798 Works

Data from: NEMBASE4: the nematode transcriptome resource

Mark L. Blaxter, James Wasmuth, Benjamin Elsworth & Mark Blaxter
Nematode parasites are of major importance in human health and agriculture, and free-living species deliver essential ecosystem services. The genomics revolution has resulted in the production of many datasets of expressed sequence tags (ESTs) from a phylogenetically wide range of nematode species, but these are not easily compared. NEMBASE4 presents a single portal onto extensively functionally annotated, EST-derived transcriptomes from over sixty species of nematodes, including plant and animal parasites and free-living taxa. Using the...

Data from: Quantitative genetics of immunity and life history under different photoperiods

Katrin Hammerschmidt, Peter Deines, Alastair J. Wilson & Jens Rolff
Insects with complex life-cycles should optimize age and size at maturity during larval development. When inhabiting seasonal environments, organisms have limited reproductive periods and face fundamental decisions: individuals that reach maturity late in season have to either reproduce at a small size or increase their growth rates. Increasing growth rates is costly in insects due to higher juvenile mortality, decreased adult survival, or increased susceptibility to parasitism by bacteria and viruses via compromised immune function....

Data from: Out of the Andes: patterns of diversification in clearwing butterflies

Marianne Elias, Mathieu Joron, Keith Willmott, Vera Kaiser, Karina Silva-Brandão, Carlos Arias, Luz Miryam Gomez Piñeres, Sandra Uribe, Andrew Brower, André Freitas & Chris Jiggins
Global biodiversity peaks in the tropical forests of the Andes, a striking geological feature that has likely been instrumental in generating biodiversity by providing opportunities for both vicariant and ecological speciation. However, the role of these mountains in the diversification of insects, which dominate biodiversity, has been poorly explored using phylogenetic methods. Here we study the role of the Andes in the evolution of a diverse Neotropical insect group, the clearwing butterflies. We used dated...

Data from: Does nasal echolocation influence the modularity of the mammal skull?

Sharlene E. Santana & Sarah E. Lofgren
In vertebrates, changes in cranial modularity can evolve rapidly in response to selection. However, mammals have apparently maintained their pattern of cranial integration throughout their evolutionary history and across tremendous morphological and ecological diversity. Here, we use phylogenetic, geometric morphometric and comparative analyses to test the hypothesis that the modularity of the mammalian skull has been remodelled in rhinolophid bats due to the novel and critical function of the nasal cavity in echolocation. We predicted...

Data from: Costs of crowding for the transmission potential in malaria parasites

Laura C. Pollitt, Thomas S. Churcher, Emma J. Dawes, Shahid M. Khan, Mohammed Sajid, Maria-Gloria Basáñez, Nick Colegrave & Sarah E. Reece
The utility of using evolutionary and ecological frameworks to understand the dynamics of infectious diseases is gaining increasing recognition. However, integrating evolutionary ecology and infectious disease epidemiology is challenging because within-host dynamics can have counterintuitive consequences for between-host transmission, especially for vector-borne parasites. A major obstacle to linking within- and between-host processes is that the drivers of the relationships between the density, virulence, and fitness of parasites are poorly understood. By experimentally manipulating the intensity...

Data from: Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer

Katie V. Stopher, Craig A. Walling, Alison Morris, Fiona E. Guinness, Tim H. Clutton-Brock, Josephine M. Pemberton & Daniel H. Nussey
Social structure, limited dispersal and spatial heterogeneity in resources are ubiquitous in wild vertebrate populations. As a result, relatives share environments as well as genes, and environmental and genetic sources of similarity between individuals are potentially confounded. Quantitative genetic studies in the wild therefore typically account for easily captured shared environmental effects (e.g. parent, nest or region). Fine-scale spatial effects are likely to be just as important in wild vertebrates, but have been largely ignored....

Data from: Mechanisms and fitness effects of antibacterial defenses in a carrion beetle

Andres N. Arce, Paul R. Johnston, Per T. Smiseth & Daniel E. Rozen
Parents of many species care for their offspring by protecting them from a wide range of environmental hazards, including desiccation, food shortages, predators, competitors, and parasites and pathogens. Currently, little is known about the mechanisms and fitness consequences of parental defenses against bacterial pathogens and competitors. Here we combine approaches from microbiology and behavioural ecology to investigate the role and mechanistic basis of antibacterial secretions applied to carcasses by parents of the burying beetle Nicrophorus...

Data from: Signatures of diversifying selection in European pig breeds

Samantha Wilkinson, Zen H. Lu, Hendrik-Jan Megens, Alan L. Archibald, Chris Haley, Ian J. Jackson, Martien A. M. Groenen, Richard P. M. A. Crooijmans, Rob Ogden & Pamela Wiener
Porcine_60K_Data_Wilkinsonetal2013.tarMapping and variant calling data on SSC5:98000000-99000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_98000000-99000000.tarMapping and variant calling data on SSC5:3100000-34000000This file shares the same REAME as SSC11_53500000-55500000.tarSSC5_3100000-34000000.tarMapping and variant calling data on SSC11:53500000-55500000SSC11_53500000-55500000.tar

Data from: Existing infection facilitates establishment and density of malaria parasites in their mosquito vector

Laura C. Pollitt, Joshua T. Bram, Simon Blanford, Matthew J. Jones & Andrew F. Read
Very little is known about how vector-borne pathogens interact within their vector and how this impacts transmission. Here we show that mosquitoes can accumulate mixed strain malaria infections after feeding on multiple hosts. We found that parasites have a greater chance of establishing and reach higher densities if another strain is already present in a mosquito. Mixed infections contained more parasites but these larger populations did not have a detectable impact on vector survival. Together...

Data from: Contrasting responses of male and female foraging effort to year-round wind conditions

Sue Lewis, Richard A. Phillips, Sarah J. Burthe, Sarah Wanless & Francis Daunt
1. There is growing interest in the effects of wind on wild animals, given evidence that wind speeds are increasing and becoming more variable in some regions, particularly at temperate latitudes. Wind may alter movement patterns or foraging ability, with consequences for energy budgets and, ultimately, demographic rates. 2. These effects are expected to vary among individuals due to intrinsic factors such as sex, age or feeding proficiency. Furthermore, this variation is predicted to become...

Data from: Multivariate immune defences and fitness in the wild: complex but ecologically important associations among plasma antibodies, health and survival

Daniel H. Nussey, Kathryn A. Watt, Abigail Clark, Jill G. Pilkington, Josephine M. Pemberton, Andrea L. Graham & Tom N. McNeilly
Despite our rapidly advancing mechanistic understanding of vertebrate immunity under controlled laboratory conditions, the links between immunity, infection and fitness under natural conditions remain poorly understood. Antibodies are central to acquired immune responses, and antibody levels circulating in vivo reflect a composite of constitutive and induced functional variants of diverse specificities (e.g. binding antigens from prevalent parasites, self tissues or novel non-self sources). Here, we measured plasma concentrations of 11 different antibody types in adult...

Data from: Fine with heat, problems with water: microclimate alters water loss in a thermally adapted insular lizard

Anat Belasen, Kinsey Brock, Binbin Li, Dimitra Chremou, Efstratios Valakos, Panayiotis Pafilis, Barry Sinervo & Johannes Foufopoulos
Global change, including habitat isolation and climate change, has both short- and long-term impacts on wildlife populations. For example, genetic drift and inbreeding result in genetic impoverishment in small, isolated populations, while species undergo range shifts or adaptive phenotypic change in response to shifts in environmental temperatures. In this study, we utilize a model system in which Holocene landscape changes have occurred to examine long-term effects of population isolation. To examine how isolation may constrain...

Data from: Age, oxidative stress exposure and fitness in a long-lived seabird

Katherine A. Herborn, Francis Daunt, Britt J. Heidinger, Hanna M. V. Granroth-Wilding, Sarah J. Burthe, Mark A. Newell & Pat Monaghan
The need to manage exposure to oxidative stress, which can damage macromolecules, is thought to influence the resolution of life history trade-offs. Oxidative damage is expected to increase with age as a consequence of changes in the optimal investment in defences or repair, and/or because of senescence in antioxidant defence systems, though the pattern might differ between short and long-lived species. However, data on age related changes in damage levels in wild populations are rare....

Data from: The global antigenic diversity of swine influenza A viruses

Nicola S. Lewis, Colin A. Russell, Tavis K. Anderson, Kathryn Berger, David F. Burke, Judith M. Fonville, Ronald A.M. Fouchier, Paul Kellam, Bjorn F. Koel, Tung Nguyen, Bundit Nuansrichy, J. S. Malik Peiris, Takehiko Saito, Gaelle Simon, Eugene Skepner, Nobuhiro Takemae, ESNIP3 Consortium, Richard J. Webby, Kristien Van Reeth, Sharon M. Brookes, Lars Larsen, Ian H. Brown, Amy L. Vincent, Pinky Langat, Filip Bielejec … & JS Malik Peiris
Swine influenza presents a substantial disease burden for pig populations worldwide and poses a potential pandemic threat to humans. There is considerable diversity in both H1 and H3 influenza viruses circulating in swine due to the frequent introductions of viruses from humans and birds coupled with geographic segregation of global swine populations. Much of this diversity is characterized genetically but the antigenic diversity of these viruses is poorly understood. Critically, the antigenic diversity shapes the...

Data from: Genetic loci inherited from hens lacking maternal behaviour both inhibit and paradoxically promote this behaviour

Ian C. Dunn
Background: A major step towards the success of chickens as a domesticated species was the separation between maternal care and reproduction. Artificial incubation replaced the natural maternal behaviour of incubation and, thus, in certain breeds, it became possible to breed chickens with persistent egg production and no incubation behaviour; a typical example is the White Leghorn strain. Conversely, some strains, such as the Silkie breed, are prized for their maternal behaviour and their willingness to...

Data from: Use of novel psychoactive substances by inpatients on general adult psychiatric wards

Jack L. Stanley, Daniel V. Mogford, Rebecca J. Lawrence & Stephen M. Lawrie
Objectives: Non-illicit alternatives to controlled drugs, known as Novel Psychoactive Substances (NPS) have recently risen to prominence. They are readily available with uncertain pharmacology and no widely available assay. Given that psychiatric patients are at risk of comorbid substance abuse, we hypothesized that NPS use would be present in the psychiatric population, and sought to determine its prevalence and investigate the characteristics of those who use these drugs with a retrospective review of discharge letters....

Data from: Maternal effects alter the severity of inbreeding depression in the offspring

Natalie Pilakouta & Per T. Smiseth
A maternal effect is a causal influence of the maternal phenotype on the offspring phenotype over and above any direct effects of genes. There is abundant evidence that maternal effects can have a major impact on offspring fitness. Yet, no previous study has investigated the potential role of maternal effects in influencing the severity of inbreeding depression in the offspring. Inbreeding depression is a reduction in the fitness of inbred offspring relative to outbred offspring....

Data from: Testing models of speciation from genome sequences: divergence and asymmetric admixture in Island Southeast Asian Sus species during the Plio-Pleistocene climatic fluctuations

Laurent A. F. Frantz, Ole Madsen, Hendrik-Jan Megens, Martien A. M. Groenen & Konrad Lohse
In many temperate regions, ice ages promoted range contractions into refugia resulting in divergence (and potentially speciation), while warmer periods led to range expansions and hybridization. However, the impact these climatic oscillations had in many parts of the tropics remains elusive. Here, we investigate this issue using genome sequences of three pig (Sus) species, two of which are found on islands of the Sunda-shelf shallow seas in Island Southeast Asia (ISEA). A previous study revealed...

Data from: Image analysis of weaverbird nests reveals signature weave textures

Ida E. Bailey, André Backes, Patrick T. Walsh, Kate V. Morgan, Simone L. Meddle & Susan D. Healy
In nature, many animals build structures that can be readily measured at the scale of their gross morphology (e.g. length, volume and weight). Capturing individuality as can be done with the structures designed and built by human architects or artists, however, is more challenging. Here, we tested whether computer-aided image texture classification approaches can be used to describe textural variation in the nests of weaverbirds (Ploceus species) in order to attribute nests to the individual...

Data from: Phylogenetic eigenvectors and non-stationarity in the evolution of theropod dinosaur skulls

Jose A. F. Diniz-Filho, Davi M. C. C. Alves, Fabricio Villalobos, Manabu Sakamoto, Steve L. Brusatte & Luis M. Bini
Despite the longstanding interest in non-stationarity of both phenotypic evolution and diversification rates, only recently have methods been developed to study this property. Here, we propose a methodological expansion of the Phylogenetic Signal Representation (PSR) curve based on phylogenetic eigenvectors to test for non-stationarity. The PSR is built by plotting the coefficients of determination R2 from Phylogenetic Eigenvector Regression (PVR) models increasing the number of phylogenetic eigenvectors against the accumulated eigenvalues. The PSR curve is...

Data from: The cranial endocast of the Middle Devonian dipnonan Dipterus valenciennesi and a fossilized dipnoan otoconial mass

Tom J. Challands & Thomas J. Challands
The well known Middle Devonian (Eifelian–Givetian) lungfish Dipterus valenciennesi from Scotland, UK, has been studied for more than one hundred years though our understanding of the neurocranium and cranial cavity is incomplete. Micro-CT scanning demonstrates that the internal cast of the cranial cavity, the endocast, possesses a mix of primitive and derived characters. The olfactory bulbs are sessile, as in the derived extant Lepidosirenidae. However, Dipterus valenciennesi possesses the primitive condition of a shallow telencephalon...

Data from: Repeatability of adaptation in experimental populations of different sizes

Josianne Lachapelle, Joshua Reid & Nick Colegrave
The degree to which evolutionary trajectories and outcomes are repeatable across independent populations depends on the relative contribution of selection, chance and history. Population size has been shown theoretically and empirically to affect the amount of variation that arises among independent populations adapting to the same environment. Here, we measure the contribution of selection, chance and history in different-sized experimental populations of the unicellular alga Chlamydomonas reinhardtii adapting to a high salt environment to determine...

Data from: Genome-wide tests for introgression between cactophilic Drosophila implicate a role of inversions during speciation

Konrad Lohse, Magnus Clarke, Michael G. Ritchie & William J. Etges
Models of speciation-with-gene-flow have shown that the reduction in recombination between alternative chromosome arrangements can facilitate the fixation of locally adaptive genes in the face of gene flow and contribute to speciation. However, it has proven frustratingly difficult to show empirically that inversions have reduced gene flow and arose during or shortly after the onset of species divergence rather than represent ancestral polymorphisms. Here we present an analysis of whole genome data from a pair...

Data from: Variation in early life testosterone in a wild population of red deer

Alyson T. Pavitt, Craig A. Walling, Alan S. McNeilly, Josephine M. Pemberton & Loeske E. B. Kruuk
1. Individual differences in circulating hormone concentrations can affect life history traits throughout an animal’s life. Despite this, relatively little is known about the potential drivers or consequences of individual variation in hormone levels, particularly in early life. In animals showing maternal care, early development is often dependent on maternal characteristics and condition. It is therefore possible that individual hormone profiles early in life are dependent on condition-linked characteristics of the mother. 2. Using data...

Data from: Early life expenditure in sexual competition is associated with increased reproductive senescence in male red deer

Jean-François Lemaître, Jean-Michel Gaillard, Josephine M. Pemberton, Tim H. Clutton-Brock, Daniel H. Nussey, J.-F. Lemaitre & J.-M. Gaillard
The evolutionary theories of senescence predict that investment in reproduction in early life should come at the cost of reduced somatic maintenance, and thus earlier or more rapid senescence. There is now growing support for such trade-offs in wild vertebrates, but these exclusively come from females. Here, we test this prediction in male red deer (Cervus elaphus) using detailed longitudinal data collected over a 40-year field study. We show that males which had larger harems...

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