37 Works

Data from: Seawater environmental DNA reflects seasonality of a coastal fish community

Eva Egelyng Sigsgaard, Ida Broman Nielsen, Henrik Carl, Marcus Anders Krag, Steen Wilhelm Knudsen, Yingchun Xing, Tore Hejl Holm-Hansen, Peter Rask Møller & Philip Francis Thomsen
Coastal marine fish populations are in decline due to overfishing, habitat destruction, climate change and invasive species. Seasonal monitoring is important for detecting temporal changes in the composition of fish communities, but current monitoring is often non-existent or limited to annual or semi-annual surveys. In the present study, we investigate the potential of using environmental DNA (eDNA) metabarcoding of seawater samples to detect the seasonal changes in a coastal marine fish community. Water sampling and...

Data from: Identifying the most surprising victims of mass extinction events: an example using Late Ordovician brachiopods

Seth Finnegan, Christian M. Ø. Rasmussen & David A. T. Harper
Mass extinction events are recognized by increases in extinction rate and magnitude and, often, by changes in the selectivity of extinction. When considering the selective fingerprint of a particular event, not all taxon extinctions are equally informative: some would be expected even under a ‘background’ selectivity regime, whereas others would not and thus require special explanation. When evaluating possible drivers for the extinction event, the latter group is of particular interest. Here, we introduce a...

Data from: The genus Gennadas (Benthesicymidae: Decapoda): morphology of copulatory characters, phylogeny and coevolution of genital structures

Alexander L. Vereshchaka, Anastasia A. Lunina & Jørgen Olesen
Species within Gennadas differ from each other largely only in male (petasma) and female (thelycum) copulatory characters, which were restudied in scanning electron microscopy and used as a basis for phylogenetic analyses. Twenty-six petasma characters and 49 thelycum characters were identified. All sixteen recognized species of Gennadas and Aristaeomorpha foliacea (outgroup) were included as terminals. Four robust monophyletic clades were retrieved, described and diagnosed as new species groups. The thelycum characters had greater impact on...

Data from: Isotopic methods for non-destructive assessment of carbon dynamics in shrublands under long-term climate change manipulation

Louise C. Andresen, Maria T. Dominguez, Sabine Reinsch, Andy R. Smith, Inger Kappel Schmidt, Per Ambus, Claus Beier, Pascal Boeckx, Roland Bol, Giovanbattista De Dato, Bridget A. Emmett, Marc Estiarte, Mark H. Garnett, György Kröel-Dulay, Sharon L. Mason, Cecilie S. Nielsen, Josep Penuelas, Albert Tietema & Andrew R. Smith
1.Long-term climate change experiments are extremely valuable for studying ecosystem responses to environmental change. Examination of the vegetation and the soil should be non-destructive to guarantee long-term research. In this paper, we review field methods using isotope techniques for assessing carbon dynamics in the plant-soil-air continuum, based on recent field experience and examples from a European climate change manipulation network. 2.Eight European semi-natural shrubland ecosystems were exposed to warming and drought manipulations. One field site...

Data from: Population genetic structure of the endemic rosewoods Dalbergia cochinchinensis and D. oliveri at a regional scale reflects the Indochinese landscape and life-history traits

Ida Hartvig, Thea So, Suchitra Changtragoon, Hoa Thi Tran, Somsanith Bouamanivong, Ida Theilade, Erik Dahl Kjaer & Lene Rostgaard Nielsen
Indochina is a biodiversity hot spot and harbors a high number of endemic species, most of which are poorly studied. This study explores the genetic structure and reproductive system of the threatened endemic timber species Dalbergia cochinchinensis and Dalbergia oliveri using microsatellite data from populations across Indochina and relates it to landscape characteristics and life-history traits. We found that the major water bodies in the region, Mekong and Tonle Sap, represented barriers to gene flow...

Data from: Local and regional specialization in plant–pollinator networks

Daniel Wisbech Carstensen, Kristian Trøjelsgaard, Jeff Ollerton & Leonor Patricia C. Moraletto
Specialization of species is often studied in ecology but its quantification and meaning is disputed. More recently, ecological network analysis has been widely used as a tool to quantify specialization, but here its true meaning is also debated. However, irrespective of the tool used, the geographic scale at which specialization is measured remains central. Consequently, we use data sets of plant–pollinator networks from Brazil and the Canary Islands to explore specialization at local and regional...

Data from: Deciphering conjugative plasmid permissiveness dynamics in wastewater microbiomes

Samuel Jacquiod, Asker Brjenrod, Stefan M. Morberg, Waleed Abu Al-Soud, Søren J. Sørensen, Leise Riber & Asker Brejnrod
Wastewater treatment plants (WWTPs) are designed to robustly treat polluted water. They are characterized by ceaseless flows of organic, chemical and microbial matter, followed by treatment steps before environmental release. WWTPs are hotspots of horizontal gene transfer (HGT) between bacteria via conjugative plasmids, leading to dissemination of potentially hazardous genetic material such as antimicrobial resistance genes (AMRGs). While current focus is on the threat of AMRGs spreading and environmental maintenance, conjugative plasmid transfer dynamics within...

Data from: Interaction rewiring and the rapid turnover of plant-pollinator networks

Paul J. CaraDonna, William K. Petry, Ross M. Brennan, James L. Cunningham, Judith L. Bronstein, Nickolas M. Waser & Nathan J. Sanders
Whether species interactions are static or change over time has wide-reaching ecological and evolutionary consequences. However, species interaction networks are typically constructed from temporally aggregated interaction data, thereby implicitly assuming that interactions are fixed. This approach has advanced our understanding of communities, but it obscures the timescale at which interactions form (or dissolve) and the drivers and consequences of such dynamics. We address this knowledge gap by quantifying the within-season turnover of plant–pollinator interactions from...

Data from: Gene flow and effective population sizes of the butterfly Maculinea alcon in a highly fragmented, anthropogenic landscape

An Vanden Broeck, Dirk Maes, Andreas Kelager, Irma Wynhoff, Michiel WallisDeVries, David R. Nash, Gerard Oostermeijer, Hans Van Dyck & Joachim Mergeay
Understanding connectivity among populations in fragmented landscapes is of paramount importance in species conservation because it determines their long-term viability and helps to identify and prioritize populations to conserve. Rare and sedentary species are particularly vulnerable to habitat fragmentation as they occupy narrow niches or restricted habitat ranges. Here, we assess contemporary interpopulation connectedness of the threatened, myrmecophilous butterfly, Maculinea alcon, in a highly fragmented landscape. We inferred dispersal, effective population sizes, genetic diversity and...

Data from: Rat retinal vasomotion assessed by laser speckle imaging

Anastasiia Y. Neganova, Dmitry D. Postnov, Olga Sosnovtseva & Jens Christian Brings Jacobsen
Vasomotion is spontaneous or induced rhythmic changes in vascular tone or vessel diameter that lead to rhythmic changes in flow. While the vascular research community debates the physiological and pathophysiological consequence of vasomotion, there is a great need for experimental techniques that can address the role and dynamical properties of vasomotion in vivo. We apply laser speckle imaging to study spontaneous and drug induced vasomotion in retinal network of anesthetized rats. The results reveal a...

Data from: Agriculture shapes the trophic niche of a bat preying on multiple pest arthropods across Europe: evidence from DNA metabarcoding

Ostaizka Aizpurua, Ivana Budinski, Panagiotis Georgiakakis, Shyam Gopalakrishnan, Carlos Ibáñez, Vanessa Mata, Hugo Rebelo, Danilo Russo, Farkas Szodoray-Parádi, Violeta Zhelyazkova, Vida Zrncic, M. Thomas P. Gilbert & Antton Alberdi
The interaction between agricultural production and wildlife can shape, and even condition, the functioning of both systems. In this study we i) explored the degree to which a widespread European bat, namely the common bent-wing bat Miniopterus schreibersii, consumes crop-damaging insects at a continental scale, and ii) tested whether its dietary niche is shaped by the extension and type of agricultural fields. We employed a dual-primer DNA metabarcoding approach to characterise arthropod 16S and COI...

Data from: Transient negative biochar effects on plant growth are strongest after microbial species loss

W. H. Gera Hol, Mette Vestergård, Freddy Ten Hooven, Henk Duyts, Tess F. J. Van De Voorde & T. Martijn Bezemer
Biochar has been explored as an organic amendment to improve soil quality and benefit plant growth. The overall positive effects of biochar on crop yields are generally attributed to abiotic changes, while the alternative causal pathway via changes in soil biota is unexplored. We compared plant growth effects of legumes in sterile soil inoculated with dilutions of soil and soil microbial suspensions to determine the direct effects of biochar-induced changes in soil biota on plant...

Data from: Transcriptome-wide patterns of divergence during allopatric evolution

Ricardo J. Pereira, Felipe S. Barreto, N. Tessa Pierce, Miguel Carneiro & Ronald S. Burton
Recent studies have revealed repeated patterns of genomic divergence associated with species formation. Such patterns suggest that natural selection tends to target a set of available genes, but is also indicative that closely related taxa share evolutionary constraints that limit genetic variability. Studying patterns of genomic divergence among populations within the same species may shed light on the underlying evolutionary processes. Here, we examine transcriptome-wide divergence and polymorphism in the marine copepod Tigriopus californicus, a...

Data from: Trait-dependent distributional shifts in fruiting of common British fungi

Alan C. Gange, Einar Heegaard, Lynne Boddy, Carrie Andrew, Paul Kirk, Rune Halvorsen, Thomas W. Kuyper, Claus Bässler, Jeffrey Diez, Jacob Heilman-Clausen, Klaus Høiland, Ulf Büntgen & Håvard Kauserud
Despite the dramatic phenological responses of fungal fruiting to recent climate warming, it is unknown whether spatial distributions of fungi have changed and to what extent such changes are influenced by fungal traits, such as ectomycorrhizal (ECM) or saprotrophic lifestyles, spore characteristics, or fruit body size. Our overall aim was to understand how climate and fungal traits determine whether and how species-specific fungal fruit body abundances have shifted across latitudes over time, using the UK...

Data from: Asymmetric winter warming advanced plant phenology to a greater extent than symmetric warming in an alpine meadow

Ji Suonan, Aimée T. Classen, Zhenhua Zhang & Jin-Sheng He
The warming of terrestrial high-latitude ecosystems, while increasing, will likely be asymmetric across seasons – where winter non-growing seasons will warm more than summer growing seasons. Asymmetric winter warming in temperature-sensitive ecosystems may delay spring phenological events by reducing the opportunity that a plants’ chilling requirement is met. Similarly, symmetric warming can advance spring phenology. To explore the impact of asymmetric warming on plant phenology, we applied a year-round warming and a winter warming treatment...

Data from: Coordinated responses of soil communities to elevation in three subarctic vegetation types

G. F. Ciska Veen, Jonathan R. De Long, Paul Kardol, Maja K. Sundqvist, L. Basten Snoek & David A. Wardle
Global warming has begun to have a major impact on the species composition and functioning of plant and soil communities. However, long-term community and ecosystem responses to increased temperature are still poorly understood. In this study, we used a well-established elevational gradient in northern Sweden to elucidate how plant, microbial and nematode communities shift with elevation and associated changes in temperature in three highly contrasting vegetation types (i.e. heath, meadow and Salix vegetation). We found...

Data from: Exploring the impact of multidecadal environmental changes on the population genetic structure of a marine primary producer

Nina Lundholm, Sofia Ribeiro, Anna Godhe, Lene Rostgaard Nielsen & Marianne Ellegaard
Many marine protists form resting stages that can remain viable in coastal sediments for several decades. Their long-term survival offers the possibility to explore the impact of changes in environmental conditions on population dynamics over multidecadal time scales. Resting stages of the phototrophic dinoflagellate Pentapharsodinium dalei were isolated and germinated from five layers in dated sediment cores from Koljö fjord, Sweden, spanning ca. 1910–2006. This fjord has, during the last century, experienced environmental fluctuations linked...

Data from: Algorithm for post-clustering curation of DNA amplicon data yields reliable biodiversity estimates

Tobias Guldberg Frøslev, Rasmus Kjøller, Hans Henrik Bruun, Rasmus Ejrnæs, Ane Kirstine Brunbjerg, Carlotta Pietroni & Anders Johannes Hansen
DNA metabarcoding is promising for cost-effective biodiversity monitoring, but reliable diversity estimates are difficult to achieve and validate. Here we present and validate a method, called LULU, for removing erroneous molecular operational taxonomic units (OTUs) from community data derived by high-throughput sequencing of amplified marker genes. LULU identifies errors by combining sequence similarity and co-occurrence patterns. To validate the LULU method, we use a unique data set of high quality survey data of vascular plants...

Data from: Routine blood tests are associated with short term mortality and can improve emergency department triage: a cohort study of >12,000 patients

Michael Kristensen & Kasper Iversen
Background: Prioritization of acutely ill patients in the Emergency Department remains a challenge. We aimed to evaluate whether routine blood tests can predict mortality in unselected patients in an emergency department and to compare risk prediction with a formalized triage algorithm. Methods: A prospective observational cohort study of 12,661 consecutive admissions to the Emergency Department of Nordsjælland University Hospital during two separate periods in 2010 (primary cohort, n = 6279) and 2013 (validation cohort, n...

Data from: Hemimetabolous genomes reveal molecular basis of termite eusociality

Mark C Harrison, Evelien Jongepier, Hugh M. Robertson, Nicolas Arning, Tristan Bitard-Feildel, Hsu Chao, Christopher P. Childers, Huyen Dinh, Harshavardhan Doddapaneni, Shannon Dugan, Johannes Gowin, Carolin Greiner, Yi Han, Haofu Hu, Daniel S.T. Hughes, Ann-Kathrin Huylmans, Carsten Kemena, Lukas P.M. Kremer, Sandra L. Lee, Alberto Lopez-Ezquerra, Ludovic Mallet, Jose M. Monroy-Kuhn, Annabell Moser, Shwetha C. Murali, Donna M. Muzny … & Erich Bornberg-Bauer
Around 150 million years ago, eusocial termites evolved from within the cockroaches, 50 million years before eusocial Hymenoptera, such as bees and ants, appeared. Here, we report the 2-Gb genome of the German cockroach, Blattella germanica, and the 1.3-Gb genome of the drywood termite Cryptotermes secundus. We show evolutionary signatures of termite eusociality by comparing the genomes and transcriptomes of three termites and the cockroach against the background of 16 other eusocial and non-eusocial insects....

Data from: Explaining sex differences in lifespan in terms of optimal energy allocation in the baboon

Annette Maria King, Thomas B.L. Kirkwood, Daryl P. Shanley & Thomas B. L. Kirkwood
We provide a quantitative test of the hypothesis that sex role specialisation may account for sex differences in lifespan in baboons if such specialisation causes the dependency of fitness upon longevity, and consequently the optimal resolution to an energetic trade-off between somatic maintenance and other physiological functions, to differ between males and females. We present a model in which females provide all offspring care and males compete for access to reproductive females and in which...

Aboveground plant biomass and soil respiration for seven European shrublands under drought and warming manipulations (1998-2012)

S. Reinsch, E. Koller, A. Sowerby, G. De Dato, M. Estiarte, G. Guidolotti, E. Kovács-Láng, G Kröel-Dula, E. Lellei-Kovács, K.S. Larsen, D. Liberati, R Ogaya, J. Peñuelas, J. Ransijn, D.A. Robinson, I.K. Schmidt, A.R. Smith, A. Tietema, J.S. Dukes, C. Beier & B.A. Emmett
The data consists of annual measurements of standing aboveground plant biomass, annual aboveground net primary productivity and annual soil respiration between 1998 and 2012. Data were collected from seven European shrublands that were subject to the climate manipulations drought and warming. Sites were located in the United Kingdom (UK), the Netherlands (NL), Denmark ( two sites, DK-B and DK-M), Hungary (HU), Spain (SP) and Italy (IT). All field sites consisted of untreated control plots, plots...

Data from: Climate change and human colonization triggered habitat loss and fragmentation in Madagascar.

Jordi Salmona, Rasmus Heller, Erwan Quéméré & Lounès Chikhi
The relative effect of past climate fluctuations and anthropogenic activities on current biome distribution is subject to increasing attention, notably in biodiversity hot spots. In Madagascar, where humans arrived in the last ~4 to 5,000 years, the exact causes of the demise of large vertebrates that cohabited with humans are yet unclear. The prevailing narrative holds that Madagascar was covered with forest before human arrival and that the expansion of grasslands was the result of...

Data from: Neurons in primate visual cortex alternate between responses to multiple stimuli in their receptive field

Kang Li, Vladislav Kozyrev, Søren Kyllingsbæk, Stefan Treue, Susanne Ditlevsen & Claus Bundesen
A fundamental question concerning representation of the visual world in our brain is how a cortical cell responds when presented with more than a single stimulus. We find supportive evidence that most cells presented with a pair of stimuli respond predominantly to one stimulus at a time, rather than a weighted average response. Traditionally, the firing rate is assumed to be a weighted average of the firing rates to the individual stimuli (response-averaging model) (Bundesen...

Data from: Ranking and characterization of established BMI and lipid associated loci as candidates for gene-environment interactions

Dmitry Shungin, Wei Q. Deng, Tibor V. Varga, Jian'an Luan, Evelin Mihailov, Andres Metspalu, Andrew P. Morris, Nita G. Forouhi, Cecilia Lindgren, Patrik K. E. Magnusson, Nancy L. Pedersen, Göran Hallmans, Audrey Y. Chu, Anne E. Justice, Mariaelisa Graff, Thomas W. Winkler, Lynda M. Rose, Claudia Langenberg, L. Adrienne Cupples, Paul M. Ridker, Nicholas J. Wareham, Ken K. Ong, Ruth J. F. Loos, Daniel I. Chasman, Erik Ingelsson … & Paul W. Franks
Phenotypic variance heterogeneity across genotypes at a single nucleotide polymorphism (SNP) may reflect underlying gene-environment (G·E) or gene-gene interactions. We modeled variance heterogeneity for blood lipids and BMI in up to 44,211 participants and investigated relationships between variance effects (Pv), G·E interaction effects (with smoking and physical activity), and marginal genetic effects (Pm). Correlations between Pv and Pm were stronger for SNPs with established marginal effects (Spearman's ρ=0.401 for triglycerides, and ρ=0.236 for BMI) compared...

Registration Year

  • 2017
    37

Resource Types

  • Dataset
    37

Affiliations

  • University of Copenhagen
    37
  • Natural History Museum
    4
  • Wageningen University & Research
    3
  • Bangor University
    2
  • University of Cambridge
    2
  • University of Vermont
    2
  • University of California, Berkeley
    2
  • Smithsonian Institution
    2
  • University of Gothenburg
    2
  • Swedish University of Agricultural Sciences
    2