40 Works

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: Next-generation monitoring of aquatic biodiversity using environmental DNA metabarcoding

Alice Valentini, Pierre Taberlet, Claude Miaud, Raphaël Civade, Jelger Herder, Philip Francis Thomsen, Eva Bellemain, Aurélien Besnard, Eric Coissac, Frédéric Boyer, Coline Gaboriaud, Pauline Jean, Nicolas Poulet, Nicolas Roset, Gordon H. Copp, Philippe Geniez, Didier Pont, Christine Argillier, Jean-Marc Baudoin, Tiphaine Peroux, Alain J. Crivelli, Anthony Olivier, Manon Acqueberge, Matthieu Le Brun, Peter Rask Møller … & Tony Dejean
Global biodiversity in freshwater and the oceans is declining at high rates. Reliable tools for assessing and monitoring aquatic biodiversity, especially for rare and secretive species, are important for efficient and timely management. Recent advances in DNA sequencing have provided a new tool for species detection from DNA present into the environment. In this study, we tested if an environmental DNA (eDNA) metabarcoding approach, using water samples, can be used for addressing significant questions in...

Data from: Sixty-year legacy of human impacts on a high Arctic ecosystem

Michael S. Becker & Wayne H. Pollard
The high Arctic is the world's fasting warming biome, allowing access to sections of previously inaccessible land for resource extraction. Starting in 2011, exploration of one of the Earth's largest undeveloped coal seams was initiated in a relatively pristine, polar desert environment in the Canadian high Arctic. Due to the relative lack of historic anthropogenic disturbance, significant gaps in knowledge exist on how the landscape will be impacted by development. At an abandoned airstrip located...

Data from: The phylogenetics of succession can guide restoration: an example from abandoned mine sites in the subarctic

Stephanie Shooner, Chelsea Chisholm & Thomas Jonathan Davies
1. Phylogenetic tools have increasingly been used in community ecology to describe evolutionary relationships among co-occurring species. In studies of succession, such tools may allow us to identify evolutionary lineages most suited for particular stages of succession and habitat rehabilitation. However, to date these two applications have been largely separate. Here, we suggest that information on phylogenetic community structure might help inform community restoration strategies following major disturbance. 2. Our study examined phylogenetic patterns of...

Data from: A supermatrix phylogeny of corvoid passerine birds (Aves: Corvides)

Knud Andreas Jønsson, Pierre-Henri Fabre, Jonathan D. Kennedy, Ben G. Holt, Michael K. Borregaard, Carsten Rahbek & Jon Fjeldså
The Corvides (previously referred to as the core Corvoidea) are a morphologically diverse clade of passerine birds comprising nearly 800 species. The group originated some 30 million years ago in the proto-Papuan archipelago, to the north of Australia, from where lineages have dispersed and colonized all of the world’s major continental and insular landmasses (except Antarctica). During the last decade multiple species-level phylogenies have been generated for individual corvoid families and more recently the inter-familial...

Data from: Bacterial symbiont sharing in Megalomyrmex social parasites and their fungus-growing ant hosts

Joanito Liberti, Panagiotis Sapountzis, Lars H. Hansen, Søren J. Sørensen, Rachelle M. M. Adams & Jacobus J. Boomsma
Bacterial symbionts are important fitness determinants of insects. Some hosts have independently acquired taxonomically related microbes to meet similar challenges, but whether distantly related hosts that live in tight symbiosis can maintain similar microbial communities has not been investigated. Varying degrees of nest sharing between Megalomyrmex social parasites (Solenopsidini) and their fungus-growing ant hosts (Attini) from the genera Cyphomyrmex, Trachymyrmex and Sericomyrmex allowed us to address this question, as both ant lineages rely on the...

Data from: The shepherds' tale: a genome-wide study across 9 dog breeds implicates two loci in the regulation of fructosamine serum concentration in Belgian shepherds

Simon K. G. Forsberg, Marcin Kierczak, Ingrid Ljungvall, Anne-Christine Merveille, Vassiliki Gouni, Maria Wiberg, Jakob Lundgren Willesen, Sofia Hanås, Anne-Sophie Lequarré, Louise Mejer Sørensen, Laurent Tiret, Kathleen McEntee, Eija Seppälä, Jørgen Koch, Géraldine Battaille, Hannes Lohi, Merete Fredholm, Valerie Chetboul, Jens Häggström, Örjan Carlborg, Kerstin Lindblad-Toh & Katja Höglund
Diabetes mellitus is a serious health problem in both dogs and humans. Certain dog breeds show high prevalence of the disease, whereas other breeds are at low risk. Fructosamine and glycated hemoglobin (HbA1c) are two major biomarkers of glycaemia where serum concentrations reflect glucose turnover over the past few weeks to months. In this study, we searched for genetic factors influencing variation in serum fructosamine concentration in healthy dogs using data from nine dog breeds....

Data from: ICE1 demethylation drives range expansion of a plant invader through cold-tolerance divergence

H. J. Xie, H. Li, L. L. Liu, W. M. Dai, J. Y. He, S. Lin, H. Duan, S. G. Chen, X. L. Song, B. E. Valverde & S. Qiang
Cold tolerance of alien invasive plants is a crucial determinant for their establishment and expansion into new cold environments. A close relationship between cold-tolerance level of 34 populations represented by 147 accessions and latitude, extreme lowest temperature, coldest month average temperature and invasion age revealed that cold-tolerance divergence is a key factor driving the spreading of Ageratina adenophora, a highly invasive plant in China, to subtropical areas northeastward from the first-colonized southwestern region. Four epialles...

Data from: Geographic and temporal dynamics of a global radiation and diversification in the killer whale

Phillip A. Morin, Kim M. Parsons, Frederick I. Archer, María C. Ávila-Arcos, Lance G. Barrett-Lennard, Luciano Dalla Rosa, Sebastián Duchêne, John W. Durban, Graeme M. Ellis, Steven H. Ferguson, John K. Ford, Michael J. Ford, Cristina Gabrilao, M. Thomas P. Gilbert, Kristin Kaschner, Craig O. Matkin, Stephen D. Petersen, Kelly M. Robertson, Ingrid N. Visser, Paul R. Wade, Simon Y. W. Ho & Andrew D. Foote
Global climate change during the Late Pleistocene periodically encroached and then released habitat during the glacial cycles, causing range expansions and contractions in some species. These dynamics have played a major role in geographic radiations, diversification and speciation. We investigate these dynamics in the most widely distributed of marine mammals, the killer whale (Orcinus orca), using a global data set of over 450 samples. This marine top predator inhabits coastal and pelagic ecosystems ranging from...

Data from: Comparative analyses of QTLs influencing obesity and metabolic phenotypes in pigs and humans

Sameer D. Pant, Peter Karlskov-Mortensen, Mette J. Jacobsen, Susanna Cirera, Lisette J. A. Kogelman, Camilla S. Bruun, Thomas Mark, Claus B. Jørgensen, Niels Grarup, Emil V. R. Appel, Ehm A. A. Galjatovic, Torben Hansen, Oluf B. Pedersen, Maryse Guerin, Thierry Huby, Philippe Lesnik, Theo H. E. Meuwissen, Haja N. Kadarmideen, Merete Fredholm & Oluf Pedersen
The pig is a well-known animal model used to investigate genetic and mechanistic aspects of human disease biology. They are particularly useful in the context of obesity and metabolic diseases because other widely used models (e.g. mice) do not completely recapitulate key pathophysiological features associated with these diseases in humans. Therefore, we established a F2 pig resource population (n = 564) designed to elucidate the genetics underlying obesity and metabolic phenotypes. Segregation of obesity traits...

Registration Year

  • 2015
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Resource Types

  • Dataset
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Affiliations

  • University of Copenhagen
    40
  • Swedish University of Agricultural Sciences
    4
  • McGill University
    3
  • Curtin University
    3
  • Natural History Museum
    3
  • University of Cambridge
    2
  • University of Otago
    2
  • Smithsonian Institution
    2
  • Uppsala University
    2
  • Umeå University
    2