163 Works

Data from: Population genetic analysis of a global collection of Fragaria vesca using microsatellite markers

Hrannar Smári Hilmarsson, Timo Hytönen, Sachiko Isobe, Magnus Göransson, Tuomas Toivainen & Jón Hallsteinn Hallsson
The woodland strawberry, Fragaria vesca, holds great promise as a model organism. It not only represents the important Rosaceae family that includes economically important species such as apples, pears, peaches and roses, but it also complements the well-known model organism Arabidopsis thaliana in key areas such as perennial life cycle and the development of fleshy fruit. Analysis of wild populations of A. thaliana has shed light on several important developmental pathways controlling, for example, flowering...

Data from: Monitoring of plant-environment interactions by high throughput FTIR spectroscopy of pollen

Murat Bağcıoğlu, Achim Kohler, Stephan Seifert, Janina Kneipp & Boris Zimmermann
Fourier transform infrared (FTIR) spectroscopy enables chemical analysis of pollen samples for plant phenotyping to study plant–environment interactions, such as influence of climate change or pathogens. However, current approach, such as microspectroscopy and attenuated total reflection spectroscopy, does not allow for high-throughput protocols. This study at hand suggests a new spectroscopic method for high-throughput characterization of pollen. Samples were measured as thin films of pollen fragments using a Bruker FTIR spectrometer with a high-throughput eXTension...

Data from: A high-throughput FTIR spectroscopy approach to assess adaptive variation in the chemical composition of pollen

Boris Zimmermann, Murat Bağcıoğlu, Valeria Tafinstseva, Achim Kohler, Mikael Ohlson & Siri Fjellheim
The two factors defining male reproductive success in plants are pollen quantity and quality, but our knowledge about the importance of pollen quality is limited due to methodological constraints. Pollen quality in terms of chemical composition may be either genetically fixed for high performance independent of environmental conditions, or it may be plastic to maximize reproductive output under different environmental conditions. In this study, we validated a new approach for studying the role of chemical...

Data from: Across population genomic prediction scenarios in which Bayesian variable selection outperforms GBLUP

Sanne Van Den Berg, Mario P. L. Calus, Theo H. E. Meuwissen & Yvonne C. J. Wientjes
Background: The use of information across populations is an attractive approach to increase the accuracy of genomic prediction for numerically small populations. However, accuracies of across population genomic prediction, in which reference and selection individuals are from different populations, are currently disappointing. It has been shown for within population genomic prediction that Bayesian variable selection models outperform GBLUP models when the number of QTL underlying the trait is low. Therefore, our objective was to identify...

Data from: Using network analysis to study behavioural phenotypes: an example using domestic dogs

Conor Goold, Judit Vas, Christine Olsen & Ruth C. Newberry
Phenotypic integration describes the complex interrelationships between organismal traits, traditionally focusing on morphology. Recently, research has sought to represent behavioural phenotypes as composed of quasi-independent latent traits. Concurrently, psychologists have opposed latent variable interpretations of human behaviour, proposing instead a network perspective envisaging interrelationships between behaviours as emerging from causal dependencies. Network analysis could also be applied to understand integrated behavioural phenotypes in animals. Here, we assimilate this cross-disciplinary progression of ideas by demonstrating the...

Data from: Anthrax outbreaks in the humans-livestock and wildlife interface areas of northern Tanzania: a retrospective review 2006 - 2016

Elibariki Reuben Mwakapeje, Sol Hoegset, Robert Fyumagwa, Hezron E Nonga, Robinson Mdegela & Eystein Skjerve
BACKGROUND: Anthrax outbreaks in Tanzania have been reported from the human, livestock and wildlife sectors over several years, and is among the notifiable diseases. Despite frequent anthrax outbreaks, there is no comprehensive dataset indicating the magnitude and distribution of the disease in susceptible species. This study is a retrospective review of anthrax outbreaks from the human, livestock, and wildlife surveillance systems from 2006 to 2016. The objectives were to identify hotspot districts, describe anthrax epidemiology...

Data from: Ancient hybridizations among the ancestral genomes of bread wheat

Thomas Marcussen, Simen R. Sandve, Lise Heier, Manuel Spannagl, Matthias Pfeifer, The International Wheat Genome Sequencing Consortium, Kjetill S. Jakobsen, Brande B. H. Wulff, Burkhard Steuernagel, Klaus F. X. Mayer & Odd-Arne Olsen
The allohexaploid bread wheat genome consists of three closely related subgenomes (A, B, and D), but a clear understanding of their phylogenetic history has been lacking. We used genome assemblies of bread wheat and five diploid relatives to analyze genome-wide samples of gene trees, as well as to estimate evolutionary relatedness and divergence times. We show that the A and B genomes diverged from a common ancestor ~7 million years ago and that these genomes...

Data from: Parallel and nonparallel genome-wide divergence among replicate population pairs of freshwater and anadromous Atlantic salmon

Charles Perrier, Vincent Bourret, Matthew P. Kent & Louis Bernatchez
Little is known about the genetic basis differentiating resident and anadromous forms found in many salmonid species. Using a medium-density SNP array, we documented genomic diversity and divergence at 2336 genetically mapped loci among three pairs of North American anadromous and freshwater Atlantic salmon populations. Our results show that across the genome, freshwater populations have lower diversity and a smaller proportion of private polymorphism relative to anadromous populations. Moreover, differentiation was more pronounced among freshwater...

Data from: Ethnolinguistic structuring of sorghum genetic diversity in Africa and the role of local seed systems

Ola T. Westengen, Mark Atam Okongo, Leo Onek, Trygve Berg, Hari Upadhyaya, Siri Dharma Kaur Khalsa, Siri Birkeland, Nils C. Stenseth & Anne K. Brysting
Sorghum is a drought-tolerant crop with a vital role in the livelihoods of millions of people in marginal areas. We examined genetic structure in this diverse crop in Africa. On the continent-wide scale, we identified three major sorghum populations (Central, Southern, and Northern) that are associated with the distribution of ethnolinguistic groups on the continent. The codistribution of the Central sorghum population and the Nilo-Saharan language family supports a proposed hypothesis about a close and...

Expanding forests in alpine regions lead to a corresponding shift in belowground fungal communities

Synnøve Smebye Botnen, Lea-Rebekka Tonjer, Ella Thoen, Sunil Mundra, Luis Morgado, Line Nybakken, Anders Bryn & Håvard Kauserud
Climate change causes upward shift of forest lines worldwide, with consequences on soil biota and carbon sequestration (C). We here analyse compositional changes in the soil biota across the forest line ecotone, an important transition zone between different ecosystems. We collected soil samples along transects stretching from subalpine mountain birch forests to low-alpine vegetation. Soil fungi and micro-eukaryotes were surveyed using DNA metabarcoding of the 18S and ITS2 markers, while ergosterol was used to quantify...

Arthropod OTUs in fruit bodies of wood decay fungi

Lisa Lunde & Sundy Maurice
Biological communities within living organisms are structured by their host’s traits. How host traits affect biodiversity and community composition is poorly explored for some associations, such as arthropods within fungal fruit bodies. Using DNA metabarcoding, we revealed the arthropod communities in living fruit bodies of eleven wood-decay fungi from boreal forests and investigated how they were affected by different fungal traits. Arthropod diversity was higher in fruit bodies with a larger surface area-to-volume ratio, suggesting...

A test of frequency dependent selection in the evolution of a generalist phenotype

Stephanie Blain, Louise Chavarie, Mackenzie Kinney & Dolph Schluter
A solitary population of consumers frequently evolves to the middle of a resource gradient and an intermediate mean phenotype compared to a sympatric pair of competing species that diverge to either side via character displacement. The forces governing the distribution of phenotypes in these allopatric populations, however, are little investigated. Theory predicts that the intermediate mean phenotype of the generalist should be maintained by negative frequency dependent selection, whereby alternate extreme phenotypes are favored because...

Data from: Traits mediate niches and co-occurrences of forest beetles in ways that differ among bioclimatic regions

Ryan C. Burner, Jörg G. Stephan, Lukas Drag, Tone Birkemoe, Jörg Muller, Tord Snäll, Otso Ovaskainen, Mária Potterf, Juha Siitonen, Olav Skarpaas, Inken Doerfler, Martin M. Gossner, Peter Schall, Wolfgang W. Weisser & Anne Sverdrup-Thygeson
Aim To investigate the role of traits in beetle community assembly and test for consistency in these effects among several bioclimatic regions. We asked (1) whether traits predicted species’ responses to environmental gradients (i.e., their niches), (2) whether these same traits could predict co-occurrence patterns, and (3) how consistent were niches and the role of traits among study regions. Location Boreal forests in Norway and Finland, temperate forests in Germany. Methods We complied capture records...

MetaComNet: A random forest-based framework for making spatial prediction of plant-pollinator interactions

Markus Arne Kjær Sydenham, Zander Venter, Trond Reitan, Claus Rasmussen, Astrid Skrindo, Daniel Skoog, Kaj-Andreas Hanevik, Stein Joar Hegland, Yoko Dupont, Anders Nielsen, Joseph Chipperfield & Graciela Rusch
1. Predicting plant-pollinator interaction networks over space and time will improve our understanding of how environmental change is likely to impact the functioning of ecosystems. Here we propose a framework for producing spatially explicit predictions of the occurrence and number of pairwise plant-pollinator interactions and of the species richness, diversity, and abundance of pollinators visiting flowers. We call the framework ‘MetaComNet’ because it aims to link metacommunity dynamics to the assembly of ecological networks. 2....

Data from: Future suitability of habitat in a migratory ungulate under climate change

Inger Maren Rivrud, Erling L. Meisingset, Leif Egil Loe & Atle Mysterud
With climate change, the effect of global warming on snow cover is expected to cause range expansion and enhance habitat suitability for species at their northern distribution limits. However, how this depend on landscape topography and sex in size-dimorphic species remains uncertain, and is further complicated for migratory animals following climate-driven seasonal resource fluctuations across vast landscapes. Using 11 years of data from a partially migratory ungulate at their northern distribution ranges, the red deer...

Data for: Parasitoids indicate major climate-induced shifts in Arctic communities

Tuomas Kankaanpää, Eero Vesterinen, Bess Hardwick, Niels Martin Martin Schmidt, Tommi Andersson, Paul Eric Aspholm, Isabel Barrio, Niklas Beckers, Joël Bêty, Tone Birkemoe, Melissa DeSiervo, Katherine Drotos, Dorothee Ehrich, Olivier Gilg, Vladimir Gilg, Nils Hein, Toke Høye, Kristian Jakobsen, Camille Jodouin, Jesse Jorna, Mikhail Kozlov, Jean-Claude Kresse, Don-Jean Leandri-Breton, Nicolas Lecomte, Maia Olsen … & Tomas Roslin
Climatic impacts are especially pronounced in the Arctic, which as a region is warming twice as fast as the rest of the globe. Here, we investigate how mean climatic conditions and rates of climatic change impact parasitoid insect communities in 16 localities across the Arctic. We focus on parasitoids in a wide-spread habitat, Dryas heathlands, and describe parasitoid community composition in terms of larval host use (i.e. parasitoid use of herbivorous Lepidoptera versus pollinating Diptera)...

Opposing fitness consequences of habitat use in a harvested moose population

Endre Grüner Ofstad, Endre Ofstad, Stine Markussen, Bernt-Erik Sæther, Erling Johan Solberg, Morten Heim, Hallvard Haanes, Knut Røed & Ivar Herfindal
1. Landscape changes are happening at an unprecedented pace, and together with high levels of wildlife harvesting humans have a large effect on wildlife populations. A thorough knowledge of their combined influence on individual fitness is important in order to understand factors affecting population dynamics. 2. The goal of the study was to assess the individual consistency in the use of risky habitat types, and how habitat use was related to fitness components and life-history...

Modular chromosome rearrangements reveal parallel and nonparallel adaptation in a marine fish

Tony Kess, Paul Bentzen, Sarah Lehnert, Emma Sylvester, Sigbjørn Lien, Matthew Kent, Marion Sinclair-Waters, Corey Morris, Brendan Wringe, Robert Fairweather & Ian Bradbury
Genomic architecture and standing variation can play a key role in ecological adaptation, and contribute to the predictability of evolution. In Atlantic cod (Gadus morhua), four large chromosomal rearrangements have been associated with ecological gradients and migratory behaviour in regional analyses. However, the degree of parallelism , the extent of independent inheritance, and functional distinctiveness of these rearrangements remains poorly understood. Here, we use a 12K single nucleotide polymorphism (SNP) array to demonstrate extensive individual...

Data from: Introduced Scotch broom (Cytisus scoparius) invades the genome of native populations in vulnerable heathland habitats

Lene Rostgaard Nielsen, Ursula Brandes, Erik Dahl Kjær, Siri Fjellheim & Erik Dahl Kjaer
Cytisus scoparius is a global invasive species that affects local flora and fauna at the intercontinental level. Its natural distribution spans across Europe, but seeds have also been moved among countries, mixing plants of native and non-native genetic origins. Hybridization between the introduced and native gene pool is likely to threaten both the native gene pool and the local flora. In this study, we address the potential threat of invasive C. scoparius to local gene...

Data from: Definition and estimation of vital rates from repeated censuses: choices, comparisons and bias corrections focusing on trees

Takashi S. Kohyama, Tetsuo I. Kohyama, Douglas Sheil & Takashi Kohyama
1.Mortality and recruitment rates are fundamental measures of population dynamics. Ecologists and others have defined and estimated these vital rates in various ways. We review these alternatives focusing on tree population census data in fixed area plots, though many aspects have wider application when similar data characteristics and assumptions apply: our goal is to guide choices and facilitate comparisons. 2.We divide our estimates into ‘instantaneous’ and ‘annual’ rates, corresponding to continuous- or discrete-time dynamics respectively....

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: Sociodemographic factors modulate the spatial response of brown bears to vacancies created by hunting

Shane C. Frank, Martin Leclerc, Fanie Pelletier, Frank Rosell, Jon E. Swenson, Richard Bischof, Jonas Kindberg, Hans Geir Eiken, Snorre B. Hagen, Andreas Zedrosser & Jon. E. Swenson
1.There is a growing recognition of the importance of indirect effects from hunting on wildlife populations, e.g., social and behavioral changes due to harvest, which occur after the initial offtake. Nonetheless, little is known about how the removal of members of a population influences the spatial configuration of the survivors. 2.We studied how surviving brown bears (Ursus arctos) used former home ranges that had belonged to casualties of the annual bear hunting season in southcentral...

Data from: Controlling for p-value inflation in allele frequency change in experimental evolution and artificial selection experiments

Petri Kemppainen, Bernt Rønning, Thomas Kvalnes, Ingerid J. Hagen, Thor Harald Ringsby, Anna M. Billing, Henrik Pärn, Sigbjorn Lien, Arild Husby, Bernt-Erik Sæther, Henrik Jensen & Bernt-Erik Saether
Experimental evolution studies can be used to explore genomic response to artificial and natural selection. In such studies, loci that display larger allele frequency change than expected by genetic drift alone are assumed to be directly or indirectly associated with traits under selection. However, such studies report surprisingly many loci under selection, suggesting that current tests for allele frequency change may be subject to p-value inflation and hence be anti-conservative. One factor known from genome...

Data from: Climate change and bird reproduction: warmer springs benefit breeding success in boreal forest grouse

Per Wegge & Jorund Rolstad
Global warming is predicted to adversely affect reproduction of birds, especially in northern latitudes. A recent study in Finland inferred that declining populations of black grouse Tetrao tetrix could be attributed to advancement of the time of mating and chicks hatching too early – a support of the mismatch hypothesis. Here, we examine the breeding success of sympatric capercaillie T. urogallus and black grouse over a 38-year period in southeast Norway. Breeding season temperatures increased,...

Data from: Harvest-induced phenotypic selection in an island population of moose, Alces alces

Thomas Kvalnes, Bernt-Erik Sæther, Hallvard Haanes, Knut H. Røed, Steinar Engen, Erling J. Solberg & Bernt-Erik Saether
Empirical evidence strongly indicates that human exploitation has frequently led to rapid evolutionary changes in wild populations, yet the mechanisms involved are often poorly understood. Here we applied a recently developed demographic framework for analysing selection to data from a 20-year study of a wild population of moose, Alces alces. In this population, a genetic pedigree has been established all the way back to founders. We demonstrate harvest-induced directional selection for delayed birth dates in...

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