37 Works

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...

Data from: Extinctions, genetic erosion and conservation options for the black rhinoceros (Diceros bicornis)

Yoshan Moodley, Isa-Rita M. Russo, Desiré L. Dalton, Antoinette Kotzé, Shadrack Muya, Patricia Haubensak, Boglárka Bálint, Gopi K. Munimanda, Caroline Deimel, Andrea Setzer, Kara Dicks, Barbara Herzig-Straschil, Daniela C. Kalthoff, Hans R. Siegismund, Jan Robovský, Paul O’Donoghue & Michael W. Bruford
The black rhinoceros is again on the verge of extinction due to unsustainable poaching in its native range. Despite a wide historic distribution, the black rhinoceros was traditionally thought of as depauperate in genetic variation, and with very little known about its evolutionary history. This knowledge gap has hampered conservation efforts because hunting has dramatically reduced the species’ once continuous distribution, leaving five surviving gene pools of unknown genetic affinity. Here we examined the range-wide...

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: Latitudinal variation in plant chemical defences drives latitudinal patterns of leaf herbivory

Xoaquón Moreira, Bastien Castagneyrol, Luis Abdala-Roberts, Jorge C. Berny-Mier Y Terán, Bart G. H. Timmermans, Hans Henrik Kehlet Bruun, Felisa Covelo, Gaétan Glauser, Sergio Rasmann, Ayco J. M. Tack & Hans Henrik Bruun
A long-standing paradigm in ecology holds that herbivore pressure and thus plant defences increase towards lower latitudes. However, recent work has challenged this prediction where studies have found no relationship or opposite trends where herbivory or plant defences increase at higher latitudes. Here we tested for latitudinal variation in herbivory, chemical defences (phenolic compounds), and nutritional traits (phosphorus and nitrogen) in leaves of a long-lived tree species, the English oak Quercus robur. We further investigated...

Data from: Scrutinizing key steps for reliable metabarcoding of environmental samples

Antton Alberdi, Ostaizka Aizpurua, M. Thomas P. Gilbert & Kristine Bohmann
1. Metabarcoding of environmental samples has many challenges and limitations that require carefully considered laboratory and analysis pipelines to ensure reliable results. We explore how decisions regarding study design, laboratory work and bioinformatic processing affect the final results, and provide guidelines for reliable study of environmental samples. 2. We evaluate the performance of four primer sets targeting COI and 16S regions characterising arthropod diversity in bat faecal samples, and investigate how metabarcoding results are affected...

Data from: Idiosyncratic responses to climate-driven forest fragmentation and marine incursions in reed frogs from Central Africa and the Gulf of Guinea Islands

Rayna C. Bell, Juan L. Parra, Gabriel Badjedjea, Michael F. Barej, David C. Blackburn, Marius Burger, Alan Channing, J. Maximilian Dehling, Eli Greenbaum, Václav Gvoždík, Jos Kielgast, Chifundera Kusamba, Stefan Lötters, Patrick J. McLaughlin, Zoltán T. Nagy, Mark-Oliver Rödel, Daniel M. Portik, Bryan L. Stuart, Jeremy VanDerWal, Ange-Ghislain Zassi Boulou & Kelly R. Zamudio
Organismal traits interact with environmental variation to mediate how species respond to shared landscapes. Thus, differences in traits related to dispersal ability or physiological tolerance may result in phylogeographic discordance among co-distributed taxa, even when they are responding to common barriers. We quantified climatic suitability and stability, and phylogeographic divergence within three reed frog species complexes across the Guineo-Congolian forests and Gulf of Guinea archipelago of Central Africa to investigate how they responded to a...

Data from: Environmental variation is a major predictor of global trait turnover in mammals

Ben G. Holt, Gabriel C. Costa, Caterina Penone, Jean-Philippe Lessard, Thomas M. Brooks, Ana D. Davidson, S. Blair Hedges, Volker C. Radeloff, Carsten Rahbek, Carlo Rondinini & Catherine H. Graham
Aim: To evaluate how environment and evolutionary history interact to influence global patterns of mammal trait diversity (a combination of 14 morphological and life-history traits). Location: The global terrestrial environment. Taxon: Terrestrial mammals. Methods: We calculated patterns of spatial turnover for mammalian traits and phylogenetic lineages using the mean nearest taxon distance. We then used a variance partitioning approach to establish the relative contribution of trait conservatism, ecological adaptation and clade specific ecological preferences on...

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: Evaluating the impact of domestication and captivity on the horse gut microbiome

Jessica L. Metcalf, Se Jin Song, James T. Morton, Sophie Weiss, Andaine Seguin-Orlando, Frédéric Joly, Claudia Feh, Pierre Taberlet, Eric Coissac, Amnon Amir, Eske Willerslev, Rob Knight, Valerie McKenzie & Ludovic Orlando
The mammal gut microbiome, which includes host microbes and their respective genes, is now recognized as an essential second genome that provides critical functions to the host. In humans, studies have revealed that lifestyle strongly influences the composition and diversity of the gastrointestinal microbiome. We hypothesized that these trends in humans may be paralleled in mammals subjected to anthropogenic forces such as domestication and captivity, in which diets and natural life histories are often greatly...

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: An integrated framework to identify wildlife populations under threat from climate change

Orly Razgour, John B. Taggart, Stéphanie Manel, Javier Juste, Carlos Ibáñez, Hugo Rebelo, Antton Alberdi, Gareth Jones & Kirsty Park
Climate change is a major threat to global biodiversity that will produce a range of new selection pressures. Understanding species responses to climate change requires an interdisciplinary perspective, combining ecological, molecular and environmental approaches. We propose an applied integrated framework to identify populations under threat from climate change based on their extent of exposure, inherent sensitivity due to adaptive and neutral genetic variation and range shift potential. We consider intraspecific vulnerability and population-level responses, an...

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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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...

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