356 Works

Data from: Current methods for automated filtering of multiple sequence alignments frequently worsen single-gene phylogenetic inference

Ge Tan, Matthieu Muffato, Christian Ledergerber, Javier Herrero, Nick Goldman, Manuel Gil & Christophe Dessimoz
Phylogenetic inference is generally performed on the basis of multiple sequence alignments (MSA). Because errors in an alignment can lead to errors in tree estimation, there is a strong interest in identifying and removing unreliable parts of the alignment. In recent years several automated filtering approaches have been proposed, but despite their popularity, a systematic and comprehensive comparison of different alignment filtering methods on real data has been lacking. Here, we extend and apply recently...

Data from: How random is social behaviour? Disentangling social complexity through the study of a wild house mouse population

Nicolas Perony, Claudio J. Tessone, Barbara König & Frank Schweitzer
Out of all the complex phenomena displayed in the behaviour of animal groups, many are thought to be emergent properties of rather simple decisions at the individual level. Some of these phenomena may also be explained by random processes only. Here we investigate to what extent the interaction dynamics of a population of wild house mice (Mus domesticus) in their natural environment can be explained by a simple stochastic model. We first introduce the notion...

Data from: Towards a common methodology for developing logistic tree mortality models based on ring-width data

Maxime Cailleret, Christof Bigler, Harald Bugmann, J. Julio Camarero, Katarina Cufar, Hendrik Davi, Ilona Mészáros, Francesco Minunno, Mikko Peltoniemi, Elisabeth Robert, María-Laura Suarez, Roberto Tognetti & Jordi Martinez-Vilalta
Tree mortality is a key process shaping forest dynamics. Thus, there is a growing need for indicators of the likelihood of tree death. During the last decades, an increasing number of tree-ring based studies have aimed to derive growth–mortality functions, mostly using logistic models. The results of these studies, however, are difficult to compare and synthesize due to the diversity of approaches used for the sampling strategy (number and characteristics of alive and death observations),...

Data from: Population genetics and adaptation along elevation gradients in invasive Solidago canadensis

Emily V. Moran, Andrea Reid & Jonathan M. Levine
Gene flow between populations may either support local adaptation by supplying genetic variation on which selection may act, or counteract it if maladapted alleles arrive faster than can be purged by selection. Although both such effects have been documented within plant species' native ranges, how the balance of these forces influences local adaptation in invasive plant populations is less clear, in part because introduced species often have lower genetic variation initially but also tend to...

Data from: Cross-scale interactions among bark beetles, climate change and wind disturbances a landscape modeling approach

Christian Temperli, Harald K. M. Bugmann, Ché Elkin & Harald Bugmann
Bark beetles are a key forest disturbance agent worldwide, with their impact shaped by climate, forest susceptibility, and interactions with other disturbances such as windthrow and fire. There is ample evidence on the interactions among these factors at small spatial and temporal scales, but projecting their long-term and landscape-scale impacts remains a challenge. We developed a spatially explicit model of European spruce bark beetle (Ips typographus) dynamics that incorporates beetle phenology and forest susceptibility, and...

Data from: Simplification of shade tree diversity reduces nutrient cycling resilience in coffee agroforestry

Maike Nesper, Christoph Kueffer, Smitha Krishnan, Cheppudira G. Kushalappa & Jaboury Ghazoul
1. Agroforestry systems are refuges for biodiversity and provide multiple ecosystem functions and services. Diverse multispecies shade tree canopies are increasingly replaced by monospecific shade, often dominated by non-native tree species. The loss of tree diversity and the nature of the dominating tree can have strong implications for ecosystem functions, e.g. nutrient cycling ultimately reducing crop production. 2. To understand direct and indirect impacts of shade trees on nutrient cycling and crop production, we studied...

Data from: An experimental study of strong reciprocity in bacteria

R. Fredrik Inglis, Stuart West & Angus Buckling
Strong reciprocity, whereby cooperators punish non-cooperators, may help to explain the evolutionary success of cooperative behaviours. However, theory suggests that selection for strong reciprocity can depend upon tight genetic linkage between cooperation and punishment, to avoid the strategy being outcompeted by non-punishing cooperators. We tested this hypothesis using experimental populations of the bacterium Pseudomonas aeruginosa, which cooperate by producing iron-scavenging siderophores and, in this context, punish non-cooperators with toxins. Consistent with theory, we show that...

Data from: Natural selection on immune defense: a field experiment

Laura Langeloh, Jasminca Maria Behrmann-Godel, Otto Seppälä & Jasminca Behrmann-Godel
Predicting the evolution of phenotypic traits requires an understanding of natural selection on them. Despite its indispensability in the fight against parasites, selection on host immune defense has remained understudied. Theory predicts immune traits to be under stabilizing selection due to associated trade-offs with other fitness-related traits. Empirical studies, however, report mainly positive directional selection. This discrepancy could be caused by low phenotypic variation in the examined individuals and/or variation in host resource level that...

Data from: Worldwide population genetic structure of the oriental fruit moth (Grapholita molesta), a globally invasive pest

Heather Kirk, Silvia Dorn & Dominique Mazzi
Background: Invasive pest species have large impacts on agricultural crop yields, and understanding their population dynamics is important for ensuring food security. The oriental fruit moth Grapholita molesta is a cosmopolitan pest of stone and pome fruit species including peach and apple, and historical records indicate that it has invaded North and South America, Europe, Australia and Africa from its putative native range in Asia over the past century. Results: We used 13 microsatellite loci,...

Data from: Loss of connectivity among island-dwelling Peary caribou following sea ice decline

Deborah A. Jenkins, Nicolas Lecomte, James A. Schaefer, Steffen M. Olsen, Didier Swingedouw, Steeve D. Côté, Loïc Pellissier & Glenn Yannic
Global warming threatens to reduce population connectivity for terrestrial wildlife through significant and rapid changes to sea ice. Using genetic fingerprinting, we contrasted extant connectivity in island-dwelling Peary caribou in northern Canada with continental-migratory caribou. We next examined if sea-ice contractions in the last decades modulated population connectivity and explored the possible impact of future climate change on long-term connectivity among island caribou. We found a strong correlation between genetic and geodesic distances for both...

Data from: Predation risk shaped by habitat and landscape complexity in urban environments

David Frey, Kevin Vega, Florian Zellweger, Jaboury Ghazoul, Dennis Hansen & Marco Moretti
1. Habitat loss and modification are hallmarks of anthropogenic ecosystems, but the consequences for ecosystem functions and services often remain unclear. Understanding these links in cities is complicated by strong but fine-scale differences in habitat structure among green space patches, and a high variance in habitat amount across urban landscapes. 2. We used airborne laser scanning (ALS) data to disentangle the effects of 3D woody habitat heterogeneity of urban home gardens, and woody habitat amount...

Data from: Are aphid parasitoids locally adapted to the prevalence of defensive symbionts in their hosts?

Christoph Vorburger & Romain Rouchet
Background: Insect parasitoids are under strong selection to overcome their hosts’ defences. In aphids, resistance to parasitoids is largely determined by the presence or absence of protective endosymbionts such as Hamiltonella defensa. Hence, parasitoids may become locally adapted to the prevalence of this endosymbiont in their host populations. To address this, we collected isofemale lines of the aphid parasitoid Lysiphlebus fabarum from 17 sites in Switzerland and France, at which we also estimated the frequency...

Data from: Measurement of infection efficiency of a major wheat pathogen using time-resolved imaging of disease progress

Petteri Karisto, Susanne Dora & Alexey Mikaberidze
Infection efficiency is a key epidemiological parameter that determines the proportion of pathogen spores able to infect and cause lesions once they have landed on a susceptible plant tissue. In this study, we present an improved method to measure infection efficiency of Zymoseptoria tritici using a replicated greenhouse experiment. Z. tritici is a fungal pathogen that infects wheat leaves and causes Septoria tritici blotch (STB), a major disease of wheat worldwide. We devised an original...

Data from: Spatiotemporal dynamics of Puumala hantavirus associated with its rodent host, Myodes glareolus

Vanessa Weber De Melo, Hanan Sheik Ali, Jona Freise, Denise Kühnert, Sandra Essbauer, Marc Mertens, Konrad M. Wanka, Stephan Drewes, Rainer G. Ulrich, Gerald Heckel & Hanan Sheikh Ali
Many viruses significantly impact human and animal health. Understanding the population dynamics of these viruses and their hosts can provide important insights for epidemiology and virus evolution. Puumala virus (PUUV) is a European hantavirus that may cause regional outbreaks of hemorrhagic fever with renal syndrome in humans. Here, we analyzed the spatiotemporal dynamics of PUUV circulating in local populations of its rodent reservoir host, the bank vole (Myodes glareolus) during eight years. Phylogenetic and population...

Data from: Genetic factors affecting food-plant specialization of an oligophagous seed predator

Liisa Laukkanen, Roosa Leimu, Anne Muola, Marianna Lilley & Pia Mutikainen
Several ecological and genetic factors affect the diet specialization of insect herbivores. The evolution of specialization may be constrained by lack of genetic variation in herbivore performance on different food plant species. By traditional view, trade-offs, i.e., negative genetic correlations between the performance of the herbivores on different food-plant species favour the evolution of specialization. To investigate whether there is genetic variation or trade-offs in herbivore performance between different food plants that may influence specialization...

Data from: The balance of canopy and soil effects determines intraspecific differences in foundation species’ effects on associated plants

Nuria Pistón, Richard Michalet, Christian Schöb, Petr Macek, Cris Armas & Francisco I. Pugnaire
1. The impact of plant-plant interactions on species diversity patterns has been broadly addressed in stressful environments, such as alpine ecosystems, where foundation species promote species richness by creating habitat for other species. However, foundation species with contrasting phenotypes might modify the microhabitat differently, which would alter the subordinate community composition, and coincide with distinct feedback effects of those subordinate species on the foundation species. However, the precise interaction mechanisms that facilitate species are not...

Data from: The roles of genetic drift and natural selection in quantitative trait divergence along an altitudinal gradient in Arabidopsis thaliana

Yonghai Luo, Alex Widmer & Sophie Karrenberg
Understanding how natural selection and genetic drift shape biological variation is a central topic in biology, yet our understanding of the agents of natural selection and their target traits is limited. We investigated to what extent selection along an altitudinal gradient or genetic drift contributed to variation in ecologically relevant traits in Arabidopsis thaliana. We collected seeds from 8 to 14 individuals from each of 14 A. thaliana populations originating from sites between 800 and...

Data from: Evolution under changing climates: climatic niche stasis despite rapid evolution in a non-native plant

Jake M. Alexander
A topic of great current interest is the capacity of populations to adapt genetically to rapidly changing climates, for example by evolving the timing of life-history events, but this is challenging to address experimentally. I use a plant invasion as a model system to tackle this question by combining molecular markers, a common garden experiment and climatic niche modelling. This approach reveals that non-native Lactuca serriola originates primarily from Europe, a climatic subset of its...

Data from: Silica Particles with Encapsulated DNA as trophic tracers

Carlos Andrea Mora, Daniela Paunescu, Robert Nikolaus Grass & Wendelin Jan Stark
Ecological networks such as food webs are extremely complex and can provide important information about the robustness and productivity of an ecosystem. In most cases it is not feasible to observe trophic interactions between predators and prey directly and with the available methods it is difficult to quantify the connections between them. Here we show that submicron-sized Silica Particles (100 – 150 nm) with Encapsulated DNA (SPED) enable accurate food and organism labeling and quantification...

Molecular data and analysis specifications for a study on Atriophallophorus parasites from New Zealand

Frida Feijen
This dataset accompanies the manuscript "Phylogeography and Cryptic Species Structure of a Locally Adapted Parasite in New Zealand". In our study we have shown that multiple species of the trematode parasite from the Atriophallophorus genus co-exist within the same lakes. When focusing on the most common of these species, Atriophallophorus winterbourni, we found that the Southern Alps and Pleistocene glaciation are a likely explanation for its phylogeographic patterns. This dataset consists of three parts: (I)...

ISIMIP3a landuse input data

Jan Volkholz & Sebastian Ostberg
The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) provides a framework for the collation of a consistent set of climate impact data across sectors and scales. It also provides a unique opportunity for considering interactions between climate change impacts across sectors through consistent scenarios.
The ISIMIP3a part of the third simulation round is dedicated to i) impact model evaluation and improvement and ii) detection and attribution of observed impacts according to the framework of IPCC AR5 Working...

Grasslands of temperate Europe in a changing world – Editorial to the 16th EDGG Special Feature in Tuexenia

Steffen Boch, Thomas Becker, Balázs Deák, Jürgen Dengler & Valentin H. Klaus
Mitglieder der Eurasian Dry Grassland Group (EDGG) und deren Vorgängerorganisationen geben seit 16 Jahren Grasland-Sonderausgaben (Special Features) in Tuexenia heraus. Das diesjährige Special Feature mit dem Titel Grasländer des gemäßigten Europas in einer sich verändernden Welt umfasst sieben Artikel, die verschiedene Aspekte der Graslandforschung beleuchten und dabei unterschiedliche Organismengruppen einbeziehen: LLUMIQUINGA et al. untersuchten Langzeiteffekte von Einsaat, Mahd und Kohlenstoffzusatz (Reduktion der Nährstoffverfügbarkeit durch Verschiebung des C/N-Verhältnis) auf den Renaturierungserfolg von pannonischem Sandgrasland auf ehemaligen...

A major combustion aerosol event had a negligible impact on the atmospheric ice-nucleating particle population

Michael Adams, Mark Tarn, Alberto Sanchez-Marroquin, Grace Porter, Daniel O'Sullivan, Alexander Harrison, Zhiqiang Cui, Jesús Vergara Temprado, Federico Carotenuto, Mark Holden, Martin Daily, Thomas Whale, Sebastien Sikora, Ian Burke, Jung-uk Shim, Jim McQuaid & Benjamin Murray
Clouds containing supercooled water are important for both climate and weather, but our knowledge of which aerosol particle types nucleate ice in these clouds is far from complete. Combustion aerosols have strong anthropogenic sources and if these aerosol types were to nucleate ice in clouds they might exert a climate forcing. Here, we quantified the atmospheric ice-nucleating particle (INP) concentrations during the UK’s annual Bonfire Night celebrations, which are characterised by strong anthropogenic emissions of...

ISIMIP3a reservoirs & dams input data

María del Rocío Rivas López, Jida Wang & Fangfang Yao
The Inter-Sectoral Impact Model Intercomparison Project (ISIMIP) provides a framework for the collation of a consistent set of climate impact data across sectors and scales. It also provides a unique opportunity for considering interactions between climate change impacts across sectors through consistent scenarios.
The ISIMIP3a part of the third simulation round is dedicated to i) impact model evaluation and improvement and ii) detection and attribution of observed impacts according to the framework of IPCC AR5 Working...

FoRCy: Rocking Shallow Foundation Performance in Slow Cyclic and Monotonic Experiments

Manouchehr Hakhamaneshi, Bruce L. Kutter, Andreas Gerasimos Gavras, Sivapalan Gajan, Angelos Tsatsis, George Gazetas, Ioannis Anastasopoulos, Tetsuya Kohno, Giovanna Pianese, Keshab Sharma, Lijun Deng, Weian Liu, Roberto Paolucci & Jonathan Monical
Numerous centrifuge experiments (e.g., Rosebrook 2001; Ugalde et al. 2007; Gajan and Kutter 2008; Deng et al. 2012; Hakhamaneshi et al. 2012; Liu et al. 2013; Allmond and Kutter 2014; Loli et al. 2014) and 1g shake-table experiments (e.g., Shirato et al. 2008; Drosos et al. 2012; Antonellis et al. 2015; Tsatsis and Anastasopoulos 2015) have demonstrated that rocking shallow foundations can be designed to provide re-centering and energy dissipation with little damage to the...

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