56 Works

The biomolecular characterisation of a finger ring contextually dated to the emergence of the Early Neolithic from Syltholm, Denmark

Theis Jensen, Meaghan Mackie, Alberto Taurozzi, Liam Lannigan, Carsten Gundelach, Jesper Olsen, Søren Sørensen, Matthew Collins, Mikkel Sørensen & Hannes Schroeder
We present the analysis of an osseous finger ring from a predominantly early Neolithic context in Denmark. To characterise the artefact and identify the raw material used for its manufacture, we performed micro-computed tomography (Micro CT) scanning, zooarchaeology by mass spectrometry (ZooMS) peptide mass fingerprinting, as well as protein sequencing by liquid chromatography tandem mass spectrometry (LC-MS/MS). We conclude that the ring was made from long bone or antler due to the presence of osteons...

Different pollination approaches to compare the seed set of diploid and tetraploid red clover (Trifolium pratense L.)

Shuxuan Jing, Per Kryger & Birte Boelt
In red clover seed production, low seed yield is limiting the commercial exploitation of tetraploid red clover. To explore if pollination is the limiting factor for the seed yield in tetraploid red clover, we investigated pollinator behaviour and plant reproductive success in diploid (2x) cultivar ‘Rajah’ and tetraploid (4x) cultivar ‘Amos’ using honey bee and hand pollination approaches. We measured the seed set at the flower head level with the increasing visitation rate in honey...

Data from: Overall dynamic body acceleration measures activity differently on large vs small aquatic animals

Lucía Martina Martín López, Natacha Aguilar De Soto, Peter Teglberg Madsen & Mark Johnson
Acceleration-based proxies for activity and energy expenditure are widely used in bio-logging studies of animal movement and locomotion to explore biomechanical strategies, energetic costs of behaviour, habitat use and the impact of anthropogenic disturbance. The foremost such proxy is Overall Dynamic Body Acceleration (ODBA) along with variants VeDBA and PDBA. This technique, which involves summing the magnitude of high-pass-filtered acceleration signals (the so-called dynamic acceleration) over a reference interval, has been applied to animals as...

Raw cutadapt miseq output - minibarcode 18S-V7 of macroalgae

Sarah Ørberg
Macroalgae are key primary producers in North Atlantic and Arctic coastal ecosystems, and tracing their fate and distribution is vital to improve our understanding of their ecological role and provision of ecosystem services. Recent advances from environmental DNA (eDNA) have added a new capacity to fingerprint and trace macroalgae. However, further development of resources for amplifying and identifying macroalgal eDNA are much needed. Here, we examined the performance in terms of resolution and specificity of...

Data for: Rapid shifts in Arctic tundra species’ distributions and inter-specific range overlap under future climate change

Floris Van Beest, Larissa Beumer, Asbjørn Andersen, Sophia Hansson & Niels Schmidt
Aim: The Arctic is one of the planet’s most rapidly warming regions, with trends expected to intensify in the future. Projections of shifts in species distributional ranges under future climate change are thus far lacking for most vertebrate species using the Arctic tundra. Our aim was to assess possible climate-induced changes in distributional ranges and inter-specific overlap of an Arctic species assemblage within the world’s largest land-based protected area. Location: During 1979-2013 location data of...

Global maps of current (1979-2013) and future (2061-2080) habitat suitability probability for 1,485 European endemic plant species

Robin Pouteau, Idoia Biurrun, Caroline Brunel, Milan Chytrý, Wayne Dawson, Franz Essl, Trevor Fristoe, Rense Haveman, Carsten Hobohm, Florian Jansen, Holger Kreft, Jonathan Lenoir, Bernd Lenzner, Carsten Meyer, Jesper Erenskjold Moeslund, Jan Pergl, Petr Pyšek, Jens-Christian Svenning, Wilfried Thuiller, Patrick Weigelt, Thomas Wohlgemuth, Qiang Yang & Mark Van Kleunen
Aims: The rapid increase in the number of species that have naturalized beyond their native range is among the most apparent features of the Anthropocene. How alien species will respond to other processes of future global changes is an emerging concern and remains largely misunderstood. We therefore ask whether naturalized species will respond to climate and land-use change differently than those species not yet naturalized anywhere in the world. Location: Global Methods: We investigated future...

Plant traits of grass and legume species for flood resilience and N2O mitigation

Natalie J. Oram, Yan Sun, Diego Abalos, Jan-Willem Van Groenigen, & Gerlinde De Deyn
Flooding threatens the functioning of managed grasslands by decreasing primary productivity and increasing nitrogen losses, notably as the potent greenhouse gas nitrous oxide (N2O). Sowing species with traits that promote flood resilience and mitigate flood-induced N2O emissions within these grasslands could safeguard their productivity while mitigating nitrogen losses. We tested how plant traits and resource acquisition strategies could predict flood resilience and N2O emissions of 12 common grassland species (eight grasses and four legumes) grown...

Deer-vehicle collisions in Denmark

Martin Mayer, Jacob Coleman Nielsen, Morten Elmeros & Peter Sunde
Vehicles collide with hundreds of thousands of deer on European roads each year. This leads to animal deaths and suffering, economic damage and risks for human safety, making the reduction of road mortality a major field in conservation biology. In order to successfully reduce roadkill, we need improved knowledge regarding spatio-temporal patterns of deer-vehicle collisions (DVCs) on a landscape scale. Here, we analyzed >85,000 DVCs collected over 17 years in Denmark to investigate changes in...

Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)

Shuxuan Jing, Per Kryger, Bo Markussen & Birte Boelt
This dataset includes hand pollination, honey bee pollination and pollen germination experiments described in the article "Pollination and plant reproductive success of two ploidy levels in red clover (Trifolium pratense L.)", published in Frontiers in Plant Science (DOI: 10.3389/fpls.2021.720069). In a series of hand pollination experiments, the influence of visitation rate (10, 20, 40, 80 pollinated florets per flower head) on the seed number per pollinated floret and seed number per flower head were investigated,...

Capturing single-copy nuclear genes, organellar genomes, and nuclear ribosomal DNA from deep genome skimming data for plant phylogenetics: A case study in Vitaceae

Bin-Bin Liu, Zhi-Yao Ma, Chen Ren, Richard Hodel, Miao Sun, Xiu-Qun Liu, Guang-Ning Liu, De-Yuan Hong, Elizabeth Zimmer & Jun Wen
With the decreasing cost and availability of many newly developed bioinformatics pipelines, next-generation sequencing (NGS) has revolutionized plant systematics in recent years. Genome skimming has been widely used to obtain high-copy fractions of the genomes, including plastomes, mitochondrial DNA (mtDNA), and nuclear ribosomal DNA (nrDNA). In this study, through simulations, we evaluated the optimal (minimum) sequencing depth and performance for recovering single-copy nuclear genes (SCNs) from genome skimming data, by subsampling genome resequencing data and...

Data on: contrasting manual and automated assessment of larval body size and thermal stress responses in black soldier flies and houseflies

Stine Frey Laursen, Laura Skrubbeltrang Hansen, Simon Bahrndorff, Hanne Marie Nielsen, Natasja Krog Noer, David Renault, Goutam Sahana, Jesper Givskov Sørensen & Torsten Nygaard Kristensen
The data files described below contains information on larval body size traits and stress tolerance traits obtained using contrasting methods (manual and automated). The species investigated are black soldier flies (Hermetia illucens) and houseflies (Musca domestica). Larval body size is estimated using manual weighing and imaging analysis software (Noldus EthoVision XT 15.0.1418, Wageningen, the Netherlands). Stress tolerance traits are obtained using manual observations of traditional thermal tolerance assays and by using software for video analysis...

Inconsistent effects of agricultural practices on soil fungal communities across twelve European long‐term experiments

S. Emilia Hannula, D. P. Di Lonardo, B. T. Christensen, F.V. Crotty, A. Elsen, P.J. Erp, E.M. Hansen, G. H. Rubæk, M. Tits, Z. Toth & A. J. Termorshuizen
Cropping practices have a great potential to improve soil quality through changes in soil biota. Yet the effects of these soil improving cropping systems on soil fungal communities are not well known. Here, we analysed soil fungal communities using standardized measurements in 12 long‐term experiments and 20 agricultural treatments across Europe. We were interested in whether the same practices (i.e. tillage, fertilization, organic amendments and cover crops) applied across different sites have predictable and repeatable...

Data supporting: Food limitation and starvation independently affect predator macronutrient selection

Søren Toft
Predators are often food limited in their habitat, and some are limited by specific macronutrients (protein, lipid or carbohydrate). It is unresolved, however, to what extent and in what way food and macronutrient limitation are connected. Using a carabid beetle (Nebria brevicollis), we compared macronutrient self-selection of the animals three times: immediately after collection in the field, after being fed to satiation and nutritional balance, and after a subsequent period of starvation. Both sexes were...

Effects of episodic nutrients enrichments on P-limited planktonic communities: Lake Redon ENEX 2013 experiment

Jordi Catalan, Marisol Felip, Pau Giménez-Grau, Aitziber Zufiaurre, Lluis Camarero & Sergi Pla-Rabés
Planktonic communities are naturally subjected to episodic nutrient enrichments that may stress or redress the imbalances in limiting nutrients. Human-enhanced atmospheric nitrogen deposition has caused profound N:P imbalance in many remote oligotrophic lakes in which phosphorus has largely become limiting. These lakes offer an opportunity to investigate the planktonic community response to nutrient fluctuations in P-limited conditions. The ENEX experiment in Lake Redon (Pyrenees), performed during August 2013, aimed to investigate the structural and stoichiometric...

The R package enerscape: A general energy landscape framework for terrestrial movement ecology

Emilio Berti, Marco Davoli, Robert Buitenwerf, Alexander Dyer, Oskar Hansen, Myriam Hirt, Jens-Christian Svenning, Jördis Terlau, Ulrich Brose & Fritz Vollrath
Ecological processes and biodiversity patterns are strongly affected by how animals move through the landscape. However, it remains challenging to predict animal movement and space use. Here we present our new R package enerscape to quantify and predict animal movement in real landscapes based on energy expenditure. Enerscape integrates a general locomotory model for terrestrial animals with GIS tools in order to map energy costs of movement in a given environment, resulting in energy landscapes...

Data from: Haplotype associated RNA expression (HARE) improves prediction of complex traits in maize

Anju Giri, Merritt Burch, Edward Buckler & Guillaume Ramstein
Genomic prediction typically relies on associations between single-site polymorphisms and traits of interest. This representation of genomic variability has been successful for prediction within populations. However, it usually cannot capture the complex effects due to combination of alleles in haplotypes. Therefore, accuracy across populations has usually been low. Here we present a novel and cost-effective method for imputing cis haplotype associated RNA expression (HARE, RNA expression of genes by haplotype), studied their transferability across tissues,...

High heart rates in hunting porpoises

Birgitte McDonald, Siri Elmegaard, Mark Johnson, Danuta Wisniewska, Laia Rojano-Donate, Anders Galatius, Ursula Siebert, Jonas Teilmann & Peter Madsen
The impressive breath-hold capabilities of marine mammals are facilitated by both enhanced O2 stores and reductions in the rate of O2 consumption via peripheral vasoconstriction and bradycardia, coined the dive response. Many studies have focused on the extreme role of the dive response in maximizing dive duration in marine mammals, but few have addressed how these adjustments may compromise the capability to hunt, digest and thermoregulate during routine dives. Here we use DTAGs which record...

Pleistocene climatic fluctuations promoted alternative evolutionary histories in Phytelephas aequatorialis, an endemic palm from western Ecuador

Sebastián Escobar, Andrew J Helmstetter, Scott Jarvie, Rommel Montúfar, Henrik Balslev & Thomas LP Couvreur
Aim: Pleistocene (2.58 Ma – 11.7 ka) climatic fluctuations have shaped intraspecific genetic patterns worldwide; however, their manifestation in many regions remains unknown. In order to determine the impact of Pleistocene climatic fluctuations on the tropical rain forests of western Ecuador, we explored the evolutionary history of the endemic palm Phytelephas aequatorialis. Location: Western Ecuador, northwestern South America. Taxon: Phytelephas aequatorialis (Arecaceae). Methods: 176 nuclear genes were sequenced in 91 individuals for phylogenomic and population...

Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

Beomseok Seo, Lin Lin & Jia Li
Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with...

Block-Wise Variable Selection for Clustering Via Latent States of Mixture Models

Beomseok Seo, Lin Lin & Jia Li
Mixture modeling is a major paradigm for clustering in statistics. In this article, we develop a new block-wise variable selection method for clustering by exploiting the latent states of the hidden Markov model on variable blocks or the Gaussian mixture model. The variable blocks are formed by depth-first-search on a dendrogram created based on the mutual information between any pair of variables. It is demonstrated that the latent states of the variable blocks together with...

Dataset for estimation of the biotic and climatic niche breadths and geographic range size of beech (Fagus) species worldwide

Qiong Cai, Erik Welk, Chengjun Ji, Wenjing Fang, Francesco Maria Sabatini, Jianxiao Zhu, Jiangling Zhu, Zhiyao Tang, Fabio Attorre, Juan Antonio Campos, Andraž Čarni, Milan Chytrý, Süleyman Çoban, Jürgen Dengler, Jiri Dolezal, Richard Field, József Pál Frink, Hamid Gholizadeh, Adrian Indreica, Ute Jandt, Dirk Nikolaus Karger, Jonathan Lenoir, Robert K. Peet, Remigiusz Pielech, Michele De Sanctis … & Helge Bruelheide
This dataset could be used to test whether the commonly observed positive range size–niche breadth relationship, as posited by the “niche breadth hypothesis”, exists for Fagus, one of the most dominant and widespread broad‐leaved deciduous tree genera in temperate forests of the Northern Hemisphere. There are many ways to estimate niche breadth. Here, we estimated biotic and climatic niche breadths per species using plot‐based co‐occurrence data and climate data, respectively. The range sizes of the...

Population ecology and dynamics of a remnant natural population of European yew (Taxus baccata) in a lowland temperate forest – implications for use in reforestation

Ditte Arp Jensen & Jens-Christian Svenning
There is increasing focus on reforestation, but the efforts still often include limited subsets of species despite evidence that tree diversity promote biodiversity and ecological resilience. In addition to these benefits, greater inclusion of rare native species in reforestation efforts would also help conserve these species in an uncertain future. Here, we investigate the population ecology and dynamics of the only remaining historical population of the shade-adapted under- and mid-story tree European yew (Taxus baccata)...

The role of deterministic succession during forest succession within a South African savanna

Samantha-Leigh Jamison-Daniels, Daniel Kissling, Monique Botha, Mathew Harris, Christopher Gordon & Michelle Greve
Bush encroachment can lead to a switch from open savannas to dense woodlands or forests. This has implications for both the composition of ecological communities and the provision of ecosystem services such as nutrient cycling and grazing capacity. The patterns and underlying drivers responsible for bush encroachment are not fully understood. Here, we investigate the underlying determinants of bush clump formation (a form of encroachment) in a South African savanna and explore whether bush clump...

Data from: Effects of climate and topography on the diversity anomaly of plants disjunctly distributed in eastern Asia and eastern North America

Xue Yin, Hong Qian, Xinghua Sui, Minhua Zhang, Lingfeng Mao, Jens-Christian Svenning, Robert E. Ricklefs & Fangliang He
Aim: Differences in physiography have been proposed to explain the diversity anomaly for vascular plants between environmentally similar regions of eastern Asia (EAS) and eastern North America (ENA). Here, we use plant species within disjunct genera to examine whether differences in topography contribute to the diversity anomaly and whether the richness–environment relationships differ between regions. Disjuncts are used to ensure that the diversity anomaly relates to post-disjunction evolution and diversification rather than regional differences in...

Global dryland vegetation memory

Erik Kusch, Alistair W. Seddon & Richard Davy
1. Vegetation memory describes the effect of antecedent environmental and ecological conditions on the present ecosystem state and has been proposed as an important proxy for vegetation resilience. In particular, strong vegetation-memory effects have been identified in dryland regions, but the factors underlying the spatial patterns of vegetation memory remain unknown. 2. We aim to map the components and drivers of vegetation memory in dryland regions using state-of-the-art climate-reanalysis data and refined approaches to identify...

Registration Year

  • 2021

Resource Types

  • Dataset


  • Aarhus University
  • Zhejiang University
  • University of Helsinki
  • University of Minnesota
  • University of La Laguna
  • Huazhong Agricultural University
  • Tongji University
  • Sun Yat-sen University
  • Central South University
  • Third Affiliated Hospital of Guangzhou Medical University