356 Works

Data from: Only helpful when required: a longevity cost of harbouring defensive symbionts

Christoph Vorburger & Alexandre Gouskov
Maternally transmitted symbionts can spread in host populations if they provide a fitness benefit to their hosts. Hamiltonella defensa, a bacterial endosymbiont of aphids, protects hosts against parasitoids but only occurs at moderate frequencies in most aphid populations. This suggests that harbouring this symbiont is also associated with costs, yet the nature of these costs has remained elusive. Here we demonstrate an important and clearly defined cost: reduced longevity. Experimental infections with six different isolates...

Data from: Back from the brink: potential for genetic rescue in a critically endangered tree

Aline Finger, Chris J Kettle, Christopher N Kaiser-Bunbury, Terence Valentin, Denis Matatiken, Damien Dudee & Jaboury Ghazoul
Rare plant species are vulnerable to genetic erosion and inbreeding associated with small population size and isolation due to increasing fragmentation, though the degree to which these problems undermine population viability remains debated. We explore genetic and reproductive processes in the critically endangered long-lived tropical tree Medusagyne oppositifolia, an endemic to the Seychelles with a naturally patchy distribution. This species is failing to recruit in three of its four populations. We evaluate whether recruitment failure...

Data from: The structural and functional connectivity of the grassland plant Lychnis flos-cuculi

Tsipe Aavik, Rolf Holderegger & Janine Bolliger
Understanding the relationship between structural and functional connectivity is essential for successful restoration and conservation management, particularly in intensely managed agricultural landscapes. We evaluated the relationship between structural and functional connectivity of the wetland plant Lychnis flos-cuculi in a fragmented agricultural landscape using landscape genetic and network approaches. First, we studied the effect of structural connectivity, such as geographic distance and various landscape elements (forest, agricultural land, settlements and ditch verges), on gene flow among...

Data from: Migration patterns and changes in population biology associated with the worldwide spread of the oilseed rape pathogen Leptosphaeria maculans

Azita Dilmaghani, Pierre Gladieux, Lilian Gout, Tatiana Giraud, Patrick C. Brunner, Anna Stachowiak, Marie-Hélène Balesdent & Thierry Rouxel
Pathogen introductions into novel areas can lead to the emergence of new fungal diseases of plants. Understanding the origin, introduction pathways, possible changes in reproductive system and population size of fungal pathogens is essential in devising an integrated strategy for the control of these diseases. We used minisatellite markers to infer the worldwide invasion history of the fungal plant pathogen Leptosphaeria maculans, which causes stem canker (blackleg) of oilseed and vegetable brassicas. Clustering analyses partitioned...

SHARE European Earthquake Catalogue (SHEEC) 1000-1899

Massimiliano Stucchi, Andrea Rovida, Augusto Antonio Gómez Capera, Pierre Alexandre, Thierry Camelbeeck, Mine Betül Demircioglu, Paolo Gasperini, Vasiliki Kouskouna, Roger M.W. Musson, Mircea Radulian, Karin Sesetyan, Susana Pires Vilanova, David Baumont, Hilmar Bungum, Donat Fäh, Wolfgang Lenhardt, Konstantinos Makropoulos, José Manuel Martínez Solares, Oona Scotti, Mladen Živčić, Paola Albini, Josep Batlló, Christos A. Papaioannou, Ruben Tatevossian, Mario Locati … & Domenico Giardini
The SHARE European Earthquake Catalogue (SHEEC) 1000-1899 has been compiled in the frame of the EC project "SHARE" (Seismic Hazard Harmonization in Europe; 2009-2012).nIt relies on the experience of the EC I3 project "Network of Research Infrastructures for European Seismology" (NERIES; 2006-2010), a module of which was dedicated to create the Europeann"Archive of Historical Earthquake Data" (AHEAD) and to establish methodologies to homogenously derive earthquake parameters from macroseismic data.nAHEAD has supplied the final earthquake list,...

Data from: Altruism can evolve when relatedness is low: evidence from bacteria committing suicide upon phage infection

Dominik Refardt, Tobias Bergmiller & Rolf Kümmerli
High relatedness among interacting individuals has generally been considered a precondition for the evolution of altruism. However, kin-selection theory also predicts the evolution of altruism when relatedness is low, as long as the cost of the altruistic act is minor compared to its benefit. Here, we demonstrate evidence for a low-cost altruistic act in bacteria. We investigated Escherichia coli responding to the attack of an obligately lytic phage by committing suicide in order to prevent...

Data from: De novo transcriptome analysis of the common New Zealand stick insect Clitarchus hookeri (Phasmatodea) reveals genes involved in olfaction, digestion and sexual reproduction

Chen Wu, Ross N Crowhurst, Alice B. Dennis, Victoria G. Twort, Shanlin Liu, Richard D. Newcomb, Howard A. Ross & Thomas R. Buckley
Phasmatodea, more commonly known as stick insects, have been poorly studied at the molecular level for several key traits, such as components of the sensory system and regulators of reproduction and development, impeding a deeper understanding of their functional biology. Here, we employ de novo transcriptome analysis to identify genes with primary functions related to female odour reception, digestion, and male sexual traits in the New Zealand common stick insect Clitarchus hookeri (White). The female...

Data from: Yield of temperate forage grassland species is either largely resistant or resilient to experimental summer drought

Daniel Hofer, Matthias Suter, Eamon Haughey, John A. Finn, Nyncke J. Hoekstra, Nina Buchmann & Andreas Lüscher
Due to climate change, an increasing frequency and severity of drought events are expected to impair grassland productivity, particularly of intensively managed temperate grasslands. To assess drought impacts, a common field experiment to manipulate precipitation was set up at three sites (two Swiss and one Irish) using monocultures and mixtures with two and four key forage species. Species differed in their functional traits: a shallow-rooted non-legume (Lolium perenne L.), a deep-rooted non-legume (Cichorium intybus L.),...

Data from: Dynamic NF-κB and E2F interactions control the priority and timing of inflammatory signalling and cell proliferation

John M. Ankers, Raheela Awais, Nicholas A. Jones, James Boyd, Sheila Ryan, Anotony D. Adamson, Claire V. Harper, Lloyd Bridge, David G. Spiller, Dean A. Jackson, Pawel Paszek, Violaine Sée & Micheal R. H. White
Dynamic cellular systems reprogram gene expression to ensure appropriate cellular fate responses to specific extracellular cues. Here we demonstrate that the dynamics of Nuclear Factor kappa B (NF-κB) signalling and the cell cycle are prioritised differently depending on the timing of an inflammatory signal. Using iterative experimental and computational analyses, we show physical and functional interactions between NF-κB and the E2 Factor 1 (E2F-1) and E2 Factor 4 (E2F-4) cell cycle regulators. These interactions modulate...

Data from: A global meta-analysis on the ecological drivers of forest restoration success

Renato Crouzeilles, Michael Curran, Mariana S. Ferreira, David B. Lindenmayer, Carlos E. V. Grelle & José M. Rey Benayas
Two billion ha have been identified globally for forest restoration. Our meta-analysis encompassing 221 study landscapes worldwide reveals forest restoration enhances biodiversity by 15–84% and vegetation structure by 36–77%, compared with degraded ecosystems. For the first time, we identify the main ecological drivers of forest restoration success (defined as a return to a reference condition, that is, old-growth forest) at both the local and landscape scale. These are as follows: the time elapsed since restoration...

Data from: Quantifying age-dependent extinction from species phylogenies

Helen K. Alexander, Amaury Lambert & Tanja Stadler
Several ecological factors that could play into species extinction are expected to correlate with species age, i.e., time elapsed since the species arose by speciation. To date, however, statistical tools to incorporate species age into likelihood-based phylogenetic inference have been lacking. We present here a computational framework to quantify age-dependent extinction through maximum likelihood parameter estimation based on phylogenetic trees, assuming species lifetimes are gamma distributed. Testing on simulated trees shows that neglecting age dependence...

Data from: Fish population genetic structure shaped by hydroelectric power plants in the upper Rhine catchment

Alexandre Gouskov, Marta Reyes, Lisa Wirthner-Bitterlin & Christoph Vorburger
The Rhine catchment in Switzerland has been transformed by a chain of hydroelectric power stations. We addressed the impact of fragmentation on the genetic structure of fish populations by focusing on the European chub (Squalius cephalus). This fish species is not stocked and copes well with altered habitats, enabling an assessment of the effects of fragmentation per se. Using microsatellites, we genotyped 2133 chub from 47 sites within the catchment fragmented by 37 hydroelectric power...

Data from: Horizontal gene acquisitions, mobile element proliferation, and genome decay in the host - restricted plant pathogen Erwinia tracheiphila

Lori R. Shapiro, Erin D. Scully, Timothy J. Straub, Jihye Park, Andrew G. Stephenson, Gwyn A. Beattie, Mark L. Gleason, Roberto Kolter, Miguel C. Coelho, Consuelo M. De Moraes, Mark C. Mescher & Olga Zhaxybayeva
Modern industrial agriculture depends on high density cultivation of genetically similar crop plants, creating favorable conditions for the emergence of novel pathogens with increased fitness in managed compared to ecologically intact settings. Here, we present the genome sequence of six strains of the cucurbit bacterial wilt pathogen Erwinia tracheiphila (Enterobacteriaceae) isolated from infected squash plants in New York, Pennsylvania, Kentucky, and Michigan. These genomes exhibit a high proportion of recent horizontal gene acquisitions, invasion and...

Data from: Bayesian total-evidence dating reveals the recent crown radiation of penguins

Alexandra Gavryushkina, Tracy A. Heath, Daniel T. Ksepka, Tanja Stadler, David Welch & Alexei J. Drummond
The total-evidence approach to divergence time dating uses molecular and morphological data from extant and fossil species to infer phylogenetic relationships, species divergence times, and macroevolutionary parameters in a single coherent framework. Current model-based implementations of this approach lack an appropriate model for the tree describing the diversification and fossilization process and can produce estimates that lead to erroneous conclusions. We address this shortcoming by providing a total-evidence method implemented in a Bayesian framework. This...

Data from: Infection-induced behavioural changes reduce connectivity and the potential for disease spread in wild mice contact networks

Patricia C. Lopes, Per Block & Barbara König
Infection may modify the behaviour of the host and of its conspecifics in a group, potentially altering social connectivity. Because many infectious diseases are transmitted through social contact, social connectivity changes can impact transmission dynamics. Previous approaches to understanding disease transmission dynamics in wild populations were limited in their ability to disentangle different factors that determine the outcome of disease outbreaks. Here we ask how social connectivity is affected by infection and how this relationship...

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: 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...

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: Hidden diversity in the freshwater planktonic diatom Asterionella formosa

Silke Van Den Wyngaert, Markus Möst, Remo Freimann, Bastiaan W. Ibelings & Piet Spaak
Many freshwater and marine algal species are described as having cosmopolitan distributions. Whether these widely distributed morphologically similar algae also share a similar gene pool remains often unclear. In the context of island biogeography theory, stronger spatial isolation deemed typical of freshwater lakes should restrict gene flow and lead to higher genetic differentiation among lakes. Using nine microsatellite loci, we investigate the genetic diversity of a widely distributed freshwater planktonic diatom, Asterionella formosa, across different...

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: Age-dependent speciation can explain the shape of empirical phylogenies

Oskar Hagen, Klaas Hartmann, Mike Steel & Tanja Stadler
Tens of thousands of phylogenetic trees, describing the evolutionary relationships between hundreds of thousands of taxa, are readily obtainable from various databases. From such trees inferences can be made about the underlying macroevolutionary processes, yet remarkably these processes are still poorly understood. Simple and widely used evolutionary null models are problematic: empirical trees show very different imbalance between the sizes of the daughter clades of ancestral taxa compared to what models predict. Obtaining a simple...

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: 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: Local human pressures influence gene flow in a hybridizing Daphnia species complex

Benjamin Alric, Markus Möst, Isabelle Domaizon, Cecile Pignol, Piet Spaak & Marie-Elodie Perga
Anthropogenic environmental changes are considered critical drivers of the genetic structure of populations and communities through, for example, the facilitation of introgressive hybridization between syntopic species. However, the mechanisms by which environmental perturbations trigger changes in the genetic structure of populations and communities, such as the processes that determine the directionality of hybridization and patterns of mitochondrial introgression over many generations, remain largely unexplored. In this study, the changes in genetic structure of hybridizing members...

Data from: Invasiveness of plant pathogens depends on the spatial scale of host distribution

Alexey Mikaberidze, Christopher C. Mundt & Sebastian Bonhoeffer
Plant diseases often cause serious yield losses in agriculture. A pathogen’s invasiveness can be quantified by the basic reproductive number, R0. Since pathogen transmission between host plants depends on the spatial separation between them, R0 is strongly influenced by the spatial scale of the host distribution.We present a proof of principle of a novel approach to estimate the basic reproductive number, R0, of plant pathogens as a function of the size of a field planted...

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