34 Works

Household composition, income and assets survey data (including environmental product collection) from Mabalane, Gurue and Marrupa districts, Mozambique in 2014 and 2015

F. Vollmer, J. Fisher, C.M. Ryan, S. Baumert, E. Woollen, A. Luz, I. Cossa, R. Stedham & H. Smith
This dataset includes data collected as part of the Abrupt Changes in Ecosystem Services (ACES) project on the composition, income (including consumption and sale of environmental resources), ownership of assets (e.g. farming equipment, household furnishings and own transport) and wellbeing of respondent households in rural Mozambique. Data are also included from a participatory wealth ranking exercise carried out in each village. Data were collected in a total of 27 villages: 7 villages in Mabalane District...

Data from: Genetic diversity, demographic history and neo-sex chromosomes in the Critically Endangered Raso lark

Elisa G. Dierickx, Simon Yung Wa Sin, Pieter Van Veelen, M. De L. Brooke, Yang Liu, Scott V. Edwards & Simon H. Martin
Small effective population sizes could expose island species to inbreeding and loss of genetic variation. Here, we investigate factors shaping genetic diversity in the Raso lark, which has been restricted to a single islet for approximately 500 years, with a population size of a few hundred. We assembled a reference genome for the related Eurasian skylark and then assessed diversity and demographic history using RAD-seq data (75 samples from Raso larks and two related mainland...

Data from: Arms races with mitochondrial genome soft sweeps in a gynodioecious plant, Plantago lanceolata

Roberta Bergero, Nick Levsen, Kirsten Wolff & Deborah Charlesworth
Biological situations involving conflict can create arms race situations with repeated fixations of different functional variants, producing selective sweeps and lowering neutral diversity in genome regions linked to the functional locus. However, they can sometimes lead to balancing selection, potentially creating long coalescent times for sites with functionally different variants, and, if recombination occurs rarely, for extended haplotypes carrying such variants. We tested between these possibilities in a gynodioecious plant, Plantago lanceolata, in which cytoplasmic...

Data from: Drought soil legacy overrides maternal effects on plant growth

Jonathan R. De Long, Marina Semchenko, William J. Pritchard, Irene Cordero, Ellen L. Fry, Benjamin G. Jackson, Ksenia Kurnosova, Nicholas J. Ostle, David Johnson, Elizabeth M. Baggs & Richard D. Bardgett
1.Maternal effects (i.e., trans‐generational plasticity) and soil legacies generated by drought and plant diversity can affect plant performance and alter nutrient cycling and plant community dynamics. However, the relative importance and combined effects of these factors on plant growth dynamics remain poorly understood. 2.We used soil and seeds from an existing plant diversity and drought manipulation field experiment in temperate grassland to test maternal, soil drought and diversity legacy effects, and their interactions, on offspring...

Data from: Preserved collagen reveals species identity in archaeological marine turtle bones from Caribbean and Florida sites

Michael Buckley, Virginia L. Harvey, Michelle J. LeFebvre, Susan D. DeFrance, Casper Toftgaard & Andrew C. Kitchener
Advancements in molecular science are continually improving our understanding of marine turtle biology and evolution. However, there are still considerable gaps in our understanding, such as past marine turtle distributions, which can benefit from advanced zooarchaeological analyses. Here we apply collagen fingerprinting to 130 archaeological marine turtle bone samples up to 2500 years old from the Caribbean and Florida’s Gulf Coast for faunal identification, finding the vast majority of samples (88%) to contain preserved collagen...

Data from: Inferring HIV-1 transmission networks and sources of epidemic spread in Africa with deep-sequence phylogenetic analysis

Oliver Ratmann, M. Kate Grabowski, Matthew Hall, Tanya Golubchik, Chris Wymant, Lucie Abeler-Dörner, David Bonsall, Anne Hoppe, Andrew Leigh Brown, Tulio De Oliveira, Astrid Gall, Paul Kellam, Deenan Pillay, Joseph Kagaayi, Godfrey Kigozi, Thomas C. Quinn, Maria J. Wawer, Oliver Laeyendecker, David Serwadda, Ronald H. Gray, Christophe Fraser, &
To prevent new infections with human immunodeficiency virus type 1 (HIV-1) in sub-Saharan Africa, UNAIDS recommends targeting interventions to populations that are at high risk of acquiring and passing on the virus. Yet it is often unclear who and where these ‘source’ populations are. Here we demonstrate how viral deep-sequencing can be used to reconstruct HIV-1 transmission networks and to infer the direction of transmission in these networks. We are able to deep-sequence virus from...

Data from: Exaggerated heterochiasmy in a fish with sex-linked male coloration polymorphisms

Roberta Bergero, Jim Gardner, Beth Bader, Lengxob Yong & Deborah Charlesworth
It is often stated that polymorphisms for mutations affecting fitness of males and females in opposite directions [sexually antagonistic (SA) polymorphisms] are the main selective force for the evolution of recombination suppression between sex chromosomes. However, empirical evidence to discriminate between different hypotheses is difficult to obtain. We report genetic mapping results in laboratory-raised families of the guppy (Poecilia reticulata), a sexually dimorphic fish with SA polymorphisms for male coloration genes, mostly on the sex...

Data from: Species richness change across spatial scales

Jonathan M. Chase, Brian J. McGill, Patrick L. Thompson, Laura H. Antão, Amanda E. Bates, Shane A. Blowes, Maria Dornelas, Andrew Gonzalez, Anne E. Magurran, Sarah R. Supp, Marten Winter, Anne D. Bjorkmann, Helge Bruelheide, Jarrett E.K. Byrnes, Juliano Sarmento Cabral, Robin Ehali, Catalina Gomez, Hector M. Guzman, Forest Isbell, Isla H. Myers-Smith, Holly P. Jones, Jessica Hines, Mark Vellend, Conor Waldock & Mary O'Connor
Humans have elevated global extinction rates and thus lowered global-scale species richness. However, there is no a priori reason to expect that losses of global species richness should always, or even often, trickle down to losses of species richness at regional and local scales, even though this relationship is often assumed. Here, we show that scale can modulate our estimates of species richness change through time in the face of anthropogenic pressures, but not in...

Data from: Environmental heterogeneity decreases reproductive success via effects on foraging behaviour

Alice Trevail, Jonathan Green, Jonathan Sharples, Jeff Polton, Peter Miller, Francis Daunt, Ellie Owen, Mark Bolton, Kendrew Colhoun, Stephen Newton, Gail Robertson & Samantha Patrick
Environmental heterogeneity shapes the uneven distribution of resources available to foragers, and is ubiquitous in nature. Optimal foraging theory predicts that an animal’s ability to exploit resource patches is key to foraging success. However, the potential fitness costs and benefits of foraging in a heterogeneous environment are difficult to measure empirically. Heterogeneity may provide higher quality foraging opportunities, or alternatively could increase the cost of resource acquisition because of reduced patch density or increased competition....

Life history evolution, species differences and phenotypic plasticity in hemiparasitic eyebrights (Euphrasia)

Max Brown, Natacha Frachon, Edgar Wong & Alex Twyford
Premise of the study: Species delimitation in parasitic organisms is challenging as traits used in the identification of species are often plastic and vary depending on the host. Here, we use species from a recent radiation of generalist hemiparasitic Euphrasia to investigate trait variation and trait plasticity. We test whether Euphrasia species show reliable trait differences, investigate whether these differences correspond to life history trade-offs between growth and reproduction, and quantify plasticity in response to...

How long does it take to fix a favorable mutation, and why should we care?

Brian Charlesworth
The time taken for a selectively favorable allele to spread through a single population was investigated early in the history of population genetics. The resulting formulae are based on deterministic dynamics, leading to inaccuracies at allele frequencies close to zero or one. To remedy this problem, the properties of the stochastic phases at either endpoint of allele frequency need to be analysed. This paper uses a heuristic approach to determining the expected times spent in...

Explaining illness with evil: Pathogen prevalence fosters moral vitalism

Brock Bastian, Christin-Melanie Vauclair, Steve Loughnan, Paul Bain, Ashwini Ashokkumar, Maja Becker, Michal Bilewicz, Emma Collier-Baker, Carla Crespo, Paul W. Eastwick, Ronald Fischer, Malte Friese, Ángel Gómez, Valeschka M. Guerra, Jose Luis Castellanos Guevara, Katja Hanke, Nic Hooper, Li-Li Huang, Shi Junqi, Minoru Karasawa, Peter Kuppens, Siri Leknes, Müjde Peker, Cesar Pelay, Afoditi Pina … & William B. Swann
Pathogens represent a significant threat to human health leading to the emergence of strategies designed to help manage their negative impact. We examined how spiritual beliefs developed to explain and predict the devastating effects of pathogens and spread of infectious disease. Analysis of existing data in Studies 1 and 2 suggests that moral vitalism (beliefs about spiritual forces of evil) is higher in geographical regions characterized by historical higher levels of pathogens. Furthermore, drawing on...

Data from: The genetic architecture of helminth-specific immune responses in a wild population of Soay sheep (Ovis aries)

Alexandra Sparks, Kathryn Watt, Rona Sinclair, Jill Pilkington, Josephine Pemberton, Tom McNeilly, Daniel Nussey & Susan Johnston
Much of our knowledge of the drivers of immune variation, and how these responses vary over time, comes from humans, domesticated livestock or laboratory organisms. While the genetic basis of variation in immune responses have been investigated in these systems, there is a poor understanding of how genetic variation influences immunity in natural, untreated populations living in complex environments. Here, we examine the genetic architecture of variation in immune traits in the Soay sheep of...

Data from: Reproduction has different costs for immunity and parasitism in a wild mammal

Gregory Albery, Kathryn Watt, Rosie Keith, Sean Morris, Alison Morris, Fiona Kenyon, Daniel Nussey & Josephine Pemberton
Life history theory predicts that reproductive allocation draws resources away from immunity, resulting in increased parasitism. However, studies of reproductive tradeoffs rarely examine multiple measures of reproduction, immunity, and parasitism. It is therefore unclear whether the immune costs of reproductive traits correlate with their resource costs, and whether increased parasitism emerges from weaker immunity. We examined these relationships in wild female red deer (Cervus elaphus) with variable reproductive allocation and longitudinal data on mucosal antibody...

Intracranial haemodynamic relationships in patients with cerebral small vessel disease

Gordon Blair, Michael Thrippleton, Yulu Shi, Iona Hamilton, Michael Stringer, Francesca Chappell, David Alexander Dickie, Peter Andrews, Ian Marshall, Fergus Doubal & Joanna Wardlaw
Objective To investigate cerebrovascular reactivity (CVR), blood flow, vascular and cerebrospinal fluid (CSF) pulsatility, and their independent relationship to cerebral small vessel disease (SVD) features, in patients with minor ischaemic stroke and MRI evidence of SVD. Methods We recruited patients with minor ischaemic stroke and assessed CVR using Blood Oxygen Level Dependent (BOLD) MRI during a hypercapnic challenge, cerebral blood flow, vascular and CSF pulsatility using phase contrast MRI, and structural MR brain imaging to...

Data from: A complex pattern of post-divergence expansion, contraction, introgression and asynchronous responses to Pleistocene climate changes in two Dipelta sister species from western China

Bin Tian, Yi Fu, Richard Milne, Kangshan Mao, Yong-Shuai Sun, Xiangguang Ma & Hang Sun
The well-known vicariance and dispersal models dominate in understanding the allopatric pattern for related species and presume the simultaneous occurrence of speciation and biogeographic events. However, the formation of allopatry may postdate the species divergence. We examined this hypothesis using DNA sequence data from 3 chloroplast fragments and 5 nuclear loci of Dipelta floribunda and D. yunnanensis, two shrub species with the circum Sichuan Basin distribution, combining the climatic niche modeling approach. The best-fit model...

Data from: The impact of uncertainty on cooperation intent in a conservation conflict

Chris R. J. Pollard, Steve Redpath, Luc F. Bussière, Aidan Keane, Des B. A. Thompson, Juliette C. Young & Nils Bunnefeld
Stakeholder cooperation can be vital in managing conservation conflicts. Laboratory experiments show cooperation is less likely in the presence of uncertainty. Much less is known about how stakeholders in real‐life conservation conflicts respond to different types of uncertainty. We tested the effects of different sources of uncertainty on cooperative behaviour using a framed field experiment and interviews. The experiment compared a baseline scenario of perfect certainty with scenarios including either: i) scientific uncertainty about the...

Data from: Maternal longevity and offspring sex in wild ungulates

Mathieu Douhard, Marco Festa-Bianchet, Sandra Hamel, Dan Nussey, Steeve Côté, Josephine Pemberton & Fanie Pelletier
In species with sexual size dimorphism, offspring of the larger sex usually have greater energy requirements and may lead to greater fitness costs for parents. The effects of offspring sex on maternal longevity, however, have only been tested in humans. Human studies produced mixed results and considerable debate mainly due to the difficulty of distinguishing the effects of sexual dimorphism from sociocultural factors. To advance this debate, we examined how the relative number of sons...

Data from: Food-deprivation affects egg laying and maternal care but not offspring performance in a beetle

Jon Richardson, Jennifer Ross & Per T. Smiseth
Individuals vary with respect to their nutritional state and such variation is an important determinant of the amount of resources individuals allocate towards reproductive functions. Currently, we have a relatively poor understanding of the downstream consequences of food deprivation on different traits associated with reproduction. Here, we address this gap by investigating how food deprivation affected different traits across the breeding cycle in the burying beetle, Nicrophorus vespilloides; a species that breeds on carcasses of...

Data from: Testing the Distraction Hypothesis: do extrafloral nectaries reduce ant‐pollinator conflict?

Nora Villamil, Karina Boege & Graham N. Stone
1. Ant guards protect plants from herbivores, but can also hinder pollination by damaging reproductive structures and/or repelling pollinators. Natural selection should favour the evolution of plant traits that deter ants from visiting flowers during anthesis, without waiving their defensive services. The Distraction Hypothesis posits that rewarding ants with extrafloral nectar could reduce their visitation of flowers, reducing ant-pollinator conflict while retaining protection of other structures. 2. We characterised the proportion of flowers occupied by...

Data from: Epigenome-wide association study of lung function level and its change

Medea Imboden, Matthias Wielscher, Faisal I Rezwan, Andre F S Amaral, Emmanuel Schaffner, Ayoung Jeong, Anna Beckmeyer-Borowko, Sarah E Harris, John M Starr, Ian J Deary, Claudia Flexeder, Melanie Waldenberger, Annette Peters, Holger Schulz, Su Chen, Shadia KHan Sunny, Wilfried J J Karmaus, Yu Jiang, Gertraud Erhart, Florian Kronenberg, Ryan Arathimos, Gemma C Sharp, Alexander John Henderson, Yu Fu, Paivi Piirila … & Nicole M Probst-Hensch
Previous reports link differential DNA methylation (DNAme) to environmental exposures which are associated with lung function. Direct evidence on lung function DNAme is however limited. We undertook an agnostic epigenome-wide association study (EWAS) on pre-bronchodilation lung function and its change in adults. In a discovery-replication EWAS design, DNAme in blood and spirometry were measured twice, six-to-15 years apart, in the same participants of three adult population-based discovery cohorts (n=2,043). Associated DNAme markers (P<5x10-7) were tested...

Data from: Temporal, spatial and household dynamics of typhoid fever in Kasese district, Uganda

Bernadette Basuta Mirembe, Stella Mazeri, Rebecca Callaby, Luke Nyakarahuka, Clovice Kankya & Adrian Muwonge
Typhoid fever affects 21 million people globally, 1% of whom succumb to the disease. The social, economic and public health consequences of this disease disproportionately affect people in Africa and Asia. In order to design context specific prevention strategies, we need to holistically characterise outbreaks in these settings. Here we used retrospective data (2013-2016) at national and district level to characterize temporal and spatial dynamics of typhoid fever outbreaks using time series and spatial analysis....

Data from: Macroevolutionary patterns in overexpression of tyrosine: an anti-herbivore defense in a speciose tropical tree genus, Inga (Fabaceae)

Phyllis D. Coley, María‐José Endara, Gabrielle Ghabash, Catherine A. Kidner, James A. Nicholls, R. Toby Pennington, Anthony G. Mills, Abrianna J. Soule, Maristerra R. Lemes, Graham N. Stone & Thomas A. Kursar
Plant secondary metabolites are a key defence against herbivores, and their evolutionary origin is likely from primary metabolites. Yet for this to occur, an intermediate step of overexpression of primary metabolites would need to confer some advantage to the plant. Here, we examine the evolution of overexpression of the essential amino acid, L‐tyrosine and its role as a defence against herbivores. We examined overexpression of tyrosine in 97 species of Inga (Fabaceae), a genus of...

Data from: Consistent within‐individual plasticity is sufficient to explain temperature responses in red deer reproductive traits

Hannah Froy, Julien Martin, Katie Stopher, Alison Morris, Sean Morris, Tim Clutton-Brock, Josephine Pemberton & Loeske Kruuk
Warming global temperatures are affecting a range of aspects of wild populations, but the exact mechanisms driving associations between temperature and phenotypic traits may be difficult to identify. Here, we use a 36‐year data set on a wild population of red deer to investigate the causes of associations between temperature and two important components of female reproduction: timing of breeding and offspring size. By separating within‐ versus between‐individual associations with temperature for each trait, we...

River Tay, Scotland, water chemistry and greenhouse gas measurements 2009-2010

A.E. Pickard, U.M. Skiba, L. Carvalho, K.V. Heal, R.M. Rees & J.F. Harley
This dataset contains concentrations of dissolved organic carbon, dissolved inorganic carbon, nutrients and concentrations of greenhouse gases CO2, CH4 and N2O from nine sites across the River Tay catchment. Water was sampled on a monthly basis between February 2009 and December 2010. The locations of sampling sites were based on existing flow gauging and water sampling sites of the Scottish Environment Protection Agency (SEPA).

Registration Year

  • 2019
    34

Resource Types

  • Dataset
    34

Affiliations

  • University of Edinburgh
    34
  • Centre for Ecology and Hydrology
    3
  • University of Cambridge
    3
  • University of Aberdeen
    3
  • University of Leeds
    3
  • University of Manchester
    3
  • University of Exeter
    3
  • Sun Yat-sen University
    2
  • Université de Sherbrooke
    2
  • University of Glasgow
    2