16 Works

Data from: Human face-off: a new method for mapping evolutionary rates on three-dimensional digital models

Silvia Castiglione, Marina Melchionna, Antonio Profico, Gabriele Sansalone, Maria Modafferi, Alessandro Mondanaro, Stephen Wroe, Paolo Piras & Pasquale Raia
Modern phylogenetic comparative methods allow estimating evolutionary rates of phenotypic change, how these rates differ across clades, and assessing whether the rate remained constant over time. Unfortunately, currently available phylogenetic comparative tools express the rate in terms of a scalar dimension, hence they do not allow us to determine rate variations among different parts of a single, complex phenotype, or charting of realized rate variation directly onto the phenotype. Herein, we present a new method...

Integrating stakeholders’ perspectives and spatial modelling to develop scenarios of future land use and land cover change in northern Tanzania

Rebecca Kariuki, Linus Munishi, Colin Courtney-Mustaphi, Claudia Capitani, Anna Shoemaker, Paul Lane & Rob Marchant
Rapid rates of land use and land cover change (LULCC) in eastern Africa and limited instances of genuinely equal partnerships involving scientists, communities and decision makers challenge the development of robust pathways toward future environmental and socioeconomic sustainability. We use a participatory modelling tool, Kesho, to assess the biophysical, socioeconomic, cultural and governance factors that influenced past (1959-1999) and present (2000-2018) LULCC in northern Tanzania and to simulate four scenarios of land cover change to...

COVID-19 patient data from a study in Singapore curated for input into an in silico infection model

Farzad Fatehi, Richard J. Bingham, Eric C. Dykeman, Peter G. Stockley & Reidun Twarock
Within-host models of COVID-19 infection dynamics enable the merits of different forms of antiviral therapy to be assessed in individual patients. A stochastic agent-based model of COVID-19 intracellular dynamics is introduced here, that incorporates essential steps of the viral life cycle targeted by treatment options. Integration of model predictions with an intercellular ODE model of within-host infection dynamics, fitted to patient data, generates a generic profile of disease progression in patients that have recovered in...

Data from: Quantifying trade-offs between butterfly abundance and movement in the management of agricultural set-aside strips

Katie Threadgill, Jenny Hodgson, Naomi Jones, Colin McClean & Jane Hill
1. Agri-environment schemes (AES) create small areas of habitat within agricultural landscapes to support biodiversity. Here, we study butterfly flight behaviour within linear AES features and examine whether differences in resource availability affect the speed, linearity or directionality of local movements, thereby affecting their contribution to landscape connectivity. 2. We surveyed butterflies within three basic (naturally regenerating) and three wildflower-sown linear field margin strips (0.09-0.15 ha) on a farm in North Yorkshire, UK, and mapped...

Narnian Virtues - Year 3 Qualitative Data

Peter Hart, Mark Pike & Anna Liddle
This dataset follows a Fouth Generation Evaluation methodology. Focus groups with students (years 7 to 9) and teachers were carried out, to understand the impact of the Narnian Virtues Character Education Curriculum

Datasets for Socio-macroeconomic impacts of implementing different post-Brexit UK energy reduction targets to 2030

Jaime Nieto Vega, Hector Pollitt, Paul Brockway, Lucy Clements, Marco Sakai & John Barrett
This file contains the following data sheets used in the following paper: Nieto, J., Pollitt, H. Brockway, P.E., Clements, L., Sakai, M., and Barrett J. “Socio-Macroeconomic Impacts of Implementing Different Post-Brexit UK Energy Reduction Targets to 2030.” Energy Policy 158, 2021, 112556. Available at: https://doi.org/10.1016/j.enpol.2021.112556 *Inputs: Exogenous inputs to the model *Results Levels:Results for the E3ME and MARCO-UK scenarios in levels *Results vs Baseline: Results for the E3ME and MARCO-UK scenarios in volume index (Baseline=100)...

Superoxide is promoted by sucrose and affects amplitude of circadian rhythms in the evening

Michael Haydon, John Davey & Ángela Román
Plants must coordinate photosynthetic metabolism with the daily environment and adapt rhythmic physiology and development to match carbon availability. Circadian clocks drive biological rhythms which adjust to environmental cues. Products of photosynthetic metabolism, including sugars and reactive oxygen species (ROS), are closely associated with the plant circadian clock and sugars have been shown to provide metabolic feedback to the circadian oscillator. Here, we report a comprehensive sugar-regulated transcriptome of Arabidopsis and identify genes associated with...

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...

Nepal Stressor Interaction Model (Nepal SIM)

Nicholas Roxburgh, Lindsay Stringer, Andrew Evans, Raj K. GC, Nick Malleson & Heppenstall Alison
"A detail-rich, ethnographically informed agent-based model of a Nepalese smallholder village that was originally created for the purpose of studying the impact of multiple stressors on mountain communities, but which can potentially be adapted to serve other purposes. The model was created in NetLogo 5.0.5 but additionally calls on R scripts and .CSV inputs that are included in the package. Example R scripts for conducting analysis of model outputs are also included, along with example...

Fine-scale genetic structure reflects limited and coordinated dispersal in the colonial monk parakeet, Myiopsitta monachus

Francesca Dawson Pell, Juan Carlos Senar, Daniel Franks & Ben Hatchwell
The genetic structure of animal populations has considerable behavioural, ecological and evolutionary implications and may arise from various demographic traits. Here, we use observational field data and molecular genetics to determine the genetic structure of an invasive population of monk parakeets, Myiopsitta monachus, at a range of spatial scales, and investigate the demographic processes that generate the observed structure. Monk parakeets construct large nests that can house several pairs occupying separate chambers; these nests are...

Testing the effectiveness of the Forest Integrity Assessment: A field-based tool for estimating the condition of tropical forest

Andrew Suggitt, Kok Yeong, Anders Lindhe, Agnes Agama, Keith Hamer, Glen Reynolds, Jane Hill & Jennifer Lucey
1. Global targets to halt biodiversity losses and mitigate climate change will require protecting rainforest beyond current protected area networks, necessitating responsible forest stewardship from a diverse range of companies, communities and private individuals. Robust assessments of forest condition are critical for successful forest management, but many existing techniques are highly technical, time-consuming, expensive, or require specialist knowledge. 2. To make assessment of tropical forests accessible to a wide range of actors, many of whom...

Proximity to forest mediates trade-offs between yields and biodiversity of birds in oil palm smallholdings

Keith C Hamer, Michael A Sasu, Linda Ofosuhene, Rebecca Asare, Benjamin Ossom, Catherine L Parr, Sarah A Scriven, Winston Asante, Rosemary Addico & Jane K Hill
There is much debate about how best to mitigate the effects of agricultural expansion on biodiversity, especially in the tropics. Recent studies have emphasised that proximity to natural habitats can enhance farmland biodiversity, yet few studies have examined whether or not such proximity mediates local trade-offs between yields and biodiversity, and hence alters conclusions about the ecological benefits of alternative farming strategies. Here we examine yield-biodiversity trade-offs, focusing on birds in oil palm smallholdings at...

New insights into early medieval Islamic cuisine: organic residue analysis of pottery from rural and urban Sicily (GCMS DATA FILES)

Jasmine Lundy
Sicily, during the 9th-12th century AD, thrived politically, economically, and culturally under Islamic political rule and the capital of Palermo stood as a cultural and political centre in the Mediterranean Islamic world. However, to what extent the lifeways of the people that experienced these regimes were impacted during this time is not well understood, particularly those from lesser studied rural contexts. This paper presents the first organic residue analysis of 134 cooking pots and other...

Data from: Social and physical environment independently affect oviposition decisions in Drosophila

Emily Churchill, Calvin Dytham, Jon Bridle & Michael Thom
In response to environmental stimuli, including variation in the presence of conspecifics, genotypes show highly plastic responses in behavioral and physiological traits influencing reproduction. Although extensively documented in males, such female responses are rather less studied. We expect females to be highly responsive to environmental variation and to differentially allocate resources to increase offspring fitness, given the major contribution of mothers to offspring number, size, and developmental conditions. Using Drosophila melanogaster, we (a) manipulate exposure...

Genetic conservation literature review

Melissa Minter, David O'Brien, Joan Cottrell, Richard Ennos, Jane Hill & Jeanette Hall
Genetic diversity is important for species persistence and Gene Conservation Units (GCUs) have been implemented for forest trees to protect genetic diversity and evolutionary processes in situ. The Convention on Biological Diversity stipulates the protection of genetic diversity as an Aichi target, and so we explore the potential for GCUs to be implemented more widely. Our global systematic review showed that GCUs are currently implemented primarily for plant species of economic importance (109/158 species studied),...

Supplementary Information for Phylogenetic analyses of ray-finned fishes (Actinopterygii) using collagen type I protein sequences

Virginia Harvey, Joseph Keating & Michael Buckley
Ray-finned fishes (Actinopterygii) are the largest and most diverse group of vertebrates, comprising over half of all living vertebrate species. Phylogenetic relationships between ray-finned fishes have historically pivoted on the study of morphology, which has notoriously failed to resolve higher-order relationships, such as within the percomorphs. More recently, comprehensive genomic analyses have provided further resolution of actinopterygian phylogeny, including higher-order relationships. Such analyses are rightfully regarded as the ‘gold standard’ for phylogenetics. However, DNA retrieval...

Registration Year

  • 2021
    16

Resource Types

  • Dataset
    16

Affiliations

  • University of York
    16
  • University of Leeds
    6
  • University of Liverpool
    2
  • University of Sheffield
    2
  • Plymouth University
    1
  • Deutsches Museum
    1
  • Nature Conservation Research Centre
    1
  • Kwame Nkrumah University of Science and Technology
    1
  • University of Cambridge
    1
  • Museum of Natural Sciences of Barcelona
    1