163 Works

Data from: A population genomics insight into the Mediterranean origins of wine yeast domestication

Pedro Almeida, Raquel Barbosa, Polona Zalar, Yumi Imanishi, Kiminori Shimizu, Benedetta Turchetti, Jean-Luc Legras, Marta Serra, Sylvie Dequin, Arnaud Couloux, Julie Guy, Douda Bensasson, Paula Gonçalves & José Paulo Sampaio
The domestication of the wine yeast Saccharomyces cerevisiae is thought to be contemporary with the development and expansion of viticulture along the Mediterranean basin. Until now, the unavailability of wild lineages prevented the identification of the closest wild relatives of wine yeasts. Here, we enlarge the collection of natural lineages and employ whole-genome data of oak-associated wild isolates to study a balanced number of anthropic and natural S. cerevisiae strains. We identified industrial variants and...

Data from: Sexual imprinting: What strategies should we expect to see in nature?

Hayes Griffin, Robert Tucker Gilman & Dalton W. Chaffee
Sexual imprinting occurs when juveniles learn mate preferences by observing the phenotypes of other members of their populations, and it is ubiquitous in nature. Imprinting strategies, that is which individuals and phenotypes are observed and how strong preferences become, vary among species. Imprinting can affect trait evolution and the probability of speciation, and different imprinting strategies are expected to have different effects. However, little is known about how and why different imprinting strategies evolve, or...

Data from: The potential influence of morphology on the evolutionary divergence of an acoustic signal.

William R. Pitchers, Chris P. Klingenberg, Tom Tregenza, John Hunt & Ian Dworkin
The evolution of acoustic behaviour and that of the morphological traits mediating its production are often coupled. Lack of variation in the underlying morphology of signalling traits has the potential to constrain signal evolution. This relationship is particularly likely in field crickets, where males produce acoustic advertisement signals to attract females by stridulating with specialized structures on their forewings. In this study, we characterize the size and geometric shape of the forewings of males from...

Data from: The walking dead: blender as a tool for palaeontologists with a case study on extinct arachnids

Russell Garwood & Jason Dunlop
This paper serves two roles. First, it acts as an introduction to Blender, an open-source computer graphics program, which can be of utility to paleontologists. To lessen the software's otherwise steep learning curve, a step-by-step guide to create an idealized reconstruction of a fossil in the form of a three-dimensional model in Blender, or to use the software to render results from ‘virtual paleontology' techniques, is provided as an online supplemental data file. Second, here...

Data from: Combined analysis of variation in core, accessory and regulatory genome regions provides a super-resolution view into the evolution of bacterial populations

Alan McNally, Yaara Oren, Darren Kelly, Ben Pascoe, Steven Dunn, Tristan Seecharan, Minna Vehkala, Niko Välimäki, Michael B. Prentice, Amgad Ashour, Oren Avram, Tal Pupko, Ulrich Dobrindt, Ivan Literak, Sebastian Guenther, Katharina Schauffler, Lothar H. Wieler, Zong Zhiyong, Samuel K. Sheppard, James O. McInerney, Jukka Corander & Tristan Sreecharan
The use of whole-genome phylogenetic analysis has revolutionized our understanding of the evolution and spread of many important bacterial pathogens due to the high resolution view it provides. However, the majority of such analyses do not consider the potential role of accessory genes when inferring evolutionary trajectories. Moreover, the recently discovered importance of the switching of gene regulatory elements suggests that an exhaustive analysis, combining information from core and accessory genes with regulatory elements could...

Data from: Change and stability in a steep morph-frequency cline in the snail Cepaea nemoralis (L.) over 43 years.

Robert A. D. Cameron, Laurence M. Cook & Jeremy J. D. Greenwood
Populations of the polymorphic land snail Cepaea nemoralis (L.) from Deepdale, Derbyshire, UK, sampled in 1965-67, showed a pattern of area effects, with steep clines among groups of populations differing in shell colour and banding morph frequencies. In 2010 most of these populations were resampled. In particular a continuous transect made in 1967 of 42 18.34m x 18.34m quadrats across a steep cline in several morph frequencies was completely resampled. In the dale as a...

Data from: Genotype-dependent responses to levels of sibling competition over maternal resources in mice

Reinmar Hager, James M. Cheverud & Jason B. Wolf
Research on phenotypic plasticity has often focused on how a given genotype responds to changing physical environments. However, for many species the social environment plays an equally important role due to competition for resources. During early development, the level of competition for limited resources will often depend critically on the number of siblings. Therefore, competition among siblings should drive the evolution of genes that allow flexible responses to realized levels of competition and maternal resource...

Data from: Citizen science reveals unexpected continental-scale evolutionary change in a model organism

Jonathan Silvertown, Laurence Cook, Robert Cameron, Mike Dodd, Kevin McConway, Jenny Worthington, Peter Skelton, Christian Anton, Oliver Bossdorf, Bruno Baur, Menno Schilthuizen, Benoît Fontaine, Helmut Sattmann, Giorgio Bertorelle, Maria Correia, Cristina Oliveira, Beata Pokryszko, Małgorzata Ożgo, Arturs Stalažs, Eoin Gill, Üllar Rammul, Péter Sólymos, Zoltan Féher & Xavier Juan
Organisms provide some of the most sensitive indicators of climate change and evolutionary responses are becoming apparent in species with short generation times. Large datasets on genetic polymorphism that can provide an historical benchmark against which to test for recent evolutionary responses are very rare, but an exception is found in the brown-lipped banded snail (Cepaea nemoralis). This species is sensitive to its thermal environment and exhibits several polymorphisms of shell colour and banding pattern...

Data from: Drop spreading with random viscosity

Feng Xu & Oliver E. Jensen
We examine theoretically the spreading of a viscous liquid drop over a thin film of uniform thickness, assuming the liquid’s viscosity is regulated by the concentration of a solute that is carried passively by the spreading flow. The solute is assumed to be initially heterogeneous, having a spatial distribution with prescribed statistical features. To examine how this variability influences the drop’s motion, we investigate spreading in a planar geometry using lubrication theory, combining numerical simulations...

Data from: Biotic and abiotic plant-soil feedback depends on nitrogen-acquisition strategy and shifts during long-term ecosystem development

Guochen Kenny Png, Hans Lambers, Paul Kardol, Benjamin L. Turner, David A. Wardle & Etienne Laliberté
1. Feedback between plants and soil is an important driver of plant community structure, but it remains unclear whether plant-soil feedback (PSF): (i) reflects changes in biotic or abiotic properties, (ii) depends on environmental context in terms of soil nutrient availability, and (iii) varies among plant functional groups. Because soil nutrient availability strongly affects plant distribution and performance, soil chemical properties and plant nutrient-acquisition strategies might serve as important drivers of PSF. 2. We used...

Data from: Genetic variation for antibiotic persistence in Escherichia coli

Balint Stewart & Daniel E Rozen
Bacterial persistence describes a heterogenous response to antibiotics in clonal populations of bacteria due to phenotypic variation within the population, with a small proportion of cells surviving treatment even at very high concentrations of drug. The aim of this study was to determine whether different natural isolates of E. coli, selected at random from a collection representing the spectrum of genetic diversity in the species, generate different fractions of persister cells. Despite comparable minimum inhibitory...

Data from: Noninvasive physiological markers demonstrate link between habitat quality, adult sex ratio and poor population growth rate in a vulnerable species, the Cape mountain zebra

Jessica M. D. Lea, Susan L. Walker, Graham I. H. Kerley, John Jackson, Shelby C. Matevich & Susanne Shultz
Effective conservation and species management requires an understanding of the causes of poor population growth. Conservation physiology uses biomarkers to identify factors that contribute to low individual fitness and population declines. Building on this, macrophysiology can use the same markers to assess how individual physiology varies with different ecological or demographic factors over large temporal and spatial scales. Here, we use a macrophysiological approach to identify the ecological and demographic correlates of poor population growth...

Data from: Evolution of mir-92a underlies natural morphological variation in Drosophila melanogaster

Saad Arif, Sophie Murat, Isabel Almudi, Maria D. S. Nunes, Diane Bortolamiol-Becet, Naomi S. McGregor, James M. S. Currie, Harri Hughes, Matthew Ronshaugen, Élio Sucena, Eric C. Lai, Christian Schlötterer & Alistair P. McGregor
eworoRL514BC_QTLPhenotype and genotype data for QTL mapping between strains e, wo, ro and RAL514.eworoRL514BC.xlsstsse_ORER_QTL_mapMap information for QTL mapping between strains st, ss, e and oregon R.ssste_ORER_QTL_crossCross information for QTL mapping between strains st, ss, e and oregon R.

Data from: The contrasting roles of host species diversity and parasite population genetic diversity in the infection dynamics of a keystone parasitic plant

Jennifer K. Rowntree & Hayley Craig
1) Diversity among species and genetic diversity within species are both important components of ecological communities that can determine the outcome of species interactions, especially between hosts and parasites. We sought to understand the impact of species diversity on host community resistance to infection by a keystone parasitic plant (Rhinanthus minor L.) and genetic diversity of the parasite on its successful establishment in a grassland community. 2) We used an experimental approach where large pots...

Data from: Biodiversity in agricultural landscapes: the effect of apple cultivar on epiphyte diversity

C. Robin Stevenson, Chantel Davies & Jennifer K. Rowntree
In natural systems, extended phenotypes of trees can be important in determining the species composition and diversity of associated communities. Orchards are productive systems where trees dominate, and can be highly biodiverse, but few studies have considered the importance of tree genetic background in promoting associated biodiversity. We tested the effect of apple cultivar (plant genetic background) on the diversity and composition of the associated epiphytic bryophyte community across a total of seven cultivars in...

Data from: Grassland invasibility varies with drought effects on soil functioning

Maarten Schrama & Richard D. Bardgett
Although it is known that ecosystems are more susceptible to invasion when disturbed, our knowledge of the mechanisms involved remains limited. Recent studies indicate that disturbance-induced changes in soil nutrient availability could influence community invasibility, but the importance of this mechanism in the real world is not known. We tested the hypotheses that (i) exotic plant species profit from drought effects on soil functioning more than do natives; and (ii) grassland invasibility depends on soil...

Data from: Decoupled diversity dynamics in green and brown webs during primary succession in a salt marsh

Maarten Schrama, Fons Van Der Plas, Matty P. Berg & Han Olff
Terrestrial ecosystems are characterized by a strong functional connection between the green (plant–herbivore-based) and brown (detritus–detritivore-based) parts of the food web, which both develop over successional time. However, the interlinked changes in green and brown food web diversity patterns in relation to key ecosystem processes are rarely studied. Here, we demonstrate changes in species richness, diversity and evenness over a wide range of invertebrate green and brown trophic groups during 100 years of primary succession...

Data from: Copy-when-uncertain: bumblebees rely on social information when rewards are highly variable

Marco Smolla, Sylvain Alem, Lars Chittka & Susanne Shultz
To understand the relative benefits of social and personal information use in foraging decisions, we developed an agent-based model of social learning that predicts social information should be more adaptive where resources are highly variable and personal information where resources vary little. We tested our predictions with bumblebees and found that foragers relied more on social information when resources were variable than when they were not. We then investigated whether socially salient cues are used...

Data from: Testes size increases with sperm competition risk and intensity in bony fish and sharks

Amy G. Rowley, Toby S. Daly-Engel & John L. Fitzpatrick
Female multiple mating provides the opportunity for sexual selection to continue after gamete release, generating strong selection on male reproductive traits. In particular, in species where female multiple mating is common, males are expected to invest more in testicular tissue to afford them a numerical advantage during sperm competition. However, although testes size (correcting for body size) is a commonly used proxy of the strength of sperm competition, there is surprisingly scant direct evidence linking...

Data from: The peripheral olfactory code in Drosophila larvae contains temporal information and is robust over multiple timescales

Micheline Grillet, Dario Campagner, Rasmus Petersen, Catherine McCrohan & Matthew Cobb
We studied the electrophysiological activity of two classes of Drosophila melanogaster larval olfactory sensory neurons (OSNs), Or24a and Or74a, in response to 1 s stimulation with butanol, octanol, 2-heptanone, and propyl acetate. Each odour/OSN combination produced unique responses in terms of spike count and temporal profile. We used a classifier algorithm to explore the information content of OSN activity, and showed that as well as spike count, the activity of these OSNs included temporal information...

Data from: Self-cannulation for haemodialysis: patient attributes, clinical correlates and self-cannulation predilection models

Anuradha Jayanti, Philip Foden, Alison Wearden, Julie Morris, Paul Brenchley & Sandip Mitra
Background and objectives: With emerging evidence in support of home haemodialysis (HHD), patient factors which determine uptake of the modality need to be better understood. Self-cannulation (SC) is a major step towards enabling self-care ‘in-centre’ and home HD and remains the foremost barrier to its uptake. Human factors governing this aspect of HD practice are poorly understood. The aim of this study is to better understand self-cannulation preferences and factors which define them in end...

Data from: Plasticity in plant functional traits is shaped by variability in neighbourhood species composition

Maria Abakumova, Kristjan Zobel, Anu Lepik & Marina Semchenko
Plant functional traits can vary widely as a result of phenotypic plasticity to abiotic conditions. Trait variation may also reflect responses to the identity of neighbours, although not all species are equally responsive to their biotic surroundings. We hypothesized that responses to neighbours are shaped by spatial community patterns and resulting variability in neighbour composition. More precisely, we tested the theoretical prediction that plasticity is most likely to evolve if alternative environments (in this case,...

Data from: Pigmented anatomy in Carboniferous cyclostomes and the evolution of the vertebrate eye

Sarah E. Gabbott, Philip C.J. Donoghue, Robert S. Sansom, Jakob Vinther, Andrei Dolocan, Mark A. Purnell & Philip C. J. Donoghue
The success of vertebrates is linked to the evolution of a camera-style eye and sophisticated visual system. In the absence of useful data from fossils, scenarios for evolutionary assembly of the vertebrate eye have been based necessarily on evidence from development, molecular genetics and comparative anatomy in living vertebrates. Unfortunately, steps in the transition from a light-sensitive ‘eye spot’ in invertebrate chordates to an image-forming camera-style eye in jawed vertebrates are constrained only by hagfish...

Ecosystem function and vegetation data from Parsonage Down, UK, in 2013

E.L. Fry, A.L. Hall, J. Savage, R.D. Bardgett, N. Ostle, R.F. Pywell & J.M. Bullock
This dataset contains vegetation survey data and nitrate and ammonium concentrations, microbial biomass data, particle size, and nitrification and mineralisation rates within soils from an experiment based at Parsonage Down, UK. The vegetation survey comprises total species percentage cover and species richness data from four 50 cm by 50 cm quadrats. The experiment investigated the effect of different plant groups on soil carbon stores and nutrient cycling, by using a mixture of hand weeding and...

Data from: A new Devonian euthycarcinoid evidences the use of different respiratory strategies during the marine-to-terrestrial transition in the myriapod lineage

Pierre Gueriau, James C. Lamsdell, Roy A. Wogelius, Phillip L. Manning, Victoria M. Egerton, Uwe Bergmann, Loïc Bertrand & Julien Denayer
Myriapods were, together with arachnids, the earliest animals to occupy terrestrial ecosystems, by at least the Silurian. The origin of myriapods and their land colonization have long remained puzzling until euthycarcinoids, an extinct group of aquatic arthropods considered amphibious, were shown to be stem group myriapods, extending the lineage to the Cambrian and evidencing a marine-to-terrestrial transition. Although possible respiratory structures comparable to the air-breathing tracheal system of myriapods are visible in several euthycarcinoids, little...

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