40 Works

Data from: Functional role of phenylacetic acid from metapleural gland secretions in controlling fungal pathogens in evolutionarily derived leafcutter ants

Hermógenes Fernández-Marín, David R. Nash, Sara Higginbotham, Catalina Estrada, Jelle S. Van Zweden, Patrizia D'Ettorre, William T. Wcislo, Jacobus J. Boomsma & H. Fernandez-Marin
Fungus-farming ant colonies vary four to five orders of magnitude in size. They employ compounds from actinomycete bacteria and exocrine glands as antimicrobial agents. Atta colonies have millions of ants and are particularly relevant for understanding hygienic strategies as they have abandoned their ancestors' prime dependence on antibiotic-based biological control in favour of using metapleural gland (MG) chemical secretions. Atta MGs are unique in synthesizing large quantities of phenylacetic acid (PAA), a known but little...

Data from: An assessment of ancient DNA preservation in Holocene-Pleistocene fossil bone excavated from the world heritage Naracoorte Caves, South Australia

Alicia Grealy, Amy Macken, Morten E. Allentoft, Nicolas J. Rawlence, Elizabeth Reed & Michael Bunce
Although there is a long history of research into the fossil deposits of the Naracoorte Caves (South Australia), ancient DNA (aDNA) has not been integrated into any palaeontological study from this World Heritage site. Here, we provide the first evidence of aDNA preservation in Holocene- and Pleistocene-aged fossil bone from a deposit inside Robertson Cave. Using a combination of metabarcoding and shotgun next-generation sequencing approaches, we demonstrate that aDNA from diverse taxa can be retrieved...

Data from: Identification of multiple QTL hotspots in sockeye salmon (Oncorhynchus nerka) using genotyping-by-sequencing and a dense linkage map

Wesley A. Larson, Garrett J. McKinney, Morten T. Limborg, Meredith V. Everett, Lisa W. Seeb & James E. Seeb
Understanding the genetic architecture of phenotypic traits can provide important information about the mechanisms and genomic regions involved in local adaptation and speciation. Here, we used genotyping-by-sequencing and a combination of previously published and newly generated data to construct sex-specific linkage maps for sockeye salmon (Oncorhynchus nerka). We then used the denser female linkage map to conduct quantitative trait locus (QTL) analysis for 4 phenotypic traits in 3 families. The female linkage map consisted of...

Data from: Interaction specificity between leaf-cutting ants and vertically transmitted Pseudonocardia bacteria

Sandra B. Andersen, Sze Huei Yek, David R. Nash & Jacobus J. Boomsma
Background: The obligate mutualism between fungus-growing ants and microbial symbionts offers excellent opportunities to study the specificity and stability of multi-species interactions. In addition to cultivating fungus gardens, these ants have domesticated actinomycete bacteria to defend gardens against the fungal parasite Escovopsis and possibly other pathogens. Panamanian Acromyrmex echinatior leaf-cutting ants primarily associate with actinomycetes of the genus Pseudonocardia. Colonies are inoculated with one of two vertically transmitted phylotypes (Ps1 or Ps2), and maintain the...

Data from: Convergent evolution of highly reduced fruiting bodies in Pezizomycotina suggests key adaptations to the bee habitat

Anja Amtoft Wynns
Background: Among the understudied fungi found in nature are those living in close association with social and solitary bees. The bee-specialist genera Bettsia, Ascosphaera and Eremascus are remarkable not only for their specialized niche but also for their simple fruiting bodies or ascocarps, which are morphologically anomalous in Pezizomycotina. Bettsia and Ascosphaera are characterized by a unicellular cyst-like cleistothecium known as a spore cyst, while Eremascus is characterized by completely naked asci, or asci not...

Data from: Environmental factors and traits that drive plant litter decomposition do not determine home-field advantage effects

Ciska G. F. Veen, Maja K. Sundqvist, David A. Wardle & G. F. Ciska Veen
The ‘home-field advantage’ (HFA) hypothesis predicts that plant litter is decomposed faster than expected underneath the plant from which it originates (‘home’) than underneath other plants (‘away’), because decomposer communities are specialized to break down litter from the plants they associate with. However, empirical evidence shows that the occurrence of HFA is highly variable, and the reasons for this are little understood. In our study we progress our understanding by investigating whether HFA is stronger...

Data from: Plant defenses against ants provide a pathway to social parasitism in butterflies

Dario Patricelli, Francesca Barbero, Andrea Occhipinti, Cinzia M. Bertea, Simona Bonelli, Luca P. Casacci, Simon A. Zebelo, Christoph Crocoll, Jonathan Gershenzon, Massimo E. Maffei, Jeremy A. Thomas & Emilio Balletto
Understanding the chemical cues and gene expressions that mediate herbivore–host-plant and parasite–host interactions can elucidate the ecological costs and benefits accruing to different partners in tight-knit community modules, and may reveal unexpected complexities. We investigated the exploitation of sequential hosts by the phytophagous–predaceous butterfly Maculinea arion, whose larvae initially feed on Origanum vulgare flowerheads before switching to parasitize Myrmica ant colonies for their main period of growth. Gravid female butterflies were attracted to Origanum plants...

Data from: The genomes of two key bumblebee species with primitive eusocial organisation

Ben M. Sadd, Seth M. Barribeau, Guy Bloch, Dirk C. De Graaf, Peter Dearden, Christine Elsik, Jurgen Gadau, Cornelius Grimmelikhuijzen, Martin Hasselmann, Jeffrey Lozier, Hugh Robertson, Guy Smagghe, Eckart Stolle, Matthias Van Vaerenbergh, Robert Waterhouse, Erich Bornberg-Bauer, Steffan Klasberg, Anna Bennett, Francisco Camara, Roderic Guigo, Katharina Hoff, Marco Mariotti, Monica Munos-Torres, Terence Murphy, Didac Santesmasses … & Kim C. Worley
Background: The shift from solitary to social behavior is one of the major evolutionary transitions. Primitively eusocial bumblebees are uniquely placed to illuminate the evolution of highly eusocial insect societies. Bumblebees are also invaluable natural and agricultural pollinators, and there is widespread concern over recent population declines in some species. High-quality genomic data will inform key aspects of bumblebee biology, including susceptibility to implicated population viability threats. Results: We report the high quality draft genome...

Data from: Resource specialists lead local insect community turnover associated with temperature – analysis of an 18-year full-seasonal record of moths and beetles

Philip Francis Thomsen, Peter Søgaard Jørgensen, Hans Henrik Bruun, Jan Pedersen, Torben Riis-Nielsen, Krzysztof Jonko, Iwona Słowińska, Carsten Rahbek & Ole Karsholt
Insect responses to recent climate change are well documented, but the role of resource specialization in determining species vulnerability remains poorly understood. Uncovering local ecological effects of temperature change with high-quality, standardized data provides an important first opportunity for predictions about responses of resource specialists, and long-term time series are essential in revealing these responses. Here, we investigate temperature-related changes in local insect communities, using a sampling site with more than a quarter-million records from...

Data from: A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins

Ruth Fernández, Mikkel Schubert, A. M. Vargas-Velázquez, Andrew Brownlow, Gisli A. Víkingsson, Ursula Siebert, Lasse Fast Jensen, Nils Øien, Dave Wall, Emer Rogan, Bjarni Mikkelsen, Willy Dabin, Gilles Guillot, Ludovic Orlando, A. H. Alfarhan, S. A. Alquraishi & K. A. S. Al-Rasheid
The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover genomewide genotypes from 70 white-beaked (Lagenorhynchus albirostris) and 43 Atlantic white-sided dolphins (L. acutus) gathered throughout their north-east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38...

Data from: Genetic consequences of population expansions and contractions in the common hippopotamus (Hippopotamus amphibius) since the Late Pleistocene

Céline Stoffel, Christophe Dufresnes, John B. A. Okello, Christian Noirard, Pierre Joly, Silvester Nyakaana, Vincent B. Muwanika, Nicolas Alcala, Séverine Vuilleumier, Hans R. Siegismund & Luca Fumagalli
Over the past two decades, an increasing amount of phylogeographic work has substantially improved our understanding of African biogeography, in particular the role played by Pleistocene pluvial–drought cycles on terrestrial vertebrates. However, still little is known on the evolutionary history of semi-aquatic animals, which faced tremendous challenges imposed by unpredictable availability of water resources. In this study, we investigate the Late Pleistocene history of the common hippopotamus (Hippopotamus amphibius), using mitochondrial and nuclear DNA sequence...

Data from: Tag jumps illuminated – reducing sequence-to-sample misidentifications in metabarcoding studies

Ida Bærholm Schnell, Kristine Bohmann, M. Thomas P. Gilbert & Ida Baerholm Schnell
Metabarcoding of environmental samples on second-generation sequencing platforms has rapidly become a valuable tool for ecological studies. A fundamental assumption of this approach is the reliance on being able to track tagged amplicons back to the samples from which they originated. In this study, we address the problem of sequences in metabarcoding sequencing outputs with false combinations of used tags (tag jumps). Unless these sequences can be identified and excluded from downstream analyses, tag jumps...

Data from: Diet is the primary determinant of bacterial community structure in the guts of higher termites

Aram Mikaelyan, Carsten Dietrich, Tim Köhler, Michael Poulsen, David Sillam-Dussès & Andreas Brune
The gut microbiota of termites plays critical roles in the symbiotic digestion of lignocellulose. While phylogenetically ‘lower termites’ are characterized by a unique association with cellulolytic flagellates, higher termites (family Termitidae) harbour exclusively prokaryotic communities in their dilated hindguts. Unlike the more primitive termite families, which primarily feed on wood, they have adapted to a variety of lignocellulosic food sources in different stages of humification, ranging from sound wood to soil organic matter. In this...

Data from: Breeding system evolution influenced the geographic expansion and diversification of the core Corvoidea (Aves: Passeriformes)

Petter Z. Marki, Pierre-Henri Fabre, Knud A. Jønsson, Carsten Rahbek, Jon Fjeldså & Jonathan D. Kennedy
Birds vary greatly in their life-history strategies, including their breeding systems, which range from brood parasitism to a system with multiple non-breeding helpers at the nest. By far the most common arrangement, however, is where both parents participate in raising the young. The traits associated with parental care have been suggested to affect dispersal propensity and lineage diversification, but to date tests of this potential relationship at broad temporal and spatial scales have been limited....

Data from: No deep diving: evidence of predation on epipelagic fish for a stem beaked whale from the late Miocene of Peru

Olivier Lambert, Alberto Collareta, Walter Landini, Klaas Post, Benjamin Ramassamy, Claudio Di Celma, Mario Urbina-Schmitt & Giovanni Bianucci
Although modern beaked whales (Ziphiidae) are known to be highly specialized toothed whales that predominantly feed at great depths upon benthic and benthopelagic prey, only limited palaeontological data document this major ecological shift. We report on a ziphiid–fish assemblage from the Late Miocene of Peru that we interpret as the first direct evidence of a predator–prey relationship between a ziphiid and epipelagic fish. Preserved in a dolomite concretion, a skeleton of the stem ziphiid Messapicetus...

Data from: Ancient DNA microsatellite analyses of the extinct New Zealand giant moa (Dinornis robustus) identify relatives within a single fossil site

Morten E. Allentoft, Rasmus Heller, Richard N. Holdaway & Michael Bunce
By analysing ancient DNA (aDNA) from 74 14C-dated individuals of the extinct South Island giant moa (Dinornis robustus) of New Zealand, we identified four dyads of closely related adult females. Although our total sample included bones from four fossil deposits located within a 10 km radius, these eight individuals had all been excavated from the same locality. Indications of kinship were based on high pairwise genetic relatedness (rXY) in six microsatellite markers genotyped from aDNA,...

Data from: Chronic Trichuris muris Infection Decreases Diversity of the Intestinal Microbiota and Concomitantly Increases the Abundance of Lactobacilli

Jacob Bak Holm, Daniel Sorobetea, Pia Kiilerich, Yuliaxis Ramayo-Caldas, Jordi Estellé, Tao Ma, Lise Madsen, Karsten Kristiansen & Marcus Svensson-Frej
The intestinal microbiota is vital for shaping the local intestinal environment as well as host immunity and metabolism. At the same time, epidemiological and experimental evidence suggest an important role for parasitic worm infections in maintaining the inflammatory and regulatory balance of the immune system. In line with this, the prevalence of persistent worm infections is inversely correlated with the incidence of immune-associated diseases, prompting the use of controlled parasite infections for therapeutic purposes. Despite...

Data from: Natural genetic variation in Arabidopsis thaliana defense metabolism genes modulate field fitness

Rachel Kerwin, Julie Feusier, Jason Corwin, Matthew Rubin, Catherine Lin, Alise Muok, Brandon Larson, Baohua Li, Bindu Joseph, Marta Francisco, Daniel Copeland, Cynthia Weinig & Daniel J. Kliebenstein
Natural populations persist in complex environments, where biotic stressors, such as pathogen and insect communities, fluctuate temporally and spatially. These shifting biotic pressures generate heterogeneous selective forces that can maintain standing natural variation within a species. To directly test if genes containing causal variation for the Arabidopsis thaliana defensive compounds, glucosinolates (GSL) control field fitness and are therefore subject to natural selection, we conducted a multi-year field trial using lines that vary in only specific...

Data from: Effects of elevation and nitrogen and phosphorus fertilization on plant defence compounds in subarctic tundra heath vegetation

Jonathan R. De Long, Maja K. Sundqvist, Michael J. Gundale, Reiner Giesler & David A. Wardle
1. Plant chemical and structural defence compounds are well known to impact upon herbivory of fresh leaves and influence decomposition rates after leaf senescence. A number of theories predict that alleviating nutrient limitation and reducing other environmental stressors will result in decreased production of plant chemical defences. 2. In this study, we measured plant defence properties [total polyphenols (TP), condensed tannins (CT) and lignin concentrations, and protein complexation capacity (PCC)] in both fresh and senesced...

Data from: Relative impacts of environmental variation and evolutionary history on the nestedness and modularity of tree-herbivore networks.

Kathryn M. Robinson, Céline Hauzy, Nicolas Loeuille & Benedicte R. Albrectsen
Nestedness and modularity are measures of ecological networks whose causative effects are little understood. We analyzed antagonistic plant–herbivore bipartite networks using common gardens in two contrasting environments comprised of aspen trees with differing evolutionary histories of defence against herbivores. These networks were tightly connected owing to a high level of specialization of arthropod herbivores that spend a large proportion of the life cycle on aspen. The gardens were separated by ten degrees of latitude with...

Data from: Computing the local field potential (LFP) from integrate-and-fire network models

Alberto Mazzoni, Henrik Anders Lindén, Hermann Cuntz, Anders Lansner, Stefano Panzeri, Gaute Tomas Einevoll & Henrik Lindén
Leaky integrate-and-fire (LIF) network models are commonly used to study how the spiking dynamics of neural networks changes with stimuli, tasks or dynamic network states. However, neurophysiological studies in vivo often rather measure the mass activity of neuronal microcircuits with the local field potential (LFP). Given that LFPs are generated by spatially separated currents across the neuronal membrane, they cannot be computed directly from quantities defined in models of point-like LIF neurons. Here, we explore...

Data from: Dramatic niche shifts and morphological change in two insular bird species

Per Alström, Jon Fjeldså, Knud Andreas Jønsson, Anders Ödeen, Per G. P. Ericson, Martin Irestedt, J. Fjeldsa, K. A. Jonsson, P. Alstrom & A. Odeen
Colonizations of islands are often associated with rapid morphological divergence. We present two previously unrecognized cases of dramatic morphological change and niche shifts in connection with colonization of tropical forest-covered islands. These evolutionary changes have concealed the fact that the passerine birds madanga, Madanga ruficollis, from Buru, Indonesia, and São Tomé shorttail, Amaurocichla bocagii, from São Tomé, Gulf of Guinea, are forest-adapted members of the family Motacillidae (pipits and wagtails). We show that Madanga has...

Data from: Ground ice melt in the high Arctic leads to greater ecological heterogeneity

Michael S. Becker, T. Jonathan Davies, Wayne H Pollard & Wayne H. Pollard
1. The polar desert biome of the Canadian high Arctic Archipelago is currently experiencing some of the greatest mean annual air temperature increases on the planet, threatening the stability of ecosystems residing above temperature-sensitive permafrost. 2. Ice wedges are the most widespread form of ground ice, occurring in up to 25% of the world's terrestrial near-surface, and their melting (thermokarst) may catalyze a suite of biotic and ecological changes, facilitating major ecosystem shifts. 3. These...

Data from: Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas

Yung Hae Kim, Hjalte List Larsen, Pau Rué, Laurence A. Lemaire, Jorge Ferrer & Anne Grapin-Botton
Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells. In the mouse pancreas, lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine, ductal, and acinar cells but become bipotent by embryonic day 13.5, giving rise to endocrine cells and ductal cells. However, the dynamics of individual progenitors balancing self-renewal and lineage-specific differentiation has never been...

Data from: Genetic diversity, virulence and fitness evolution in an obligate fungal parasite of bees

Sophie. E. F. Evison, Kirsten Foley, Annette Bruun Jensen & William O. H. Hughes
Within-host competition is predicted to drive the evolution of virulence in parasites, but the precise outcomes of such interactions are often unpredictable due to many factors including the biology of the host and the parasite, stochastic events and co-evolutionary interactions. Here, we use a serial passage experiment (SPE) with three strains of a heterothallic fungal parasite (Ascosphaera apis) of the Honey bee (Apis mellifera) to assess how evolving under increasing competitive pressure affects parasite virulence...

Registration Year

  • 2015

Resource Types

  • Dataset


  • University of Copenhagen
  • Swedish University of Agricultural Sciences
  • McGill University
  • Curtin University
  • Natural History Museum
  • University of Cambridge
  • University of Otago
  • Smithsonian Institution
  • Uppsala University
  • Umeå University