56 Works

Field spectroscopy and leaf trait data from a field experiment in Surrey [HMTF]

D.A. Coomes, M. Davey & M.H. Nunes
The dataset comprises a range of leaf traits, measured from leaf samples collected from trees growing on deep alluvial soils and shallow chalk soils, near Mickleham in Surrey, UK. Across both sites, leaves were collected from 66 trees, representing six species. The six species common to both sites were: Acer campestre (field maple), Acer pseudoplatanus (sycamore), Corylus avellana (hazel), Crataegus monogyna (hawthorn), Fraxinus excelsior (ash) and Sambucus nigra (elder). Data were collected under the NERC...

Data from: Why on earth did I buy that? A study of regretted appliance purchases

Thomas Roberts, Aimie Hope & Alexandra Skelton
If targets to reduce greenhouse gas emissions and thereby tackle climate change are to be achieved, it will be necessary to reduce both embodied energy costs (e.g. in terms of producing and manufacturing the products and services that society consumes) and operational energy costs. Reducing the number of purchases that people regret could be a first step in changing the overall dynamic of consumption patterns. This research looks at some potentially adverse effects of consumption...

Data from: Oral microbiomes from hunter-gatherers and traditional farmers reveal shifts in commensal balance and pathogen load linked to diet

Florent Lassalle, Matteo Spagnoletti, Matteo Fumagalli, Liam Shaw, Mark Dyble, Catherine Walker, Mark G. Thomas, Andrea Bamberg Migliano & Francois Balloux
Maladaptation to modern diets has been implicated in several chronic disorders. Given the higher prevalence of disease such as dental caries and chronic gum diseases in industrialized societies, we sought to investigate the impact of different subsistence strategies on oral health and physiology, as documented by the oral microbiome. To control for confounding variables such as environment and host genetics, we sampled saliva from three pairs of populations of hunter-gatherers and traditional farmers living in...

Data from: DNA methylation and gene expression changes derived from assisted reproductive technologies can be decreased by reproductive fluids

Sebastian Canovas, Elena Ivanova, Raquel Romar, Soledad García-Martínez, Cristina Soriano-Úbeda, Francisco Alberto A. García-Vázquez, Heba Saadeh, Simon Andrews, Gavin Kelsey & Pilar Coy
The number of children born since the origin of Assisted Reproductive Technologies (ART) exceeds 5 million. The majority seem healthy, but a higher frequency of defects has been reported among ART-conceived infants, suggesting an epigenetic cost. We report the first whole-genome DNA methylation datasets from single pig blastocysts showing differences between in vivo and in vitro produced embryos. Blastocysts were produced in vitro either without (C-IVF) or in the presence of natural reproductive fluids (Natur-IVF)....

Data from: Urban development, land sharing and land sparing: the importance of considering restoration

Lydia Collas, Rhys E. Green, Alexander Ross, Josie H. Wastell & Andrew Balmford
1. At present, there is limited knowledge of how best to reconcile urban development with biodiversity conservation, and in particular whether populations of wild species would be greater under low-density housing (with larger gardens), or high-density housing (allowing more area to be left as undeveloped green spaces). The land sharing/sparing framework – originally developed in the context of farming – can be applied to address this question. 2. We sampled the abundance of trees in...

Data from: Childhood adiposity and type 1 diabetes: a Mendelian randomization study

J. C. Censin, Christoph Nowak, Nicholas Cooper, Peter Bergsten, John A. Todd & Tove Fall
BACKGROUND: The incidence of type 1 diabetes (T1D) is increasing globally. One hypothesis is that increasing childhood obesity rates may explain part of this increase, but, as T1D is rare, intervention studies are challenging to perform. The aim of this study was to assess this hypothesis with a Mendelian randomization approach that uses genetic variants as instrumental variables to test for causal associations. METHODS AND FINDINGS: We created a genetic instrument of 23 single nucleotide...

Data from: Experimental evidence that primate trichromacy is well suited for detecting primate social colour signals

Chihiro Hiramatsu, Amanda D. Melin, William L. Allen, Constance Dubuc & James P. Higham
Primate trichromatic colour vision has been hypothesized to be well tuned for detecting variation in facial coloration, which could be due to selection on either signal wavelengths or the sensitivities of the photoreceptors themselves. We provide one of the first empirical tests of this idea by asking whether, when compared with other visual systems, the information obtained through primate trichromatic vision confers an improved ability to detect the changes in facial colour that female macaque...

Data from: Routine habitat switching alters the likelihood and persistence of infection with a pathogenic parasite

David R. Daversa, Andrea Manica, Jaime Bosch, Jolle W. Jolles & Trenton W. J. Garner
1.Animals switch habitats on a regular basis, and when habitats vary in suitability for parasitism, routine habitat switching alters the frequency of parasite exposure and may affect post-infection parasite proliferation. However, the effects of routine habitat switching on infection dynamics are not well understood. 2.We performed infection experiments, behavioural observations, and field surveillance to evaluate how routine habitat switching by adult alpine newts (Ichthyosaura alpestris) influences infection dynamics of the pathogenic parasite, Batrachochytrium dendrobatidis (Bd)....

Data from: Function and flexibility of object exploration in kea and New Caledonian crows

Megan L. Lambert, Martina Schiestl, Raoul Schwing, Alex H. Taylor, Gyula K. Gajdon, Katie E. Slocombe & Amanda M. Seed
A range of nonhuman animals frequently manipulate and explore objects in their environment, which may enable them to learn about physical properties and potentially form more abstract concepts of properties such as weight and rigidity. Whether animals can apply the information learned during their exploration to solve novel problems, however, and whether they actually change their exploratory behaviour to seek functional information about objects have not been fully explored. We allowed kea (Nestor notabilis) and...

Data from: Habitat disturbance selects against both small and large species across varying climates

Heloise Gibb, Nathan J. Sanders, Robert R. Dunn, Xavier Arnan, Heraldo L. Vasconcellos, David A. Donoso, Alan N. Andersen, Rogerio R. Silva, Tom R. Bishop, Crisanto Gomez, Blair F. Grossman, Kalsum M. Yusah, Sarah H. Luke, Renata Pacheco, Jessica Pearce-Duvet, Javier Retana, Melanie Tista, Catherine L. Parr & H. L. Vasconcelos
Global extinction drivers, including habitat disturbance and climate change, are thought to affect larger species more than smaller species. However, it is unclear if such drivers interact to affect assemblage body size distributions. We asked how these two key global change drivers differentially affect the interspecific size distributions of ants, one of the most abundant and ubiquitous animal groups on earth. We also asked whether there is evidence of synergistic interactions and whether effects are...

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...

Foraging behaviour of Parus major held in temporary captivity

R Thorogood, H Kokko & J Mappes
The data set describes foraging decisions by great tits (Parus major), held in temporary captivity. Data were collected from birds caught from forest at the University of Jyväskylä Research Station, Konnevesi (62°37.7'N 026°17'E), Finland, and were collected during the winter of 2013-2014. Birds were presented with (1) two different coloured plastic cups, or (2) two different artificial prey (almond pieces inside a paper packet and printed with a black and white symbol). One symbol was...

Data from: Empirical phylogenies and species abundance distributions are consistent with pre-equilibrium dynamics of neutral community models with gene flow

Anne-Sophie Bonnet-Lebrun, Andrea Manica, Anders Eriksson, Ana S.L. Rodrigues & Ana S. L. Rodrigues
Community characteristics reflect past ecological and evolutionary dynamics. Here, we investigate whether it is possible to obtain realistically shaped modelled communities – i.e., with phylogenetic trees and species abundance distributions shaped similarly to typical empirical bird and mammal communities – from neutral community models. To test the effect of gene flow, we contrasted two spatially explicit individual-based neutral models: one with protracted speciation, delayed by gene flow, and one with point mutation speciation, unaffected by...

Data from: Does coevolution with a shared parasite drive hosts to partition their defences among species?

Eleanor M. Caves, Martin Stevens & Claire N. Spottiswoode
When mimicry imposes costs on models, selection may drive the model's phenotype to evolve away from its mimic. For example, brood parasitism often drives hosts to diversify in egg appearance among females within a species, making mimetic parasitic eggs easier to detect. However, when a single parasite species exploits multiple host species, parasitism could also drive host egg evolution away from other co-occurring hosts, to escape susceptibility to their respective mimics. This hypothesis predicts that...

Data from: Is bigger better? The relationship between size and reproduction in female Asian elephants

J. A. H. Crawley, H. S. Mumby, S. N. Chapman, M. Lahdenperä, K. U. Mar, W. Htut, A. Thura Soe, H. H. Aung & V. Lummaa
The limited availability of resources is predicted to impose trade-offs between growth, reproduction and self-maintenance in animals. However, although some studies have shown that early reproduction suppresses growth, reproduction positively correlates with size in others. We use detailed records from a large population of semi-captive elephants in Myanmar to assess the relationships between size (height and weight), reproduction and survival in female Asian elephants, a species characterized by slow, costly life history. Although female height...

Data from: Disparity, diversity, and duplications in the Caryophyllales

Stephen A. Smith, Joseph W. Brown, Ya Yang, Riva Bruenn, Chloe P. Drummond, Samuel F. Brockington, Joseph F. Walker, Noah Last, Norman A. Douglas & Michael J. Moore
The role played by whole genome duplication (WGD) in plant evolution is actively debated. WGDs have been associated with advantages such as superior colonization, various adaptations, and increased effective population size. However, the lack of a comprehensive mapping of WGDs within a major plant clade has led to uncertainty regarding the potential association of WGDs and higher diversification rates. Using seven chloroplast and nuclear ribosomal genes, we constructed a phylogeny of 5036 species of Caryophyllales,...

Data from: Bird and bat species' global vulnerability to collision mortality at wind farms revealed through a trait-based assessment

Chris B. Thaxter, Graeme M. Buchanan, Carr Jamie, Stuart H.M. Butchart, Tim Newbold, Rhys E. Green, Joseph A. Tobias, Wendy B. Foden, Sue O'Brien & James W. Pearce-Higgins
Mitigation of anthropogenic climate change involves deployments of renewable energy worldwide, including wind farms, which can pose a significant collision risk to volant animals. Most studies into the collision risk between species and wind turbines, however, have taken place in industrialized countries. Potential effects for many locations and species therefore remain unclear. To redress this gap, we conducted a systematic literature review of recorded collisions between birds and bats and wind turbines within developed countries....

Data from: Improved transcriptome sampling pinpoints 26 ancient and more recent polyploidy events in Caryophyllales, including two allopolyploidy events

Ya Yang, Michael J. Moore, Samuel F. Brockington, Jessica Mikenas, Julia Olivieri, Joseph F. Walker & Stephen A. Smith
• Studies of the macroevolutionary legacy of polyploidy are limited by an incomplete sampling of these events across the tree of life. To better locate and understand these events, we need comprehensive taxonomic sampling as well as homology inference methods that accurately reconstruct the frequency and location of gene duplications. • We assembled a dataset of transcriptomes and genomes from 169 species in Caryophyllales, of which 43 were newly generated for this study, representing one...

Data from: Resolving recent plant radiations: power and robustness of genotyping-by-sequencing

Mario Fernández-Mazuecos, Greg Mellers, Beatriz Vigalondo, Llorenç Sáez, Pablo Vargas & Beverley J. Glover
Disentangling species boundaries and phylogenetic relationships within recent evolutionary radiations is a challenge due to the poor morphological differentiation and low genetic divergence between species, frequently accompanied by phenotypic convergence, inter-specific gene flow and incomplete lineage sorting. Here we employed a genotyping-by-sequencing (GBS) approach, in combination with morphometric analyses, to investigate a small western Mediterranean clade in the flowering plant genus Linaria that radiated in the Quaternary. After confirming the morphological and genetic distinctness of...

Data from: When do trade-offs occur? The roles of energy constraints and trait flexibility in a bushcricket

Flavia Barbosa, Darren Rebar & Michael D. Greenfield
In many animal species, the expression of sexually-selected traits is negatively correlated with survival traits such as immune function, a relationship termed a ‘trade-off’. But an alternative in which sexually-selected traits are positively correlated with survival traits is also widespread. The nature of inter-trait relationships may be largely determined by overall energy expenditure, energy availability, and trait flexibility, with trade-offs expected when individuals are subject to energy constraints. We tested this hypothesis in Ephippiger diurnus,...

Data from: Jumping without slipping: leafhoppers (Hemiptera: Cicadellidae) possess special tarsal structures for jumping from smooth surfaces

Christofer J. Clemente, Hanns Hagen Goetzke, James M. R. Bullock, Gregory P. Sutton, Malcolm Burrows & Walter Federle
Many hemipteran bugs can jump explosively from plant substrates, which can be very smooth. We therefore analysed the jumping performance of froghoppers (Philaenus spumarius, Aphrophoridae) and leafhoppers (Aphrodes bicinctus/makarovi, Cicadellidae) taking off from smooth (glass) and rough (sandpaper, 30 µm asperity size) surfaces. On glass, the propulsive hind legs of Philaenus froghoppers slipped, resulting in uncontrolled jumps with a fast forward spin, a steeper angle and only a quarter of the velocity compared with jumps...

Data from: TAPBPR bridges UDP-glucose:glycoprotein glucosyltransferase 1 onto MHC class I to provide quality control in the antigen presentation pathway

Andreas Neerincx, Clemens Hermann, Robin Antrobus, Andy Van Hateren, Cao Huan, Nico Trautwein, Stefan Stevanović, Tim Elliott, Janet E. Deane, Louise H. Boyle & Huan Cao
Recently we revealed that TAPBPR is a peptide exchange catalyst important for optimal peptide selection by MHC class I molecules. Here we asked if any other co-factors associate with TAPBPR which would explain its effect on peptide selection. We identify an interaction between TAPBPR and UDP-glucose:glycoprotein glucosyltransferase 1 (UGT1), a folding sensor in the calnexin/calreticulin quality control cycle known to regenerate the Glc1Man9GlcNAc2 moiety on glycoproteins. Our results suggest the formation of a multimeric complex,...

Data from: Unravelling seed dispersal through fragmented landscapes: frugivore species operate unevenly as mobile links

Juan P. González-Varo, Carolina Carvalho, Juan M. Arroyo, Pedro Jordano & Carolina S. Carvalho
Seed dispersal constitutes a pivotal process in an increasingly fragmented world, promoting population connectivity, colonization and range shifts in plants. Unveiling how multiple frugivore species disperse seeds through fragmented landscapes, operating as mobile links, has remained elusive owing to methodological constraints for monitoring seed dispersal events. We combine for the first time DNA barcoding and DNA microsatellites to identify, respectively, the frugivore species and the source trees of animal-dispersed seeds in forest and matrix of...

Data from: DNA recovery from wild chimpanzee tools

Fiona A. Stewart, Alexander K. Piel, Lydia Luncz, Joanna Osborne, Yingying Li, Beatrice H. Hahn, Michael Haslam & Joanna Osborn
Most of our knowledge of wild chimpanzee behaviour stems from fewer than 10 long-term field sites. This bias limits studies to a potentially unrepresentative set of communities known to show great behavioural diversity on small geographic scales. Here, we introduce a new genetic approach to bridge the gap between behavioural material evidence in unhabituated chimpanzees and genetic advances in the field of primatology. The use of DNA analyses has revolutionised archaeological and primatological fields, whereby...

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
    56

Resource Types

  • Dataset
    56

Affiliations

  • University of Cambridge
    56
  • Lund University
    5
  • University of Oxford
    5
  • University of Michigan-Ann Arbor
    3
  • Oberlin College
    3
  • Estación Biológica de Doñana
    2
  • University of North Carolina
    2
  • Royal Society for the Protection of Birds
    2
  • New York University
    2
  • British Antarctic Survey
    2