163 Works

Data from: A method to generate multi-locus barcodes of pinned insect specimens using MiSeq

Trace Akankunda, Hien To, Carlos R Lopez, Remko Leijs & Katja Hogendoorn
For molecular insect identification, amplicon sequencing methods are recommended because they offer a cost effective approach for targeting small sets of informative genes from multiple samples. In this context, high-throughput multilocus amplicon sequencing has been achieved using the MiSeq Illumina sequencing platform. However, this approach generates short gene fragments of less than 500 bp, which then have to be overlapped using bioinformatics to achieve longer sequence lengths. This increases the risk of generating chimeric sequences...

Data from: Comparative transcriptomics reveals domestication-associated features of Atlantic salmon lipid metabolism

Yang Jin, Rolf Erik Olsen, Thomas Nelson Harvey, Mari-Ann Østensen, Keshuai Li, Nina Santi, Olav Vadstein, Atle Magnar Bones, Jon Olav Vik, Simen Rød Sandve & Yngvar Olsen
Domestication of animals imposes strong targeted selection for desired traits but can also result in unintended selection due to new domestic environments. Atlantic salmon was domesticated in the 1970s and has subsequently been selected for faster growth in systematic breeding programmes. More recently, salmon aquaculture has replaced fish oils (FO) with vegetable oils (VO) in feed, radically changing the levels of essential long-chain polyunsaturated fatty acids (LC-PUFA). Our aim was to study the impact of...

Diet of the brown bear in Himalaya: combining classical and molecular genetic techniques

Muhammad Ali Nawaz, Alice Valentini, Noor Kamal Khan, Christian Miquel, Pierre Taberlet & Jon E. Swenson
The ecological requirements of brown bears are poorly known in the Himalaya region, which complicates conservation efforts. We documented the diet of the Himalayan brown bear ( Ursus arctos isabellinus ) by combining classical scat analysis and a newly developed molecular genetic technique (the trn L approach), in Deosai National Park, Pakistan. Brown bears consumed over 50 plant species, invertebrates, ungulates, and several rodents. Eight plant families; Poaceae, Polygonaceae, Cyperaceae, Apiaceae, Asteraceae, Caryophyllaceae, Lamiaceae, and...

Expert-based assessment of rewilding indicates progress at site-level, yet challenges for upscaling

Josiane Segar, Henrique Pereira, Raquel Filgueiras, Alexandros Karamanlidis, Deli Saavedra & Néstor Fernández
Rewilding is gaining importance across Europe, as agricultural abandonment trajectories provide opportunities for large-scale ecosystem restoration. However, its effective implementation is hitherto limited, in part due to a lack of monitoring of rewilding interventions and their interactions. Here, we provide a first assessment of rewilding progress across seven European sites. Using an iterative and participatory Delphi technique to standardize and analyze expert-based knowledge of these sites, we 1) map rewilding interventions onto the three central...

Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima

Donovan Anderson, Yuki Negishi, Hiroko Ishiniwa, Kei Okuda, Thomas Hinton, Rio Toma, Junco Nagata, Hidetoshi Tamate & Shingo Kaneko
Natural and anthropogenic disasters have the capability to cause sudden extrinsic environmental changes and long-lasting perturbations including invasive species, species expansion, and influence evolution as selective pressures force adaption. Such disasters occurred on March 11th 2011, in Fukushima, Japan when an earthquake, tsunami, and meltdown of a nuclear power plant all drastically reformed anthropogenic land use. Here, we demonstrate, using genetic data, how wild boar (Sus scrofa leucomystax) have persevered against these environmental changes, including...

Time-series covering up to four decades reveals major changes and drivers of marine growth and proportion of repeat spawners in an Atlantic salmon population

Alison Harvey, Øystein Skaala, Reidar Borgstrøm, Per Tommy Fjeldheim, Kaja Fjeldheim, Kjell Utne, Ingrid Johnsen, Peder Fiske, Synne Winterthun, Sofie Knutar, Harald Sægrov, Kurt Urdal & Kevin Glover
1. Wild Atlantic salmon populations have declined in many regions and are affected by diverse natural and anthropogenic factors. To facilitate management guidelines, precise knowledge of mechanisms driving population changes in demographics and life history traits is needed. 2. Our analyses were conducted on a) age and growth data from scales of salmon caught by angling in the river Etneelva, Norway, covering smolt year classes from 1980 to 2018, b) extensive sampling of the whole...

Strategies to Mitigate Enteric Methane Emissions by Ruminants

C. Arndt, A.N. Hristov, W.J. Price, S.C. McClelland, A.M. Pelaez, A.R. Bayat, L.A. Crompton, J. Dijkstra, M.A. Eugène, D. Enahoro, E. Kebreab, M. Kreuzer, M. McGee, C. Martin, C.J. Newbold, C.K. Reynolds, A. Schwarm, K.J. Shingfield, J.B. Veneman, D.R. Yáñez-Ruiz & Z. Yu
To meet the 1.5°C target, methane (CH4) from ruminants must be reduced by 11 to 30% of the 2010 level by 2030 and by 24 to 47% by 2050. A meta-analysis identified strategies to decrease product-based [PB; CH4 per unit meat or milk (CH4I)] and absolute (ABS) enteric CH4 emissions while maintaining or increasing animal productivity (AP; weight gain and milk yield). Next the potential of different adoption rates of one PB and/or ABS strategies...

Asynchronous Saturation of the Carbon Sink in African and Amazonian tropical forests

Wannes Hubau, Simon Lewis, Oliver Phillips, Kofi Kofi Affum-Baffoe, Hans Hans Beeckman, Aida Cuni-Sanchez, Corneille Ewango, Sophie Fauset, Douglas Sheil, Bonaventure Sonké, Martin Sullivan, Terry Sunderland, Sean Thomas, Katharine Abernethy, Stephen Adu-Bredu, Christian Amani, Timothy Baker, Lindsay Banin, Fidèle Baya, Serge Begne, Amy Bennett, Fabrice Benedet, Robert Bitariho & Yannick Bocko
Data and R-code from Hubau W et al. 2020. 'Asynchronous Saturation of the Carbon Sink in African and Amazonian tropical forests'. Nature 579, 80-87. 2020. DOI: 10.1038/s41586-020-2035-0. ABSTRACT: Structurally intact tropical forests sequestered ~50% of global terrestrial carbon uptake over the 1990s and early 2000s, offsetting ~15% of anthropogenic CO2 emissions1-3. Climate-driven vegetation models typically predict that this tropical forest ‘carbon sink’ will continue for decades4,5. However, recent inventories of intact Amazonian forests show declining...

Data from: Genetic isolation within the malaria mosquito Anopheles melas

Kevin C. Deitz, Giridhar Athrey, Michael R. Reddy, Hans J. Overgaard, Abrahan Matias, Jawara Musa, Alessandra Della Torre, Vincenzo Petrarca, Joao Pinto, Anthony E. Kiszewski, Pierre Kengne, Carlo Costantini, Adalgisa Caccone, Michel A. Slotman, Musa Jawara & Giri Athrey
Anopheles melas is a brackish water-breeding member of the An. gambiae complex that is distributed along the coast of West Africa and is a major malaria vector within its range. Because little is known about the population structure of this species, we analyzed 15 microsatellite markers and 1,161 bp of mtDNA in 11 An. melas populations collected throughout its range. Compared to its sibling species An. gambiae, An. melas populations have a high level of...

Data from: Population structure, genetic variation and linkage disequilibrium in perennial ryegrass populations divergently selected for freezing tolerance

Mallikarjuna Rao Kovi, Siri Fjellheim, Simen R. Sandve, Arild Larsen, Heidi Rudi, Torben Asp, Matthew Peter Kent & Odd Arne Rognli
Low temperature is one of the abiotic stresses seriously affecting the growth of perennial ryegrass (Lolium perenne L. Understanding the genetic control of freezing tolerance would aid in the development of cultivars of perennial ryegrass with improved adaptation to frost. A total number of 80 individuals (24 of High frost [HF]; 29 of Low frost [LF] and 27 of Unselected [US]) from the second generation of the two divergently selected populations and an unselected control...

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...

European soil seed bank communities across a climate and land-cover gradient

Jan Plue, Hans Van Calster, Inger Auestad, Sofia Basto, Reneé M. Bekker, Hans Henrik Bruun, Richard Chevalier, Guillaume Decocq, Ulf Grandin, Martin Hermy, Hans Jacquemyn, Anna Jakobsson, Rein Kalamees, Rob H. Marrs, Bryndis Marteinsdóttir, Per Milberg, Robin J. Pakeman, Gareth Phoenix, Ken Thompson, Vigdis Vandvik, Markus Wagner, Sara A.O. Cousins, Ove Eriksson, Jamshid Ghorbani, Małgorzata Jankowska-Błaszczuk … & Alistair G. Auffret
This is the data set used for the publication Buffering effects of soil seed banks on plant community composition in response to land use and climate, published in the journal Global Ecology and Biogeography. Aim. Climate and land use are key determinants of biodiversity, with past and ongoing changes posing serious threats to global ecosystems. Unlike most other organism groups, plant species can possess dormant life-history stages such as soil seed banks, which may help...

Data from: Neighborhood bully: no difference in territorial response towards neighbors or strangers in marmots

Mariona Ferrandiz-Rovira, Timothée Zidat, Pierre Dupont, Vérane Berger, Célia Rézouki & Aurélie Cohas
Territorial animals are expected to adjust their response to intruders according to the perceived threat-level. One of the factors that drives threat-level is the identity of the intruder. The dear enemy phenomenon theory postulates that individuals should respond with lower intensity to neighbors, already possessing a territory, than to strangers that may fight to evict them. In social species, the hierarchical status of the intruder might also mediate this response. Such behavioral adjustments presuppose a...

Data from: The standard metabolic rate of a land snail (Cepaea hortensis) is a repeatable trait and influences winter survival

Claus Bech, Maren Trones Christiansen, Pernille Kvernland, Randi Marie Nygård, Eline Rypdal, Sara Kjeldsø Sneltorp, Liv Monica Trondrud & Øyvind Gjønnes Tvedten
Phenotypic selection on physiological parameters is an underrepresented topic in studies of evolutionary biology. There is especially a lack of studies involving invertebrate organisms. We studied the repeatability of the standard metabolic rate (SMR) and the effect of individual variation in SMR on the subsequent winter survival in a terrestrial shell-bearing mollusc, the white-lipped snail (Cepaea hortensis) in mid-Norway. SMR was measured twice during the autumn and – after an experimental overwintering at controlled conditions...

Determinants of heart rate in Svalbard reindeer reveal mechanisms of seasonal energy management

L. Monica Trondrud, Gabriel Pigeon, Steve Albon, Walter Arnold, Alina L. Evans, R. Justin Irvine, Elżbieta Król, Erik Ropstad, Audun Stien, Vebjørn Veiberg, John R. Speakman & Leif Egil Loe
Seasonal energetic challenges may constrain an animal’s ability to respond to changing individual and environmental conditions. Here we investigated variation in heart rate, a well-established proxy for metabolic rate, in Svalbard reindeer, a species with strong seasonal changes in foraging and metabolic activity. In 19 adult females we recorded heart rate, subcutaneous temperature and activity using biologgers. Mean heart rate more than doubled from winter to summer. Typical drivers of energy expenditure, such as reproduction...

Fat storage influences fasting endurance more than body size in an ungulate

L. Monica Trondrud, Gabriel Pigeon, Elżbieta Król, Steve Albon, Alina L. Evans, Walter Arnold, Catherine Hambly, R. Justin Irvine, Erik Ropstad, Audun Stien, Vebjørn Veiberg, John R. Speakman & Leif Egil Loe
1. The fasting endurance hypothesis (FEH) predicts strong selection for large body size in mammals living in environments where food supply is interrupted over prolonged periods of time. The Arctic is a highly seasonal and food restricted environment, but contrary to predictions from the FEH, empirical evidence shows that Arctic mammals are often smaller than their temperate conspecifics. Intraspecific studies integrating physiology and behaviour of different-sized individuals, may shed light on this paradox. 2. We...

Data from: Evolution of the immune system influences speciation rates in teleost fishes

Martin Malmstrøm, Michael Matschiner, Ole K. Tørresen, Bastiaan Star, Lars G. Snipen, Thomas F. Hansen, Helle T. Baalsrud, Alexander J. Nederbragt, Reinhold Hanel, Walter Salzburger, Nils C. Stenseth, Kjetill S. Jakobsen & Sissel Jentoft
Teleost fishes constitute the most species-rich vertebrate clade and exhibit extensive genetic and phenotypic variation, including diverse immune defense strategies. The genomic basis of a particularly aberrant strategy is exemplified by Atlantic cod, in which a loss of major histocompatibility complex (MHC) II functionality coincides with a marked expansion of MHC I genes. Through low-coverage genome sequencing (9–39×), assembly and comparative analyses for 66 teleost species, we show here that MHC II is missing in...

Data from: A genome-wide association study identifies a region strongly associated with symmetrical onychomadesis on chromosome 12 in dogs

Stina Dahlgren, Martine Lund Ziener & Frode Lingaas
Symmetrical onychomadesis causes periodic loss of claws in otherwise healthy dogs. Genome-wide association analysis in 225 Gordon Setters identified a single region associated with symmetrical onychomadesis on chromosome 12 (spanning about 3.3 mb). A meta-analysis including also English Setters indicated that this genomic region predisposes for symmetrical onychomadesis in English Setters as well. The associated region spans most of the major histocompatibility complex and nearly 1 Mb downstream. Like many other autoimmune diseases, associations of...

Data from: Genomic signatures of parasite-driven natural selection in north European Atlantic salmon (Salmo salar)

Ksenia J. Zueva, Jaakko Lumme, Alexei E Veselov, Matthew P. Kent & Craig R. Primmer
Understanding the genomic basis of host-parasite adaptation is important for predicting the long-term viability of species and developing successful management practices. However, in wild populations, identifying specific signatures of parasite-driven selection often presents a challenge, as it is difficult to unravel the molecular signatures of selection driven by different, but correlated, environmental factors. Furthermore, separating parasite-mediated selection from similar signatures due to genetic drift and population history can also be difficult. Populations of Atlantic salmon...

Data from: Circadian rhythmicity persists through the Polar night and midnight sun in Svalbard reindeer

Walter Arnold, Thomas Ruf, Leif Egil Loe, R. Justin Irvine, Erik Ropstad, Vebjørn Veiberg & Steve D. Albon
Studies of locomotor activity in Svalbard reindeer reported the temporary absence of diel rhythms under Arctic photic conditions. However, using Lomb-Scargle periodogram analyses with high statistical power we found diel or circadian rhythmicity throughout the entire year in measures of behaviour, temperature in the rumen and heart rate in free-living Svalbard reindeer. Significant diel rhythmicity was only lacking during some of the 15-day intervals analysed in the less frequently measured heart rate. During Polar Night...

Data from: A local evaluation of the individual state-space to scale up Bayesian spatial capture recapture

Cyril Milleret, Pierre Dupont, Christophe Bonenfant, Henrik Brøseth, Øystein Flagstad, Chris Sutherland & Richard Bischof
1. Spatial capture-recapture models (SCR) are used to estimate animal density and to investigate a range of problems in spatial ecology that cannot be addressed with traditional non-spatial methods. Bayesian approaches in particular offer tremendous flexibility for SCR modelling. Increasingly, SCR data are being collected over very large spatial extents making analysis computational intensive, sometimes prohibitively so. 2. To mitigate the computational burden of large-scale SCR models, we developed an improved formulation of the Bayesian...

Data from: Contrasting the roles of section length and instream habitat enhancement for river restoration success: a field study on 20 European restoration projects

Daniel Hering, Jukka Aroviita, Annette Baattrup-Pedersen, Karel Brabec, Tom Buijse, Frauke Ecke, Nikolai Friberg, Marek Gielczewski, Kathrin Januschke, Jan Köhler, Benjamin Kupilas, Armin W. Lorenz, Susanne Muhar, Amael Paillex, Michaela Poppe, Torsten Schmidt, Stefan Schmutz, Jan Vermaat, Piet F. M. Verdonschot, Ralf C. M. Verdonschot, Jochem Kail & Christian Wolter
1. Restoration of river hydromorphology often has limited detected effects on river biota. One frequently discussed reason is that the restored river length is insufficient to allow populations to develop and give the room for geomorphologic processes to occur. 2. We investigated ten pairs of restored river sections of which one was a large project involving a long, intensively restored river section and one represented a smaller restoration effort. The restoration effect was quantified by...

Data from: Berry production drives bottom-up effects on body mass and reproductive success in an omnivore

Anne G. Hertel, Richard Bischof, Ola Langvall, Atle Mysterud, Jonas Kindberg, Jon E. Swenson, Andreas Zedrosser & Ola Langval
Obligate herbivores dominate studies of the effects of climate change on mammals, however there is limited empirical evidence for how changes in the abundance or quality of plant food affect mammalian omnivores. Omnivores can exploit a range of different food resources over the course of a year, but they often rely on seasonally restricted highly nutritious fruiting bodies during critical life stages. Brown bears Ursus arctos in Sweden are dependent on berries for fattening before...

Data from: Genome-wide SNP analysis reveals a genetic basis for sea-age variation in a wild population of Atlantic salmon (Salmo salar)

Susan E. Johnston, Panu Orell, Victoria L. Pritchard, Matthew P. Kent, Sigbjørn Lien, Eero Niemelä, Jaakko Erkinaro, Craig Primmer & Craig R. Primmer
Delaying sexual maturation can lead to larger body size and higher reproductive success, but carries an increased risk of death before reproducing. Classical life history theory predicts that trade-offs between reproductive success and survival should lead to the evolution of an optimal strategy in a given population. However, variation in mating strategies generally persists, and in general, there remains a poor understanding of genetic and physiological mechanisms underlying this variation. One extreme case of this...

Data from: Mapping and validation of a major QTL affecting resistance to pancreas disease (salmonid alphavirus) in Atlantic salmon (Salmo salar)

Serap Gonen, Matthew Baranski, Ingunn Thorland, Ashie Norris, Harald Grove, Petter Arnesen, Håvard Bakke, Sigbjørn Lien, Stephen C. Bishop & Ross D. Houston
Pancreas disease (PD), caused by a salmonid alphavirus (SAV), has a large negative economic and animal welfare impact on Atlantic salmon aquaculture. Evidence for genetic variation in host resistance to this disease has been reported, suggesting that selective breeding may potentially form an important component of disease control. The aim of this study was to explore the genetic architecture of resistance to PD, using survival data collected from two unrelated populations of Atlantic salmon; one...

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  • Norwegian University of Life Sciences
  • Norwegian Institute for Nature Research
  • University of Oslo
  • Swedish University of Agricultural Sciences
  • Norwegian University of Science and Technology
  • Norwegian Institute of Bioeconomy Research
  • Natural Resources Institute Finland
  • University of Helsinki
  • Université de Sherbrooke
  • James Hutton Institute