313 Works

A Multi-Type Birth-Death model for Bayesian inference of lineage-specific birth and death rates

Joëlle Barido-Sottani, Timothy Vaughan & Tanja Stadler
Heterogeneous populations can lead to important differences in birth and death rates across a phylogeny. Taking this heterogeneity into account is necessary to obtain accurate estimates of the underlying population dynamics. We present a new multi-type birth-death model (MTBD) that can estimate lineage-specific birth and death rates. This corresponds to estimating lineage-dependent speciation and extinction rates for species phylogenies, and lineage-dependent transmission and recovery rates for pathogen transmission trees. In contrast with previous models, we...

Assessing the impact of incomplete species sampling on estimates of speciation and extinction rates

Rachel C. M. Warnock, Tracy A. Heath & Tanja Stadler
Estimating speciation and extinction rates is essential for understanding past and present biodiversity, but is challenging given the incompleteness of the rock and fossil records. Interest in this topic has led to a divergent suite of independent methods—paleontological estimates based on sampled stratigraphic ranges and phylogenetic estimates based on the observed branching times in a given phylogeny of living species. The fossilized birth–death (FBD) process is a model that explicitly recognizes that the branching events...

Data from: Nutrient availability controls the impact of mammalian herbivores on soil carbon and nitrogen pools in grasslands

Judith Sitters, E.R. Jasper Wubs, Elisabeth S. Bakker, Thomas W. Crowther, Peter B. Adler, Sumanta Bagchi, Jonathan D. Bakker, Lori Biederman, Elizabeth T. Borer, Elsa E. Cleland, Nico Eisenhauer, Jennifer Firn, Laureano Gherardi, Nicole Hagenah, Yann Hautier, Sarah E. Hobbie, Johannes M.H. Knops, Andrew S. MacDougall, Rebecca L. McCulley, Joslin L. Moore, Brent Mortensen, Pablo L. Peri, Suzanne M. Prober, Charlotte Riggs, Anita C. Risch … &
Grasslands have been subject to considerable alteration due to human activities globally, including widespread changes in populations and composition of large mammalian herbivores and elevated supply of nutrients. Grassland soils remain important reservoirs of carbon (C) and nitrogen (N). Herbivores may affect both C and N pools and these changes likely interact with increases in soil nutrient availability. Given the scale of grassland soil fluxes, such changes can have striking consequences for atmospheric C concentrations...

Adaptation to drought is coupled with slow growth, but independent from phenology in marginal silver fir (Abies alba Mill.) populations

Katalin Csillery, Nina Buchmann & Bruno Fady
Drought is one of the most important selection pressures for forest trees in the context of climate change. Yet, the different evolutionary mechanisms, and their environmental drivers, by which certain populations become more drought tolerant than others is still little understood. We studied adaptation to drought in 16 silver fir (Abies alba Mill.) populations from the French Mediterranean Alps by combining observations on seedlings from a large scale greenhouse experiment (N=8199) and on adult tress...

Mating patterns influence vulnerability to the extinction vortex

Joanne Godwin, Alyson J. Lumley, Łukasz Michalczyk, Oliver Y. Martin & Matthew J. G. Gage
Earth’s biodiversity is undergoing mass extinction due to anthropogenic compounding of environmental, demographic and genetic stresses. These different stresses can trap populations within a reinforcing feedback loop known as the extinction vortex, in which synergistic pressures build upon one another through time, driving down population viability. Sexual selection, the widespread evolutionary force arising from competition, choice and reproductive variance within animal mating patterns, could have vital consequences for population viability and the extinction vortex: 1)...

Plant volatiles induced by herbivore eggs prime defenses and mediate shifts in the reproductive strategy of receiving plants

Foteini Paschalidou, Lisa Eyman, James Sims, James Buckley, Nina Fatouros, Consuelo De Moraes & Mark Mescher
Plants can detect cues associated with the risk of future herbivory and modify defense phenotypes accordingly; however, our current understanding is limited both with respect to the range of early warning cues to which plants respond and the nature of the responses. Here we report that exposure to volatile emissions from plant tissues infested with herbivore eggs promotes stronger defense responses to subsequent herbivory in two Brassica species. Furthermore, exposure to these volatile cues elicited...

Data from: Genomic signatures of convergent adaptation to Alpine environments in three Brassicaceae species

Christian Rellstab, Stefan Zoller, Christian Sailer, Andrew Tedder, Felix Gugerli, Kentaro K. Shimizu, Rolf Holderegger, Alex Widmer & Martin C. Fischer
It has long been discussed to what extent related species develop similar genetic mechanisms to adapt to similar environments. Most studies documenting such convergence have either used different lineages within species or surveyed only a limited portion of the genome. Here, we investigated whether similar or different sets of orthologous genes were involved in genetic adaptation of natural populations of three related plant species to similar environmental gradients in the Alps. We used whole-genome pooled...

Immune challenges increase network centrality in a queenless ant

Giacomo Alciatore, Line V. Ugelvig, Erik Frank, Jérémie Bidaux, Asaf Gal, Thomas Schmitt, Daniel J.C. Kronauer & Yuko Ulrich
Social animals display a wide range of behavioural defences against infectious diseases, some of which inherently increase social contacts with infectious individuals (e.g., mutual grooming), while others decrease them (e.g., social exclusion). These defences often rely on the detection of infectious individuals, but this can be achieved in several ways that are difficult to differentiate. Here, we combine non-pathogenic immune challenges with automated tracking in colonies of the clonal raider ant to ask whether ants...

Data for: Immobilization of molecular catalysts on electrode surfaces using host–guest interactions

S. David Tilley, Laurent Sévery, Jacek Szczerbiński, Mert Taskin, Isik Tuncay, Fernanda Nunes, Chiara Cignarella, Gabriele Tocci, Olivier Blacque, Juerg Osterwalder, Renato Zenobi & Marcella Iannuzzi
Anchoring molecular catalysts on electrode surfaces combines the high selectivity and activity of molecular systems with the practicality of heterogeneous systems. Molecular catalysts, however, are far less stable than traditional heterogeneous electrocatalysts, and therefore a method to easily replace anchored molecular catalysts that have degraded could make such electrosynthetic systems more attractive. Here, we apply a non-covalent ‘click’ chemistry approach to reversibly bind molecular electrocatalysts to electrode surfaces through host–guest complexation with surface-anchored cyclodextrins. The...

Genomic vulnerability to rapid climate warming in a tree species with a long generation time

Benjamin Dauphin, Christian Rellstab, Max Schmid, Stefan Zoller, Dirk Karger, Sabine Brodbeck, Frédéric Guillaume & Felix Gugerli
The ongoing increase in global temperature affects biodiversity, especially in mountain regions where climate change is exacerbated. As sessile, long-lived organisms, trees are especially challenged in terms of adapting to rapid climate change. Here, we show that low rates of allele frequency shifts in Swiss stone pine (Pinus cembra) occurring near the treeline result in high genomic vulnerability to future climate warming, presumably due to the species’ long generation time. Using exome sequencing data from...

Data from: Fitness benefits to bacteria of carrying prophages and prophage-encoded antibiotic-resistance genes peak in different environments

Carolin Wendling, Alex Hall & Dominik Refardt
Understanding the role of horizontal gene transfer (HGT) in adaptation is a key challenge in evolutionary biology. In microbes, an important mechanism of HGT is prophage acquisition (phage genomes integrated into bacterial chromosomes). Prophages can influence bacterial fitness via transfer of beneficial genes (including antibiotic-resistance genes, ARGs), protection from superinfecting phages, or switching to a lytic lifecycle which releases free phages infectious to competitors. We expect these effects to depend on environmental conditions because of,...

Impacts of beekeeping on wild bee diversity and pollination networks in the Aegean Archipelago

Amparo Lázaro, Andreas Mueller, Andreas Ebmer, Holger Dathe, Erwin Scheuchl, Maximilian Schwarz, Stephan Risch, Alain Pauly, Jelle Devalez, Thomas Tscheulin, Carmelo Gómez-Martínez, Evangelos Papas, John Pickering, Nickolas Waser & Theodora Petanidou
Maintaining the diversity of wild bees is a priority for preserving ecosystem function and promoting stability and productivity of agroecosystems. However, wild bee communities face many threats and beekeeping could be one of them, because honey bees may have a strong potential to outcompete wild pollinators when placed at high densities. Yet, we still know little about how beekeeping intensity affects wild bee diversity and their pollinator interactions. Here, we explore how honey bee density...

Data from: Population genomics of the 'Arcanum' species group in wild tomatoes: evidence for separate origins of two self-compatible lineages

Mathias Scharmann, Ana M Florez-Rueda, Morgane Roth & Thomas Städler
Given their diverse mating systems and recent divergence, wild tomatoes (Solanum section Lycopersicon) have become an attractive model system to study ecological divergence, the build-up of reproductive barriers, and the causes and consequences of the breakdown of self-incompatibility. Here we report on a lesser-studied group of species known as the ‘Arcanum’ group, comprising the nominal species Solanum arcanum, S. chmielewskii and S. neorickii. The latter two taxa are self-compatible but are thought to self-fertilize at...

Human-associated microbiota suppress invading bacteria even under disruption by antibiotics

Andrew Letten, Michael Baumgartner, Katia Pfrunder-Cardozo, Jonathan Levine & Alex Hall
In light of their adverse impacts on resident microbial communities, it is widely predicted that broad-spectrum antibiotics can promote the spread of resistance by releasing resistant strains from competition with other strains and species. We investigated the competitive suppression of a resistant strain of Escherichia coli inoculated into human-associated communities in the presence and absence of the broad and narrow spectrum antibiotics rifampicin and polymyxin B, respectively. We found strong evidence of community-level suppression of...

Behavioral interactions between bacterivorous nematodes and predatory bacteria in a synthetic community

Nicola Mayrhofer, Gregory J. Velicer, Kaitlin A. Schaal & Marie Vasse
Theory and empirical studies in metazoans predict that apex predators should shape the behavior and ecology of mesopredators and prey at lower trophic levels. Despite the ecological importance of microbial communities, few studies of predatory microbes examine such behavioral responses and the multiplicity of trophic interactions. Here, we sought to assemble a three-level microbial food chain and to test for behavioral interactions between the predatory nematode Caenorhabditis elegans and the predatory social bacterium Myxococcus xanthus...

Evolution of honey resistance in experimental populations of bacteria depends on the type of honey, and has no major side effects for antibiotic susceptibility

Anna M. Bischofberger, Katia R. Pfrunder Cardozo, Michael Baumgartner & Alex R. Hall
With rising antibiotic resistance, alternative treatments for communicable diseases are increasingly relevant. One possible alternative for some types of infections is honey, used in wound care since before 2000 BCE and more recently in licensed, medical-grade products. However, it is unclear whether medical application of honey results in the evolution of bacterial honey resistance, and whether this has collateral effects on other bacterial traits such as antibiotic resistance. Here, we used single-step screening assays and...

FGF-2-dependent signaling activated in aged human skeletal muscle promotes intramuscular adipogenesis

Sebastian Mathes, Alexandra Fahrner, Umesh Ghoshdastider, Hannes A. Rüdiger, Michael Leunig, Christian Wolfrum & Jan Krützfeldt
Aged skeletal muscle is markedly affected by fatty muscle infiltration and strategies to reduce the occurrence of intramuscular adipocytes are urgently needed. Here, we show that fibroblast growth factor-2 (FGF-2) not only stimulates muscle growth, but also promotes intramuscular adipogenesis. Using multiple screening assays upstream and downstream of microRNA (miR)-29a signaling, we located the secreted protein and adipogenic inhibitor SPARC to an FGF-2 signaling pathway that is conserved between skeletal muscle cells from mice and...

Data from: Putting vascular epiphytes on the traits map

Peter Hietz, Katrin Wagner, Flavio Nunes Ramos, Juliano Sarmento Cabral, Gerhard Zotz, Claudia Agudelo, Ana Maria Benavides, Manuel Cach Pérez, Catherine Cardelús, Nahelli Chilpa Galván, Lucas Costa, Rodolfo De Paula Oliveiras, Helena Einzmann, Rafael Farias, Valeria Guzmán Jacob, Michael Kessler, Catherine Kirby, Holger Kreft, Thorsten Krömer, Jamie Males, Samuel Monsalve Correa, Maria Moreno, Gunnar Petter, Casandra Reyes, Alfredo Saldaña … & Carrie Woods
Epiphyte trait data for the paper Hietz et al. 2021 Putting vascular epiphytes on the traits map. Journal of Ecology Plant functional traits impact the fitness and environmental niche of plants. Major plant functional types have been characterized by their trait spectrum, and the environmental and phylogenetic imprints on traits have advanced several ecological fields. Yet very few trait data on epiphytes, which represent almost 10% of vascular plants, are available. We collated >80,000 mostly...

Data from: Predicting species occurrences with habitat network models

Damian Omar Ortiz-Rodríguez, Antoine Guisan, Rolf Holderegger & Maarten Van Strien
1. Biodiversity conservation requires modelling tools capable of predicting the presence or absence (i.e. occurrence-state) of species in habitat patches. Local habitat characteristics of a patch (lh), the cost of traversing the landscape matrix between patches (weighted connectivity; (wc), and the position of the patch in the habitat network topology (nt) all influence occurrence-state. Existing models are data demanding or consider only local habitat characteristics. We address these shortcomings and present a network-based modelling approach,...

Similar cost of Hamiltonella defensa in experimental and natural aphid-endosymbiont associations

Heidi Kaech, Christoph Vorburger & Stephanie Jud
Endosymbiont-conferred resistance to parasitoids is common in aphids, but comes at a cost to the host in the absence of parasitoids. In black bean aphids (Aphis fabae), costs in terms of reduced lifespan and lifetime reproduction were demonstrated by introducing eleven isolates of the protective symbiont Hamiltonella defensa into previously uninfected aphid clones. Transfection of H. defensa isolates into a common genetic background allows to compare the costs of different endosymbiont isolates unconfounded by host...

COSMO Technical Report No. 24: Online Trajectory Module in COSMO: A short user guide

A. K. Miltenberger, A. Roches, S. Pfahl & H. Wernli
The Technical Reports are intended mainly for internal use within the COSMO group (COSMO = Consortium for Small Scale Modeling), but also to inform other groups on model changes and research activities. The purpose of the Technical Reports is 1. to document scientific research activities, 2. to document technical changes to the model system, 3. to give an overview on new components of the model system.

Wenn Kühe auf Roboter treffen - Agrarwissenschaften an der ETH Zürich

Sophie Graf, Gilgen Anna & Sandra Flatt

ISIMIP3b population input data

Stefan Lange & Tobias Geiger
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 ISIMIP3b part of the third simulation round is dedicated to a quantification of climate-related risks at different levels of global warming and socio-economic change. ISIMIP3b group I simulations are based on historical...

Dataset of nanoplastic transport in soil via bioturbation by Lumbricus terrestris

Wiebke Mareile Heinze, Denise M. Mitrano, Elma Lahive, John Koestel & Geert Cornelis
The dataset comprises data acquired in laboratory-based process-studies with microcosms on the transport of nanoplastics (polystyrene, 256 nm diameter) in an agricultural soil via bioturbation over the course of 4 weeks. Transport of nanoplastics was monitored through the use of palladium (Pd)-doped nanoplastics (0.24 % w/w) by analyzing soil samples at specific depths (0-2 cm, 2-6 cm, 6-15 cm, 15-29 cm) after defined experimental times (7, 14, 21, 28 days). Microcosms consisted of 30 cm...

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  • Swiss Federal Institute of Technology in Zurich
  • ETH Zurich
  • University of Zurich
  • Swiss Federal Institute of Aquatic Science and Technology
  • Swiss Federal Institute for Forest, Snow and Landscape Research
  • Potsdam Institute for Climate Impact Research
  • University of Oxford
  • Columbia University
  • French National Centre for Scientific Research
  • Spanish National Research Council