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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Xiao, Chengfeng; Fard, Niki Bayat; Brzezinski, Kaylen; Robertson, R. Meldrum; +1 Authors

    Many insects enter coma upon exposure to anoxia, a feature routinely exploited by experimentalists to handle them. But the genetic and physiological bases of anoxic coma induction and recovery are only partially understood, as are the long-term consequences for the animal's performance. We examined three populations of Drosophila melanogaster (designated B) that have been inadvertently under selection for rapid recovery from CO2 exposure for nearly 40 years (around 1,000 generations) resulting from routine maintenance practices. We contrasted CO2 and N2 (presumed a less reactive gas) knockdown and recovery times of these B flies with six populations of common ancestry (A and C populations) that were not exposed to CO2 over the same period. We found that B populations showed faster and more consistent locomotor recovery than A or C populations after CO2 knockdown, a result also observed with N2 knockdown. A and C populations showed much higher variance in recovery time after CO2 exposure than after N2 exposure, suggesting gas-specific effects on pathways associated with locomotor recovery. While these selection treatments result in considerable variation in life history attributes and body size, with the characteristic intermediacy of B populations, their superiority in resistance to gas exposure and locomotor recovery suggests that it is a direct consequence of prior repeated exposure to anoxia, broadly, and CO2, specifically. Hence we describe a powerful new evolutionary model for the genetic and physiological investigation of anoxic coma in insects. JEXBIO199521_Data_IData associated with the publication: https://doi.org/10.1242/jeb.199521JEXBIO199521_Data.xlsx

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODO; DRYADarrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    ZENODO; DRYAD
    Dataset . 2019
    License: CC 0
    Data sources: ZENODO; Datacite
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ ZENODO; DRYADarrow_drop_down
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      ZENODO; DRYAD
      Dataset . 2019
      License: CC 0
      Data sources: ZENODO; Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Matabos, Marjolaine; Tunnicliffe, Verena; Juniper, S. Kim; Dean, Courtney;

    Changes in ocean ventilation driven by climate change result in loss of oxygen in the open ocean that, in turn, affects coastal areas in upwelling zones such as the northeast Pacific. Saanich Inlet, on the west coast of Canada, is a natural seasonally hypoxic fjord where certain continental shelf species occur in extreme hypoxia. One study site on the VENUS cabled subsea network is located in the hypoxic zone at 104 m depth. Photographs of the same 5 m2 area were taken with a remotely-controlled still camera every 2/3 days between October 6th 2009 and October 18th 2010 and examined for community composition, species behaviour and microbial mat features. Instruments located on a near-by platform provided high-resolution measurements of environmental variables. We applied multivariate ordination methods and a principal coordinate analysis of neighbour matrices to determine temporal structures in our dataset. Responses to seasonal hypoxia (0.1–1.27 ml/l) and its high variability on short time-scale (hours) varied among species, and their life stages. During extreme hypoxia, microbial mats developed then disappeared as a hippolytid shrimp, Spirontocaris sica, appeared in high densities (200 m22) despite oxygen below 0.2 ml/l. The slender sole Lyopsetta exilis was abundant in severe hypoxia and diminished as oxygen increased in the summer. This planktivore may be responding to changes in the depth of the diurnal migration of zooplankton. While the squat lobster Munida quadrispina was common at all times, juveniles disappeared in fluctuating conditions. Despite low oxygen conditions, animal densities were high indicating that the risk from hypoxia is balanced by factors such as food availability and escape from less tolerant predators. As hypoxia increases on the continental shelf, we expect benthic communities to become dominated by low diversity, hypoxia-tolerant species of low commercial significance. CHONe_MB08_Matabos_data_year

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DRYAD; Federated Res...arrow_drop_down
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DRYAD; Federated Res...arrow_drop_down
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      DANS-EASY
      Dataset . 2014
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Ivy, Catherine M.; Robertson, Cayleih E.; Bernier, Nicholas J.;

    Eutrophication and climate change are increasing the incidence of severe hypoxia in fish nursery habitats, yet the programming effects of hypoxia on stress responsiveness in later life are poorly understood. In this study, to investigate whether early hypoxia alters the developmental trajectory of the stress response, zebrafish embryos were exposed to 4 h of anoxia at 36 h post-fertilization and reared to adults when the responses to secondary stressors were assessed. While embryonic anoxia did not affect basal cortisol levels or the cortisol response to hypoxia in later life, it had a marked effect on the responses to a social stressor. In dyadic social interactions, adults derived from embryonic anoxia initiated more chases, bit more often, entered fewer freezes and had lower cortisol levels. Adults derived from embryonic anoxia also performed more bites towards their mirror image, had lower gonadal aromatase gene expression and had higher testosterone levels. We conclude that acute embryonic anoxia has long-lasting consequences for the hormonal and behavioural responses to social interactions in zebrafish. Specifically, we demonstrate that acute embryonic anoxia favours the development of a dominant and aggressive phenotype, and that a disruption in sex steroid production may contribute to the programming effects of environmental hypoxia. Ivy et al. 2017 Complete Dataset for DryadComplete dataset for the following publication: Ivy, C.M., Robertson, C.E. and Bernier N.J. 2017. Acute embryonic anoxia exposure favours the development of a dominant and aggressive phenotype in adult zebrafish. Proc. R. Soc. B 20161868.

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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Toews, Shelby; Wellband, Kyle; Dixon, Brian; Heath, Daniel D.;

    Phenotypic differences among populations within a species have been reported for a variety of traits, ranging from life history to physiology to gene transcription. Population-level phenotypic variation has been attributed to genetic differences resulting from genetic drift and/or local adaptation as well as environmental differences resulting from plasticity. We studied population- and family-level variation in gene transcription for 22 fitness-related genes, comprising immune, growth, metabolic, and stress processes in Chinook salmon (Oncorhynchus tshawytscha). We created hybrid Chinook salmon families from eight populations and treated them with an immune stimulus, a handling stress challenge, and held some as a no-treatment control group. Population effects, sire effects, and narrow-sense heritability (h2) were calculated for each candidate gene within each treatment group. We expected population to have a significant effect on gene transcription for many of our genes; however, we found a population effect for transcription at only one immune gene at rest. The limited number of significant population effects on gene transcription, combined with significant additive genetic variance within each population does not support the expectation of past strong selection pressures acting on heritable transcription profiles among populations. Instead, our results indicate that Chinook salmon likely adapt to their local environment through transcriptional plasticity rather than fixed differences. The expectation for fixed population-level differences in gene transcription at fitness-related genes, reflecting accepted models of local adaptation is high; however, comparisons among multiple populations using half-sib breeding designs are rare. Our work fills an important gap in our growing understanding of the process of among and within-population divergence. READMEThis document defines all abbreviations within the other data files.Raw_qPCR_DataRaw qPCR data from a QuantStudio 12K Flex for all samples and candidate genes.Toews_2018_Raw_qPCR_Data_Chinook_Transcription.txtPCR_EfficienciesThis file contains the PCR efficiencies of all candidate genes used in the study. The efficiencies were calculated using LinRegPCR.Toews_2018_PCR_Efficiencies_Chinook_Transcription.txtProcessed_qPCR_DataThis file contains the information needed to normalize the Cq values from the raw data, as well as the final DCt values that were used in the manuscript.Toews_2018_Processed_qPCR_Data_Chinook_Transcription.txtSample_AnnotationThis file contains information for each sample in the study, including the individual sample's rearing tank, sire, population, weight, treatment group, etc.Toews_2018_Sample_Annotation_Chinook_Transcription.txtR_Source_CodeThis text file contains the R source code used for the analyses in the paper.Toews_2018_R_Source_Code_Chinook_Transcription.txt

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Federated Research D...arrow_drop_down
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    DANS-EASY
    Dataset . 2019
    Data sources: B2FIND
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      DANS-EASY
      Dataset . 2019
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Gasbarro, Ryan; Chu, Jackson W.F.; Tunnicliffe, Verena;

    As global ocean deoxygenation proceeds and the frequency of extreme low-oxygen (hypoxic) events increases, seafloor ecosystems will inevitably be affected. Our study examines how benthic community responses scale with the severity and spatial extent of hypoxia. Saanich Inlet is a natural model system for testing the effects of hypoxic conditions that determine the benthic megafaunal community structure during annual deoxygenation and reoxygenation. In 2016, an anomalously severe and widespread hypoxic event occurred in the fjord after a decade of oxygen decline at a rate of 0.07 mL L−1 y−1 as measured by a cabled seafloor observatory. We use a living ecological time-series generated from remotely operated vehicle surveys to assess how the benthic megafaunal community disassembled in response to this extreme hypoxic event. Three benthic surveys at similar times in 2013 and 2016 reveal large increases in the area of seafloor bathed in anoxic and hypoxic waters in the latter year. Both bottom oxygen and species depth distributions shoaled from 2013 to 2016, accompanied by a 56% overall decline in megafauna. The abundant habitat-forming pennatulacean octocoral, Halipteris willemoesi, decreased in abundance by 92.3% from fall 2013 to fall 2016, and pandalid shrimp disappeared from the community. Hypoxia-tolerant species experienced milder losses, and two new species occurred in 2016 – one a predator on the coral. Co-occurrence analyses revealed loss of significant community segregation from 2013 to 2016, and a re-mix of pairwise species co-occurrences in the latter year. The loss of oxygenated habitat compressed species into narrower depth ranges and led to disassembly probably through niche space constriction, while decimation of some populations eliminated key community associations. Community fragmentation and disruption of interactions is a possible outcome for many marine benthic ecosystems as marine hypoxia intensifies. Gasbarro_etal(2019_JMS)_DataData are animal counts and environment data collected during three remotely operated vehicle imagery surveys in Saanich Inlet, Vancouver Island, British Columbia, Canada in 2016. Each row entry equals a second of annotated ROV video with associated metadata (e.g. video file properties), water column data (e.g. depth, temperature, oxygen), or species data (presence/absence or counts). Extended details can be found with the associated README file.

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    DRYAD; ZENODO
    Dataset . 2019
    License: CC 0
    Data sources: ZENODO; Datacite
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      DRYAD; ZENODO
      Dataset . 2019
      License: CC 0
      Data sources: ZENODO; Datacite
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    Authors: Leger, Michelle M.; Kolisko, Martin; Kamikawa, Ryoma; Stairs, Courtney W.; +13 Authors

    Many anaerobic microbial parasites possess highly modified mitochondria known as mitochondrion-related organelles (MROs). The best-studied of these are the hydrogenosomes of Trichomonas vaginalis and Spironucleus salmonicida, which produce ATP anaerobically through substrate-level phosphorylation with concomitant hydrogen production; and the mitosomes of Giardia intestinalis, which are functionally reduced and lack any role in ATP production. However, to understand the metabolic specializations that these MROs underwent in adaptation to parasitism, data from their free-living relatives are needed. Here, we present a large-scale comparative transcriptomic study of MROs across a major eukaryotic group, Metamonada, examining lineage-specific gain and loss of metabolic functions in the MROs of Trichomonas, Giardia, Spironucleus and their free-living relatives. Our analyses uncover a complex history of ATP production machinery in diplomonads such as Giardia, and their closest relative, Dysnectes; and a correlation between the glycine cleavage machinery and lifestyles. Our data further suggest the existence of a previously undescribed biochemical class of MRO that generates hydrogen but is incapable of ATP synthesis. Protein alignmentsAlignments of organellar proteinsmito_alignments.zipPhylogenomic datasetSingle gene alignments used for phylogenomic analysisPhylogenomic.zipData SourcesFasta files with assembled transcriptomes of Carpediemonas-like organismsAssemblies.zip

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    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
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      DANS-EASY
      Dataset . 2017
      Data sources: B2FIND
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    Authors: Rahman, Ashrafur; Munther, Daniel; Fazil, Aamir; Smith, Ben; +1 Authors

    The utility of characterizing the effects of strain variation and individual/subgroup susceptibility on dose-response outcomes has motivated the search for new approaches beyond the popular use of the exponential dose-response model for listeriosis. While descriptive models can account for such variation, they have limited power to extrapolate beyond the details of particular outbreaks. In contrast, this study exhibits dose-response relationships from a mechanistic basis, quantifying key biological factors involved in pathogen-host dynamics. An efficient computational algorithm and geometric interpretation of the infection pathway are developed to connect dose-response outcomes with the underlying bistable dynamics of the model. Relying on in-vitro experiments as well as outbreak data, we estimate plausible parameters for the human context. Despite the presence of uncertainty in such parameters, sensitivity analysis reveals that the host response is most influenced by the pathogen-immune system interaction. In particular, we show how variation in this interaction across a subgroup of the population dictates the shape of dose-response curves. Finally, in terms of future experimentation, our model results provide guidelines and highlight vital aspects of the interplay between immune cells and particular strains of L. monocytogenes that should be examined. dose_response_normal_distData for figure 8CSV file contains 12 data set together with mean, standard deviation and 95% confidence interval.Dataforfigure8.csvmatlab program/code to generate the figure 8The program uses data from the CSV file 'Dataforfigure8'shaded_region.m

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    Dataset . 2018
    Data sources: B2FIND
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      Dataset . 2018
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Magpantay, Felicia Maria G.; King, Aaron A.; Rohani, Pejman;

    Mathematical models of childhood diseases date back to the early twentieth century. In several cases, models that make the simplifying assumption of homogeneous time-dependent transmission rates give good agreement with data in the absence of secular trends in population demography or transmission. The prime example is afforded by the dynamics of measles in industrialized countries in the pre-vaccine era. Accurate description of the transient dynamics following the introduction of routine vaccination has proved more challenging, however. This is true even in the case of measles which has a well-understood natural history and an effective vaccine that confers long-lasting protection against infection. Here, to shed light on the causes of this problem, we demonstrate that, while the dynamics of homogeneous and age-structured models can be qualitatively similar in the absence of vaccination, they diverge subsequent to vaccine roll-out. In particular, we show that immunization induces changes in transmission rates, which in turn reshapes the age distribution of infection prevalence, which effectively modulates the amplitude of seasonality in such systems. To examine this phenomenon empirically, we fit transmission models to measles notification data from London that span the introduction of the vaccine. We find that a simple age-structured model provides a much better fit to the data than does a homogeneous model, especially in the transition period from the pre-vaccine to the vaccine era. Thus, we propose that age structure and heterogeneities in contact rates are critical features needed to accurately capture transient dynamics in the presence of secular trends. CODE_plotsR Code for Plots in "Age-structure and transient dynamics in epidemiological systems"CODE_searchR Code for an initial parameter search to fit models in "Age-structure and transient dynamics in epidemiological systems"

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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Donaldson, Michael E.; Rico, Yessica; Hueffer, Karsten; Rando, Halie M.; +2 Authors

    Pathogens are recognized as major drivers of local adaptation in wildlife systems. By determining which gene variants are favored in local interactions among populations with and without disease, spatially explicit adaptive responses to pathogens can be elucidated. Much of our current understanding of host responses to disease comes from a small number of genes associated with an immune response. High-throughput sequencing (HTS) technologies, such as genotype-by-sequencing (GBS), facilitate expanded explorations of genomic variation among populations. Hybridization-based GBS techniques can be leveraged in systems not well characterized for specific variants associated with disease outcome to “capture” specific genes and regulatory regions known to influence expression and disease outcome. We developed a multiplexed, sequence capture assay for red foxes to simultaneously assess ~300-kbp of genomic sequence from 116 adaptive, intrinsic, and innate immunity genes of predicted adaptive significance and their putative upstream regulatory regions along with 23 neutral microsatellite regions to control for demographic effects. The assay was applied to 45 fox DNA samples from Alaska, where three arctic rabies strains are geographically restricted and endemic to coastal tundra regions, yet absent from the boreal interior. The assay provided 61.5% on-target enrichment with relatively even sequence coverage across all targeted loci and samples (mean = 50×), which allowed us to elucidate genetic variation across introns, exons, and potential regulatory regions (4,819 SNPs). Challenges remained in accurately describing microsatellite variation using this technique; however, longer-read HTS technologies should overcome these issues. We used these data to conduct preliminary analyses and detected genetic structure in a subset of red fox immune-related genes between regions with and without endemic arctic rabies. This assay provides a template to assess immunogenetic variation in wildlife disease systems. Red fox immune-gene sequencesRed fox immune-gene sequences (2,229,152 bp) used to design the sequence capture assay.red_fox_immune-gene_sequences.fastaRed fox immune-gene SNPsRed fox SNP variant call information.red_fox_immune-gene_SNPs.vcfRed fox NimbleGen SeqCap EZ_probesCoordinates used to design the overlapping NimbleGen SeqCap EZ probes.red_fox_NimbleGen_SeqCap_EZ_probes.bed

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    DANS-EASY
    Dataset . 2017
    Data sources: B2FIND
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      Dataset . 2017
      Data sources: B2FIND
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Pakkala, Jesse J.; Norris, D. Ryan; Sedinger, James S.; Newman, Amy E. M.;

    1.Although laboratory studies have shown that chronic exposure to elevated glucocorticoids during development can have profound effects on the physiology and behaviour of animals, we still have a poor understanding of the proximate and ultimate consequences of early-life stress on individuals in the wild. 2. In an island population of Savannah sparrows (Passerculus sandwichensis), we examined multiple hypotheses to explain how elevated glucocorticoid exposure during the nestling period influenced both hypothalamic-pituitary-adrenal (HPA) axis function during the nestling period and the subsequent movement and survival of young after they fledged the nest. 3. We exposed nestlings to exogenous corticosterone from 2-6 d of age and then measured both baseline and stress-induced (30 min restraint) plasma corticosterone levels prior to fledging (d 7). We then recaptured young throughout the pre-migratory period and used mark-recapture analysis to estimate temporary emigration from the capture site (movement) and survival. 4. Corticosterone-treated nestlings had higher baseline corticosterone levels and lower stress reactivity than untreated individuals, and were more sensitive to inclement weather. Although there was no evidence that corticosterone treatments influenced survival, treated individuals had higher rates of temporary emigration outside of the study site than sham or controls. 5. Our results provide support for the ceiling hypothesis, which suggests that individuals with chronic elevated glucocorticoids can lead to a dampened HPA axis response. We also provide support for the CORT-activity hypothesis, which suggests that elevated glucocorticoids can increase activity levels, at least 1-2 months after leaving the nest. Our study highlights the importance of tracking individuals across multiple stages of the annual cycle to understand how early life events carry-over to influence both physiology and behaviour. Pakkala et al_individual nestling data including body measurements and steroid concentrationsHormone (corticosterone) concentrations for nestling (day 7) Savannah sparrows at baseline (within 3 minutes of disturbing the nest) and after a 30 min restraint in a cloth bag. Body measurements and precipitation values also included for each individual.Pakkala et al_individual data including steroid concentrations.csvPakkala et al_Savanah Sparrow Input for MARKInput table for Program MARK; capture/recapture data for juvenile Savannah sparrows before autumn migration from Kent Island, NB.

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    DANS-EASY
    Dataset . 2015
    Data sources: B2FIND
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      Dataset . 2015
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Xiao, Chengfeng; Fard, Niki Bayat; Brzezinski, Kaylen; Robertson, R. Meldrum; +1 Authors

    Many insects enter coma upon exposure to anoxia, a feature routinely exploited by experimentalists to handle them. But the genetic and physiological bases of anoxic coma induction and recovery are only partially understood, as are the long-term consequences for the animal's performance. We examined three populations of Drosophila melanogaster (designated B) that have been inadvertently under selection for rapid recovery from CO2 exposure for nearly 40 years (around 1,000 generations) resulting from routine maintenance practices. We contrasted CO2 and N2 (presumed a less reactive gas) knockdown and recovery times of these B flies with six populations of common ancestry (A and C populations) that were not exposed to CO2 over the same period. We found that B populations showed faster and more consistent locomotor recovery than A or C populations after CO2 knockdown, a result also observed with N2 knockdown. A and C populations showed much higher variance in recovery time after CO2 exposure than after N2 exposure, suggesting gas-specific effects on pathways associated with locomotor recovery. While these selection treatments result in considerable variation in life history attributes and body size, with the characteristic intermediacy of B populations, their superiority in resistance to gas exposure and locomotor recovery suggests that it is a direct consequence of prior repeated exposure to anoxia, broadly, and CO2, specifically. Hence we describe a powerful new evolutionary model for the genetic and physiological investigation of anoxic coma in insects. JEXBIO199521_Data_IData associated with the publication: https://doi.org/10.1242/jeb.199521JEXBIO199521_Data.xlsx

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    ZENODO; DRYAD
    Dataset . 2019
    License: CC 0
    Data sources: ZENODO; Datacite
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      Dataset . 2019
      License: CC 0
      Data sources: ZENODO; Datacite
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  • image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
    Authors: Matabos, Marjolaine; Tunnicliffe, Verena; Juniper, S. Kim; Dean, Courtney;

    Changes in ocean ventilation driven by climate change result in loss of oxygen in the open ocean that, in turn, affects coastal areas in upwelling zones such as the northeast Pacific. Saanich Inlet, on the west coast of Canada, is a natural seasonally hypoxic fjord where certain continental shelf species occur in extreme hypoxia. One study site on the VENUS cabled subsea network is located in the hypoxic zone at 104 m depth. Photographs of the same 5 m2 area were taken with a remotely-controlled still camera every 2/3 days between October 6th 2009 and October 18th 2010 and examined for community composition, species behaviour and microbial mat features. Instruments located on a near-by platform provided high-resolution measurements of environmental variables. We applied multivariate ordination methods and a principal coordinate analysis of neighbour matrices to determine temporal structures in our dataset. Responses to seasonal hypoxia (0.1–1.27 ml/l) and its high variability on short time-scale (hours) varied among species, and their life stages. During extreme hypoxia, microbial mats developed then disappeared as a hippolytid shrimp, Spirontocaris sica, appeared in high densities (200 m22) despite oxygen below 0.2 ml/l. The slender sole Lyopsetta exilis was abundant in severe hypoxia and diminished as oxygen increased in the summer. This planktivore may be responding to changes in the depth of the diurnal migration of zooplankton. While the squat lobster Munida quadrispina was common at all times, juveniles disappeared in fluctuating conditions. Despite low oxygen conditions, animal densities were high indicating that the risk from hypoxia is balanced by factors such as food availability and escape from less tolerant predators. As hypoxia increases on the continental shelf, we expect benthic communities to become dominated by low diversity, hypoxia-tolerant species of low commercial significance. CHONe_MB08_Matabos_data_year

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    DANS-EASY
    Dataset . 2014
    Data sources: B2FIND
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      Dataset . 2014
      Data sources: B2FIND
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    Authors: Ivy, Catherine M.; Robertson, Cayleih E.; Bernier, Nicholas J.;

    Eutrophication and climate change are increasing the incidence of severe hypoxia in fish nursery habitats, yet the programming effects of hypoxia on stress responsiveness in later life are poorly understood. In this study, to investigate whether early hypoxia alters the developmental trajectory of the stress response, zebrafish embryos were exposed to 4 h of anoxia at 36 h post-fertilization and reared to adults when the responses to secondary stressors were assessed. While embryonic anoxia did not affect basal cortisol levels or the cortisol response to hypoxia in later life, it had a marked effect on the responses to a social stressor. In dyadic social interactions, adults derived from embryonic anoxia initiated more chases, bit more often, entered fewer freezes and had lower cortisol levels. Adults derived from embryonic anoxia also performed more bites towards their mirror image, had lower gonadal aromatase gene expression and had higher testosterone levels. We conclude that acute embryonic anoxia has long-lasting consequences for the hormonal and behavioural responses to social interactions in zebrafish. Specifically, we demonstrate that acute embryonic anoxia favours the development of a dominant and aggressive phenotype, and that a disruption in sex steroid production may contribute to the programming effects of environmental hypoxia. Ivy et al. 2017 Complete Dataset for DryadComplete dataset for the following publication: Ivy, C.M., Robertson, C.E. and Bernier N.J. 2017. Acute embryonic anoxia exposure favours the development of a dominant and aggressive phenotype in adult zebrafish. Proc. R. Soc. B 20161868.

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
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    DANS-EASY
    Dataset . 2016
    Data sources: B2FIND
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ DANS-EASYarrow_drop_down
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      DANS-EASY
      Dataset . 2016
      Data sources: B2FIND
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    Authors: Toews, Shelby; Wellband, Kyle; Dixon, Brian; Heath, Daniel D.;

    Phenotypic differences among populations within a species have been reported for a variety of traits, ranging from life history to physiology to gene transcription. Population-level phenotypic variation has been attributed to genetic differences resulting from genetic drift and/or local adaptation as well as environmental differences resulting from plasticity. We studied population- and family-level variation in gene transcription for 22 fitness-related genes, comprising immune, growth, metabolic, and stress processes in Chinook salmon (Oncorhynchus tshawytscha). We created hybrid Chinook salmon families from eight populations and treated them with an immune stimulus, a handling stress challenge, and held some as a no-treatment control group. Population effects, sire effects, and narrow-sense heritability (h2) were calculated for each candidate gene within each treatment group. We expected population to have a significant effect on gene transcription for many of our genes; however, we found a population effect for transcription at only one immune gene at rest. The limited number of significant population effects on gene transcription, combined with significant additive genetic variance within each population does not support the expectation of past strong selection pressures acting on heritable transcription profiles among populations. Instead, our results indicate that Chinook salmon likely adapt to their local environment through transcriptional plasticity rather than fixed differences. The expectation for fixed population-level differences in gene transcription at fitness-related genes, reflecting accepted models of local adaptation is high; however, comparisons among multiple populations using half-sib breeding designs are rare. Our work fills an important gap in our growing understanding of the process of among and within-population divergence. READMEThis document defines all abbreviations within the other data files.Raw_qPCR_DataRaw qPCR data from a QuantStudio 12K Flex for all samples and candidate genes.Toews_2018_Raw_qPCR_Data_Chinook_Transcription.txtPCR_EfficienciesThis file contains the PCR efficiencies of all candidate genes used in the study. The efficiencies were calculated using LinRegPCR.Toews_2018_PCR_Efficiencies_Chinook_Transcription.txtProcessed_qPCR_DataThis file contains the information needed to normalize the Cq values from the raw data, as well as the final DCt values that were used in the manuscript.Toews_2018_Processed_qPCR_Data_Chinook_Transcription.txtSample_AnnotationThis file contains information for each sample in the study, including the individual sample's rearing tank, sire, population, weight, treatment group, etc.Toews_2018_Sample_Annotation_Chinook_Transcription.txtR_Source_CodeThis text file contains the R source code used for the analyses in the paper.Toews_2018_R_Source_Code_Chinook_Transcription.txt

    image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Federated Research D...arrow_drop_down
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    DANS-EASY
    Dataset . 2019
    Data sources: B2FIND
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/ Federated Research D...arrow_drop_down
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      image/svg+xml art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos Open Access logo, converted into svg, designed by PLoS. This version with transparent background. http://commons.wikimedia.org/wiki/File:Open_Access_logo_PLoS_white.svg art designer at PLoS, modified by Wikipedia users Nina, Beao, JakobVoss, and AnonMoos http://www.plos.org/
      DANS-EASY
      Dataset . 2019
      Data sources: B2FIND
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