184 Works

Data from: Efficient detection of novel nuclear markers for Brassicaceae by transcriptome sequencing

Reinhold Stockenhuber, Stefan Zoller, Rie Shimizu-Inatsugi, Felix Gugerli, Kentaro K. Shimizu, Alex Widmer & Martin C. Fischer
The lack of DNA sequence information for most non-model organisms impairs the design of primers that are universally applicable for the study of molecular polymorphisms in nuclear markers. Next-generation sequencing (NGS) techniques nowadays provide a powerful approach to overcome this limitation. We present a flexible and inexpensive method to identify large numbers of nuclear primer pairs that amplify in most Brassicaceae species. We first obtained and mapped NGS transcriptome sequencing reads from two of the...

Data from: Mapping the imprint of biotic interactions on β-diversity

Marc Ohlmann, Florent Mazel, Loïc Chalmandrier, Stéphane Bec, Eric Coissac, Ludovic Gielly, Johan Pansu, Vincent Schilling, Pierre Taberlet, Lucie Zinger, Jerome Chave & Wilfried Thuiller
Investigating how trophic interactions influence the β-diversity of meta-communities is of paramount importance to understanding the processes shaping biodiversity distribution. Here, we apply a statistical method for inferring the strength of spatial dependencies between pairs of species groups. Using simulated community data generated from a multi-trophic model, we showed that this method can approximate biotic interactions in multi-trophic communities based on β-diversity patterns across groups. When applied to soil multi-trophic communities along an elevational gradient...

Data from: Plant species richness negatively affects root decomposition in grasslands

Hongmei Chen, Liesje Mommer, Jasper Van Ruijven, Hans De Kroon, Christine Fischer, Arthur Gessler, Anke Hildebrandt, Michael Scherer-Lorenzen, Christian Wirth & Alexandra Weigelt
Plant diversity enhances many ecosystem functions, including root biomass production, which drives soil carbon input. Although root decomposition accounts for a large proportion of carbon input for soil, little is known about plant diversity effect on this process. Plant diversity may affect root decomposition in two non-exclusive ways: by providing roots of different substrate quality (e.g. root chemistry) and/or by altering the soil environment (e.g. microclimate). To disentangle these two pathways, we conducted three decomposition...

Data from: Directed dispersal by rotational shepherding supports landscape genetic connectivity in a calcareous grassland plant

Yessica Rico, Rolf Holderegger, Hans Juergen Boehmer & Helene H. Wagner
Directed dispersal by animal vectors has been found to have large effects on the structure and dynamics of plant populations adapted to frugivory. Yet, empirical data are lacking on the potential of directed dispersal by rotational grazing of domestic animals to mediate gene flow across the landscape. Here, we investigated the potential effect of large-flock shepherding on landscape-scale genetic structure in the calcareous grassland plant Dianthus carthusianorum, whose seeds lack morphological adaptations to dispersal to...

Data from: European phylogeography of the epiphytic lichen fungus Lobaria pulmonaria and its green algal symbiont

Ivo Widmer, Francesco Dal Grande, Laurent Excoffier, Rolf Holderegger, Christine Keller, Vladimir S. Mikryukov & Christoph Scheidegger
In lichen symbiosis, fungal and algal partners form close associations, often co-dispersed by vegetative propagules. Due to the particular interdependence, processes such as colonization, dispersal or genetic drift are expected to result in congruent patterns of genetic structure in the symbionts. To study the population structure of an obligate symbiotic system in Europe, we genotyped the fungal and algal symbionts of the epiphytic lichen Lobaria pulmonaria at eight and seven microsatellite loci, respectively, and analyzed...

Data from: Peatland vascular plant functional types affect methane dynamics by altering microbial community structure

Bjorn J. M. Robroek, Vincent E. J. Jassey, Martine A. R. Kox, Roeland L. Berendsen, Robert T. E. Mills, Lauric Cécillon, Jéremy Puissant, Marion Meima–Franke, Peter A. H. M. Bakker, Paul L. E. Bodelier & Marion Meima-Franke
1. Peatlands are natural sources of atmospheric methane (CH4), an important greenhouse gas. It is established that peatland methane dynamics are controlled by both biotic and abiotic conditions, yet the interactive effect of these drivers is less studied and consequently poorly understood. 2. Climate change affects the distribution of vascular plant functional types (PFTs) in peatlands. By removing specific PFTs, we assessed their effects on peat organic matter chemistry, microbial community composition and on potential...

Data from: Functional responses of multi-taxa communities to disturbance and stress gradients in a restored floodplain

Bertrand Fournier, François Gillet, Renée-Claire Le Bayon, Edward A. D. Mitchell & Marco Moretti
1. Trait-based approaches can reveal the mechanisms through which disturbances or stress impact communities, allowing comparisons of the role of different mechanisms in shaping communities among taxonomic groups. Such information can lead to higher comparability, transferability and predictability of the outcome of restoration projects. However, multitaxa trait-based approaches were rarely used in the context of ecosystem restoration. 2. We investigated the responses to environmental gradients of seven taxa (vascular plants, staphylinid and carabid beetles, spiders,...

Data from: Influence of parameter settings in automated scoring of AFLPs on population genetic analysis

Marc Herrmann, Rolf Holderegger & Maarten J. Van Strien
The use of procedures for the automated scoring of AFLP fragments has recently increased. Corresponding software does not only automatically score the presence or absence of AFLP fragments, but also allows an evaluation of how different settings of scoring parameters influence subsequent population genetic analyses. In this study, we used the automated scoring package RAWGENO to evaluate how five scoring parameters influence the number of polymorphic bins and estimates of pairwise genetic differentiation between populations...

Data from: Mammal-induced trophic cascades in invertebrate food webs are modulated by grazing intensity in subalpine grassland

Martijn L. Vandegehuchte, Martin Schütz, Frederic De Schaetzen & Anita C. Risch
1. Even though mammalian herbivores can exert strong indirect effects on other animals by altering the vegetation, the study of trophic cascades retains a focus on apex predators and their top-down forces. Bottom-up trophic interaction chains induced by mammalian herbivores, particularly in invertebrate food webs, remain largely unexplored. 2. We tested whether effects of mammalian herbivores on the vegetation ricochet back up several trophic levels of the invertebrate food web. We further tested two alternative...

Data from: Interactions between C:N:P stoichiometry and soil macrofauna control dung decomposition of savanna herbivores

Judith Sitters, Marc-Jacques Maechler, Peter J. Edwards, Werner Suter & Harry Olde Venterink
1. Although dung of mammalian herbivores is an important pathway for nutrient return in savanna ecosystems, differences in dung decomposition rates among species have been little studied. 2. We measured rates of dung deposition and decomposition for various herbivores in a moist Tanzanian savanna, and related differences among species to nutrient concentrations and the activities of soil macrofauna (e.g., different mesh sizes of decomposition bags, or presence and absence of dung beetles). 3. Dung C:N:P...

Data from: Genetic diversity in widespread species is not congruent with species richness in alpine plant communities

Pierre Taberlet, Niklaus E. Zimmermann, Thorsten Englisch, Andreas Tribsch, Rolf Holderegger, Nadir Alvarez, Harald Niklfeld, Zbigniew Mirek, Atte Moilanen, Wolfgang Ahlmer, Paolo Ajmone Marsan, Enzo Bona, Maurizio Bovio, Philippe Choler, Elżbieta Cieślak, Gheorghe Coldea, Licia Colli, Vasile Cristea, Jean-Pierre Dalmas, Božo Frajman, Luc Garraud, Myriam Gaudeul, Ludovic Gielly, Walter Gutermann, Nejc Jogan … & Karol Marhold
The Convention on Biological Diversity (CBD) aims at the conservation of all three levels of biodiversity, i.e. ecosystems, species and genes. Genetic diversity represents evolutionary potential and is important for ecosystem functioning. Unfortunately, genetic diversity in natural populations is hardly considered in conservation strategies because it is difficult to measure and has been hypothesized to co-vary with species richness. This means that species richness is taken as a surrogate of genetic diversity in conservation planning,...

Data from: Multiple factors modulate tree growth complementarity in central European mixed forests

Marco Mina, Markus O. Huber, David I. Forrester, Esther Thürig & Brigitte Rohner
Mixed species forests can often be more productive and deliver higher levels of ecosystem services and functions than monocultures. However, complementarity effects for any given tree species are difficult to generalize because they can vary greatly along gradients of climatic conditions and resource availability. Identifying the conditions where species diversity can positively influence productivity is crucial. To date, few studies have examined how growth complementarity across species and mixture types is modulated by stand and...

Data from: Fine-root exploitation strategies differ in tropical old-growth and logged-over forests in Ghana

Shalom D. Addo-Danso, Cindy E. Prescott, Stephen Adu-Bredu, Akwasi Duah-Gyamfi, Sam Moore, Robert D. Guy, David I. Forrester, Kennedy Owusu-Afriyie, Peter L. Marshall, Yadvinder Malhi. & Yadvinder Malhi
Understanding the changes in root exploitation strategies during post-logging recovery is important for predicting forest productivity and carbon dynamics in tropical forests. We sampled fine (diameter < 2 mm) roots using the soil-core method to quantify fine-root biomass, and architectural and morphological traits to determine root exploitation strategies in an old-growth forest and in a 54-year-old logged-over forest influenced by similar parent material and climate. Seven root traits were considered: four associated with resource exploitation...

Data from: Pine afforestation decreases the long-term performance of understory shrubs in a semiarid Mediterranean ecosystem: a stable isotope approach.

Cristina Moreno-Gutiérrez, Giovanna Battipaglia, Paolo Cherubini, Antonio Delgado Huertas & José Ignacio Querejeta
1. Plant–plant interactions shape the structure and composition of plant communities, but shifts in interaction outcomes might occur in the face of ongoing climate change. 2. We assessed the influence of Pinus halepensis plantations on the long-term ecophysiological performance of understorey vegetation, by conducting a retrospective comparison (1989–2007) of growth-ring widths, δ13C and δ18O between Rhamnus lycioides shrubs from two contrasting vegetation types: P. halepensis plantations vs. open woodlands. We also measured the leaf δ13C,...

Data from: Spatial variation in throughfall, soil, and plant water isotopes in a temperate forest

Gregory R. Goldsmith, Scott T. Allen, Sabine Braun, Nadine Engbersen, Clara Romero González-Quijano, James W. Kirchner & Rolf T.W. Siegwolf
Studies of stable isotopes of water in the environment have been fundamental to advancing our understanding of how water moves through the soil-plant-atmosphere continuum; however, much of this research focuses on how water isotopes vary in time, rather than in space. We examined the spatial variation in the δ18O and δ2H of throughfall and bulk soil water, as well as branch xylem and bulk leaf water of Picea abies (Norway Spruce) and Fagus sylvatica (Beech),...

Data from: Observed forest sensitivity to climate implies large changes in 21st century North American forest growth

Noah D. Charney, Flurin Babst, Benjamin Poulter, Sydne Record, Valerie M. Trouet, David Frank, Brian J. Enquist & Margaret E. K. Evans
Predicting long-term trends in forest growth requires accurate characterisation of how the relationship between forest productivity and climatic stress varies across climatic regimes. Using a network of over two million tree-ring observations spanning North America and a space-for-time substitution methodology, we forecast climate impacts on future forest growth. We explored differing scenarios of increased water-use efficiency (WUE) due to CO2-fertilisation, which we simulated as increased effective precipitation. In our forecasts: (1) climate change negatively impacted...

Data from: Trophic level, successional age and trait matching determine specialization of deadwood-based interaction networks of saproxylic beetles

Beate Wende, Martin M. Gossner, Ingo Grass, Tobias Arnstadt, Martin Hofrichter, Andreas Floren, Karl Eduard Linsenmair, Wolfgang W. Weisser & Ingolf Steffan-Dewenter
The specialization of ecological networks provides important insights into possible consequences of biodiversity loss for ecosystem functioning. However, mostly mutualistic and antagonistic interactions of living organisms have been studied, whereas detritivore networks and their successional changes are largely unexplored. We studied the interactions of saproxylic (deadwood-dependent) beetles with their dead host trees. In a large-scale experiment, 764 logs of 13 tree species were exposed to analyse network structure of three trophic groups of saproxylic beetles...

Data from: Estimating age-dependent extinction: contrasting evidence from fossils and phylogenies

Oskar Hagen, Tobias Andermann, Tiago B. Quental, Alexandre Antonelli & Daniele Silvestro
The estimation of diversification rates is one of the most vividly debated topics in modern systematics, with considerable controversy surrounding the power of phylogenetic and fossil-based approaches in estimating extinction. Van Valen’s seminal work from 1973 proposed the “Law of constant extinction” which states that the probability of extinction of taxa is not dependent on their age. This assumption of age-independent extinction has prevailed for decades with its assessment based on survivorship curves, which, however,...

Data from: Integrating correlation between traits improves spatial predictions of plant functional composition

Rafael O. Wüest, Tamara Muenkenmuller, Sebastien Lavergne, Laura Pollock & Wilfried Thuiller
Functional trait composition is increasingly recognized as key to better understand and predict community responses to environmental gradients. Predictive approaches traditionally model the weighted mean trait values of communities (CWMs) as a function of environmental gradients. However, most approaches treat traits as independent regardless of known trade-offs between them, which could lead to spurious predictions. To address this issue, we suggest jointly modeling a suit of functional traits along environmental gradients while accounting for relationships...

Data from: Stoichiometric N:P flexibility and mycorrhizal symbiosis favor plant resistance against drought

Pierre Mariotte, Alberto Canarini & Feike A. Dijkstra
1. Drought induces changes in the nitrogen (N) and phosphorus (P) cycle but most plant species have limited flexibility to take up nutrients under such variable or unbalanced N and P availability. Both the degree of flexibility in plant N:P ratio and of root symbiosis with arbuscular mycorrhizal (AM) fungi might control plant resistance to drought-induced changes in nutrient availability, but this has not been directly tested. 2. Here, we examined the role of plant...

Data from: Genome-wide variation in nucleotides and retrotransposons in alpine populations of Arabis alpina (Brassicaceae)

Aude Rogivue, Rimjhim Roy Choudhury, Stefan Zoller, Stéphane Joost, Francois Felber, Michel Kasser, Christian Parisod & Felix Gugerli
Advances in high-throughput sequencing have promoted the collection of reference genomes and genome-wide diversity. However, the assessment of genomic variation among populations has hitherto mainly been surveyed through single-nucleotide polymorphisms (SNPs) and largely ignored the often major fraction of genomes represented by transposable elements (TEs). Despite accumulating evidence supporting the evolutionary significance of TEs, comprehensive surveys remain scarce. Here, we sequenced the full genomes of 304 individuals of Arabis alpina sampled from four nearby natural...

Data from: Nutrient release from moose bioturbation in aquatic ecosystems

Joseph K. Bump, Brenda G. Bergman, Amy J. Schrank, Amy M. Marcarelli, Evan S. Kane, Anita C. Risch & Martin Schütz
While the ecological importance of bioturbation is well recognized and the prevalence of aquatic foraging by terrestrial ungulates is increasingly appreciated, research linking how terrestrial ungulates function as disturbance mechanisms via bioturbation in freshwater systems is lacking. The purpose of this study was to quantify potential nutrient pulses released from benthic sediments into the water column when moose Alces alces feed on aquatic plants. We also determined if we could experimentally mimic the benthic disturbance...

Data from: Environmental changes drive the temporal stability of semi-arid natural grasslands through altering species asynchrony

Zhuwen Xu, Haiyan Ren, Mai-He Li, Jasper Van Ruijven, Xingguo Han, Shiqiang Wan, Hui Li, Qiang Yu, Yong Jiang & Lin Jiang
Stability is an important property of ecological systems, many of which are experiencing increasing levels of anthropogenic environmental changes. However, how these environmental changes influence ecosystem stability remains poorly understood. We conducted an 8-year field experiment in a semi-arid natural grassland to explore the effects of two common environmental changes, precipitation and nitrogen enrichment, on the temporal stability of plant above-ground biomass. A split-plot design, with precipitation as the main plot factor and nitrogen as...

Data from: How do climate change experiments alter plot-scale climate?

Ailene Ettinger & Elizabeth M. Wolkovich
To understand and forecast biological responses to climate change, scientists frequently use field experiments that alter temperature and precipitation. Climate manipulations can manifest in complex ways, however, challenging interpretations of biological responses. We reviewed publications to compile a database of daily plot‐scale climate data from 15 active‐warming experiments. We find that the common practices of analysing treatments as mean or categorical changes (e.g. warmed vs. unwarmed) masks important variation in treatment effects over space and...

Data from: Spatial heterogeneity in species composition constrains plant community responses to herbivory and fertilization

Dorothee Hodapp, Elizabeth T. Borer, W. Stanley Harpole, Eric M. Lind, Eric W. Seabloom, Peter B. Adler, Juan Alberti, Carlos A. Arnillas, Jonathan D. Bakker, Lori Biederman, Marc Cadotte, Elsa E. Cleland, Scott Collins, Philip A. Fay, Jennifer Firn, Nicole Hagenah, Yann Hautier, Oscar Iribarne, Johannes M.H. Knops, Rebecca L. McCulley, Andrew MacDougall, Joslin L. Moore, John W. Morgan, Brent Mortensen, Kimberly J. La Pierre … & Johannes M. H. Knops
Environmental change can result in substantial shifts in community composition. The associated immigration and extinction events are likely constrained by the spatial distribution of species. Still, studies on environmental change typically quantify biotic responses at single spatial (time series within a single plot) or temporal (spatial beta-diversity at single time points) scales, ignoring their potential interdependence. Here, we use data from a global network of grassland experiments to determine how turnover responses to two major...

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