280 Works

Data from: Intestinal Ralstonia pickettii augments glucose intolerance in obesity

Shanthadevi Udayappan, Petia Kovatcheva-Datchary, Guido Bakker, Stefan Havik, Hilde Herrema, Patrice Cani, Kristien Bouter, Clara Belzer, Julia J. Witjes, Anne Vrieze, Eleonore Susanne Victoria De Sonnaville, Alice Chaplin, Daniel Van Raalte, Steven Aalvink, Geesje Dallinga-Thie, Hans Heilig, Goran Bergstrom, Suzan Van Der Meij, Bart Van Wagensveld, Joost Hoekstra, Frits Holleman, Erik Stroes, Albert Groen, Fredrik Backhed, Willem De Vos … & Daniel H. Van Raalte
An altered intestinal microbiota composition has been implicated in the pathogenesis of metabolic disease including obesity and type 2 diabetes mellitus (T2DM). Low grade inflammation, potentially initiated by the intestinal microbiota, has been suggested to be a driving force in the development of insulin resistance in obesity. Here, we report that bacterial DNA is present in mesenteric adipose tissue of obese but otherwise healthy human subjects. Pyrosequencing of bacterial 16S rRNA genes revealed that DNA...

Data from: Dairy products viscosity estimated by laser speckle correlation

Dmitry D. Postnov, Flemming Moller & Olga Sosnovtseva
Dairy products exhibit several physical properties that are crucial to define whether we like the food or not: firmness, creaminess, thickness, or lightness. Viscosity changes the flow properties of food and influences the appearance and the consistency of a product; this control variable is important in most production stages—manufacture, processing, and storage. Viscosity of heterogeneous products at a given temperature depends on its composition and physical state of its substances. Although rheology provides a method...

Data from: Nationwide prevalence and incidence study of neuromyelitis optica spectrum disorder in Denmark

Viktoria Papp, Zsolt Illes, Melinda Magyari, Nils Koch-Henriksen, Matthias Kant, Claudia Christina Pfleger, Shanu Faerch Roemer, Michael Broksgaard Jensen, Annett Evelyn Petersen, Helle Hvilsted Nielsen, Lene Rosendahl, Zsolt Mezei, Tove Christensen, Kristina Svendsen, Poul Erik Hyldgaard Jensen, Magnus Christian Lydolph, Niels Heegaard, Jette Lautrup Frederiksen, Finn Thorup Sellebjerg, Egon Stenager & Thor Petersen
Objectives: To estimate the nationwide population-based incidence, prevalence, and geographical distribution of neuromyelitis optica spectrum disorder in Denmark based on the 2015 International Panel for NMO Diagnosis (IPND) criteria Methods: We conducted a multicentre, historically prospective study. Data were sourced from the Danish National Patient Registry, the Danish Multiple Sclerosis Registry, departments of neurology and laboratories providing aquaporin 4 (AQP4) antibody test. Cases were selected based on the 2006 Wingerchuk and the 2015 IPND criteria...

Data from: Convergent evolution of the ladder-like ventral nerve cord in Annelida

Conrad Helm, Patrick Beckers, Thomas Bartolomaeus, Stephan H. Drukewitz, Ioannis Kourtesis, Anne Weigert, Günter Purschke, Katrine Worsaae, Torsten H. Struck & Christoph Bleidorn
Background: A median, segmented, annelid nerve cord has repeatedly been compared to the arthropod and vertebrate nerve cords and became the most used textbook representation of the annelid nervous system. Recent phylogenomic analyses, however, challenge the hypothesis that a subepidermal rope-ladder-like ventral nerve cord (VNC) composed of a paired serial chain of ganglia and somata-free connectives represents either a plesiomorphic or a typical condition in annelids. Results: Using a comparative approach by combining phylogenomic analyses...

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: Global distribution of Chelonid fibropapilloma-associated herpesvirus among clinically healthy sea turtles

Alonzo Alfaro-Núñez, Mads Frost Bertelsen, Anders Miki Bojesen, Isabel Rasmussen, Lisandra Zepeda-Mendoza, Morten Tange Olsen & Marcus Thomas Pius Gilbert
Background: Fibropapillomatosis (FP) is a neoplastic disease characterized by cutaneous tumours that has been documented to infect all sea turtle species. Chelonid fibropapilloma-associated herpesvirus (CFPHV) is believed to be the aetiological agent of FP, based principally on consistent PCR-based detection of herpesvirus DNA sequences from FP tumours. We used a recently described PCR-based assay that targets 3 conserved CFPHV genes, to survey 208 green turtles (Chelonia mydas). This included both FP tumour exhibiting, and clinically...

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: Modeling of kidney hemodynamics: probability-based topology of an arterial network

Dmitry D. Postnov, Donald J. Marsh, Thomas H. Braunstein, Niels-Henrik Holstein-Rathlou, Erik A. Martens & Olga Sosnovtseva
Through regulation of the extracellular fluid volume, the kidneys provide important long-term regulation of blood pressure. At the level of the individual functional unit (the nephron), pressure and flow control involves two different mechanisms that both produce oscillations. The nephrons are arranged in a complex branching structure that delivers blood to each nephron and, at the same time, provides a basis for an interaction between adjacent nephrons. The functional consequences of this interaction are not...

Data from: Activity and migratory flights of individual free-flying songbirds throughout the annual cycle: method and first case study

Johan Bäckman, Arne Andersson, Thomas Alerstam, Lykke Pedersen, Sissel Sjöberg, Kasper Thorup & Anders P. Tøttrup
We describe a method and device (< 1.2 g) for recording, processing and storing data about activity and location of individuals of free-living songbirds throughout the annual cycle. Activity level was determined every five minutes from five 100 ms samples of accelerometer data with 5 s between the sampling events. Activity levels were stored on an hourly basis throughout the annual cycle, allowing periods of resting/sleep, continuous flight and intermediate activity (foraging, breeding) to be...

Data from: Social selection parapatry in Afrotropical sunbirds

Jay P. McEntee, Joshua V. Peñalba, Chacha Werema, Elia Mulungu, Maneno Mbilinyi, David Moyer, Louis Hansen, Jon Fjeldså & Rauri C. K. Bowie
The extent of range overlap of incipient and recent species depends on the type and magnitude of phenotypic divergence that separates them, and the consequences of phenotypic divergence on their interactions. Signal divergence by social selection likely initiates many speciation events, but may yield niche-conserved lineages predisposed to limit each others’ ranges via ecological competition. Here we examine this neglected aspect of social selection speciation theory in relation to the discovery of a non-ecotonal species...

Life history predicts flight muscle phenotype and function in birds

Shane DuBay, Yongjie Wu, Graham Scott, Yanhua Qu, Qiao Liu, Joel Smith, Chao Xin, Andrew Hart Reeve, Chen Juncheng, Dylan Meyer, Jing Wang, Jacob Johnson, Zachary Cheviron, Fumin Lei & John Bates
1. Functional traits are the essential phenotypes that underlie an organism’s life history and ecology. Although biologists have long recognized that intraspecific variation is consequential to an animals’ ecology, studies of functional variation are often restricted to species-level comparisons, ignoring critical variation within species. In birds, interspecific comparisons have been foundational in connecting flight muscle phenotypes to species-level ecology, but intraspecific variation has remained largely unexplored. 2. We asked how age- and sex-dependent demands on...

Data from: Testing trade-offs and the dominance-impoverishment rule among ant communities

Julie K. Sheard, Annika S. Nelson, Jeppe Berggreen, Raphael Boulay, Robert R. Dunn & Nathan J. Sanders
Aim: Ant communities are believed to be structured by competition, with dominant species competitively excluding subordinates (the dominance-impoverishment rule). However, a high number of seemingly similar species coexist, possibly due to interspecific trade-offs. Here, we examine the evidence for the dominance-impoverishment rule across a broad latitudinal gradient and explore whether trade-offs explain coexistence within and among ant communities. Location: 40 sites in 19 countries across Europe, western North America and northern South America. Taxon: Formicidae....

Catchment properties and the photosynthetic trait composition of freshwater plant communities

Lars Lønsmann Iversen, A. Winkel, L. Baastrup-Spohr, A. B. Hinke, J. Alahuhta, A. Baattrup-Pedersen, S. Birk, P. Brodersen, P. A. Chambers, F. Ecke, T. Feldmann, D. Gebler, J. Heino, T. S. Jespersen, S. J. Moe, T. Riis, L. Sass, O. Vestergaard, S. C. Maberly, K. Sand-Jensen & O. Pedersen
Unlike in land plants, photosynthesis in many aquatic plants relies on bicarbonate in addition to carbon dioxide (CO2) to compensate for the low diffusivity and potential depletion of CO2 in water. Concentrations of bicarbonate and CO2 vary greatly with catchment geology. In this study, we investigate whether there is a link between these concentrations and the frequency of freshwater plants possessing the bicarbonate use trait. We show, globally, that the frequency of plant species with...

Targeted conservation genetics of the endangered chimpanzee

Peter Frandsen, Claudia Fontsere, Sven Nielsen, Kristian Hanghøj, Natalia Castejon-Fernandez, Esther Lizano, David Hughes, Jessica Hernandez-Rodriquez, Thorfinn Korneliussen, Frands Carlsen, Hans Siegismund, Thomas Mailund, Tomas Marques Bonet & Christina Hvilsom
Populations of the common chimpanzee (Pan troglodytes) are in an impending risk of going extinct in the wild as a consequence of damaging anthropogenic impact on their natural habitat and illegal pet and bushmeat trade. Conservation management programmes for the chimpanzee have been established outside their natural range (ex situ), and chimpanzees from these programmes could potentially be used to supplement future conservation initiatives in the wild (in situ). However, these programmes have often suffered...

Reconstructing Ecological Niche Evolution via Ancestral State Reconstruction with Uncertainty Incorporated

Hannah Owens, Vivian Ribiero, Erin Saupe, Marlon E. Cobos, Peter Hosner, Jacob Cooper, Abdallah Samy, Vijay Barve, Narayani Barve, Carlos Muñoz & A. Townsend Peterson
Reconstructing ecological niche evolution can provide insight into the biogeography and diversification of evolving lineages. However, comparative phylogenetic methods can infer the history of ecological niche evolution inaccurately because (1) species’ niches are often poorly characterized; and (2) phylogenetic comparative methods rely on niche summary statistics rather than full estimates of species’ environmental tolerances. Here we propose a new framework for coding ecological niches and reconstructing their evolution that explicitly acknowledges and incorporates the uncertainty...

Data from: Adaptive radiation and the evolution of nectarivory in a large songbird clade

Petter Zahl Marki, Jonathan D. Kennedy, Chris Cooney, Carsten Rahbek & Jon Fjeldså
The accumulation of exceptional ecological diversity within a lineage is a key feature of adaptive radiation resulting from diversification associated with the subdivision of previously underutilized resources. The invasion of unoccupied niche space is predicted to be a key determinant of adaptive diversification, and this process may be particularly important if the diversity of competing lineages within the area, in which the radiation unfolds, is already high. Here, we test whether the evolution of nectarivory...

Data from: Tropical forest type influences community assembly processes in arbuscular mycorrhizal fungi

Camilla M.R. Pereira, Álvaro López-García, Danielle Karla Alves Da Silva, Leonor C. Maia, Tobias G. Frøslev, Rasmus Kjøller & Søren Rosendahl
Aim: Plant community assembly in tropical rainforest has been shown to be largely governed by stochastic processes, but as arbuscular mycorrhizal (AM) fungi display limited host preference, they may not follow the same stochastic assembly pattern. Here, we determined the relative importance of environmental and spatial drivers responsible for the community assembly process of AM fungi in two types of tropical rainforest (semideciduous rainforest and dense ombrophilous forests). Location: Atlantic rainforest in northeastern Brazil, South...

Data from: Biocultural approaches to sustainability: a systematic review of the scientific literature

Jan Hanspach, L. Jamila Haider, Elisa Oteris-Rozas, Anton Stahl Olafsson, Natalie Gulsrud, Chris Raymond, Mario Torralba, Berta Martín-López, Claudia Bieling, María García Martín, Christian Albert, Thomas Beery, Nora Fagerholm, Isabel Díaz-Reviriego, Annika Drews-Shambroom & Tobias Plieninger
Current sustainability challenges demand approaches that acknowledge a plurality of human-nature interactions and worldviews, for which biocultural approaches are considered appropriate and timely. This systematic review analyses the application of biocultural approaches to sustainability in scientific journal articles published between 1990 and 2018 through a mixed methods approach combining qualitative content analysis and quantitative multivariate methods. The study identifies seven distinct biocultural lenses, i.e. different ways of understanding and applying biocultural approaches, which to different...

Data from: A consistent species richness-climate relationship for oaks across the Northern Hemisphere

Xiaoting Xu, Dimitar Dimitrov, Nawal Shrestha, Carsten Rahbek & Zhiheng Wang
Aim: Although the effects of climate on species richness are known, regional processes may lead to different species richness-climate relationships across continents resulting in species richness anomalies, especially for tropical groups. Phylogenetic niche conservatism may also influence species richness-climate relationships of different lineages. Here, we tested whether regional effects also exist for temperate lineages using the genus Quercus. Location: Northern Hemisphere Time period: Present day Major taxa studied: Quercus (Fagaceae) Methods: We used a dated...

Data from: Host‐derived population genomics data provides insights into bacterial and diatom composition of the killer whale skin

Rebecca Hooper, Jaelle C. Brealey, Tom Van Der Valk, Antton Alberdi, John W. Durban, Holly Fearnbach, Kelly M. Robertson, Robin W. Baird, M. Bradley Hanson, Paul Wade, M. Thomas P. Gilbert, Philip A. Morin, Jochen B. W. Wolf, Andrew D. Foote, Katerina Guschanski & Phillip A. Morin
Recent exploration into the interactions and relationship between hosts and their microbiota has revealed a connection between many aspects of the host's biology, health and associated micro‐organisms. Whereas amplicon sequencing has traditionally been used to characterize the microbiome, the increasing number of published population genomics data sets offers an underexploited opportunity to study microbial profiles from the host shotgun sequencing data. Here, we use sequence data originally generated from killer whale Orcinus orca skin biopsies...

Data from: Privatisation rescues essential function following loss of cooperation

Sandra Breum Andersen, Melanie Ghoul, Rasmus Lykke Marvig, Zhuo-Bin Lee, Søren Molin, Helle Krogh Johansen & Ashleigh S. Griffin
A single cheating mutant can lead to the invasion and eventual eradication of cooperation from a population. Consequently, cheat invasion is often considered equal to extinction in empirical and theoretical studies of cooperator-cheat dynamics. But does cheat invasion necessarily equate extinction in nature? By following the social dynamics of iron metabolism in Pseudomonas aeruginosa during cystic fibrosis lung infection, we observed that individuals evolved to replace cooperation with a ‘private’ behaviour. Phenotypic assays showed that...

Amoebocytes facilitate efficient carbon and nitrogen assimilation in the Cassiopea Symbiodiniaceae symbiosis

Niclas Heidelberg Lyndby, Nils Rädecker, Sandrine Bessette, Louise Jensen, Stéphane Escrig, Erik Trampe, Michael Kühl & Anders Meibom
The upside-down jellyfish Cassiopea engages in symbiosis with photosynthetic microalgae that facilitate uptake and recycling of inorganic nutrients. In contrast to most other symbiotic cnidarians, algal endosymbionts in Cassiopea are not restricted to the gastroderm but are found in amoebocyte cells within the mesoglea. While symbiont-bearing amoebocytes are highly abundant, their role in nutrient uptake and cycling in Cassiopea remains unknown. By combining isotopic labelling experiments with correlated SEM and NanoSIMS imaging, we quantified the...

Global patterns of the leaf economics spectrum in wetlands

Yingji Pan, Ellen Cieraad, Jean Armstrong, William Armstrong, Beverley Clarkson, Timothy Colmer, Ole Pedersen, Eric Visser, Laurentius Voesenek & Peter Van Bodegom
The leaf economics spectrum (LES) describes consistent correlations among a variety of leaf traits that reflect a gradient from conservative to acquisitive plant strategies. So far, whether the LES holds in wetland plants at a global scale has been unclear. Using data on 365 wetland species from 151 studies, we find that wetland plants in general show a shift within trait space along the same common slope as observed in non-wetland plants, with lower leaf...

Separating direct and indirect effects of rising temperatures on biogenic volatile emissions in the Arctic

Lars Lønsmann Iversen, Riikka Rinnan, Jing Tang, Ida Vedel-Petersen, Michelle Schollert & Guy Schurgers
Volatile organic compounds (VOCs) are released from biogenic sources in a temperature-dependent manner. Consequently, Arctic ecosystems are expected to greatly increase their VOC emissions with ongoing climate warming, which is proceeding at twice the rate of global temperature rise. Here, we show that ongoing warming has strong, increasing effects on Arctic VOC emissions. Using a combination of statistical modelling on data from several warming experiments in the Arctic tundra and dynamic ecosystem modelling, we separate...

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  • University of Copenhagen
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