158 Works

Decomposing demographic contributions to the effective population size with moose as a case study

Stine Svalheim Markussen, Aline Lee, Ane Myhre, Steinar Engen, Erling Solberg, Hallvard Haanes, Knut H Røed, Ivar Herfindal, Morten Heim & Bernt-Erik Sæther
Levels of random genetic drift are influenced by demographic factors, such as mating system, sex ratio and age structure. The effective population size (Ne) is a useful measure for quantifying genetic drift. Evaluating relative contributions of different demographic factors to Ne is therefore important to identify what makes a population vulnerable to loss of genetic variation. Until recently, models for estimating Ne have required many simplifying assumptions, making them unsuitable for this task. Here, using...

Tying Knots: Creating Metaphors for Interpersonal Relationships

Knut Omholt

Data from: Reference genome of Lumpfish Cyclopterus lumpus Linnaeus provides evidence of male heterogametic sex determination through the AMH pathway

Melissa Holborn, Anthony Einfeldt, Tony Kess, Steve Duffy, Amber Messmer, Barbara Langille, Johanne Gauthier, Paul Bentzen, Tim Knutsen, Matthew Kent, Danny Boyce & Ian Bradbury
Teleosts exhibit extensive diversity of sex determination (SD) systems and mechanisms, providing the opportunity to study the evolution of sex determination and sex chromosomes. Here we sequenced the genome of the Common Lumpfish (Cyclopterus lumpus Linnaeus), a species of increasing importance to aquaculture, and identified the SD region and master SD locus using a 70K SNP array and tissue-specific expression data. The chromosome-level assembly identified 25 diploid chromosomes with a total size of 572.89 Mb,...

Context dependent fitness costs of reproduction despite stable body mass costs in an Arctic herbivore

Gabriel Pigeon, Steve Albon, Leif Egil Loe, Richard Bischof, Christophe Bonenfant, Mads Farchhammer, Justine Irvine, Erik Ropstad, Vebjorn Veiberg & Audun Stein
1. The cost of reproduction on demographic rates is often assumed to operate through changing body condition. Several studies have found that reproduction depresses body mass more if the current conditions are severe, such as high population densities or adverse weather, than under benign environmental conditions. However, few studies have investigated the association between the fitness and body mass costs of reproduction. 2. Using 25 years of individual-based capture-recapture data from Svalbard reindeer (Rangifer tarandus...

Data from: Ancient chromosomal rearrangement associated with local adaptation of a post-glacially colonized population of Atlantic Cod in the northwest Atlantic

Marion Sinclair-Waters, Ian R. Bradbury, Corey J. Morris, Sigbjorn Lien, Matthew P. Kent & Paul Bentzen
Intraspecific diversity is central to the management and conservation of exploited species, yet knowledge of how this diversity is distributed and maintained in the genome of many marine species is lacking. Recent advances in genomic analyses allow for genome-wide surveys of intraspecific diversity and offer new opportunities for exploring genomic patterns of divergence. Here, we analyzed genome-wide polymorphisms to measure genetic differentiation between an offshore migratory and a non-migratory population and to define conservation units...

Data from: Managing Neotropical oil palm expansion to retain phylogenetic diversity

Graham W. Prescott, James J. Gilroy, Torbjørn Haugaasen, Claudia A. Medina Uribe, William A. Foster & David P. Edwards
The expansion of tropical agriculture is a major driver of the extinction crisis. A key question is whether biodiversity losses can be minimized by restricting future expansion to low-productivity farmland and retaining forest fragments, especially in rapidly changing Neotropical landscapes. We investigated these methods in the context of avian phylogenetic diversity, which summarizes the evolutionary history preserved within communities. Evidence suggests that phylogenetic diversity plays an important role in maintaining key ecosystem functions. We collected...

Data from: Evolution of sex determination loci in Atlantic salmon

James Kijas, Sean McWilliam, Marina Naval Sanchez, Peter Kube, Harry King, Bradley Evans, Torfin Nome, Sigbjorn Lien & Klara Verbyla
Teleost fish exhibit a remarkable diversity in the control of sex determination, offering the opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 fish and 46,501 SNP to map sex determination to three separate genomic locations in Atlantic salmon (Salmo salar). To characterize each, whole genome sequencing was performed to 30-fold depth of coverage using 20 fish representing each of three identified sex lineages. SNP polymorphism reveals male...

Data from: Does biomass growth increase in the largest trees? Flaws, fallacies and alternative analyses

Douglas Sheil, Chris S. Eastaugh, Mart Vlam, Pieter A. Zuidema, Peter Groenendijk, Peter Van Der Sleen, Alex Jay & Jerome Vanclay
The long-standing view that biomass growth in trees typically follows a rise-and-fall unimodal pattern has been challenged by studies concluding that biomass growth increases with size even among the largest stems in both closed forests and in open competition-free environments. We highlight challenges and pitfalls that influence such interpretations. The ability to observe and calibrate biomass change in large stems requires adequate data regarding these specific stems. Data checking and control procedures can bias estimates...

Data from: Host and tissue variation overshadow the response of boreal moss-associated fungal communities to increased nitrogen load

Marie L. Davey, Marte J. Skogen, Einar Heegaard, Rune Halvorsen, Håvard Kauserud & Mikael Ohlson
Human activity has more than doubled the amount of nitrogen entering the global nitrogen cycle, and the boreal forest biome is a nitrogen-limited ecosystem sensitive to nitrogen load perturbation. Although bryophyte-associated microbes contribute significantly to boreal forest ecosystem function, particularly in carbon and nitrogen cycling, little is known about their responses to anthropogenic global change. Amplicon pyrosequencing of the ITS2 region of rDNA was used to investigate how fungal communities associated with three bryophyte species...

Data from: Population closure and the bias-precision trade-off in Spatial Capture-Recapture

Pierre Dupont, Cyril Milleret, Olivier Gimenez & Richard Bischof
1. Spatial capture-recapture (SCR) is an increasingly popular method for estimating ecological parameters. This method often relies on data collected over relatively long sampling periods. While longer sampling periods can yield larger sample sizes and thus increase precision of estimates, they also increase the risk of violating the closure assumption, thereby potentially introducing bias. The sampling period characteristics are therefore likely to play an important role in this bias-precision tradeoff. Yet few studies have studied...

Data from: Genetic architecture of a hormonal response to gene knockdown in honey bees

Kate E. Ihle, Olav Rueppell, Ying Wang, M. Kim Fondrk, , Gro V. Amdam & Zachary Y. Huang
Variation in endocrine signaling is proposed to underlie the evolution and regulation of social life histories, but the genetic architecture of endocrine signaling is still poorly understood. An excellent example of a hormonally influenced set of social traits is found in the honey bee (Apis mellifera): a dynamic and mutually suppressive relationship between juvenile hormone (JH) and the yolk precursor protein vitellogenin (Vg) regulates behavioral maturation and foraging of workers. Several other traits cosegregate with...

Data from: Effect of soil pH increase by biochar on NO, N2O and N2 production during denitrification in acid soils

Alfred Obia, Gerard Cornelissen, Jan Mulder & Peter Dörsch
Biochar (BC) application to soil suppresses emission of nitrous- (N2O) and nitric oxide (NO), but the mechanisms are unclear. One of the most prominent features of BC is its alkalizing effect in soils, which may affect denitrification and its product stoichiometry directly or indirectly. We conducted laboratory experiments with anoxic slurries of acid Acrisols from Indonesia and Zambia and two contrasting BCs produced locally from rice husk and cacao shell. Dose-dependent responses of denitrification and...

Data from: A multiscale vibrational spectroscopic approach for identification and biochemical characterization of pollen

Murat Bağcıoğlu, Boris Zimmermann & Achim Kohler
Background: Analysis of pollen grains reveals valuable information on biology, ecology, forensics, climate change, insect migration, food sources and aeroallergens. Vibrational (infrared and Raman) spectroscopies offer chemical characterization of pollen via identifiable spectral features without any sample pretreatment. We have compared the level of chemical information that can be obtained by different multiscale vibrational spectroscopic techniques. Methodology: Pollen from 15 different species of Pinales (conifers) were measured by seven infrared and Raman methodologies. In order...

Data from: Characterizing aeroallergens by infrared spectroscopy of fungal spores and pollen

Boris Zimmermann, Zdenko Tkalčec, Armin Mešić & Achim Kohler
Background: Fungal spores and plant pollen cause respiratory diseases in susceptible individuals, such as asthma, allergic rhinitis and hypersensitivity pneumonitis. Aeroallergen monitoring networks are an important part of treatment strategies, but unfortunately traditional analysis is time consuming and expensive. We have explored the use of infrared spectroscopy of pollen and spores for an inexpensive and rapid characterization of aeroallergens. Methodology: The study is based on measurement of spore and pollen samples by single reflectance attenuated...

Data from: Canine mammary tumours are affected by frequent copy number aberrations, including amplification of MYC and loss of PTEN

Kaja S. Borge, Silje Nord, Peter Van Loo, Ole C. Lingjærde, Gjermund Gunnes, Grethe I. G. Alnæs, Hiroko K. Solvang, Torben Lüders, Vessela N. Kristensen, Anne-Lise Børresen-Dale & Frode Lingaas
Background: Copy number aberrations frequently occur during the development of many cancers. Such events affect dosage of involved genes and may cause further genomic instability and progression of cancer. In this survey, canine SNP microarrays were used to study 117 canine mammary tumours from 69 dogs. Results: We found a high occurrence of copy number aberrations in canine mammary tumours, losses being more frequent than gains. Increased frequency of aberrations and loss of heterozygosity were...

Data from: De novo and reference transcriptome assembly of transcripts expressed during flowering provide insight into seed setting in tetraploid red clover

Mallikarjuna Rao Kovi, Helga Amdahl, Muath Alsheikh & Odd Arne Rognli
Red clover (Trifolium pratense L.) is one of the most important legume forage species in temperate livestock agriculture. Tetraploid red clover cultivars are generally producing less seed than diploid cultivars. Improving the seed setting potential of tetraploid cultivars is necessary to utilize the high forage quality and environmentally sustainable nitrogen fixation ability of red clover. In the current study, our aim was to identify candidate genes involved in seed setting. Two genotypes, ‘Tripo’ with weak...

Data from: Proactive avoidance behaviour and pace-of-life syndrome in Atlantic salmon

Børge Damsgård, Tor H. Evensen, Øyvind Øverli, Marnix Gorissen, Lars Ebbesson, Sonia Ray & Erik Höglund
Individuals in a fish population differ in key life history traits such as growth rate and body size. This raises the question of whether such traits cluster along a fast-slow growth continuum according to a pace-of-life syndrome (POLS). Fish species like salmonids may develop a bimodal size distribution, providing an opportunity to study the relationships between individual growth and behavioural responsiveness. Here we test whether proactive characteristics (bold behaviour coupled with low post-stress cortisol production)...

Data from: Exclusion of invertebrates influences saprotrophic fungal community and wood decay rate in an experimental field study

Rannveig Margrete Jacobsen, Anne Sverdrup-Thygeson, Håvard Kauserud, Sunil Mundra & Tone Birkemoe
1. Decomposer communities perform an essential ecosystem function by recycling nutrients. However, the effect of higher trophic levels on microbial decomposer communities and rate of decomposition is poorly understood. We therefore conducted an exclusion experiment to test the effect of invertebrates on fungal decomposer communities in dead wood, repeated at 30 sites in two landscapes, and measured wood density to assess effect on decay rate. 2. Invertebrates were excluded from recently cut logs by cages...

Data from: Priority effects of early successional insects influence late successional fungi in dead wood

Rannveig Margrete Jacobsen, Tone Birkemoe & Anne Sverdrup-Thygeson
Community assembly is an integral process in all ecosystems, producing patterns of species distributions, biodiversity, and ecosystem functioning. Environmental filters and colonization history govern the assembly process, but their relative importance varies depending on the study system. Dead wood decomposition is a slow process, allowing decomposer communities to develop within a slowly changing substrate for decades. Despite this, there are few long-term studies of priority effects from colonization history in this ecosystem. In this study,...

Data from: Infanticide as a male reproductive strategy has a nutritive risk effect in brown bears

Sam M. J. G. Steyaert, Christine Reusch, Sven Brunberg, Jon E. Swenson, Klaus Hackländer, Andreas Zedrosser & K. Hacklander
Behavioral strategies to reduce predation can incur costs (i.e. risk effects). A common strategy to avoid predation is spatiotemporal avoidance of predators, in which prey typically trade optimal resources for safety. Analogous with predator-prey theory, risk effects should also arise in species with sexually selected infanticide (SSI), in which females with dependent offspring avoid infanticidal males. In brown bears (Ursus arctos), SSI is common and explains spatiotemporal segregation among reproductive classes. Here, we show that...

Data from: Seed banks are biodiversity reservoirs: species-area relationships above versus below ground

Vigdis Vandvik, Kari Klanderud, Eric Meineri, Inger E. Måren & Joachim Töpper
Soil seed banks offer plants the possibility to disperse through time. This has implications for population and community dynamics, as recognised by ecological and evolutionary theory. In contrast, the conservation and restoration literature often find seed banks to be depauperate, weedy and without much conservation value or restoration potential. One explanation for these contrasting views might lie in a systematic bias in the sampling of seed banks versus established plant communities. We use the species–area...

Data from: Y chromosome haplotype distribution of brown bears (Ursus arctos) in Northern Europe provides insight into population history and recovery (Ursus arctos)

Julia Schregel, Hans Geir Eiken, Finn Audun Grøndahl, Frank Hailer, Jouni Aspi, Ilpo Kojola, Konstantin Tirronen, Pjotr Danilov, Alexander Rykov, Eugene Poroshin, Axel Janke, Jon E. Swenson, Snorre B. Hagen & Piotr Danilov
High-resolution, male-inherited Y-chromosomal markers are a useful tool for population genetic analyses of wildlife species, but to date have only been applied in this context to relatively few species besides humans. Using nine Y-chromosomal STR and three Y-chromosomal single nucleotide polymorphism markers (Y-SNPs), we studied whether male gene flow was important for the recent recovery of the brown bear (Ursus arctos) in Northern Europe, where the species declined dramatically in numbers and geographic distribution during...

Data from: Determinants of age at first reproduction and lifetime breeding success revealed by full paternity assignment in a male ungulate

Stine S. Markussen, Ivar Herfindal, Anne Loison, Erling J. Solberg, Hallvard Haanes, Knut H. Røed, Morten Heim, Bernt-Erik Sæther & Bernt-Erik Saether
Age at first reproduction is an important determinant of individual variation in reproductive success in ungulates, but few studies have examined its relationship with later fitness-related traits in males. We used a long-term individual based study of a harvested moose population to quantify the individual reproductive performance and survival of males, as well as to examine the determinants of age at first reproduction and consequences of age at first reproduction on lifetime breeding success. The...

Data from: Extremely low genetic variability and highly structured local populations of Arabidopsis thaliana at higher latitudes

Anna Monika Lewandowska-Sabat, Siri Fjellheim & Odd Arne Rognli
The genetic diversity and population structure of Arabidopsis thaliana populations from Norway were studied and compared to a worldwide sample of A. thaliana in order to investigate the demographic history and elucidate possible colonization routes of populations at the northernmost species limit. We genotyped 282 individuals from 31 local populations using 149 single nucleotide polymorphism (SNP) markers. A high level of population subdivision (FST = 0.85 ± 0.007) was found indicating that A. thaliana is...

Data from: Little impact of over-winter parasitism on a free-ranging ungulate in the high Arctic

Anja Morven Carlsson, Steve D. Albon, Stephen J. Coulson, Erik Ropstad, Audun Stien, Ken Wilson, Leif Egil Loe, Vebjørn Veiberg, Robert Justin Irvine & Kenneth Wilson
1.Macroparasites have a central place in wildlife ecology because they have the potential to regulate host populations through effects on reproduction and/or survival. However, there remains a paucity of studies that have demonstrated the regulatory role of these parasites in free-ranging animals. 2.Previous work on Svalbard reindeer demonstrated that the experimental removal of the parasitic gastrointestinal nematode Ostertagia gruehneri transmitted in summer, improved reindeer fecundity, and that the species was capable of mediating a density-dependent...

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