25 Works

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: 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...

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: Isolation-by-distance in landscapes: considerations for landscape genetics

Maarten J. Van Strien, Rolf Holderegger & Henrikus J. Van Heck
In landscape genetics, isolation-by-distance (IBD) is regarded as a baseline pattern that is obtained without additional effects of landscape elements on gene flow. However, the configuration of suitable habitat patches determines deme topology, which in turn should affect rates of gene flow. IBD patterns can be characterized either by monotonically increasing pairwise genetic differentiation (for example, FST) with increasing interdeme geographic distance (case-I pattern) or by monotonically increasing pairwise genetic differentiation up to a certain...

Data from: An SNP-based second-generation genetic map of Daphnia magna and its application to QTL analysis of phenotypic traits

Jarkko Routtu, Matthew D. Hall, Brian Albere, Christian Beisel, R. Daniel Bergeron, Anurag Chaturvedi, Jeong-Hyeon Choi, John Colbourne, Luc De Meester, Melissa T. Stephens, Claus-Peter Stelzer, Eleanne Solorzano, W. Kelley Thomas, Michael E. Pfrender & Dieter Ebert
Background: Although Daphnia is increasingly recognized as a model for ecological genomics and biomedical research, there is, as of yet, no high-resolution genetic map for the genus. Such a map would provide an important tool for mapping phenotypes and assembling the genome. Here we estimate the genome size of Daphnia magna and describe the construction of an SNP array based linkage map. We then test the suitability of the map for life history and behavioural...

Data from: Large-scale proteomics of the cassava storage root and identification of a target gene to reduce post-harvest deterioration

Hervé Vanderschuren, Evans Nyaboga, Jacquelyne S. Poon, Katja Baerenfaller, Jonas Grossmann, Matthias Hirsch-Hoffmann, Norbert Kirchgessner, Paolo Nanni & Wilhelm Gruissem
Cassava (Manihot esculenta) is the most important root crop in the tropics, but rapid postharvest physiological deterioration (PPD) of the root is a major constraint to commercial cassava production. We established a reliable method for image-based PPD symptom quantification and used label-free quantitative proteomics to generate an extensive cassava root and PPD proteome. Over 2600 unique proteins were identified in the cassava root, and nearly 300 proteins showed significant abundance regulation during PPD. We identified...

Data from: Payoff-based learning explains the decline in cooperation in public goods games

Maxwell N. Burton-Chellew, Heinrich H. Nax & Stuart A. West
Economic games such as the public goods game are increasingly being used to measure social behaviours in humans and non-human primates. The results of such games have been used to argue that people are pro-social, and that humans are uniquely altruistic, willingly sacrificing their own welfare in order to benefit others. However, an alternative explanation for the empirical observations is that individuals are mistaken, but learn, during the game, how to improve their personal payoff....

Data from: The draft genome of Primula veris yields insights into the molecular basis of heterostyly

Michael D. Nowak, Giancarlo Russo, Ralph Schlapbach, Cuong Nguyen Huu, Michael Lenhard & Elena Conti
Annotation files for the Primula veris genome assemblyThe included files were produced with the Maker2 annotation pipeline.Pveris_Maker2_Genome_Annotation.tgz

Data from: Identification of ZEB1 as a central component of the adipogenic gene regulatory network

Carine Gubelmann, Petra C. Schwalie, Sunil K. Raghav, Eva Röder, Delessa Tenagne, Elke Kiehlmann, Sebastian M. Waszak, Andrea Corsinotti, Gilles Udin, Wiebke Holcombe, Gottfried Rudowsky, Didier Trono, Christian Wolfrum & Bart Deplancke
Adipose tissue is a key determinant of whole body metabolism and energy homeostasis. Unraveling the regulatory mechanisms underlying adipogenesis is therefore highly relevant from a biomedical perspective. Our current understanding of fat cell differentiation is centered on the transcriptional cascades driven by the C/EBP protein family and the master regulator PPARγ. To elucidate further components of the adipogenic gene regulatory network, we performed a large-scale transcription factor (TF) screen overexpressing 734 TFs in mouse pre-adipocytes...

Data from: Choice of capture and extraction methods affect detection of freshwater biodiversity from environmental DNA

Kristy Deiner, Jean-Claude Walser, Elvira Mächler & Florian Altermatt
Environmental DNA (eDNA) is used to detect biodiversity by the capture, extraction, and identification of DNA shed to the environment. However, eDNA capture and extraction protocols vary widely across studies. This use of different protocols potentially biases detection results and could significantly hinder a reliable use of eDNA to detect biodiversity. We tested whether choice of eDNA capture and extraction protocols significantly influenced biodiversity detection in aquatic systems. We sampled lake and river water, captured...

Data from: Quantifying temporal isolation: a modelling approach assessing the effect of flowering time differences on crop-to-weed pollen flow in sunflower

Marie Roumet, Adeline Cayre, Muriel Latreille & Marie-Hélène Muller
Flowering time divergence can be a crucial component of reproductive isolation between sympatric populations but few studies have quantified its actual contribution to the reduction of gene flow. In this study, we aimed at estimating pollen-mediated gene flow between cultivated sunflower and a weedy conspecific sunflower population growing in the same field, and at quantifying how it is affected by the weeds’ flowering time. For that purpose, we extended an existing mating model by including...

Data from: Forest trees in human modified landscapes: ecological and genetic drivers of recruitment failure in Dysoxylum malabaricum (Meliaceae)

Sascha A. Ismail, Jaboury Ghazoul, Gudasalamani Ravikanth, Cheppudira G. Kushalappa, Ramanan Uma Shaanker & Chris J. Kettle
Tropical agro-forest landscapes are global priority areas for biodiversity conservation. Little is known about the ability of these landscapes to sustain large late successional forest trees upon which much forest biodiversity depends. These landscapes are subject to fragmentation and additional habitat degradation which may limit tree recruitment and thus compromise numerous ecosystem services including carbon storage and timber production. Dysoxylum malabaricum is a large canopy tree species in the Meliaceae, a family including many important...

Data from: Genetic drift linked to heterogeneous landscape and ecological specialization drives diversification in the Alpine endemic columbine Aquilegia thalictrifolia

Margherita Lega, Simone Fior, Mingai Li, Stefano Leonardi & Claudio Varotto
The European Alpine system is an extensive mountain range, whose heterogeneous landscape together with Quaternary climatic oscillations significantly affected organismal diversity and distribution in Europe. The model genus Aquilegia represents a textbook example of a rapid and recent radiation through the Northern hemisphere, with the majority of the European taxa occuring in the Alpine system. However, the processes governing genetic differentiation of the genus in this complex geographic area are still widely unexplored. In this...

Data from: Experimental evolution of external immune defenses in the red flour beetle

Gerrit Joop, Olivia Roth, Paul Schmid-Hempel & Joachim Kurtz
The red flour beetle, Tribolium castaneum, secretes quinones that control the microbial flora in the surrounding environment. These secretions act as an external immune defence that provides protection against pathogens. At high concentrations, however, these secretions are harmful to the host itself, and selection may thus have optimized the level of expression under natural conditions. Here, we show that the expression of external immunity responded to selection during experimental evolution within a few generations. At...

Data from: Multifarious selection through environmental change: acidity and predator-mediated adaptive divergence in the moor frog (Rana arvalis)

Andrés Egea-Serrano, Sandra Hangartner, Anssi Laurila & Katja Räsänen
Environmental change can simultaneously cause abiotic stress and alter biological communities, yet adaptation of natural populations to co-changing environmental factors is poorly understood. We studied adaptation to acid and predator stress in six moor frog (Rana arvalis) populations along an acidification gradient, where abundance of invertebrate predators increases with increasing acidity of R. arvalis breeding ponds. First, we quantified divergence among the populations in anti-predator traits (behaviour and morphology) at different rearing conditions in the...

Data from: The influence of genetic drift and selection on quantitative traits in a plant pathogenic fungus

Tryggvi S. Stefansson, Bruce A. McDonald & Yvonne Willi
Genetic drift and selection are ubiquitous evolutionary forces acting to shape genetic variation in populations. While their relative importance has been well studied in plants and animals, less is known about their relative importance in fungal pathogens. Because agro-ecosystems are more homogeneous environments than natural ecosystems, stabilizing selection may play a stronger role than genetic drift or diversifying selection in shaping genetic variation among populations of fungal pathogens in agro-ecosystems. We tested this hypothesis by...

Data from: Preference for outbred host plants and positive effects of inbreeding on egg survival in a specialist herbivore

Aino Kalske, Anne Muola, Pia Mutikainen & Roosa Leimu
Inbreeding can profoundly affect the interactions of plants with herbivores as well as with the natural enemies of the herbivores. We studied how plant inbreeding affects herbivore oviposition preference, and whether inbreeding of both plants and herbivores alters the probability of predation or parasitism of herbivore eggs. In a laboratory preference test with the specialist herbivore moth Abrostola asclepiadis and inbred and outbred Vincetoxicum hirundinaria plants, we discovered that herbivores preferred to oviposit on outbred...

Data from: Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity and turnover rates are disconnected

Yaowu Xing, Renske E. Onstein, Richard J. Carter, Tanja Stadler & H. Peter Linder
The magnitude and extent of global change during the Cenozoic are remarkable, yet the impacts of these changes on biodiversity and the evolutionary dynamics of species diversification remain poorly understood. To investigate this question we combine palaeontological and neontological data for the angiosperm order Fagales, an ecologically important clade of c. 1370 species of trees with an exceptional fossil record. We show differences in patterns of accumulation of generic diversity, species richness, and turnover rates...

Data from: Lytic phages obscure the cost of antibiotic resistance in Escherichia coli

Samuel J. Tazzyman & Alex R. Hall
The long-term persistence of antibiotic-resistant bacteria depends on their fitness relative to other genotypes in the absence of drugs. Outside the laboratory, viruses that parasitize bacteria (phages) are ubiquitous, but costs of antibiotic resistance are typically studied in phage-free experimental conditions. We used a mathematical model and experiments with Escherichia coli to show that lytic phages strongly affect the incidence of antibiotic resistance in drug-free conditions. Under phage parasitism, the likelihood that antibiotic-resistant genetic backgrounds...

Data from: Plasmids and evolutionary rescue by drug resistance

Samuel J. Tazzyman & Sebastian Bonhoeffer
Antibiotic resistance provides evolutionary rescue for bacterial populations under the threat of extinction through antibiotics. It can arise de novo through mutation in the population, or be obtained from other bacterial populations via the transfer of a resistance-conferring plasmid. We use stochastic modelling methods to establish whether the most likely source of rescue is via a plasmid or via the chromosome, and show that contrary to what is assumed plasmids are not necessarily beneficial locations...

Data from: Quality attracts parasites: host condition-dependent chemo-orientation of trematode larvae

Otto Seppälä & Katja Leicht
1. Environmental factors impairing physiological condition of organisms are assumed to predispose them to parasite infections. This is because host immune function is typically condition-dependent. However, poor physiological condition has been reported to reduce host susceptibility to parasites in various systems. 2. We examined whether such an effect can be due to altered exposure of hosts to active parasite transmission stages by investigating chemo-orientation of free-swimming cercariae larvae of a parasite Echinoparyphium aconiatum towards its...

Data from: Genetic connectivity of the moth pollinated tree Glionnetia sericea in a highly fragmented habitat

Aline Finger, Christopher N. Kaiser-Bunbury, Chris J. Kettle, Terence Valentin & Jaboury Ghazoul
Long-distance gene flow is thought to be one prerequisite for the persistence of plant species in fragmented environments. Human influences have led to severe fragmentation of native habitats in the Seychelles islands, with many species surviving only in small and isolated populations. The endangered Seychelles endemic tree Glionnetia sericea is restricted to altitudes between 450 m and 900 m where the native forest vegetation has been largely lost and replaced with exotic invasives over the...

Data from: Experimental evolution of parasitoid infectivity on symbiont-protected hosts leads to the emergence of genotype-specificity

Romain Rouchet & Christoph Vorburger
Host-parasitoid interactions may lead to strong reciprocal selection for traits involved in host defense and parasitoid counter-defense. In aphids, individuals harboring the facultative bacterial endosymbiont Hamiltonella defensa exhibit enhanced resistance to parasitoid wasps. We used an experimental evolution approach to investigate the ability of the parasitoid wasp Lysiphlebus fabarum to adapt to the presence of H. defensa in its aphid host Aphis fabae. Sexual populations of the parasitoid were exposed for eleven generations to a...

Data from: Population structure of the invasive forest pathogen Hymenoscyphus pseudoalbidus

Andrin Gross, Tsuyoshi Hosoya & Valentin Queloz
Understanding the genetic diversity and structure of invasive pathogens in source and introduced areas is crucial to reveal hidden biological aspects of an organism, to reconstruct the course of invasions and to establish effective control measures. Hymenoscyphus pseudoalbidus (anamorph: Chalara fraxinea) is an invasive and highly destructive fungal pathogen on common ash Fraxinus excelsior in Europe and occurs natively in east Asia. To get insights into the dispersal mechanism and the history of invasion, we...

Data from: Cheaper isn’t always worse: more protective isolates of a defensive symbiont are less costly to the aphid host

Luis Cayetano, Lukas Rothacher, Jean-Christophe Simon, Christoph Vorburger & J.-C. Simon
Defences against parasites are typically associated with costs to the host that contribute to the maintenance of variation in resistance. This also applies to the defence provided by the facultative bacterial endosymbiont Hamiltonella defensa, which protects its aphid hosts against parasitoid wasps while imposing life-history costs. To investigate the cost–benefit relationship within protected hosts, we introduced multiple isolates of H. defensa to the same genetic backgrounds of black bean aphids, Aphis fabae, and we quantified...

Registration Year

  • 2014

Resource Types

  • Dataset


  • Swiss Federal Institute of Technology in Zurich
  • University of Zurich
  • Swiss Federal Institute of Aquatic Science and Technology
  • University of Oxford
  • French National Institute for Agricultural Research
  • Swiss Institute of Bioinformatics
  • National Museum
  • University of Neuchâtel
  • Augusta University
  • University of Melbourne