos Grández, Manuel Macia, Hugo Romero-Saltos, Mauricio Sanchez, Renato Valencia & Alvaro Duque
1. The extent to which historical dispersal, environmental features and geographic barriers shape the phylogenetic structure and turnover of tree communities in northwestern Amazonia at multiple spatial scales remains poorly understood. 2. We used 85 floristically standardized 0.1-ha plots (DBH ³ 2.5 cm) distributed in three subregions of northwestern (NW) Amazonia across three main habitat types (floodplain, swamp, terra firme forests), to hypothesize that: i) historical dispersal overcome geographical barriers, which meant low local phylogenetic...

Data from: Subsampling reveals that unbalanced sampling affects STRUCTURE results in a multi-species dataset

Patrick G. Meirmans
Studying the genetic population structure of species can reveal important insights into several key evolutionary, historical, demographic, and anthropogenic processes. One of the most important statistical tools for inferring genetic clusters is the program STRUCTURE. Recently, several papers have pointed out that STRUCTURE may show a bias when the sampling design is unbalanced, resulting in spurious joining of underrepresented populations and spurious separation of overrepresented populations. Suggestions to overcome this bias include subsampling and changing...

Data from: Evolution of size-dependent intraspecific competition predicts body size scaling of metabolic rate

Vincent Hin & Andre M. De Roos
1. Growth in body size is accompanied by changes in foraging capacity and metabolic costs, which lead to changes in competitive ability during ontogeny. The resulting size-dependent competitive asymmetry influences population dynamics and community structure, but it is not clear whether natural selection leads to asymmetry in intraspecific competition. 2. We address this question by using a size-structured consumer-resource model, in which the strength and direction of competitive asymmetry between different consumer individuals depends on...

Data from: Canopy height explains species richness in the largest clade of Neotropical lianas

Leila Meyer, José Alexandre F. Diniz-Filho, Lúcia G. Lohmann, Joaquín Hortal, Elisa Barreto, Thiago Rangel & W. Daniel Kissling
Aim: Tall and structurally complex forests can provide ample habitat and niche space for climbing plants, supporting high liana species richness. We test to what extent canopy height (as proxy of 3D habitat structure), climate and soil interact to determine species richness in the largest clade of Neotropical lianas. We expect that the effect of canopy height on species richness is higher for lianas from closed tropical rainforests compared to riparian and savanna habitats. Location:...

Data from: PalmTraits 1.0, a species-level functional trait database for palms worldwide

W. Daniel Kissling, Henrik Balslev, William J. Baker, John Dransfield, Bastian Göldel, Jun Ying Lim, Renske E. Onstein & Jens-Christian Svenning
Plant traits are critical to plant form and function —including growth, survival and reproduction— and therefore shape fundamental aspects of population and ecosystem dynamics as well as ecosystem services. Here, we present a global species-level compilation of key functional traits for palms (Arecaceae), a plant family with keystone importance in tropical and subtropical ecosystems. We derived measurements of essential functional traits for all (>2500) palm species from key sources such as monographs, books, other scientific...

Climate drives community-wide divergence within species over a limited spatial scale: evidence from an oceanic island

Antonia Salces-Castellano, Jairo Patiño, Nadir Alvarez, Carmelo Andújar, Paula Arribas, Juan J. Braojos-Ruiz, Marcelino Del Arco-Aguilar, Víctor García-Olivares, Dirk Karger, Heriberto López, Ioanna Manolopoulou, Pedro Oromí, Antonio J. Pérez-Delgado, William W. Peterman, Kenneth F. Rijsdijk & Brent C. Emerson
Geographic isolation substantially contributes to species endemism on oceanic islands when speciation involves the colonisation of a new island. However, less is understood about the drivers of speciation within islands. What is lacking is a general understanding of the geographic scale of gene flow limitation within islands, and thus the geographic scale and drivers of geographical speciation within insular contexts. Using a community of beetle species, we show that when dispersal ability and climate tolerance...

Less is more: on-board lossy compression of accelerometer data increases biologging capacity

Rascha Nuijten, Theo Gerrits, Judy Shamoun-Baranes & Bart Nolet
GPS-tracking devices have been used in combination with a wide range of additional sensors to study animal behaviour, physiology and interaction with their environment. Tri-axial accelerometers allow researchers to remotely infer the behaviour of individuals, at all places and times. Collection of accelerometer data is relatively cheap in terms of energy usage, but the amount or raw data collected generally requires much storage space and is particularly demanding in terms of energy needed for data...

Palm fruit colours are linked to the broad-scale distribution and diversification of primate colour vision systems

Renske Onstein, Daphne Vink, Jorin Veen, Christopher Barratt, Suzette Flantua, Serge Wich & Daniel Kissling
A long-standing hypothesis in ecology and evolution is that trichromatic colour vision (the ability to distinguish red from green) in frugivorous primates has evolved as an adaptation to detect conspicuous (reddish) fruits. This could provide a competitive advantage over dichromatic frugivores which cannot distinguish reddish colours from a background of green foliage. Here, we test whether the origin, distribution and diversity of trichromatic primates is positively associated with the availability of conspicuous palm fruits, i.e....

Data from: Predicting optimal outcomes in cognitive therapy or interpersonal psychotherapy for depressed individuals using the Personalized Advantage Index approach

Marcus J. H. Huibers, Zachary D. Cohen, Lotte H. J. M. Lemmens, Arnoud Arntz, Frenk P. M. L. Peeters, Pim Cuijpers & Robert J. DeRubeis
Introduction: Although psychotherapies for depression produce equivalent outcomes, individual patients respond differently to different therapies. Predictors of outcome have been identified in the context of randomized trials, but this information has not been used to predict which treatment works best for the depressed individual. In this paper, we aim to replicate a recently developed treatment selection method, using data from an RCT comparing the effects of cognitive therapy (CT) and interpersonal psychotherapy (IPT). Methods: 134...

Data from: Seasonal detours by soaring migrants shaped by wind regimes along the East Atlantic Flyway

Wouter M. G. Vansteelant, Judy Shamoun-Baranes, Willem Van Manen, Jan Van Diermen & Willem Bouten
Avian migrants often make substantial detours between their seasonal destinations. It is likely some species do this to make the most of predictable wind regimes along their respective flyways. We test this hypothesis by studying orientation behaviour of a long-distance soaring migrant in relation to prevailing winds along the East Atlantic Flyway. We tracked 62 migratory journeys of 12 adult European Honey Buzzards Pernis apivorus with GPS loggers. Hourly fixes were annotated with local wind...

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

Wilm Daniel Kissling, Lars Dalby, Camilla Fløjgaard, Jonathan Lenoir, Brody Sandel, Christopher Sandom, Kristian Trøjelsgaard, Jens-Christian Svenning & Jens-Christian Svenning
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...

Data from: Nectar accessibility determines fitness, flower choice and abundance of hoverflies that provide natural pest control

Paul C.J. Van Rijn, Felix L. Wäckers & Paul C. J. Van Rijn
1. In modern agricultural landscapes many organisms providing ecosystem services such as pollination and natural pest control are likely constrained by shortage of nectar and/or pollen required for adult nutrition. More and more flower-rich field margin strips and other habitats are created to eliminate these constraints. For most target organisms, however, it is not well known which (types of) flowers are effective in providing suitable pollen and nectar. 2. We studied the suitability of a...

Data from: Differential recycling of coral and algal dissolved organic matter via the sponge loop

Laura Rix, Jasper M. De Goeij, Dick Van Oevelen, Ulrich Struck, Fuad A. Al-Horani, Christian Wild & Malik S. Naumann
Corals and macroalgae release large quantities of dissolved organic matter (DOM), one of the largest sources of organic matter produced on coral reefs. By rapidly taking up DOM and transforming it into particulate detritus, coral reef sponges are proposed to play a key role in transferring the energy and nutrients in DOM to higher trophic levels via the recently discovered sponge loop. DOM released by corals and algae differs in quality and composition, but the...

Data from: Interacting effects of unobserved heterogeneity and individual stochasticity in the life-history of the Southern fulmar

Stéphanie Jenouvrier, Lise M. Aubry, Christophe Barbraud, Henri Weimerskirch & Hal Caswell
1.Individuals are heterogeneous in many ways. Some of these differences are incorporated as individual states (e.g., age, size, breeding status) in population models. However, substantial amounts of heterogeneity may remain unaccounted for, due to unmeasurable genetic, maternal, or environmental factors. 2.Such unobserved heterogeneity (UH) affects the behavior of heterogeneous cohorts via intra-cohort selection and contributes to inter-individual variance in demographic outcomes such as longevity and lifetime reproduction. Variance is also produced by individual stochasticity, due...

Data from: Holocene variability of an Amazonian hyperdominant

Mark B. Bush & Crystal N. H. McMichael
Little is known regarding the long-term stability or instability of Amazonian plant communities. We assessed whether the most abundant species, hyperdominants, may have risen to prominence at the Pleistocene–Holocene transition, following subsequent changes in moisture regimes, or as a result of human activity later in the Holocene. The fossil pollen history of the commonest western Amazonian tree, Iriartea deltoidea (hereafter Iriartea), is investigated using fossil pollen data from 13 lakes. Iriartea is a monospecific genus...

Data from: Use and categorization of Light Detection and Ranging vegetation metrics in avian diversity and species distribution research

Tristan R. M. Bakx, Zsófia Koma, Arie C. Seijmonsbergen & W. Daniel Kissling
Aim: Vegetation structure is a key determinant of animal diversity and species distributions. The introduction of Light Detection and Ranging (LiDAR) has enabled the collection of massive amounts of point cloud data for quantifying habitat structure at fine resolution. Here, we review the current use of LiDAR-derived vegetation metrics in diversity and distribution research of birds, a key group for understanding animal-habitat relationships. Location: Global. Methods: We review 50 relevant papers and quantify where, in...

Data from: Factors essential for L,D-transpeptidase-mediated peptidoglycan cross-linking and β-lactam resistance in Escherichia coli

Christiane Bouchier, Jean-Emmanuel Hugonnet, Michel Arthur, Dominique Mengin-Lecreulx, Yves Brun, Michael Van Nieuwenhze, Louis B Rice, Alejandro Monton, Tanneke Den Blaauwen, Etienne Carbonnelle, Carole Veckerlé & Kuyek Tu
The target of β-lactam antibiotics is the D,D-transpeptidase activity of penicillin-binding proteins (PBPs) for synthesis of 4→3 cross-links in the peptidoglycan of bacterial cell walls. Unusual 3→3 cross-links formed by L,D-transpeptidases were first detected in Escherichia coli more than four decades ago, however no phenotype has previously been associated with their synthesis. Here we show that production of the L,D-transpeptidase YcbB in combination with elevated synthesis of the (p)ppGpp alarmone by RelA lead to full...

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  • 2012

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  • University of Amsterdam
  • Nederlands Instituut voor Ecologie
  • Hansen Experimental Physics Laboratory, Stanford University
  • Electrical Engineering and Computer Science Department, University of Michigan
  • SUPA School of Physics and Astronomy, University of Glasgow
  • Aarhus University
  • NASA Goddard Space Flight Center
  • Wageningen University & Research
  • Center for Data Science, New York University
  • Lockheed Martin Solar & Astrophysics Laboratory