56 Works

Genome-scale target capture of mitochondrial and nuclear environmental DNA from water samples

Mads Reinholdt Jensen & Philip Francis Thomsen
Environmental DNA (eDNA) provides a promising supplement to traditional sampling methods for population genetic inferences, but current studies have almost entirely focused on short mitochondrial markers. Here, we develop one mitochondrial and one nuclear set of target capture probes for the whale shark (Rhincodon typus) and test them on seawater samples collected in Qatar to investigate the potential of target capture for eDNA-based population studies. The mitochondrial target capture successfully retrieved ~235x (90x-352x per base...

Data from: Arthropods as vertebrate predators: a review of global patterns

Jose Valdez
Aim: Arthropods as vertebrate predators is generally overlooked in ecology due to the cryptic nature of these events, the relatively small size of arthropods, and the difficulty in finding published data. This study represents the largest global assessment of arthropods preying on vertebrates to provide a conceptual framework, identify global patterns, and provide a searchable database. Location: Global. Time period: Present. Major taxa studied: Arthropods and vertebrates. Methods: A systematic literature review was conducted. Results:...

Data from: Vessel noise levels drive behavioural responses of humpback whales with implications for whale-watching

Kate Sprogis
Disturbance from whale-watching can cause significant behavioural changes with fitness consequences for targeted whale populations. However, the sensory stimuli triggering these responses are unknown, preventing effective mitigation. Here, we test the hypothesis that vessel noise level is a driver of disturbance, using humpback whales (Megaptera novaeangliae) as a model species. We conducted controlled exposure experiments (n= 42) on resting mother-calf pairs on a resting ground off Australia, by simulating whale-watch scenarios with a research vessel...

Data from : Historical legacies and ecological determinants of grass naturalizations worldwide

Anne-Christine Monnet, Maria S. Vorontsova, Rafaël H. A. Govaerts, Jens-Christian Svenning & Brody Sandel
The global distribution of exotic species is the result of abiotic, biotic and dispersal filtering processes that shape the movement and success of species outside their native range. In this study we aim to understand how these filtering processes drive the fluxes of grass species among regions, the factors that influence which species establish outside of their native range, and where they do so. We used national and subnational checklists of native and introduced grass...

Data from: Vessel noise levels drive behavioural responses of humpback whales with implications for whale-watching

Kate Sprogis
Disturbance from whale-watching can cause significant behavioural changes with fitness consequences for targeted whale populations. However, the sensory stimuli triggering these responses are unknown, preventing effective mitigation. Here, we test the hypothesis that vessel noise level is a driver of disturbance, using humpback whales (Megaptera novaeangliae) as a model species. We conducted controlled exposure experiments (n= 42) on resting mother-calf pairs on a resting ground off Australia, by simulating whale-watch scenarios with a research vessel...

Nutrient digestibility and balance studies

Sadjad Danesh Mesgaran, Björn Kuhla, René Baumont, Gonzalo Cantalapiedra-Hijar, Pierre Noziére, Peter Lund, David Humphries & Jan Dijkstra
The nutritional value of a feed for cattle depends on its nutrient and energy contents, the extent of rumen fermentation and degradation, and the post-ruminal digestibility. Efficiency of digestion depends on different factors, for example, the apparent digestibility (estimated by subtracting the nutrients contained in faeces from the nutrients contained in dietary intake – unlike true digestibility where the endogenous and microbial amount is taken into account and corrected in final outcome) usually decreases when...

The fate of Meconopsis species in the Tibeto-Himalayan region under future climate change

Wen-Ting Wang, Wen-Yong Guo, Scott Jarvie & Jens-Christian Svenning
High-mountain areas such as the Tibeto-Himalayan region (THR) host cold-adapted biota expected to be sensitive to anthropogenic climate change. Meconopsis is a representative endangered genus confined to alpine meadow or subnival habitats in the THR. To obtain occurrence data for Meconopsis species found in the THR and adjacent regions, we used records from the Chinese Virtual Herbarium (CVH: http://www.cvh.org.cn/), the Global Biodiversity Information Facility (GBIF: http://www.gbif.org/), and the published literature (He et al., 2019). We...

Rumen fluid sampling via oral stomach tubing method

Sanne van Gastelen, Wouter Muizelaar, Paolo Bani, Björn Kuhla, Mogens Larsen & David Yáñez-Ruiz
There are different purposes for collecting rumen fluid, e.g. assessment of rumen fermentation characteristics and rumen microbiota, as well as ex vivo incubations for feed analysis. Collecting rumen content through the fistula from rumen cannulated ruminants is considered the reference method for the collection of representative samples of rumen digesta, but access to surgically-modified animals is not universal and restricted to research facilities. Hence, a less invasive alternative has been developed: the oral stomach tubing...

Dark diversity reveals importance of biotic resources and competition for plant diversity across habitats

Camilla Fløjgaard, José Valdez, Lars Dalby, Jesper Erenskjold Moeslund, Kevin Clausen, Rasmus Ejrnæs, Meelis Partel & Ane Kirstine Brunbjerg
Species richness is the most commonly used metric to quantify biodiversity. However, examining dark diversity, the group of missing species which can potentially inhabit a site, can provide a more thorough understanding of the processes influencing observed biodiversity and help evaluate the restoration potential of local habitats. So far, dark diversity has mainly been studied for specific habitats or largescale landscapes while less attention has been given to variation across broad environmental gradients or as...

Criteria for defining interictal epileptiform discharges in EEG: a clinical validation study

Mustafa Aykut Kural, Lene Duez, Vibeke Sejer Hansen, Pål Gunnar Larsson, Stefan Rampp, Reinhard Schulz, Hatice Tankisi, Richard Wennberg, Bo Bibby, Michael Scherg & Sandor Beniczky
Objective: To define and validate criteria for accurate identification of EEG interictal epileptiform discharges (IEDs) using: (a) the six sensor space criteria proposed by the International Federation of Clinical Neurophysiology (IFCN), and, (b) a novel source space method. Criteria yielding high specificity are needed because EEG “over-reading” is a common cause of epilepsy misdiagnosis. Methods: Seven raters reviewed EEG segments containing sharp waveforms from 100 patients with and without epilepsy. Clinical diagnosis gold standard was...

Introduction to citizen science. The case of Fangstjournalen.dk

Jitka Stilund Hansen, Signe Gadegaard, Karsten Kryger Hansen, Gertrud Stougård Thomsen, Asger Væring Larsen & Katrine Flindt Holmstrand

FAIR data in a Citizen Science project “Fangstjournalen”

Katrine Flindt Holmstrand, Asger Væring Larsen, Signe Gadegaard, Jitka Stilund Hansen, Karsten Kryger Hansen & Gertrud Stougård Thomsen
In this video Researcher Christian Skov from DTU Aqua tells about the Citizen Science project “Fangstjournalen” and how Research Data Management, data sharing and following the FAIR guiding principles for research data can increase the impact and the value of the research - even beyond the scope of the project. This video is produced by four Danish Universities as part of a project financially supported by DEFF. The aim of the project is to identify...

Genotypes of Swan Geese Anser cygnoides using 17 nuclear microsatellite loci at 14 locations.

Qin Zhu, Iderbat Damaba, Qingshan Zhao, Kunpeng Yi, Nyambayar Batbayar, Tseveenmyadag Natsagdorj, Davaasuren Batmunkh, Xin Wang, Sonia Rozenfeld, Sachiko Moriguchi, Aibin Zhan, Lei Cao & Anthony David Fox
Dispersal affects the spatial distribution and population structure of species.Dispersal is often male-biased in mammals while female-biased in birds, with the notable exception of the Anatidae. In this study, we tested genetic evidence for sex-biased dispersal (SBD) in the Swan Goose Anser cygnoides, an Asian endemic and IUCN vulnerable species, which has been increasingly restricted to breeding on Mongolian steppe wetlands. We analyzed the genotypes of 278 Swan Geese samples from 14 locations at 14...

Food quality of Ephestia eggs, the aphid Rhopalosiphum padi and mixed diet for Orius majusculus

Søren Toft, Kim Jensen, Jesper Sørensen, Lene Sigsgaard & Martin Holmstrup
We studied the food quality of the aphid Rhopalosiphum padi to the pirate bug Orius majusculus using Ephestia eggs as high‐quality comparison prey. Several performance parameters were tested on individuals that had been reared and maintained on each of the two single‐prey diets or on a mixed diet. All fitness parameters were lower in individuals fed aphids only, indicating poor food quality of this prey. Compared with the pure Ephestia egg diet, the mixed diet...

Data from: Facile fabrication of Mn2+ doped ZnO photocatalysts by electrospinning

Yuting Wang, Xin Hao, Zegao Wang, Mingdong Dong & Lifeng Cui
In this study, we report a high efficiency photocatalyst synthesized by Mn2+ doped ZnO nanofibers (NFs) fabricated by facile electrospinning and a following annealing process, in which Mn2+ successes incorporate to ZnO NFs lattice without changing any morphology and crystalline structure of ZnO. The photodegradation properties were studied for ZnO doping with different concentrations of Mn2+ (5, 10, 15 and 50 at.%). The 50 % Mn2+-doped ZnO NFs owns excellent active photocatalytic performance (quantum efficiency...

Harbour porpoise (Phocoena phocoena) reaction to a 3D seismic airgun survey in the North Sea

Joanna Sarnocinska, Jonas Teilmann, Jeppe Balle, Floris Van Beest, Matthieu Delefosse & Jakob Tougaard
The most common cetacean in the North Sea is the harbor porpoise (Phocoena phocoena). Underwater noise is increasingly recognized as a source of impact on the marine environment and seismic airguns were one of the first man-made high intensity sound source to receive attention with respect to potential impact on marine mammals. In this study, we investigate the effects of a 3D seismic survey on harbor porpoise echolocation activity in the Danish sector of the...

Data from: Genetic structuring in a Neotropical palm analyzed through an Andean orogenesis‐scenario

Sebastián Escobar, Jean‐Christophe Pintaud, Henrik Balslev, Rodrigo Bernal, Mónica Moraes Ramírez, Betty Millán & Rommel Montúfar
Andean orogenesis has driven the development of very high plant diversity in the Neotropics through its impact on landscape evolution and climate. The analysis of the intraspecific patterns of genetic structure in plants would permit inferring the effects of Andean uplift on the evolution and diversification of Neotropical flora. In this study, using microsatellite markers and Bayesian clustering analyses, we report the presence of four genetic clusters for the palm Oenocarpus bataua var. bataua which...

Canopy structure and forest understory conditions in a wet Amazonian forest – no change over the last 20 years

Jacob Nabe-Nielsen & Renato Valencia
Climate change is altering forest dynamics in the tropics, with large potential impacts on forest structure and understory conditions. However, we found that canopy height distribution and openness remained stable over two decades in the western Amazon, and that gap creation rates would need to increase 300% before affecting equilibrium.

Data from: Accelerating homogenization of the global plant–frugivore meta-network

Evan Fricke & Jens-Christian Svenning
Introductions of species by humans are causing the homogenization of species composition across biogeographic barriers. The ecological and evolutionary consequences of introduced species derive from their effects on networks of species interactions, but we lack a quantitative understanding of the impacts of introduced species on ecological networks and their biogeographic patterns globally. Here we address this data gap by analysing mutualistic seed-dispersal interactions from 410 local networks, encompassing 24,455 unique pairwise interactions between 1,631 animal...

Environmental DNA metabarcoding of cow dung reveals taxonomic and functional diversity of invertebrate assemblages

Eva Egelyng Sigsgaard, Kent Olsen, Morten D. D. Hansen, Oskar Liset Pryds Hansen, Toke Thomas Høye, Jens-Christian Svenning & Philip Francis Thomsen
Insects and other terrestrial invertebrates are declining in species richness and abundance. This includes the invertebrates associated with herbivore dung, which have been negatively affected by grazing abandonment and the progressive loss of large herbivores since the Late Pleistocene. Importantly, traditional monitoring of these invertebrates is time-consuming and requires considerable taxonomic expertise, which is becoming increasingly scarce. In this study, we investigated the potential of environmental DNA (eDNA) metabarcoding of cow dung samples for biomonitoring...

Data from: First measurements of field metabolic rate in wild juvenile fishes show strong thermal sensitivity but variations between sympatric ecotypes

Ming-Tsung Chung, Kris‐Emil Mose Jørgensen, Clive N. Trueman, Halvor Knutsen, Per Erik Jorde & Peter Grønkjær
The relationship between physiology and temperature has a large influence on population-level responses to climate change. In natural settings, direct thermal effects on metabolism may be exaggerated or offset by behavioural responses influencing individual energy balance. Drawing on a newly developed proxy, we provide the first estimates of the thermal performance curve of field metabolism in a wild fish. We investigate the thermal sensitivity of field metabolic rate in two sympatric, genetically distinct ecotypes of...

What can physiological capacity and behavioral choice tell us about thermal adaptation?

Paul Vinu Salachan, Jesper Sørensen & Heidi MacLean
To date, behavioral responses and their role for thermal adaptation have been largely overlooked in small ectotherms. Here, we measure reproductive output using four adult acclimation temperatures in Drosophila melanogaster and quantify egg-laying at restricted temperatures (thermal capacity) and across a thermal gradient (thermal preference). We demonstrate that different conclusions about insect responses to changing environmental temperatures can be drawn based on whether individuals were temperature restricted or were allowed a behavioral choice of temperature....

Data from: Movement and seasonal energetics mediate vulnerability to disturbance in marine mammal populations

Cara Gallagher, Volker Grimm, Line Kyhn, Carl Kinze & Jacob Nabe-Nielsen
In marine environments noise from human activities is increasing dramatically, causing animals to alter their behavior and forage less efficiently. These alterations incur energetic costs that can result in reproductive failure, death, and may ultimately influence population viability; yet the link between population dynamics and individual energetics is poorly understood. We present an energy budget model for simulating effects of acoustic disturbance on populations. It accounts for environmental variability and individual state, while incorporating realistic...

Lameness detection and scoring

Sadjad Danesh Mesgaran, Juan Haladjian, Stefan Nüske, Dorothée Ledoux, Dave Humphries, Lene Munksgaard & Isabelle Veissier
Enting concluded lameness, from an economic perspective, as the third most costly health disease, following mastitis and reproductive failure issues, in cattle units. Archer estimated the incidence rate of lameness in the United Kingdom cattle herds roughly 50 cases/100 cows in a year; nevertheless, due to poor correlation between incidence rates and records of treatments in farms, the actual number seems to be higher. Surprisingly, the significance of lameness associated with cattle welfare, health and...

Bodyweight, body condition and anatomy

Sadjad Danesh Mesgaran, Martin Weisbjerg, Alex Bach, Jennifer Salau, Jan Henning Haas, Wolfgang Junge, Georg Thaller & Björn Kuhla
Measuring bodyweight (BW) in cattle is essential for many research and management activities such as calculating dietary energy requirements for maintenance, calculating average daily gain and evaluating breeding values which include BW as a trait. Frequent monitoring of BW in dairy cows is necessary as changes in BW can help assess the energy balance of an animal. Precise understanding of BW gain of growing and fattening cattle or body mass changes during lactation is crucial...

Registration Year

  • 2020

Resource Types

  • Dataset
  • Text
  • Audiovisual


  • Aarhus University
  • Leibniz Institute for Farm Animal Biology
  • University of Reading
  • National Research Institute for Agriculture, Food and Environment
  • University of Clermont Auvergne
  • Wageningen University & Research
  • Pontificia Universidad Católica del Ecuador
  • University of Gothenburg
  • Aalborg University
  • Technical University of Denmark