88 Works

Data from: The landscape of anthropogenic mortality: how African lions respond to spatial variation in risk

Andrew J. Loveridge, Marion Valeix, Nicholas B. Elliot & David W. Macdonald
1. Demography and conservation status of many wild organisms are increasingly shaped by interactions with humans. This is particularly the case for large, wide ranging carnivores. 2. Using 206 mortality records (1999-2012) of lions in Hwange National Park, Zimbabwe, we calculated mortality rates for each source of anthropogenic mortality, modelled risk of anthropogenic mortality across the landscape accounting for time lions spent in different parts of the landscape, and assessed whether subsets of the population...

Data from: Global population divergence and admixture of the brown rat (Rattus norvegicus)

Emily E. Puckett, Jane Park, Matthew Combs, Michael J. Blum, Juliet E. Bryant, Adalgisa Caccone, Federico Costa, Eva E. Deinum, Alexandra Esther, Chelsea G. Himsworth, Peter D. Keightley, Albert Ko, Ake Lundkvist, Lorraine M. McElhinney, Serge Morand, Judith Robins, James Russell, Tanja M. Strand, Olga Suarez, Lisa Yon & Jason Munshi-South
Native to China and Mongolia, the brown rat (Rattus norvegicus) now enjoys a worldwide distribution. While black rats and the house mouse tracked the regional development of human agricultural settlements, brown rats did not appear in Europe until the 1500s, suggesting their range expansion was a response to relatively recent increases in global trade. We inferred the global phylogeography of brown rats using 32 k SNPs, and detected 13 evolutionary clusters within five expansion routes....

Data from: Experimental contact zones reveal causes and targets of sexual selection in hybridizing lizards

Hannah E. A. MacGregor, Geoffrey M. While, Jade Barrett, Guillem Pérez I De Lanuza, Pau Carazo, Sozos Michaelides & Tobias Uller
Divergence in sexually selected traits in allopatry should affect the degree and direction of hybridization. However, few studies have established the causes and targets of sexual selection during secondary contact. Common wall lizards (Podarcis muralis) from north-central Italy have highly exaggerated male sexual traits compared to populations in Western Europe. Using experimental populations, we show that this creates asymmetries in male dominance, spatial habitat use and reproductive success upon secondary contact. Hybridization occurred almost exclusively...

Data from: Probabilistic divergence time estimation without branch lengths: dating the origins of dinosaurs, avian flight and crown birds

Graeme T. Lloyd, David W. Bapst, Matt Friedman & Katie E. Davis
Branch lengths—measured in character changes—are an essential requirement of clock-based divergence estimation, regardless of whether the fossil calibrations used represent nodes or tips. However, a separate set of divergence time approaches are typically used to date palaeontological trees, which may lack such branch lengths. Among these methods, sophisticated probabilistic approaches have recently emerged, in contrast with simpler algorithms relying on minimum node ages. Here, using a novel phylogenetic hypothesis for Mesozoic dinosaurs, we apply two...

Data from: Counting cats: spatially explicit population estimates of cheetah (Acinonyx jubatus) using unstructured sampling data

Femke Broekhuis & Arjun M. Gopalaswamy
Many ecological theories and species conservation programmes rely on accurate estimates of population density. Accurate density estimation, especially for species facing rapid declines, requires the application of rigorous field and analytical methods. However, obtaining accurate density estimates of carnivores can be challenging as carnivores naturally exist at relatively low densities and are often elusive and wide-ranging. In this study, we employ an unstructured spatial sampling field design along with a Bayesian sex-specific spatially explicit capture-recapture...

Data from: Biofilm morphotypes and population structure among Staphylococcus epidermidis from commensal and clinical samples

Llinos Harris, Susan Murray, Ben Pascoe, James Bray, Guillaume Meric, Leonardos Magerios, Thomas S. Wilkinson, Rose E. Jeeves, Holger Rohde, Stefan Schwarz, Herminia De Lencastre, Maria Miragaia, Joana Rolo, Rory Bowden, Keith A. Jolley, Martin C. J. Maiden, Dietrich Mack, Samuel Sheppard, Llinos G. Harris, Rose Jeeves & Samuel K. Sheppard
Bacterial species comprise related genotypes that can display divergent phenotypes with important clinical implications. Staphylococcus epidermidis is a common cause of nosocomial infections and, critical to its pathogenesis, is its ability to adhere and form biofilms on surfaces, thereby moderating the effect of the host’s immune response and antibiotics. Commensal S. epidermidis populations are thought to differ from those associated with disease in factors involved in adhesion and biofilm accumulation. We quantified the differences in...

Data from: Information use and resource competition: an integrative framework

Alexander E. G. Lee, James P. Ounsley, Timothy Coulson, J. Marcus Rowcliffe, Guy Cowlishaw & Tim Coulson
Organisms may reduce uncertainty regarding how best to exploit their environment by collecting information about resource distribution. We develop a model to demonstrate how competition can facilitate or constrain an individual’s ability to use information when acquiring resources. Since resource distribution underpins both selection on information use and the strength and nature of competition between individuals, we demonstrate interdependencies between the two that should be common in nature. Individuals in our model can search for...

Data from: Evaluation of Xpert® MTB/RIF assay in induced sputum and gastric lavage samples from young children with suspected tuberculosis from the MVA85A TB vaccine trial

Erick Wekesa Bunyasi, Michele Tameris, Hennie Geldenhuys, Bey-Marrie Schmidt, Angelique Kany Kany Luabeya, Humphrey Mulenga, Thomas J. Scriba, Willem A. Hanekom, Hassan Mahomed, Helen McShane & Mark Hatherill
Objective: Diagnosis of childhood tuberculosis is limited by the paucibacillary respiratory samples obtained from young children with pulmonary disease. We aimed to compare accuracy of the Xpert® MTB/RIF assay, an automated nucleic acid amplification test, between induced sputum and gastric lavage samples from young children in a tuberculosis endemic setting. Methods: We analyzed standardized diagnostic data from HIV negative children younger than four years of age who were investigated for tuberculosis disease near Cape Town,...

Data from: Spatially coordinated dynamic gene transcription in living pituitary tissue

Karen Featherstone, Kirsty Hey, Hiroshi Momiji, Anne V. McNamara, Amanda L. Patist, Joanna Woodburn, David G. Spiller, Helen C. Christian, Alan S. McNeilly, John J. Mullins, Barbel F. Finkenstadt, David A. Rand, Michael R. H. White & Julian R. E. Davis
Transcription at individual genes in single cells is often pulsatile and stochastic. A key question emerges regarding how this behaviour contributes to tissue phenotype, but it has been a challenge to quantitatively analyse this in living cells over time, as opposed to studying snap-shots of gene expression state. We have used imaging of reporter gene expression to track transcription in living pituitary tissue. We integrated live-cell imaging data with statistical modelling for quantitative real-time estimation...

Data from: A global bionomic database for the dominant vectors of human malaria

N. Claire Massey, Gala Garrod, Antoinette Wiebe, Andrew J. Henry, Zhi Huang, Catherine L. Moyes & Marianne E. Sinka
Anopheles mosquitoes were first recognised as the transmitters of human malaria in the late 19th Century and have been subject to a huge amount of research ever since. Yet there is still much that is unknown regarding the ecology, behaviour (collectively ‘bionomics’) and sometimes even the identity of many of the world’s most prominent disease vectors, much less the within-species variation in their bionomics. Whilst malaria elimination remains an ambitious goal, it is becoming increasingly...

Data from: Zika virus in the Americas: early epidemiological and genetic findings

Nuno Rodrigues Faria, Raimunda Do Socorro Da Silva Azevedo, Moritz U. G. Kraemer, Renato Souza, Mariana Sequetin Cunha, Sarah C. Hill, Julien Thezé, Michael B. Bonsall, Thomas A. Bowden, Ilona Rissanen, Iray Maria Rocco, Juliana Silva Nogueira, Adriana Yurika Maeda, Fernanda Giseli Da Silva Vasami, Fernando Luiz De Lima Macedo, Akemi Suzuki, Sueli Guerreiro Rodrigues, Ana Cecilia Ribeiro Cruz, Bruno Tardeli Diniz, Daniele Barbosa De Almeida Medeiros, Daniela Sueli Guerreiro Rodrigues, Alice Louize Nunes Queiroz, Eliana Vieira Pinto Da Silva, Daniele Freitas Henriques, Elisabeth Salbe Travassos Da Rosa … & Pedro F. C. Vasconcelos
Brazil has experienced an unprecedented epidemic of Zika virus (ZIKV), with ~30,000 cases reported to date. ZIKV was first detected in Brazil in May 2015 and cases of microcephaly potentially associated with ZIKV infection were identified in November 2015. Using next generation sequencing we generated seven Brazilian ZIKV genomes, sampled from four self-limited cases, one blood donor, one fatal adult case, and one newborn with microcephaly and congenital malformations. Phylogenetic and molecular clock analyses show...

Data from: Dispersal in the sub-Antarctic: king penguins show remarkably little population genetic differentiation across their range

Gemma V. Clucas, Jane L. Younger, Damian Kao, Alex D. Rogers, Jonathan Handley, Gary D. Miller, Pierre Jouventin, Paul Nolan, Karim Gharbi, Karen J. Miller & Tom Hart
Background: Seabirds are important components of marine ecosystems, both as predators and as indicators of ecological change, being conspicuous and sensitive to changes in prey abundance. To determine whether fluctuations in population sizes are localised or indicative of large-scale ecosystem change, we must first understand population structure and dispersal. King penguins are long-lived seabirds that occupy a niche across the sub-Antarctic zone close to the Polar Front. Colonies have very different histories of exploitation, population...

Data from: Tropical ancient DNA from bulk archaeological fish bone reveals the subsistence practices of a historic coastal community in southwest Madagascar

Alicia Grealy, Kristina Douglass, James Haile, Chriselle Bruwer, Charlotte Gough & Michael Bunce
Taxonomic identification of archaeological fish bones provides important insights into the subsistence practices of ancient coastal peoples. However, it can be difficult to execute robust morphological identification of fish bones from species-rich fossil assemblages, especially from post-cranial material with few distinguishing features. Fragmentation, weathering and burning further impede taxonomic identification, resulting in large numbers of unidentifiable bones from archaeological sites. This limitation can be somewhat mitigated by taking an ancient DNA (aDNA) bulk-bone metabarcoding (BBM)...

Data from: Invasive plant species are locally adapted just as frequently and at least as strongly as native plant species

Ayub M. O. Oduor, Roosa Leimu & Mark Van Kleunen
Concerns over the ecological impacts of invasive alien plant species have generated great research interest in understanding the mechanisms that underlie the capacity of such plants to occupy a broad range of habitats. It has been repeatedly suggested that rapid evolution of local adaptation to novel environments may enable invasive plants to occupy a broad range of habitats. However, the classical Darwinian view on evolution by natural selection is that the process is slow and...

Data from: Divergent evolution peaks under intermediate population bottlenecks during bacterial experimental evolution

Tom Vogwill, Robyn L. Phillips, Danna R. Gifford & R. Craig MacLean
There is growing evidence that parallel molecular evolution is common, but its causes remain poorly understood. Demographic parameters such as population bottlenecks are predicted to be major determinants of parallelism. Here, we test the hypothesis that bottleneck intensity shapes parallel evolution by elucidating the genomic basis of adaptation to antibiotic-supplemented media in hundreds of populations of the bacterium Pseudomonas fluorescens Pf0-1. As expected, bottlenecking decreased the rate of phenotypic and molecular adaptation. Surprisingly, bottlenecking had...

Data from: Discrimination behavior mediates foraging quality versus quantity trade-offs: nut choice in wild rodents

Wenwen Chen, Ze Zhang, Christina D. Buesching, Chris Newman, David W. Macdonald, Zongqiang Xie, Shucun Sun & Youbing Zhou
Discrimination, the ability to distinguish sensory stimuli and respond accordingly, is a critical factor underscoring optimal foraging decisions. Nevertheless, little is known about how mammals discriminate between apparently similar foods of different quality. Here, we compared the foraging behavior of Chinese white-bellied rats, Niviventer confucianus, and Edwards’s long-tailed giant rats, Leopoldamys edwardsi, under natural conditions in the field and in a captive enclosure without predation/competition. We examined the behavioral processes involved in discriminating between sound...

Data from: Habitat saturation promotes delayed dispersal in a social reptile

Ben Halliwell, Tobias Uller, David G. Chapple, Michael G. Gardner, Erik Wapstra & Geoffrey M. While
When and where offspring disperse has important implications for the evolutionary emergence and maintenance of group living. In non-cooperative breeders, direct benefits of delayed dispersal are relatively limited, suggesting that decisions regarding whether or not to remain in the parental territory are largely driven by the availability of suitable habitat in which to settle. While there is ample evidence of correlations between habitat saturation and delayed dispersal, experimental tests are rare, particularly for species with...

Data from: Carry-over effects on the annual cycle of a migratory seabird: an experimental study

Annette L. Fayet, Robin Freeman, Akiko Shoji, Holly L. Kirk, Oliver Padget, Chris M. Perrins & Tim Guilford
Long-lived migratory animals must balance the cost of current reproduction with their own condition ahead of a challenging migration and future reproduction. In these species, carry-over effects, which occur when events in one season affect the outcome of the subsequent season, may be particularly exacerbated. However, how carry-over effects influence future breeding outcomes and whether (and how) they also affect behaviour during migration and wintering is unclear. Here we investigate carry-over effects induced by a...

Data from: Pleiotropy and the low cost of individual traits promote cooperation

Sara Mitri & Kevin R. Foster
The evolution of cooperation is thought to be promoted by pleiotropy, whereby cooperative traits are co-regulated with traits that are important for personal fitness. However, this hypothesis faces a key challenge: what happens if mutation targets a cooperative trait specifically rather than the pleiotropic regulator? Here we explore this question with the bacterium Pseudomonas aeruginosa, which cooperatively digests complex proteins using elastase. We empirically measure and theoretically model the fate of two mutants – one...

Data from: Lifespan and reproductive cost explain interspecific variation in the optimal onset of reproduction

Emeline Mourocq, Pierre Bize, Sandra Bouwhuis, Russell Bradley, Anne Charmantier, Carlos De La Cruz, Szymon Marian Obniak, Richard H. M. Espie, Márton Herenyi, Hermann Hötker, Oliver Kruger, John Marzluff, Anders P. Møller, Shinichi Nakagawa, Richard A. Phillips, Andrew N. Radford, Alexandre Roulin, János Török, Juliana Valencia, Martijn Van De Pol, Ian G. Warkentin, Isabel S. Winney, Andrew G. Wood, Michael Griesser & Szymon M. Drobniak
Fitness can be profoundly influenced by the age at first reproduction (AFR), but to date the AFR-fitness relationship only has been investigated intraspecifically. Here we investigated the relationship between AFR and average lifetime reproductive success (LRS) across 34 bird species. We assessed differences in the deviation of the Optimal AFR (i.e., the species-specific AFR associated with the highest LRS) from the age at sexual maturity, considering potential effects of life-history as well as social and...

Data from: A trait-based trade-off between growth and mortality: evidence from 15 tropical tree species using size-specific RGRs

Christopher D. Philipson, Daisy H. Dent, Michael J. O’Brien, Juliette Chamagne, Dzaeman Dzulkifli, Reuben Nilus, Sam Philips, Glen Reynolds, Philippe Saner, Andy Hector & Michael J. O'Brien
A life-history trade-off between low mortality in the dark and rapid growth in the light is one of the most widely accepted mechanisms underlying plant ecological strategies in tropical forests. Differences in plant functional traits are thought to underlie these distinct ecological strategies; however, very few studies have shown relationships between functional traits and demographic rates within a functional group. We present 8 years of growth and mortality data from saplings of 15 species of...

Data from: The contrasting role of male relatedness in different mechanisms of sexual selection in red junglefowl

Cedric Tan Kai Wei, Philippa Doyle, Emma Bagshaw, David S. Richardson, Stuart L. Wigby, Tom Pizzari, Cedric Kai Wei Tan, Stuart Wigby & Tommaso Pizzari
In structured populations, competition for reproductive opportunities should be relaxed among related males. The few tests of this prediction often neglect the fact that sexual selection acts through multiple mechanisms, both before and after mating. We performed experiments to study the role of within-group male relatedness across pre- and postcopulatory mechanisms of sexual selection in social groups of red junglefowl, Gallus gallus, in which two related males and one unrelated male competed over females unrelated...

Data from: A transmission-virulence evolutionary trade-off explains attenuation of HIV-1 in Uganda

François Blanquart, Mary Kate Grabowski, Joshua Herbeck, Fred Nalugoda, David Serwadda, Michael A. Eller, Merlin L. Robb, Ronald Gray, Godfrey Kigozi, Oliver Laeyendecker, Katrina A. Lythgoe, Gertrude Nakigozi, Thomas C. Quinn, Steven J. Reynolds, Maria J. Wawer & Christophe Fraser
Evolutionary theory hypothesizes that intermediate virulence maximizes pathogen fitness as a result of a trade-off between virulence and transmission, but empirical evidence remains scarce. We bridge this gap using data from a large and long-standing HIV-1 prospective cohort, in Uganda. We use an epidemiological-evolutionary model parameterised with this data to derive evolutionary predictions based on analysis and detailed individual-based simulations. We robustly predict stabilising selection towards a low level of virulence, and rapid attenuation of...

Data from: Conditional cooperation and confusion in public-goods experiments

Maxwell N. Burton-Chellew, Claire El Mouden & Stuart A. West
Economic experiments are often used to study if humans altruistically value the welfare of others. A canonical result from public-good games is that humans vary in how they value the welfare of others, dividing into fair-minded conditional cooperators, who match the cooperation of others, and selfish noncooperators. However, an alternative explanation for the data are that individuals vary in their understanding of how to maximize income, with misunderstanding leading to the appearance of cooperation. We...

Data from: Epistasis between antibiotic resistance mutations and genetic background shape the fitness effect of resistance across species of Pseudomonas

Tom Vogwill, Mila Kojadinovic & R. Craig MacLean
Antibiotic resistance often evolves by mutations at conserved sites in essential genes, resulting in parallel molecular evolution between divergent bacterial strains and species. Whether these resistance mutations are having parallel effects on fitness across bacterial taxa, however, is unclear. This is an important point to address, because the fitness effects of resistance mutations play a key role in the spread and maintenance of resistance in pathogen populations. We address this idea by measuring the fitness...

Registration Year

  • 2016
    88

Resource Types

  • Dataset
    88

Affiliations

  • University of Oxford
    88
  • University of Zurich
    6
  • Imperial College London
    5
  • University of Washington
    4
  • University of Groningen
    4
  • University of Tasmania
    4
  • University of Southampton
    4
  • Centre for Ecology & Hydrology
    3
  • University of Georgia
    3
  • Lund University
    3