365 Works

Data from: Robustness of the outcome of adult bumblebee infection with a trypanosome parasite after varied parasite exposures during larval development

Gabriel Cisarovsky, Paul Schmid-Hempel & Ben M. Sadd
The outcome of defence by the invertebrate immunity has recently been shown to be more complex than previously thought. In particular, the outcome is affected by biotic and abiotic environmental variation, host genotype, parasite genotype, and their interaction. Knowledge of conditions under which environmental variation affects the outcome of an infection is one important question that relates to this complexity. We here use the model system of the bumblebee, Bombus terrestris infected by the trypanosome,...

Data from: Estimating speciation and extinction rates for phylogenies of higher taxa

Tanja Stadler & Folmer Bokma
Speciation and extinction rates can be estimated from molecular phylogenies. Recently, a number of methods have been published showing that these rates can be estimated even if the phylogeny is incomplete, that is, if not all extant species are included. We show that the accuracy of such methods strongly depends on making the correct assumptions about how the sampling process was performed. We focus on phylogenies that are incomplete because some subclades (e.g., genera and...

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: 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: 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: 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: 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: 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: 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: 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: 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 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: 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: 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: 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: 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: 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: Manipulation of light spectral quality disrupts host location and attachment by parasitic plants in the genus Cuscuta

Beth I. Johnson, Consuelo M. De Moraes & Mark C. Mescher
Parasitic plants in the genus Cuscuta (dodders) make their living by extracting resources from other plants. While relatively few dodder species are agricultural pests, those that are can be challenging to control, in part due to their intimate physical and physiological association with host plants. Consequently, dodders remain pervasive and economically damaging pests in a variety of crop systems. The development of improved management strategies would be facilitated by greater understanding of the ecological and...

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: Nesting sites of giant honey bees modulated by landscape patterns

Charlotte Pavageau, Cédric Gaucherel, Claude Garcia & Jaboury Ghazoul
1. The composition of agro-ecological landscapes is thought to have important implications for the production of major crops through its effects on pollinator abundance and behaviour. 2. We explored the roles of land cover and land cover heterogeneity on bee nest distribution for Apis dorsata, a key species for coffee pollination, in a complex agroforest landscape. We emphasized scaling and non-uniform effects by combining two different approaches of spatial analysis, the point-pattern analysis and surface-pattern...

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: 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: Cryptic lineages of a common alpine mayfly show strong life-history divergence

Marie Leys, Irene Keller, Christopher T. Robinson & Katja Räsänen
Understanding ecological divergence of morphologically similar but genetically distinct species – previously considered as a single morphospecies – is of key importance in evolutionary ecology and conservation biology. Despite their morphological similarity, cryptic species may have evolved distinct adaptations. If such ecological divergence is unaccounted for, any predictions about their responses to environmental change and biodiversity loss may be biased. We used spatio-temporally replicated field surveys of larval cohort structure and population genetic analyses (using...

Data from: The predictability of a lake phytoplankton community, over time-scales of hours to years

Mridul K. Thomas, Simone Fontana, Marta Reyes, Michael Kehoe & Francesco Pomati
Forecasting changes to ecological communities is one of the central challenges in ecology. However, nonlinear dependencies, biotic interactions and data limitations have limited our ability to assess how predictable communities are. We used a machine learning approach and environmental monitoring data (biological, physical and chemical) to assess the predictability of phytoplankton cell density in one lake across an unprecedented range of time scales. Communities were highly predictable over hours to months: model R2 decreased from...

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