505 Works

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: Simple chained guide trees give poorer multiple sequence alignments than inferred trees in simulation and phylogenetic benchmarks

Ge Tan, Manuel Gil, Ari P. Löytynoja, Nick Goldman & Christophe Dessimoz
Multiple sequence aligners typically work by progressively aligning the most closely related sequences or group of sequences according to guide trees. In PNAS, Boyce et al. report that alignments reconstructed using simple chained trees (i.e., comb-like topologies) with random leaf assignment performed better in protein structure-based benchmarks than those reconstructed using phylogenies estimated from the data as guide trees. The authors state that this result could turn decades of research in the field on its...

Data from: Transition from one- to two-dimensional development facilitates maintenance of multicellularity

Alejandra M. Manjarrez-Casas, Homayoun C. Bagheri & Akos Dobay
Filamentous organisms represent an example where incomplete separation after cell division underlies the development of multicellular formations. With a view to understanding the evolution of more complex multicellular structures, we explore the transition of multicellular growth from one to two dimensions. We develop a computational model to simulate multicellular development in populations where cells exhibit density-dependent division and death rates. In both the one- and two-dimensional contexts, multicellular formations go through a developmental cycle of...

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: Evidence for nonconsumptive effects from a large predator in an ungulate prey?

Benedikt Gehr, Elizabeth J. Hofer, Andreas Ryser, Eric Vimercati, Kristina Vogt & Lukas F. Keller
Pedators can indirectly affect prey survival and reproduction by evoking costly anti-predator responses. Such non-consumptive effects may be as strong or stronger than consumptive predator effects. However, evidence for this in large terrestrial vertebrate systems is equivocal and few studies quantify the actual fitness costs of non-consumptive effects. Here we investigated whether non-consumptive effects elicited by Eurasian lynx (Lynx lynx), a large terrestrial predator, reduced survival in an ungulate prey, the European roe deer (Capreolus...

Data from: How well can body size represent effects of the environment on demographic rates? Disentangling correlated explanatory variables

Mollie E. Brooks, Marianne Mugabo, Gwendolen M. Rogers, Timothy G. Benton, Arpat Ozgul & Gwendolen M. Rodgers
Demographic rates are shaped by the interaction of past and current environments that individuals in a population experience. Past environments shape individual states via selection and plasticity, and fitness-related traits (e.g. individual size) are commonly used in demographic analyses to represent the effect of past environments on demographic rates. We quantified how well the size of individuals captures the effects of a population's past and current environments on demographic rates in a well-studied experimental system...

Data from: The diversity of population responses to environmental change

Fernando Colchero, Owen R. Jones, Dalia A. Conde, Dave Hodgson, Felix Zajitschek, Benedikt R. Schmidt, Aurelio F. Malo, Susan C. Alberts, Peter H. Becker, Sandra Bouwhuis, Anne M. Bronikowski, Kristel M. De Vleeschouwer, Richard J. Delahay, Stefan Dummermuth, Eduardo Fernández-Duque, John Frisenvænge, Martin Hesselsøe, Sam Larson, Jean-Francois Lemaitre, Jennifer McDonald, David A.W. Miller, Colin O'Donnell, Craig Packer, Becky E. Raboy, Christopher J. Reading … & Chris J. Reading
The current extinction and climate change crises pressure us to predict population dynamics with ever-greater accuracy. Although predictions rest on the well-advanced theory of age-structured populations, two key issues remain poorly-explored. Specifically, how the age-dependency in demographic rates and the year-to-year interactions between survival and fecundity affect stochastic population growth rates. We use inference, simulations, and mathematical derivations to explore how environmental perturbations determine population growth rates for populations with different age-specific demographic rates and...

Data from: A new paleoecological look at the Dinwoody Formation (Lower Triassic, western U.S.): intrinsic versus extrinsic controls on ecosystem recovery after the end-Permian mass extinction

Richard Hofmann, Michael Hautmann & Hugo Bucher
The Dinwoody Formation of the Western U.S. represents an important archive of Early Triassic ecosystems in the immediate aftermath of the end-Permian mass extinction. We present a systematic description and a quantitative paleoecological analysis of its benthic faunas in order to reconstruct benthic associations and to explore the temporal and spatial variations of diversity, ecological structure and taxonomic composition throughout the earliest Triassic of the western U.S. A total of 15 bivalve species, two gastropod...

Data from: Experimental evolution for generalists and specialists reveals multivariate genetic constraints on thermal reaction norms

David Berger, Richard J. Walters & Wolf U. Blanckenhorn
Theory predicts the emergence of generalists in variable environments and antagonistic pleiotropy to favour specialists in constant environments, but empirical data seldom support such generalist–specialist trade-offs. We selected for generalists and specialists in the dung fly Sepsis punctum (Diptera: Sepsidae) under conditions that we predicted would reveal antagonistic pleiotropy and multivariate trade-offs underlying thermal reaction norms for juvenile development. We performed replicated laboratory evolution using four treatments: adaptation at a hot (31 °C) or a...

Data from: Land-use intensity and the effects of organic farming on biodiversity: a hierarchical meta-analysis

Sean L. Tuck, Camilla Winqvist, Flávia Mota, Johan Ahnström, Lindsay A. Turnbull & Janne Bengtsson
The benefits of organic farming to biodiversity in agricultural landscapes continue to be hotly debated, emphasising the importance of precisely quantifying the effect of organic vs. conventional farming. We conducted an updated hierarchical meta-analysis of studies that compared biodiversity under organic and conventional farming methods, measured as species richness. We calculated effect sizes for 184 observations garnered from 94 studies, and for each study we obtained three standardised measures reflecting land-use intensity. We investigated the...

Data from: Dendritic network structure and dispersal affect temporal dynamics of diversity and species persistence

Mathew Seymour, Emanuel A. Fronhofer & Florian Altermatt
Landscape connectivity structure, specifically the dendritic network structure of rivers, is expected to influence community diversity dynamics by altering dispersal patterns, and subsequently the unfolding of species interactions. However, previous comparative and experimental work on dendritic metacommunities has studied diversity mostly from an equilibrium perspective. Here we investigated the effect of dendritic versus linear network structure on local (α-diversity), among (β-diversity) and total (γ-diversity) temporal species community diversity dynamics. Using a combination of microcosm experiments,...

Data from: Polymorphisms at the innate immune receptor TLR2 are associated with Borrelia infection in a wild rodent population

Barbara Tschirren, Martin Andersson, Kristin Scherman, Helena Westerdahl, Peer R. E. Mittl & Lars Raberg
The discovery of the key role of Toll-like receptors (TLRs) in initiating innate immune responses and modulating adaptive immunity has revolutionised our understanding of vertebrate defence against pathogens. Yet, despite their central role in pathogen recognition and defence initiation, there is little information on how variation in TLRs influences disease susceptibility in natural populations. Here we assessed the extent of naturally occurring polymorphisms at TLR2 in wild bank voles (Myodes glareolus) and tested for associations...

Data from: Pedigree error due to extra-pair reproduction substantially biases estimates of inbreeding depression

Jane M. Reid, Lukas F. Keller, Amy B. Marr, Pirmin Nietlisbach, Rebecca J. Sardell & Peter Arcese
Understanding the evolutionary dynamics of inbreeding and inbreeding depression requires unbiased estimation of inbreeding depression across diverse mating systems. However, studies estimating inbreeding depression often measure inbreeding with error, for example, based on pedigree data derived from observed parental behavior that ignore paternity error stemming from multiple mating. Such paternity error causes error in estimated coefficients of inbreeding (f) and reproductive success and could bias estimates of inbreeding depression. We used complete “apparent” pedigree data...

Data from: Red and orange flags for secondary headaches in clinical practice: SNNOOP10 list

Thien Phu Do, Angelique Remmers, Henrik Winther Schytz, Christoph Schankin, Sarah E. Nelson, Mark Obermann, Jakob Møller Hansen, Alexandra J. Sinclair, Andreas R. Ganteinbein & Guus G. Schoonman
A minority of headache patients have a secondary headache disorder. The medical literature presents and promotes red flags to increase the likelihood of identifying a secondary etiology. In this review, we aim to discuss the incidence and prevalence of secondary headaches as well as the data on sensitivity, specificity, and predictive value of red flags for secondary headaches. We review the following red flags: (1) systemic symptoms including fever; (2) neoplasm history; (3) neurologic deficit...

Data from: The evolution of costly mate choice against segregation distorters

Andri Manser, Anna K. Lindholm, Franjo J. Weissing & Franz J. Weissing
The evolution of female preference for male genetic quality remains a controversial topic in sexual selection research. One well-known problem, known as the lek paradox, lies in understanding how variation in genetic quality is maintained in spite of natural selection and sexual selection against low-quality alleles. Here, we theoretically investigate a scenario where females pay a direct fitness cost to avoid males carrying an autosomal segregation distorter. We show that preference evolution is greatly facilitated...

Data from: Enhancing plant diversity in agricultural landscapes promotes both rare bees and dominant crop-pollinating bees through complementary increase in key floral resources

Louis Sutter, Philippe Jeanneret, Agustín M. Bartual, Gionata Bocci & Matthias Albrecht
1. Enhancing key floral resources is essential to effectively mitigate the loss of pollinator diversity and associated provisioning of pollination functions in agro-ecosystems. However, effective floral provisioning measures may diverge among different pollinator conservation targets, such as the conservation of rare species or the promotion of economically important crop pollinators. We examined to what extent such diverging conservation goals could be reconciled. 2. We analysed plant–bee visitation networks of 64 herbaceous semi-natural habitats representing a...

Data from: Small-scale spatial variation in infection risk shapes the evolution of a Borrelia resistance gene in wild rodents

Luca Cornetti, Daniela Hilfiker, Mélissa Lemoine & Barbara Tschirren
Spatial variation in pathogen-mediated selection is predicted to influence the evolutionary trajectory of host populations and lead to spatial variation in their immunogenetic composition. However, to date few studies have been able to directly link small-scale spatial variation in infection risk to host immune gene evolution in natural, non-human populations. Here we use a natural rodent-Borrelia system to test for associations between landscape-level spatial variation in Borrelia infection risk along replicated elevational gradients in the...

Data from: Extra-pair paternity and the variance in male fitness in song sparrows (Melospiza melodia)

Christophe Lebigre, Peter Arcese, Rebecca J. Sardell, Lukas F. Keller & Jane M. Reid
The variance in fitness across population members can influence major evolutionary processes. In socially monogamous but genetically polygynandrous species, extra-pair paternity (EPP) is widely hypothesized to increase the variance in male fitness compared to that arising given the socially monogamous mating system. This hypothesis has not been definitively tested because comprehensive data describing males’ apparent (social) and realized (genetic) fitness have been lacking. We used 16 years of comprehensive social and genetic paternity data for...

Data from: Polyandry and the decrease of a selfish genetic element in a wild house mouse population

Andri Manser, Anna K. Lindholm, Barbara König & Homayoun C. Bagheri
Despite deleterious effects on individuals, the t haplotype is a selfish genetic element present in many house mouse populations. By distorting the transmission ratio, +/t males transmit the t haplotype to up to 90% of their offspring. However, t/t individuals perish in utero. Theoretical models based on these properties predict a much higher t frequency than observed, leading to the t paradox. Here, we use empirical field data and theoretical approaches to investigate whether polyandry...

Data from: Lifespan and reproductive cost explain interspecific variation in the optimal onset of reproduction

Emeline Mourocq, Pierre Bize, Sandra Bouwhuis, Russell Bradley, Anne Charmantier, Carlos De La Cruz, Szymon Marian Obniak, Richard H. M. Espie, Márton Herenyi, Hermann Hötker, Oliver Kruger, John Marzluff, Anders P. Møller, Shinichi Nakagawa, Richard A. Phillips, Andrew N. Radford, Alexandre Roulin, János Török, Juliana Valencia, Martijn Van De Pol, Ian G. Warkentin, Isabel S. Winney, Andrew G. Wood, Michael Griesser & Szymon M. Drobniak
Fitness can be profoundly influenced by the age at first reproduction (AFR), but to date the AFR-fitness relationship only has been investigated intraspecifically. Here we investigated the relationship between AFR and average lifetime reproductive success (LRS) across 34 bird species. We assessed differences in the deviation of the Optimal AFR (i.e., the species-specific AFR associated with the highest LRS) from the age at sexual maturity, considering potential effects of life-history as well as social and...

Data from: A reassessment of explanations for discordant introgressions of mitochondrial and nuclear genomes

Timothée Bonnet, Raphaël Leblois, Francois Rousset & Pierre-André Crochet
Hybridization is increasingly recognized as a significant evolutionary process, in particular because it can lead to introgression of genes from one species to another. A striking pattern of discordance in the amount of introgression between mitochondrial and nuclear markers exists such that substantial mitochondrial introgression is often found in combination with no or little nuclear introgression. Multiple mechanisms have been proposed to explain this discordance, including positive selection for introgressing mitochondrial variants, several types of...

Data from: Group cohesion in foraging meerkats: follow the moving ‘vocal hot spot’

Gabriella E.C. Gall, Marta B. Manser & Gabriella E. C. Gall
Group coordination, when ‘on the move’ or when visibility is low, is a challenge faced by many social living animals. While some animals manage to maintain cohesion solely through visual contact, the mechanism of group cohesion through other modes of communication, a necessity when visual contact is reduced, is not yet understood. Meerkats (Suricata suricatta), a small, social carnivore, forage as a cohesive group while moving continuously. While foraging, they frequently emit ‘close calls’, soft...

Data from: Agreements between industry and academia on publication rights: a retrospective study of protocols and publications of randomized clinical trials

Benjamin Kasenda, Erik Von Elm, John J. You, Anette Blümle, Yuki Tomonaga, Ramon Saccilotto, Alain Amstutz, Theresa Bengough, Joerg J. Meerpohl, Mihaela Stegert, Kelechi K. Olu, Kari A. O. Tikkinen, Ignacio Neumann, Alonso Carrasco-Labra, Markus Faulhaber, Sohail M. Mulla, Dominik Mertz, Elie A. Akl, Dirk Bassler, Jason W. Busse, Ignacio Ferreira-González, Francois Lamontagne, Alain Nordmann, Viktoria Gloy, Heike Raatz … & Matthias Briel
Background: Little is known about publication agreements between industry and academic investigators in trial protocols and the consistency of these agreements with corresponding statements in publications. We aimed to investigate (i) the existence and types of publication agreements in trial protocols, (ii) the completeness and consistency of the reporting of these agreements in subsequent publications, and (iii) the frequency of co-authorship by industry employees. Methods and Findings: We used a retrospective cohort of randomized clinical...

Electrophysiological recordings showing allosteric modulation of LRRC8 channels by targeting their cytoplasmic domains with specific sybodies

Sonja Rutz, Dawid Deneka, Raimund Dutzler & Marta Sawicka
Members of the LRRC8 family form heteromeric assemblies, which function as volume-regulated anion channels. These modular proteins consist of a transmembrane pore and cytoplasmic leucine-rich repeat (LRR) domains. Despite their known molecular architecture, the mechanism of activation and the role of the LRR domains in this process has remained elusive. Here we have addressed this question by generating synthetic nanobodies, termed sybodies, which target the LRR domain of the obligatory subunit LRRC8A.We used these binders...

Image stack, PLY-files and a NEX-file accompanying: A new symmoriiform from the Late Devonian of Morocco: novel jaw function in ancient sharks

Linda Frey, Michael I. Coates, Kristen Tietjen, Martin Rücklin & Christian Klug
We describe the small chondrichthyan Ferromirum oukherbouchi n.gen. et sp. from the Famennian (Late Devonian) of the Maïder region in Morocco. This chondrichthyan is exceptionally well preserved and displays not only mineralized soft tissues but also undeformed cartilages of the head, gills, and shoulder girdle. A reconstruction of the head using 3D-prints revealed a previously unknown kind of jaw articulation. Here, we make the original cropped image stack and PLY-files of the single cartilaginous elements...

Registration Year

  • 2022
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  • 2013

Resource Types

  • Dataset


  • University of Zurich
  • Swiss Federal Institute of Technology in Zurich
  • Swiss Federal Institute of Aquatic Science and Technology
  • University of Oxford
  • University of Bern
  • Uppsala University
  • University of Cambridge
  • University of Lausanne
  • University of Basel
  • University of Exeter