596 Works

Supporting data for ‘DFENS: Diffusion chronometry using Finite Elements and Nested Sampling’

Euan Mutch, John Maclennan, Oliver Shorttle, John Rudge & David Neave
This is supporting data for the manuscript entitled 'DFENS: Diffusion chronometry using Finite Elements and Nested Sampling' by E. J. F. Mutch, J. Maclennan, O. Shorttle, J. F. Rudge and D. Neave. Preprint here: https://doi.org/10.1002/essoar.10503709.1 Data Set S1. ds01.csv Electron probe microanalysis (EPMA) profile data of olivine crystals used in this study. Standard deviations are averaged values of standard deviations from counting statistics and repeat measurements of secondary standards. Data Set S2. ds02.csv Plagioclase compositional...

Sunflower seed predation rates in Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) plots, Kandista and Ujun Tanjung estates, Indonesia

A. E. Eycott, E.C. Turner, S. H. Luke & A. D. Advento
Data comprise sunflower seed predation rates (i.e. number of seeds remaining) after 24 hours under different treatments in 18 experimental plots plots established in 2013 as part of the Biodiversity and Ecosystem Function in Tropical Agriculture (BEFTA) programme. Eighteen plots were examined across three estates – plots in Ujung Tanjung and Kandista estates were planted in 1987 to 1992 and are mature or over-mature oil palm, while Libo plots were replanted in 2014. Plots were...

Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) projected area of vegetation in saltmarsh habitats

B.R. Evans, I. Möller & T. Spencer
The dataset contains estimates of the projected area of vegetation derived from the analysis of side-on photographs through the vegetation canopy and recorded for survey quadrats at six UK saltmarsh sites. Three of the sites were in Morecambe Bay, North West England and three of the sites were in Essex, South East England, each of these sites consisted of a saltmarsh area and adjacent mudflat area. Each site comprised 22 quadrats in the vegetated area...

Derived global responses of annual river flow to catchment forestation through time, between 1900 and 2018

L. Bentley & D.A. Coomes
This dataset reports the responses of annual river flow to forestation in 43 catchments and contains 770 data points. Data shows the change in river flow following forestation at annual time scales, along control river flow measurements and associated metadata from primary and secondary sources. Data collection, processing and interpretation were performed by Laura Bentley and David A. Coomes between January 2018 and October 2019. Forestation was defined as a change in land cover from...

Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) global positioning system (GPS) locations of survey quadrats in saltmarsh and mudflat habitats

B.R. Evans, T. Spencer & I. Möller
The dataset details global positioning system (GPS) locations recorded for survey quadrats at six UK saltmarsh sites. Three of the sites were in Morecambe Bay, North West England and three of the sites were in Essex, South East England, each of these sites consisted of a salt marsh area and adjacent mudflat area. Each site comprised 22 quadrats on the unvegetated mudflat and 22 quadrats on the salt marsh. The locations indicated by this dataset...

Oak-associated biodiversity in the UK (OakEcol)

R.J. Mitchell, P.E. Bellamy, C.J. Ellis, R.L. Hewison, N.G. Hodgetts, G.R. Iason, N.A. Littlewood, S. Newey, J.A. Stockan & A.F.S. Taylor
This dataset contains a list of all known birds, bryophytes, fungi, invertebrates, lichens and mammals that use oak (Quercus petraea and Quercus robur) in the UK. In total 2300 species are listed in the dataset. For each species we provide a level of association with oak, ranging from obligate (only found on oak) to cosmopolitan (found on a wide range of other tree species). Data on the ecology of each oak associated species is provided:...

Coastal Biodiversity and Ecosystem Service Sustainability (CBESS) global positioning system (GPS) locations for instruments and features associated with wave monitoring and sedimentation-erosion table installations in saltmarsh and mudflat habitats

B.R. Evans, I. Möller & T. Spencer
The dataset details global positioning system (GPS) locations recorded for instruments and locations of interest associated with equipment installed for the monitoring of wave energy, surface elevation changes and sedimentation at five UK saltmarsh sites. Two of the sites were in Morecambe Bay, North West England and three of the sites were in Essex, South East England, each of these sites consisted of a salt marsh area and adjacent mudflat area. Rod Sedimentation-Erosion Tables (rSETs)...

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...

Solutions to BAS-PRO model runs for Modelling 1-10MeV Proton Phase Space Density

Alexander Lozinski, Richard Horne, Sarah Glauert, Giulio Del Zanna & Seth Claudepierre
This dataset contains solution data produced by the BAS-PRO proton radiation belt model for the study "Modelling Inner Proton Belt Variability at Energies 1 to 10MeV using BAS-PRO". The solution data is in the form of 3D grids describing phase space density computed during dynamic simulations of Earth's proton belt over the modelling period 2014 to 2018. Three model runs are included: SA19, J81 and S16. Files were produced in May 2021. This work was...

Changes in gene expression and encapsulation in Drosophila melanogaster caused by exposure to parasitoid wasps

A.B. Leitão, A. Ramesh, J.P. Day, N. Hanna, A. Devi, M.P. Hayes & F.M. Jiggins
Data consists of gene expression estimates and encapsulation rates in wild caught Drosophila melanogaster larvae following exposure to different treatments. Treatments include injection with wasp homogenate, injection with oil and no injection. Also provided are functional enrichment categories for differentially expressed genes and library generation and read mapping metrics. The data were produced under the grant: NE/P00184X/1

HadCM3 and HadGEM3 LIG model outputs: A sea ice-free Arctic

Maria Vittoria Guarino & Louise Sime
The HadGEM3 (HadGEM3-GC3.1 or HadGEM3-GC3.1-N96ORCA1) PI simulation was initialized using the standard CMIP6 protocol using constant 1850 GHGs, ozone, solar, tropospheric aerosol, stratospheric volcanic aerosol and land-use forcing. The PI spin-up was 700 model-years, which allowed the land and oceanic masses to attain approximate steady state. The HadGEM3 LIG (Last Interglacial) simulation was initialized from the end of the spin-up phase of the equivalent pre-industrial (PI) simulation. After initialization, the LIG was run for 350...

Last Interglacial summer air temperature observations for the Arctic

Maria Vittoria Guarino & Louise Sime
These 21 Last Interglacial (LIG) summer surface air temperature (SSAT) observations were compiled to assess LIG Arctic sea ice (Guarino et al 2020). Twenty of the observations were also previously used in the IPCC-AR5 report. Each observation is thought to be of summer LIG air temperature anomaly relative to present day and is located in the circum-Arctic region. All sites are from north of 51N. There are 7 terrestrial based temperature records; 8 lacustrine records;...

Data from: Rapid evolutionary response to a transmissible cancer in Tasmanian devils

Brendan Epstein, Menna Jones, Rodrigo Hamede, Sarah Hendricks, Hamish McCallum, Elizabeth P. Murchison, Barbara Schönfeld, Cody Wiench, Paul Hohenlohe & Andrew Storfer
Although cancer rarely acts as an infectious disease, a recently emerged transmissible cancer in Tasmanian devils (Sarcophilus harrisii) is virtually 100% fatal. Devil facial tumour disease (DFTD) has swept across nearly the entire species’ range, resulting in localized declines exceeding 90% and an overall species decline of more than 80% in less than 20 years. Despite epidemiological models that predict extinction, populations in long-diseased sites persist. Here we report rare genomic evidence of a rapid,...

Data from: From cacti to carnivores: improved phylotranscriptomic sampling and hierarchical homology inference provide further insight into the evolution of Caryophyllales

Joseph Frederic Walker, Ya Yang, Tao Feng, Alfonso Timoneda, Jessica Mikenas, Vera Hutchison, Caroline Edwards, Ning Wang, Sonia Ahluwalia, Julia Olivieri, Nathanael Walker-Hale, Lucas C. Majure, Raúl Puente, Gudrun Kadereit, Maximillian Lauterbach, Urs Eggli, Hilda Flores-Olvera, Helga Ochoterena, Samuel F. Brockington, Michael J. Moore & Stephen A. Smith
Premise of the Study— The Caryophyllales contains ~12,500 species and is known for its cosmopolitan distribution, convergence of trait evolution, and extreme adaptations. Some relationships within the Caryophyllales, like those of many large plant clades, remain unclear and phylogenetic studies often recover alternative hypotheses. We explore the utility of broad and dense transcriptome sampling across the order for resolving evolutionary relationships in Caryophyllales. Methods— We generated 84 transcriptomes and combined these with 224 publicly available...

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: 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: Allatostatin A signalling in Drosophila regulates feeding and sleep and is modulated by PDF

Jiangtian Chen, Wencke Reiher, Christiane Hermann-Luibl, Azza Sellami, Paola Cognigni, Shu Kondo, Charlotte Helfrich-Förster, Jan A. Veenstra & Christian Wegener
Feeding and sleep are fundamental behaviours with significant interconnections and cross-modulations. The circadian system and peptidergic signals are important components of this modulation, but still little is known about the mechanisms and networks by which they interact to regulate feeding and sleep. We show that specific thermogenetic activation of peptidergic Allatostatin A (AstA)-expressing PLP neurons and enteroendocrine cells reduces feeding and promotes sleep in the fruit fly Drosophila. The effects of AstA cell activation are...

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: Fine-scale genetic structure reflects sex-specific dispersal strategies in a population of sociable weavers (Philetairus socius)

René E. Van Dijk, Rita Covas, Claire Doutrelant, Claire N. Spottiswoode & Ben J. Hatchwell
Dispersal is a critical driver of gene flow, with important consequences for population genetic structure, social interactions and other biological processes. Limited dispersal may result in kin-structured populations in which kin selection may operate, but it may also increase the risk of kin competition and inbreeding. Here, we use a combination of long-term field data and molecular genetics to examine dispersal patterns and their consequences for the population genetics of a highly social bird, the...

Data from: Cell cycle-dependent differentiation dynamics balances growth and endocrine differentiation in the pancreas

Yung Hae Kim, Hjalte List Larsen, Pau Rué, Laurence A. Lemaire, Jorge Ferrer & Anne Grapin-Botton
Organogenesis relies on the spatiotemporal balancing of differentiation and proliferation driven by an expanding pool of progenitor cells. In the mouse pancreas, lineage tracing at the population level has shown that the expanding pancreas progenitors can initially give rise to all endocrine, ductal, and acinar cells but become bipotent by embryonic day 13.5, giving rise to endocrine cells and ductal cells. However, the dynamics of individual progenitors balancing self-renewal and lineage-specific differentiation has never been...

Data from: Angiosperm wood structure: global patterns in vessel anatomy and their relationship to wood density and potential conductivity

Amy E. Zanne, Mark Westoby, Daniel S. Falster, David D. Ackerly, Scott R Loarie, Sarah E. J. Arnold & David A. Coomes
Woody stems comprise a large biological carbon fraction and determine water transport between roots and leaves; their structure and function can influence both carbon and hydrological cycles. While angiosperm wood anatomy and density determine hydraulic conductivity and mechanical strength, little is known about interrelations across many species. We compiled a global dataset comprising two anatomical traits for 3005 woody angiosperms: mean vessel lumen area ( ) and number per unit area (N). From these, we...

Data from: The comparative landscape of duplications in Heliconius melpomene and Heliconius cydno

Ana Pinharanda, Simon H. Martin, Sarah L. Barker, John W. Davey & Chris D. Jiggins
Gene duplications can facilitate adaptation and may lead to inter-population divergence, causing reproductive isolation. We used whole-genome re-sequencing data from 34 butterflies to detect duplications in two Heliconius species, H. cydno and H. melpomene. Taking advantage of three distinctive signals of duplication in short-read sequencing data, we identified 744 duplicated loci in H. cydno and H. melpomene, 96% of which were validated with single molecule sequencing. We have found that duplications overlap genes significantly less...

Data from: Sharp acoustic boundaries across an altitudinal avian hybrid zone despite asymmetric introgression

Wouter Halfwerk, Caroline Dingle, Dusan M. Brinkhuizen, Jelmer W. Poelstra, Jan Komdeur & Hans Slabbekoorn
Birdsong is a sexually selected trait that could play an important evolutionary role when related taxa come into secondary contact. Many songbird species however learn their songs through copying one or more tutors, which complicates the evolutionary outcome of such contact. Two subspecies of a presumed vocal learner, the grey-breasted wood-wren (Henicorhina leucophrys), replace each other altitudinally across the western slope of the Ecuadorian Andes. These subspecies are morphologically very similar, but show striking differences...

Data from: Tree-centric mapping of forest carbon density from airborne laser scanning and hyperspectral data

Michele Dalponte & David A. Coomes
Forests are a major component of the global carbon cycle, and accurate estimation of forest carbon stocks and fluxes is important in the context of anthropogenic global change. Airborne laser scanning (ALS) data sets are increasingly recognized as outstanding data sources for high-fidelity mapping of carbon stocks at regional scales. We develop a tree-centric approach to carbon mapping, based on identifying individual tree crowns (ITCs) and species from airborne remote sensing data, from which individual...

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