363 Works

Data from: Use of ancient sedimentary DNA as a novel conservation tool for high-altitude tropical biodiversity

Sanne Boessenkool, Gayle McGlynn, Laura S. Epp, David Taylor, Manuel Pimentel, Abel Gizaw, Sileshi Nemomissa, Christian Brochmann & Magnus Popp
Conservation of biodiversity may in the future increasingly depend upon the availability of scientific information to set suitable restoration targets. In traditional paleoecology, sediment-based pollen provides a means to define preanthropogenic impact conditions, but problems in establishing the exact provenance and ecologically meaningful levels of taxonomic resolution of the evidence are limiting. We explored the extent to which the use of sedimentary ancient DNA (sedaDNA) may complement pollen data in reconstructing past alpine environments in...

Data from: Fungi ahoy! Diversity on marine wooden substrata in the high North

Teppo Rämä, Jenni Nordén, Marie L. Davey, Geir H. Mathiassen, Joseph W. Spatafora & Håvard Kauserud
Marine fungi are severely understudied in the polar regions. We used molecularly identified cultures to study fungi inhabiting 50 intertidal and sea-floor logs along the North Norwegian coast. The aim was to explore the taxonomic and ecological diversity and to examine factors shaping the marine wood-inhabiting fungal communities. The 577 pure cultures analyzed clustered into 147 operational taxonomic units (OTUs) based on 97 % ITS sequence similarity. Ascomycota dominated, but OTUs belonging to Basidiomycota, Mucoromycotina...

Data from: Diversity patterns of uncultured Haptophytes unravelled by pyrosequencing in Naples Bay

Lucie Bittner, Angélique Gobet, Stéphane Audic, Sarah Romac, Elianne S. Egge, Sébastien Santini, Hiroyuki Ogata, Ian Probert, Bente Edvardsen & Colomban De Vargas
Haptophytes are a key phylum of marine protists, including ~300 described morphospecies and 80 morphogenera. We used 454 pyrosequencing on large subunit ribosomal DNA (LSU rDNA) fragments to assess the diversity from size-fractioned plankton samples collected in the Bay of Naples. One group-specific primer set targeting the LSU rDNA D1/D2 region was designed to amplify Haptophyte sequences from nucleic acid extracts (total DNA or RNA) of two size fractions (0.8–3 or 3–20 μm) and two...

Data from: DNA from soil mirrors plant taxonomic and growth form diversity

Nigel G. Yoccoz, Kari-Anne Brathen, Ludovic Gielly, James Haile, Mary E. Edwards, Tomasz Goslar, H. Von Stedingk, Anne K. Brysting, Eric Coissac, Francois Pompanon, J. H. Sønstebø, Christian Miquel, Alice Valentini, Francesco De Bello, Jérôme Chave, Wilfried Thuiller, Patrick Wincker, Corinne Cruaud, Frederick Gavory, Morten Rasmussen, M. Thomas P. Gilbert, Ludovic Orlando, Christian Brochmann, Eske Willerslev & Pierre Taberlet
Ecosystems across the globe are threatened by climate change and human activities. New rapid survey approaches for monitoring biodiversity would greatly advance assessment and understanding of these threats. Taking advantage of next-generation DNA sequencing, we tested an approach we call metabarcoding: high-throughput and simultaneous taxa identification based on a very short (usually less than 100 base pairs) but informative DNA fragment. Short DNA fragments allow the use of degraded DNA from environmental samples. All analyses...

Data from: Strong and consistent natural selection associated with armour reduction in sticklebacks

Arnaud Le Rouzic, Kjartan Østbye, Tom O. Klepaker, Thomas F. Hansen, Louis Bernatchez, Dolph Schluter & Leif Asbjørn Vøllestad
Measuring the strength of natural selection is tremendously important in evolutionary biology, but remains a challenging task. In this work, we analyse the characteristics of selection for a morphological change (lateral-plate reduction) in the threespine stickleback Gasterosteus aculeatus. Adaptation to freshwater, leading to the reduction or loss of the bony lateral armor, has indeed occurred in parallel on numerous occasions in this species. Completely-plated and low-plated sticklebacks were introduced into a pond, and the phenotypic...

Data from: Functional coupling constrains craniofacial diversification in Lake Tanganyika cichlids

Masahito Tsuboi, Alejandro Gonzalez-Voyer & Niclas Kolm
Functional coupling, where a single morphological trait performs multiple functions, is a universal feature of organismal design. Theory suggests that functional coupling may constrain the rate of phenotypic evolution, yet empirical tests of this hypothesis are rare. In fish, the evolutionary transition from guarding the eggs on a sandy/rocky substrate (i.e. substrate guarding) to mouthbrooding introduces a novel function to the craniofacial system and offers an ideal opportunity to test the functional coupling hypothesis. Using...

Data from: Climate and fishing steer ecosystem regeneration to uncertain economic futures

Thorsten Blenckner, Marcos Llope, Christian Möllmann, Rudi Voss, Martin F. Quaas, Michele Casini, Martin Lindegren, Carl Folke, Nils Chr. Stenseth & C. Mollmann
Overfishing of large predatory fish populations has resulted in lasting restructurings of entire marine food webs worldwide, with serious socio-economic consequences. Fortunately, some degraded ecosystems show signs of recovery. A key challenge for ecosystem management is to anticipate the degree to which recovery is possible. By applying a statistical food-web model, using the Baltic Sea as a case study, we show that under current temperature and salinity conditions, complete recovery of this heavily altered ecosystem...

Data from: Phosphorus limitation enhances parasite impact: feedback effects at the population level

Katja Pulkkinen, Marcin W. Wojewodzic & Dag O. Hessen
Background: Nutrient deficiency affects the growth and population dynamics of consumers. Endoparasites can be seen as consumers that drain carbon (C) or energy from their host while simultaneously competing for limiting resources such as phosphorus (P). Depending on the relative demands of the host and the parasite for the limiting nutrient, intensified resource competition under nutrient limitation can either reduce the parasite?s effect on the host or further reduce the fitness of the nutrient-limited host....

Data from: Effects of large-scale releases on the genetic structure of red sea bream (Pagrus major, Temminck et Schlegel) populations in Japan

Enrique Blanco Gonzalez, Masato Aritaki, Halvor Knutsen & Nobuhiko Taniguchi
Genotype dataGenotype dataRelease dataRelease data

Data from: The potential for spatial distribution indices to signal thresholds in marine fish biomass

Emilie Reuchlin-Hugenholtz, Nancy L. Shackell & Jeffrey A. Hutchings
The frequently observed positive relationship between fish population abundance and spatial distribution suggests that changes in distribution can be indicative of trends in abundance. If contractions in spatial distribution precede declines in spawning stock biomass (SSB), spatial distribution reference points could complement the SSB reference points that are commonly used in marine conservation biology and fisheries management. When relevant spatial distribution information is integrated into fisheries management and recovery plans, risks and uncertainties associated with...

Data from: Mortality and lamb body mass growth in free-ranging domestic sheep – environmental impacts including lethal and non-lethal impacts of predators

Geraldine Mabille, Audun Stien, Torkild Tveraa, Atle Mysterud, Henrik Brøseth & John D. C. Linnell
The management and recovery of large predator populations in areas where human persecution has driven them to ecological extinction requires a solid understanding of the effects of both predation and food limitation on prey populations. We used 11 yr of data on reported losses among 17.3 million free-ranging sheep Ovis aries in the Norwegian farming industry to elucidate the relative roles of climate, vegetation characteristics, sheep densities, lamb body mass and densities of predators and...

Data from: Plastic and evolutionary gene expression responses are correlated in European grayling (Thymallus thymallus) sub-populations adapted to different thermal environments

Hannu Mäkinen, Spiros Papakostas, Leif Asbjørn Vøllestad, Erica H. Leder & Craig R. Primmer
Understanding how populations adapt to changing environmental conditions is a long-standing theme in evolutionary biology. Gene expression changes have been recognized as an important driver of local adaptation, but relatively little is known regarding the direction of change and in particular, about the interplay between plastic and evolutionary gene expression. We have previously shown that the gene expression profiles of European grayling (Thymallus thymallus) populations inhabiting different thermal environments include both plastic and evolutionary components....

Data from: Enhanced B-cell receptor recognition of the autoantigen transglutaminase 2 by efficient catalytic self-multimerization

Jorunn Stamnaes, Rasmus Iversen, M. Fleur Du Pré, Xi Chen & Ludvig M. Sollid
A hallmark of the gluten-driven enteropathy celiac disease is autoantibody production towards the enzyme transglutaminase 2 (TG2) that catalyzes the formation of covalent protein-protein cross-links. Activation of TG2-specific B cells likely involves gluten-specific CD4 T cells as production of the antibodies is dependent on disease-associated HLA-DQ allotypes and dietary intake of gluten. IgA plasma cells producing TG2 antibodies with few mutations are abundant in the celiac gut lesion. These plasma cells and serum antibodies to...

Data from: Evidence accumulation and choice maintenance are dissociated in human perceptual decision making

Mads Lund Pedersen, Tor Endestad & Guido Biele
Perceptual decision making in monkeys relies on decision neurons, which accumulate evidence and maintain choices until a response is given. In humans, several brain regions have been proposed to accumulate evidence, but it is unknown if these regions also maintain choices. To test if accumulator regions in humans also maintain decisions we compared delayed and self-paced responses during a face/house discrimination decision making task. Computational modeling and fMRI results revealed dissociated processes of evidence accumulation...

Data from: Parasite-mediated selection drives an immunogenetic tradeoff in plains zebras (Equus quagga)

Pauline L. Kamath, Wendy C. Turner, Martina Küsters & Wayne M. Getz
Pathogen evasion of the host immune system is a key force driving extreme polymorphism in genes of the major histocompatibility complex (MHC). Although this gene family is well characterized in structure and function, there is still much debate surrounding the mechanisms by which MHC diversity is selectively maintained. Many studies have investigated relationships between MHC variation and specific pathogens, and have found mixed support for and against the hypotheses of heterozygote advantage, frequency-dependent or fluctuating...

Data from: Genomics of speciation and introgression in Princess cichlid fishes from Lake Tanganyika

Hugo F. Gante, Michael Matschiner, Martin Malmstrøm, Kjetill S. Jakobsen, Sissel Jentoft & Walter Salzburger
How variation in the genome translates into biological diversity and new species originate has endured as the mystery of mysteries in evolutionary biology. African cichlid fishes are prime model systems to address speciation-related questions for their remarkable taxonomic and phenotypic diversity, and the possible role of gene flow in this process. Here, we capitalize on genome sequencing and phylogenomic analyses to address the relative impacts of incomplete lineage sorting, introgression and hybrid speciation in the...

Data from: Population structure in Atlantic cod in the eastern North Sea-Skagerrak-Kattegat: early life stage dispersal and adult migration

Carl André, Henrik Svedäng, Halvor Knutsen, Geir Dahle, Patrik Jonsson, Anna-Karin Ring, Mattias Sköld & Per Erik Jorde
Background: In marine fish species, where pelagic egg and larvae drift with ocean currents, population structure has been suggested to be maintained by larval retention due to hydrographic structuring and by homing of adult fish to natal areas. Whilst natal homing of adults has been demonstrated for anadromous and coral reef fishes, there are few documented examples of philopatric migration in temperate marine fish species. Results: Here, we demonstrate temporally stable genetic differentiation among spawning...

Data from: The Pillars of Hercules as a bathymetric barrier to gene-flow promoting isolation in a global deep-sea shark (Centroscymnus coelolepis)

Diana Catarino, Halvor Knutsen, Ana Veríssimo, Esben Moland Olsen, Per Erik Jorde, Gui Menezes, Hanne Sannæs, David Stanković, Joan Batista Company, Francis Neat, Roberto Danovaro, Antonio Dell'Anno, Bastien Rochowski, Sergio Stefanni, Joan Baptista Company & Hanne Sannaes
Knowledge of the mechanisms limiting connectivity and gene-flow in deep-sea ecosystems is limited, especially for deep-sea sharks. The Portuguese dogfish (Centroscymnus coelolepis) is a globally distributed and Near Threatened deep-sea shark. C. coelolepis population structure was studied using 11 nuclear microsatellite markers and a 497 bp fragment from the mtDNA Control Region. High levels of genetic homogeneity across the Atlantic (ΦST=-0.0091, FST= 0.0024, P > 0.05) were found suggesting one large population unit at this...

Data from: Multiple stressors in a top predator seabird: potential ecological consequences of environmental contaminants, population health and breeding conditions

Jan Ove Bustnes, Sophie Bourgeon, Eliza H. K. Leat, Ellen Magnusdottir, Hallvard Strøm, Sveinn A. Hanssen, Aevar Petersen, Kristin Olafsdottir, Katrine Borgå, Geir W. Gabrielsen & Robert W. Furness
Environmental contaminants may have impacts on reproduction and survival in wildlife populations suffering from multiple stressors. This study examined whether adverse effects of persistent organic pollutants (POPs) increased with poor population health and breeding conditions in three colonies (60–74°N) of great skua (Stercorarius skua) in the north-eastern Atlantic (Shetland, Iceland and Bjørnøya [Bear Island]). POPs (organochlorines [OCs] and polybrominated diphenyl ethers [BDEs]) were measured in plasma of incubating birds (n = 222), concentrations differing nearly...

Data from: Temporal variation of Bistorta vivipara-associated ectomycorrhizal fungal communities in the High Arctic

Sunil Mundra, Mohammad Bahram, Leho Tedersoo, Håvard Kauserud, Rune Halvorsen, Pernille Eidesen & Pernille Bronken Eidesen
Ectomycorrhizal (ECM) fungi are important for efficient nutrient uptake of several widespread arctic plant species. Knowledge of temporal variation of ECM fungi, and the relationship of these patterns to environmental variables, is essential to understand energy and nutrient cycling in Arctic ecosystems. We sampled roots of Bistorta vivipara ten times over two years; three times during the growing-season (June, July and September) and twice during winter (November and April) of both years. We found 668...

Data from: The role of plasma and urine metabolomics in identifying new biomarkers in severe newborn asphyxia: a study of asphyxiated newborn pigs following cardiopulmonary resuscitation

Daniel Sachse, Anne Lee Solevåg, Jens Petter Berg & Britt Nakstad
Background: Optimizing resuscitation is important to prevent morbidity and mortality from perinatal asphyxia. The metabolism of cells and tissues is severely disturbed during asphyxia and resuscitation, and metabolomic analyses provide a snapshot of many small molecular weight metabolites in body fluids or tissues. In this study metabolomics profiles were studied in newborn pigs that were asphyxiated and resuscitated using different protocols to identify biomarkers for subject characterization, intervention effects and possibly prognosis. Methods: A total...

Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

Alan McNally, Yaara Oren, Darren Kelly, Ben Pascoe, Steven Dunn, Tristan Seecharan, Minna Vehkala, Niko Välimäki, Michael B. Prentice, Amgad Ashour, Oren Avram, Tal Pupko, Ulrich Dobrindt, Ivan Literak, Sebastian Guenther, Katharina Schauffler, Lothar H. Wieler, Zong Zhiyong, Samuel K. Sheppard, James O. McInerney, Jukka Corander & Tristan Sreecharan
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could...

Data from: BsRADseq: screening DNA methylation in natural populations of non-model species

Emiliano Trucchi, Anna B. Mazzarella, Gregor D. Gilfillan, Maria T. Lorenzo, Peter Schönswetter & Ovidiu Paun
Epigenetic modifications are expected to occur at a much faster rate than genetic mutations, potentially causing isolated populations to stochastically drift apart, or if they are subjected to different selective regimes, to directionally diverge. A high level of genome-wide epigenetic divergence between individuals occupying distinct habitats is therefore predicted. Here, we introduce bisulfite-converted restriction site associated DNA sequencing (bsRADseq), an approach to quantify the level of DNA methylation differentiation across multiple individuals. This reduced representation...

Data from: The fungus that came in from the cold: dry rot’s pre-adapted ability to invade buildings

Sudhagard V. Balasundaram, Jaqueline Hess, Michael B. Durling, S. C. Moody, Lisbeth Thorbek, Cinzia Progida, Kurt LaButti, Andrea Aerts, Kerrie Barry, Igor V. Grigoriev, Lynne Boddy, Nils Högberg, Håvard Kauserud, Daniel C. Eastwood & Inger Skrede
Many organisms benefit from being pre-adapted to niches shaped by human activity, and have successfully invaded man-made habitats. One such species is the dry rot fungus Serpula lacrymans, which has a wide distribution in buildings in temperate and boreal regions, where it decomposes coniferous construction wood. Comparative genomic analyses and growth experiments using this species and its wild relatives revealed that S. lacrymans evolved a very effective brown rot decay compared to its wild relatives,...

Data from: Different contributions of local- and distant-regulatory changes to transcriptome divergence between stickleback ecotypes

Asano Ishikawa, Makoto Kusakabe, Kohta Yoshida, Mark Ravinet, Takashi Makino, Atsushi Toyoda, Asao Fujiyama & Jun Kitano
Differential gene expression can play an important role in phenotypic evolution and divergent adaptation. Although differential gene expression can be caused by both local- and distant-regulatory changes, we know little about their relative contribution to transcriptome evolution in natural populations. Here, we conducted expression quantitative trait loci (eQTL) analysis to investigate the genetic architecture underlying transcriptome divergence between marine and stream ecotypes of threespine sticklebacks (Gasterosteus aculeatus). We identified both local and distant eQTLs, some...

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