105 Works

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: How little data is enough? Phase-diagram analysis of sparsity-regularized X-ray computed tomography

Jakob S. Jørgensen, Emil Y. Sidky & J. S. Jorgensen
We introduce phase-diagram analysis, a standard tool in compressed sensing (CS), to the X-ray computed tomography (CT) community as a systematic method for determining how few projections suffice for accurate sparsity-regularized reconstruction. In CS, a phase diagram is a convenient way to study and express certain theoretical relations between sparsity and sufficient sampling. We adapt phase-diagram analysis for empirical use in X-ray CT for which the same theoretical results do not hold. We demonstrate in...

Data from: A genomewide catalogue of single nucleotide polymorphisms in white-beaked and Atlantic white-sided dolphins

Ruth Fernández, Mikkel Schubert, A. M. Vargas-Velázquez, Andrew Brownlow, Gisli A. Víkingsson, Ursula Siebert, Lasse Fast Jensen, Nils Øien, Dave Wall, Emer Rogan, Bjarni Mikkelsen, Willy Dabin, Gilles Guillot, Ludovic Orlando, A. H. Alfarhan, S. A. Alquraishi & K. A. S. Al-Rasheid
The field of population genetics is rapidly moving into population genomics as the quantity of data generated by high-throughput sequencing platforms increases. In this study, we used restriction-site-associated DNA sequencing (RADSeq) to recover genomewide genotypes from 70 white-beaked (Lagenorhynchus albirostris) and 43 Atlantic white-sided dolphins (L. acutus) gathered throughout their north-east Atlantic distribution range. Both species are at a high risk of being negatively affected by climate change. Here, we provide a resource of 38...

Data from: Shifts in North Sea forage fish productivity and potential fisheries yield

Lotte W. Clausen, Anna Rindorf, Mikael Van Deurs, Mark Dickey-Collas & Niels T. Hintzen
Forage fish populations support large scale fisheries and are key components of marine ecosystems across the world, linking secondary production to higher trophic levels. While climate-induced changes in the North Sea zooplankton community are described and documented in literature, the associated bottom-up effects and consequences for fisheries remain largely unidentified. We investigated the temporal development in forage fish productivity and the associated influence on fisheries yield of herring, sprat, Norway pout and sandeel in the...

Data from: The predictability of a lake phytoplankton community, over time-scales of hours to years

Mridul K. Thomas, Simone Fontana, Marta Reyes, Michael Kehoe & Francesco Pomati
Forecasting changes to ecological communities is one of the central challenges in ecology. However, nonlinear dependencies, biotic interactions and data limitations have limited our ability to assess how predictable communities are. We used a machine learning approach and environmental monitoring data (biological, physical and chemical) to assess the predictability of phytoplankton cell density in one lake across an unprecedented range of time scales. Communities were highly predictable over hours to months: model R2 decreased from...

Data from: Polyphasic data support the splitting of Aspergillus candidus into two species; proposal of Aspergillus dobrogensis sp. nov.

Vit Hubka, Alena Nováková, Željko Jurjević, František Sklenář, Jens C. Frisvad, Jos Houbraken, Maiken C. Arendrup, João P. Z. Siqueira, Josepa Gené & Miroslav Kolařík
Aspergillus candidus is a species frequently isolated from stored grain, food, indoor environments, soil and occasionally also from clinical material. Recent bioprospecting studies highlighted the potential of using A. candidus and its relatives in various industrial sectors as a result of their significant production of enzymes and bioactive compounds. A high genetic variability was observed among A. candidus isolates originating from various European countries and the USA, that were mostly isolated from indoor environments, caves...

Data from: Sixty years of anthropogenic pressure: a spatio-temporal genetic analysis of brown trout populations subject to stocking and population declines

Michael Hansen, Dylan Fraser, Kristian Meier & Karen-Lise Mensberg
Analyses of historical samples can provide invaluable information on changes to the genetic composition of natural populations resulting from human activities. Here, we analyze 21 microsatellite loci in historical (archived scales from 1927-1956) and contemporary samples of brown trout (Salmo trutta) from six neighbouring rivers in Denmark, to compare the genetic structure of wild populations before and after population declines and stocking with non-local strains of hatchery trout. We show that all populations have been...

Data from: Evolution determines how global warming and pesticide exposure will shape predator–prey interactions with vector mosquitoes

Tam T. Tran, Lizanne Janssens, Khuong V. Dinh, Lin Op De Beeck & Robby Stoks
How evolution may mitigate the effects of global warming and pesticide exposure on predator–prey interactions is directly relevant for vector control. Using a space-for-time substitution approach, we addressed how 4°C warming and exposure to the pesticide endosulfan shape the predation on Culex pipiens mosquitoes by damselfly predators from replicated low- and high-latitude populations. Although warming was only lethal for the mosquitoes, it reduced predation rates on these prey. Possibly, under warming escape speeds of the...

Data from: Genome- and transcriptome-assisted development of nuclear insertion/deletion markers for Calanus species (Copepoda: Calanoida) identification

Irina Smolina, Spyros Kollias, Marloes Poortvliet, Torkel Nielsen, Penelope Lindeque, Claudia Castellani, Eva Møller, Leocadio Blanco-Bercial & Galice Hoarau
Copepods of the genus Calanus are key zooplankton species in temperate to arctic marine ecosystems. Despite their ecological importance, species identification remains challenging. Furthermore, the recent report of hybrids among Calanus species highlights the need for diagnostic nuclear markers in order to efficiently identify parental species and hybrids. Using Next Generation Sequencing analysis of both the genome and transcriptome from two sibling species, C. finmarchichus and C. glacialis, we developed a panel of 12 nuclear...

Data from: Do North Atlantic Eels show parallel patterns of spatially varying selection?

Malene G. Ulrik, José Martín Pujolar, Anne-Laure Ferchaud, Magnus W. Jacobsen, Thomas D. Als, Pierre Alexandre Gagnaire, Jane Frydenberg, Peder K. Bøcher, Bjarni Jónsson, Louis Bernatchez & Michael M. Hansen
Background: The two North Atlantic eel species, the European and the American eel, represent an ideal system in which to study parallel selection patterns due to their sister species status and the presence of ongoing gene flow. A panel of 80 coding-gene SNPs previously analyzed in American eel was used to genotype European eel individuals (glass eels) from 8 sampling locations across the species distribution. We tested for single-generation signatures of spatially varying selection in...

Data from: Marine ecosystem connectivity mediated by migrant–resident interactions and the concomitant cross-system flux of lipids

Mikael Van Deurs, Anders Persson, Martin Lindegren, Charlotte Jacobsen, Stefan Neuenfeldt, Christian Jørgensen & P. Anders Nilsson
Accumulating research argues that migrants influence the functioning and productivity of local habitats and ecosystems along migration routes and potentially drive cross-system energy fluxes of considerable magnitude, yet empirical documentation of local ecological effects and descriptions of the underlying mechanisms are surprisingly rare. In this study, we discovered migrant–resident interactions and substantial cross-system lipid transportation in the transition zone between the Baltic Sea and the North Sea where a resident cod population (predators) was found...

Data from: Signatures of natural selection between life cycle stages separated by metamorphosis in European eel

Jose Martin Pujolar, Magnus W. Jacobsen, Dorte Bekkevold, Javier Lobón-Cervia, Bjarni Jónsson, Louis Bernatchez & Michael M. Hansen
Background: Species showing complex life cycles provide excellent opportunities to study the genetic associations between life cycle stages, as selective pressures may differ before and after metamorphosis. The European eel presents a complex life cycle with two metamorphoses, a first metamorphosis from larvae into glass eels (juvenile stage) and a second metamorphosis into silver eels (adult stage). We tested the hypothesis that different genes and gene pathways will be under selection at different life stages...

Data from: Escaping peril: perceived predation risk affects migratory propensity

Kaj Hulthén, Ben B. Chapman, P. Anders Nilsson, Jerker Vinterstare, Lars-Anders Hansson, Christian Skov, Jakob Brodersen, Henrik Baktoft & Christer Brönmark
Although migratory plasticity is increasingly documented, the ecological drivers of plasticity are not well understood. Predation risk can influence migratory dynamics, but whether seasonal migrants can adjust their migratory behaviour according to perceived risk is unknown. We used electronic tags to record the migration of individual roach (Rutilus rutilus), a partially migratory fish, in the wild following exposure to manipulation of direct (predator presence/absence) and indirect (high/low roach density) perceived predation risk in experimental mesocosms....

Data from: Genetic diversity and connectivity within Mytilus spp. in the subarctic and Arctic

Sofie Smedegaard Mathiesen, Jakob Thyrring, Jakob Hemmer-Hansen, Jørgen Berge, Alexey Sukhotin, Peter Leopold, Michaël Bekaert, Mikael Kristian Sejr & Einar E. Nielsen
Climate changes in the Arctic are predicted to alter distributions of marine species. However, such changes are difficult to quantify because information on present species distribution and the genetic variation within species is lacking or poorly examined. Blue mussels, Mytilus spp. are ecosystem engineers in the coastal zone globally. In order to improve knowledge of distribution and genetic structure of the Mytilus edulis complex in the Arctic, we analyzed 81 SNPs in 534 Mytilus spp....

Data from: Genome architecture enables local adaptation of Atlantic cod despite high connectivity

Julia M. I. Barth, Paul R. Berg, Per R. Jonsson, Sara Bonanomi, Hanna Corell, Jakob Hemmer-Hansen, Kjetill S. Jakobsen, Kerstin Johannesson, Per Erik Jorde, Halvor Knutsen, Per-Olav Moksnes, Bastiaan Star, Nils Chr. Stenseth, Henrik Svedäng, Sissel Jentoft & Carl André
Adaptation to local conditions is a fundamental process in evolution; however, mechanisms maintaining local adaptation despite high gene flow are still poorly understood. Marine ecosystems provide a wide array of diverse habitats that frequently promote ecological adaptation even in species characterized by strong levels of gene flow. As one example, populations of the marine fish Atlantic cod (Gadus morhua) are highly connected due to immense dispersal capabilities but nevertheless show local adaptation in several key...

Supporting fisheries management with genomic tools: a case study of kingklip (Genypterus capensis) off southern Africa

Melissa Jane Schulze, Sophie Von Der Heyden & Romina Henriques
Kingklip, Genypterus capensis, is a valuable fish resource in southern African waters, with a wide geographic distribution spanning South Africa and Namibia. Previous studies have provided evidence for multiple stocks in South Africa, but the extent of stock structuring across the Southern African region remains unclear. In this study, we genotyped over 40 000 SNPs to characterise the spatial distribution of genomic variation for G. capensis throughout its core distribution. Results suggest that fish sampled...

Data from: Restoring marine ecosystems: spatial reef configuration triggers taxon-specific responses among early colonizers

Tim J. G. Wilms, Pauli H. Norðfoss, Henrik Baktoft, Josianne G. Støttrup, Bo M. Kruse & Jon C. Svendsen
1. The longstanding debate in conservation biology on the importance of single large or several small (SLOSS) habitats for preserving biodiversity remains highly relevant, given the ongoing degradation and loss of natural habitats worldwide. Restoration efforts are often constrained by limited resources, and insights from SLOSS studies therefore have important implications if restoration efforts can be optimized by manipulating the spatial configuration of restored habitats. Yet, the relevance of SLOSS for habitat restoration remains largely...

The tale of two ice shelves: Zachariae Isstrøm and Nioghalvfjerdsfjorden, Northeast Greenland

Lu An, Eric Rignot, Michael Wood, Josh Willis, Jeremie Mouginot & Shfaqat Khan
Oceanography and gravity data of Northeastern Greenland reveal ocean temperature and bathymetry in front of Zachariae Isstrøm (ZI) and Nioghalvfjerdsfjorden (79N), which hold a 1.1-m sea-level rise ice volume equivalent but underwent different evolutions. Sub-surface, warm, salty water of Atlantic origin has easier access to ZI than to 79N because of bathymetric barriers. We reconstruct ice removal by the ocean at the grounding line and floatation retreat from thinning to explain the observed grounding line...

Data from: Linkage mapping reveals strong chiasma interference in sockeye salmon: implications for interpreting genomic data

Morten T. Limborg, Ryan K. Waples, Fred W. Allendorf & James E. Seeb
Meiotic recombination is fundamental for generating new genetic variation and for securing proper disjunction. Further, recombination plays an essential role during the rediploidization process of polyploid-origin genomes because crossovers between pairs of homeologous chromosomes retain duplicated regions. A better understanding of how recombination affects genome evolution is crucial for interpreting genomic data; unfortunately, current knowledge mainly originates from a few model species. Salmonid fishes provide a valuable system for studying the effects of recombination in...

Data from: Evolutionary prediction of medicinal properties in the genus Euphorbia L.

Madeleine Ernst, C. Haris Saslis-Lagoudakis, Olwen M. Grace, Niclas Nilsson, Henrik Toft Simonsen, James W. Horn & Nina Rønsted
The current decrease of new drugs brought to the market has fostered renewed interest in plant-based drug discovery. Given the alarming rate of biodiversity loss, systematic methodologies in finding new plant-derived drugs are urgently needed. Medicinal uses of plants were proposed as proxy for bioactivity, and phylogenetic patterns in medicinal plant uses have suggested that phylogeny can be used as predictive tool. However, the common practice of grouping medicinal plant uses into standardised categories may...

Data from: Spatiotemporal SNP analysis reveals pronounced biocomplexity at the northern range margin of Atlantic cod Gadus morhua

Nina Overgaard Therkildsen, Jakob Hemmer-Hansen, Rasmus Berg Hedeholm, Mary S. Wisz, Dorte Meldrup, Sara Bonanomi, Anja Retzel, Steffen Malskær Olsen, Einar Eg Nielsen & Christophe Pampoulie
Accurate prediction of species distribution shifts in the face of climate change requires a sound understanding of population diversity and local adaptations. Previous modeling has suggested that global warming will lead to increased abundance of Atlantic cod (Gadus morhua) in the ocean around Greenland, but the dynamics of earlier abundance fluctuations are not well understood. We applied a retrospective spatiotemporal population genomics approach to examine the temporal stability of cod population structure in this region...

Data from: Sperm performance limits the reproduction of an invasive fish in novel salinities

Leon Green, Jan Niemax, Jens-Peter Herrmann, Axel Temming, Jane W. Behrens, Jonathan N. Havenhand, Erica Leder & Charlotta Kvarnemo
Aim: The few fish species able to reproduce across wide osmotic ranges either plastically acclimate sperm performance to, or are locally adapted to, different salinities. The invasive round goby (Neogobius melanostomus) is spreading in Eurasia and the Americas, into both fresh and brackish water. We aim to understand if reproduction in different salinities is affected an ability to acclimate. Location: Brackish and freshwater systems of northern Europe and the Baltic Sea. Methods: We cross-exposed round...

GNSS uplift time series and ice surface elevation changes

Shfaqat Abbas Khan & Karina Hansen
We use Global Navigation Satellite System (GNSS) stations attached to bedrock to measure elastic displacements of the solid Earth caused by dynamic thinning near the glacier terminus. When we compare our results with discharge, we find a time lag between glacier speedup/slowdown and onset of dynamic thinning/thickening. Our results show that dynamic thinning/thickening on Jakobshavn Isbræ occurs 0.87 ± 0.07 years before speedup/slowdown. This implies that using GNSS time series we are able to predict...

Genetic response to human‐induced habitat changes in the marine environment: A century of evolution of European sprat in Landvikvannet, Norway

María Quintela, Cecilie Kvamme, Dorte Bekkevold, Richard D. M. Nash, Eeva Jansson, Geir Dahle, Kevin A. Glover, Àlex Richter‐Boix, Florian Berg & François Besnier
Habitat changes represent one of the five most pervasive threats to biodiversity. However, anthropogenic activities also have the capacity to create novel niche spaces to which species respond differently. In 1880, one such habitat alterations occurred in Landvikvannet, a freshwater lake on the Norwegian coast of Skagerrak, which became brackish after being artificially connected to the sea. This lake is now home to the European sprat, a pelagic marine fish that managed to develop a...

Marine fish traits follow fast-slow continuum across oceans

Esther Beukhof, Romain Frelat, Laurene Pecuchet, Aurore Maureaud, Tim Spaanheden Dencker, Jón Sólmundsson, Antonio Punzón, Raul Primicerio, Manuel Hidalgo, Christian Möllmann & Martin Lindegren
A fundamental challenge in ecology is to understand why species are found where they are and predict where they are likely to occur in the future. Trait-based approaches may provide such understanding, because it is the traits and adaptations of species that determine which environments they can inhabit. It is therefore important to identify key traits that determine species distributions and investigate how these traits relate to the environment. Based on scientific bottom-trawl surveys of...

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