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23 Research products, page 1 of 3

  • Canada
  • Research data
  • 2012-2021
  • Open Access
  • Federated Research Data Repository / Dépôt fédéré de données de recherche
  • MSpace at the University of Manitoba

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  • Open Access
    Authors: 
    Fudge, Neva J.; Mearow, Karen M.;
    Publisher: Dryad
    Project: NSERC , CIHR

    Background: In our previous investigations of the role of the extracellular matrix (ECM) in promoting neurite growth we have observed that a permissive laminin (LN) substrate stimulates differential growth responses in subpopulations of mature dorsal root ganglion (DRG) neurons. DRG neurons expressing Trk and p75 receptors grow neurites on a LN substrate in the absence of neurotrophins, while isolectin B4-binding neurons (IB4+) do not display significant growth under the same conditions. We set out to determine whether there was an expression signature of the LN-induced neurite growth phenotype. Using a lectin binding protocol IB4+ neurons were isolated from dissociated DRG neurons, creating two groups - IB4+ and IB4-. A small-scale microarray approach was employed to screen the expression of a panel of ECM-associated genes following dissociation (t=0) and after 24 hr culture on LN (t=24LN). This was followed by qRT-PCR and immunocytochemistry of selected genes. Results: The microarray screen showed that 36 of the 144 genes on the arrays were consistently expressed by the neurons. The array analyses showed that six genes had lower expression in the IB4+ neurons compared to the IB4- cells at t=0 (CTSH, Icam1, Itgβ1, Lamb1, Plat, Spp1), and one gene was expressed at higher levels in the IB4+ cells (Plaur). qRT-PCR was carried out as an independent assessment of the array results. There were discrepancies between the two methods, with qRT-PCR confirming the differences in Lamb1, Plat and Plaur, and showing decreased expression of AdamTs1, FN, and Icam in the IB4+ cells at t=0. After 24 hr culture on LN, there were no significant differences detected by qRT-PCR between the IB4+ and IB4- cells. However, both groups showed upregulation of Itgβ1 and Plaur after 24 hr on LN, the IB4+ group also had increased Plat, and the IB4- cells showed decreased Lamb1, Icam1 and AdamTs1. Further, the array screen also detected a number of genes (not subjected to qRT-PCR) expressed similarly by both populations in relatively high levels but not detectably influenced by time in culture (Bsg, Cst3, Ctsb, Ctsd, Ctsl, Mmp14, Mmp19, Sparc. We carried out immunohistochemistry to confirm expression of proteins encoded by a number of these genes. Conclusions:Our results show that 1B4+ and IB4- neurons differ in the expression of several genes that are associated with responsiveness to the ECM prior to culturing (AdamTs1, FN, Icam1, Lamb1, Plat, Plaur). The data suggest that the genes expressed at higher levels in the IB4- neurons could contribute to the initial growth response of these cells in a permissive environment and could also represent a common injury response that subsequently promotes axon regeneration. The differential expression of several extracellular matrix molecules (FN, Lamb1, Icam) may suggest that the IB4- neurons are capable of maintaining /secreting their local extracellular environment which could aid in the regenerative process. Overall, these data provide new information on potential targets that could be manipulated to enhance axonal regeneration in the mature nervous system.

  • Open Access English
    Authors: 
    Lamaze, Fabien C.; Pavey, Scott A.; Normandeau, Eric; Roy, Gabriel; Garant, Dany; Bernatchez, Louis;
    Publisher: Dryad
    Project: NSERC

    2009 dataThis dataset contains: gene expression values, physiological parameters, Q_values, Minisatellites length, MHCIIb alleles, parasitological parameters.data_2009_MEC-13-1125.xlsx2008-2009_parasites_dataThis dataset contains parasitological informations for the individuals sampled in 2008 and 2009. The lakes, refere to Amanites (AMA), Belles de jour (BEL), Caribou (Car), Méthot (MET), Main de fer (MAI) and Petit Saint-Bernard (BER).data_2008-2009_parasites_MEC-13-1125.xlsxMHCIIb_genotypes_dataThis dataset was generated with the genotyping pipeline described in the manuscript. It contains MHCIIb genotypes for all populations. Lakes refere to : Amanites (AMA), Belles-de-Jour (BEL), Methot (MET), Arcand (ARC), Rivard (RIV), Veillette (VEI), Caribou (CAR), Main de fer (MAI), Sorbier (SOR) and Petit saint Bernard (BER).data_genotype_2008_MHCII.xlsxData of the laboratory experimentThis dataset contains the following variables: MHCIIb gene expression values, physiological parameters (weight, length and Fulton condition index), Minisatellites groups (either long or short based on the number of repeat), family and temperature.data_laboratory-experiment.xlsx454 raw MHC2b sequencesThis file contains raw 454 sequences of the MHC2b gene.454_seq_2011090210000039.zipMHC_alleles_sequencesSequences of the 29 MHC2b alleles described in the study. These sequences were aligned with muscle, using MEGAv5 and are in the fasta format.MHC_alleles_aligned_10-04-2012.fasta The capacity of an individual to battle infection is an important fitness determinant in wild vertebrate populations. The major histocompatibility complex (MHC) genes are crucial for a host’s adaptive immune system to detect pathogens. However, anthropogenic activities may disrupt natural cycles of co-evolution between hosts and pathogens. In this study we investigated the dynamic sequence and expression variation of host parasite interactions in brook charr (Salvelinus fontinalis) in a context of past human disturbance via population supplementation from domestic individuals. To do so, we developed a new method to examine selection shaping MHC diversity within and between populations and found a complex interplay between neutral and selective processes that varied among lakes that were investigated. We provided evidence for a lower introgression rate of domestic alleles and found that parasite infection increased with domestic genomic background of individuals. We also documented an association between individual MHC alleles and parasite taxa. Finally, longer cis regulatory minisatellites were positively correlated with MHC II down-regulation and domestic admixture, suggesting that inadvertent selection during domestication resulted in a lower immune response capacity, through a trade-off between growth and immunity, which explained the negative selection of domestic alleles at least under certain circumstances.

  • Open Access
    Authors: 
    Chu, Jackson W. F.; Gale, Katie S. P.;
    Project: NSERC

    Expansion of oxygen deficient waters (hypoxia) in the northeast Pacific Ocean (NEP) will have marked impacts on marine life. The response of the resident communities will be a function of their ecophysiological constraints in low oxygen, although this remains untested in the NEP due to a lack of integrative studies. Here, we combine in situ surveys and lab-based respirometry experiments were conducted on three indicator species (spot prawn Pandalus platyceros, slender sole Lyopsetta exilis, squat lobster Munida quadrispina) of seasonally hypoxic systems in the NEP to test if metabolic constraints determine distributions and energy sequestration in a hypoxic setting. These experiments were integrated with a global review of critical oxygen levels ( math formula; lower threshold of aerobic metabolism) for crustaceans to determine if math formula-based hypoxia thresholds are different among ocean basins. Our results show that species-specific differences in math formula and standard metabolic rates (1) determine the lowest environmental oxygen ([O2]env) at which in situ populations occur, (2) result in disproportionate shifts in distributions among co-occurring species during summer hypoxia expansion events, and (3) characterize shifts in megafaunal community respiration rates due to marked spatio-temporal variability in [O2]env. Our results show that math formula-based hypoxia thresholds are significantly lower in the East Pacific Ocean relative to other major ocean basins, which suggests that the physiological response of local fauna to deoxygenation can be determined by the natural variability and oxygen exposure in a region. In order to establish realistic predictions on the biological consequences of marine deoxygenation, we suggest integrating metabolism-based traits to calculate hypoxia thresholds for marine ecosystems. CHONe_EF-13_ChuJ_Data_LnO2016Data are from lab-based respirometry experiments designed to measure metabolic rates (oxygen consumption) and critical oxygen tensions (O2crit or Pcrit) for slender sole, spot prawn, and squat lobster. Data was collected as part of a PhD thesis (J.W.F. Chu).

  • Open Access
    Authors: 
    Schott, Ryan K.; Panesar, Bhawandeep; Card, Daren C.; Preston, Matthew; Castoe, Todd A.; Chang, Belinda S. W.;
    Project: NSERC

    Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function. Supplementary File 2 - Probe Design and SequencesComplete set of probes used for cross-species targeted capture and associated dataSupplementary File 3 - Assembly and Analysis Pipelines and ScriptsCustom pipelines and scripts for the assembly and analysis of cross-species targeted capture dataSupplementary File 4 - Anolis ReferenceReference file used for assemblySupplementary File 5 - Snake ReferenceReference file used for assemblySupplementary File 6 - Gekko ReferenceReference file used for assembly

  • Open Access English
    Authors: 
    Shahsavarifard, Mohammad; Bibeau, Eric Louis;
    Country: Canada

    Dataset includes power and thrust coefficients of a 19.8 cm diameter horizontal axis hydrokinetic model turbine measured experimentally in a water tunnel. Tests are done at 0.7, 0.9, and 1.1 m/s water speeds for three turbine configurations: turbine blade alone and then with two shrouds. Output power of the turbine and its thrust force are measured experimentally. Results are corrected using a theoretical model that accounts for free surface proximity and blockage effects of the water tunnel. Please see the description file on details of the experiment.

  • Open Access
    Authors: 
    Moore, Kayla; Holländer, Hartmut;
    Country: Canada

    The data was collected during laboratory experiments in a 2-D porous media, in a 0.9 m x 0.3 m x 0.12 m box. Sand hydraulic conductivity was 2.3E-3 m/s. A salt core was placed along the bottom third of the tank. A constant head boundary was applied at the top left and top right corners of the tank. Gradients of 2%, 5% and 10% were used. Salt concentrations were collected using resistance measurements which were calibrated against standards.

  • Open Access
    Authors: 
    Martin, Paul R.; Bonier, Frances;
    Project: NSERC

    Urbanization represents an extreme transformation of more natural systems. Populations of most species decline or disappear with urbanization, and yet some species persist and even thrive in cities. What determines which species persist or thrive in urban habitats? Direct competitive interactions among species can influence their distributions and resource use, particularly along gradients of environmental challenge. Given the challenges of urbanization, similar interactions may be important for determining which species persist or thrive in cities; however, their role remains poorly understood. Here we use a global dataset to test among three alternative hypotheses for how direct competitive interactions and behavioral dominance may influence the breeding occurrence of birds in cities. We find evidence to support the Competitive Interference Hypothesis: behaviorally dominant species were more widespread in urban habitats than closely-related subordinate species, but only in taxa that thrive in urban environments (hereafter, urban-adapted), and only when dominant and subordinate species overlapped their geographic ranges. This result was evident across diverse phylogenetic groups, but varied significantly with a country’s level of economic development. Urban-adapted, dominant species were more widespread than closely-related subordinate species in cities in developed, but not developing, countries; countries in economic transition showed an intermediate pattern. Our results provide evidence that competitive interactions broadly influence species responses to urbanization, and that these interactions have asymmetric effects on subordinate species that otherwise could be widespread in urban environments. Results further suggest that economic development might accentuate the consequences of competitive interactions, thereby reducing local diversity in cities. Behavioural dominance dataDetails of behavioural dominance relationships among focal species pairs.urban.data.dominance.txtDataset used in analysisDataset used in analysis, corresponding to the R code.urban.data.for.analysis.csvFull raw datasetRaw dataset including all responses entered separately.urban.data.raw.responses.csvSubset of dataset for species pairs with quantitative dominance dataSubset of dataset for species pairs with either accessible, quantitative data on dominance relationships, or whose dominance relationships are based on the results of experiments. Dataset corresponds to a supplemental analysis (see R code line 2344).subset.quant.urban.data.for.analysis.csvR code for analysisR code for all analyses and figures.urban.analysis.RPhylogenyPhylogeny of focal species used in analyses, in Newick formaturban.tree.final

  • Open Access
    Authors: 
    Gonsamo, Alemu; Sothe, Camile; Snider, James; Finkelstein, Sarah; Arabian, Joyce; Kurz, Werner;
    Publisher: 4TU.ResearchData
    Country: Netherlands
    Project: NSERC

    *** Carbon storage and distribution in terrestrial ecosystems of Canada *** Authors: C. Sothe,1* A. Gonsamo,1 J. Arabian,2 W. A. Kurz,3 S. A. Finkelstein,4 J. Snider2 1School of Earth, Environment & Society, McMaster University, Hamilton, Ontario, Canada. 2World Wildlife Fund Canada, Toronto, Ontario, Canada. 3Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia, Canada. 4Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada. Corresponding author: Camile Sothe (sothec@mcmaster.ca) ***General Introduction*** This dataset contains the updated version of maps with the spatial distribution of soil carbon stock in Canada and associated uncertainties. It is being made public to act as supplementary data for the publication 'Large soil carbon storage in terrestrial ecosystems of Canada'. The maps were produced in the Remote Sensing Lab, McMaster University, between January 2020 and October 2021. This research project was made possible by a grant from the World Wildlife Fund (WWF)- Canada ***Purpose of the project*** This project aimed to produce the first wall-to-wall estimate of carbon stocks in plants and soils of Canada at 250 m spatial resolution using multisource satellite, climate and topographic data and a machine-learning algorithm. ***Methods*** To generate the soil carbon stock map, we used 39,323 ground samples of soil organic carbon concentration (g/kg) distributed in 6,533 sites, 11,068 ground samples of bulk density (kg/dm3) distributed in 2,157 sites, long-term climate data, multisource remote sensing data, topographic information, soil type, depth, and a 3D random forest regression model. The uncertainty map was generated using the random forest quantile regression approach difference between 95th and 5th quantiles (90% confidence interval) of soil organic carbon and bulk density predictions. ***Description of the data*** -250m spatial resolution -WGS-84 projection -Area= 8.4 million km² -Units= kg/m² -0-30cm and 0-1m soil depth -water and ice/snow areas were masked based on the 2015 Land Cover of Canada (https://open.canada.ca/data/en/dataset/4e615eae-b90c-420b-adee-2ca35896caf6) -SOC stock in permafrost areas was discounted according to ice abundance using the 'Ground ice map of Canada' (O'Neill et al., 2020 - https://doi.org/10.4095/326885) -shallow soils were discounted using the rooting depth fraction from the National Soil Database (http://sis.agr.gc.ca/cansis/nsdb/slc/index.html) This project aimed to produce the first wall-to-wall estimate of C stocks in plants and soils of Canada at 250 m spatial resolution. This dataset contains the map with the soil organic carbon (SOC) in kg/m² for entire Canada in 30cm and 1m depth, and the uncertainty in SOC predictions. The SOC stock map was produced using 39,323 ground samples of soil organic carbon concentration (g/kg) distributed in 6,533 sites, 11,068 ground samples of bulk density (kg/dm3) distributed in 2,157 sites, long-term climate data, remote sensing observations and a machine learning model. The soil samples containing the x and y coordinates, depth and SOC (in g/kg) information were overlaid with the stacked covariates (soil forming factors) to compose the regression matrix. Random forest models were trained using a recursive feature elimination scheme and a cross-validation assessment. The best model was used for spatial prediction of SOC over Canada in intermediate depths between 0 and 1 m (0cm, 5cm, 15cm, 30cm, 60cm, 100cm). Afterwards, the SOC stock of each depth increment was computed using SOC concentration and bulk density maps, and corrected with coarse fragment information. The depth increments have been added to compose the 0-30cm and 0-1m depth intervals multiplied by rooting depths fraction to discount shallow soils. Water and ice/snow areas were removed using a mask based on the Land Cover of Canada map. Ground ice in permafrost areas was discounted according to ice abundance using the ground ice map of Canada. The SOC stock uncertainty map is the difference between the first and third quantiles of a quantile regression forest approach of SOC concentration and bulk density prediction (90% confidence interval).

  • Open Access
    Authors: 
    Kay, Sharon; Gehman, Alyssa-Lois; Harley, Christopher;
    Publisher: Data Archiving and Networked Services (DANS)
    Project: NSERC

    EvasteriasPisasterSurvey_Table_2_Fig_1_dataLong term Evasterias and Pisaster population data in Burrard Inlet, British Columbia, Canada. Percent of maximum abundance (denoted as “percent_max”) for each species and proportion of each species within the sea star community (denoted as “prop_sp”), during winter surveys from 2008 to 2017. Each survey’s percent of maximum abundance was calculated using the maximum abundance recorded for that site during our surveys from 2008 to 2017. Data are split into “pre” and “post” estimated time of outbreak of wasting disease, n = 9 surveys for years before wasting and n = 40 surveys for years after wasting. Surveys are from 5 sites, and estimates of area surveyed at each site are provided. Salinity is opportunistically reported.Table_2_Fig_1_data.csvTable3_Fig_2_dataBreakdown of disease progression in Evasterias and Pisaster over 28 days, in terms of number of asymptomatic (“num_healthy”) and the number of surviving individuals remaining in a tank “(num_alive”), after experimental exposure to conspecifics with signs of SSWD. “Day” indicates the duration of experiment and “tank” indicates the replicate tanks of initially uninfected sea stars. “Census_sick” and “census_dead” indicates a binary assignment of 0 or 1, where 0 denotes more than half the population of 5 sea stars is healthy/alive and 1 denotes more than half the population is sick/dead. See supplement S1.2 for more details on the methods of the experiments.TableS3_FigS3_dataMean percent change in wet weight (grams) across competition treatments, from all three experiment rounds. Competition treatments are labeled by the number of sea stars held in a tank, and of what species. Evasterias is abbreviated with “Eva” and Pisaster is abbreviated with “Pi”. The interspecific treatment for Evasterias response was “Eva (2 Eva + 2 Pi)” and for Pisaster response was “Pi (2 Eva + 2 Pi)”. Each treatment was replicated three times per experiment (denoted as “tank” number), with the exception of experiment three, where the interspecific treatment was replicated four times, for a total of 9 replications and 10 replications respectively across all three experiments. Sample size varied per treatment as some sea stars developed signs of SSWD and thus were removed and replaced with uninfected sea stars. Replacement sea star weights were not included in the data set or growth analysis. For more details on the methods see supplement section S1.3.Fig_S4_dataSeasonal abundance data for Pisaster and Evasterias for April 2016 to March 2017. Mean percent of maximum abundance (denoted as “percent_max”) and mean proportion of species in community (denoted as “prop_sp”), over the months of one year. Each survey’s percent of maximum abundance was calculated using the maximum abundance recorded for that site during our surveys in 2016/2017.Surveys are from 5 sites, and estimates of area surveyed at each site are provided. Salinity is opportunistically reported. See supplement section S1.1 for more details on the methods. Disease emergence occurs within the context of ecological communities, and disease driven declines in host populations can lead to complex direct and indirect ecological effects. Varying effects of a single disease among multiple susceptible hosts could benefit relatively resistant species. Beginning in 2013, an outbreak of sea star wasting disease (SSWD) led to population declines of many sea star species along the west coast of North America. Through field surveys and laboratory experiments, we investigated how and why the relative abundances of two co-occurring sea star species, Evasterias troschelii and Pisaster ochraceus, shifted during the ongoing wasting epidemic in Burrard Inlet, British Columbia, Canada. We hypothesized that Evasterias is competitively inferior to Pisaster but more resistant to SSWD. Thus, we predicted that SSWD-induced declines of Pisaster could mitigate the negative effects of SSWD on Evasterias, as the latter would experience competitive release. We document shifts in sea star abundance from 2007-2017: Pisaster abundance and mean size declined during the outbreak, while Evasterias abundance increased from relatively rare to numerically dominant within the intertidal. When exposed to symptomatic sea stars, Pisaster and Evasterias both showed signs of SSWD, but transmission and susceptibility was lower in Evasterias. Despite diet overlap documented in our field surveys, Evasterias was not outcompeted by Pisaster in laboratory trails conducted with the relatively small Pisaster available after the outbreak. Interference competition with larger Pisaster, or prey exploitation by Pisaster during summer when Evasterias is primarily subtidal, may explain the rarity of Evasterias prior to Pisaster declines. Our results suggest that indirect effects mediated by competition can mask some of the direct effects of disease outbreaks, and the combination of direct and indirect effects will determine the restructuring of a community after disturbance.

  • Research data . 2012
    Open Access English
    Authors: 
    Bibeau, Eric;
    Publisher: MSpace University of Manitoba Institutional Repository
    Country: Canada

    Dataset of driving behaviour within the perimeter of Winnipeg collected from May 2009 to May 2010.

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The following results are related to Canada. Are you interested to view more results? Visit OpenAIRE - Explore.
23 Research products, page 1 of 3
  • Open Access
    Authors: 
    Fudge, Neva J.; Mearow, Karen M.;
    Publisher: Dryad
    Project: NSERC , CIHR

    Background: In our previous investigations of the role of the extracellular matrix (ECM) in promoting neurite growth we have observed that a permissive laminin (LN) substrate stimulates differential growth responses in subpopulations of mature dorsal root ganglion (DRG) neurons. DRG neurons expressing Trk and p75 receptors grow neurites on a LN substrate in the absence of neurotrophins, while isolectin B4-binding neurons (IB4+) do not display significant growth under the same conditions. We set out to determine whether there was an expression signature of the LN-induced neurite growth phenotype. Using a lectin binding protocol IB4+ neurons were isolated from dissociated DRG neurons, creating two groups - IB4+ and IB4-. A small-scale microarray approach was employed to screen the expression of a panel of ECM-associated genes following dissociation (t=0) and after 24 hr culture on LN (t=24LN). This was followed by qRT-PCR and immunocytochemistry of selected genes. Results: The microarray screen showed that 36 of the 144 genes on the arrays were consistently expressed by the neurons. The array analyses showed that six genes had lower expression in the IB4+ neurons compared to the IB4- cells at t=0 (CTSH, Icam1, Itgβ1, Lamb1, Plat, Spp1), and one gene was expressed at higher levels in the IB4+ cells (Plaur). qRT-PCR was carried out as an independent assessment of the array results. There were discrepancies between the two methods, with qRT-PCR confirming the differences in Lamb1, Plat and Plaur, and showing decreased expression of AdamTs1, FN, and Icam in the IB4+ cells at t=0. After 24 hr culture on LN, there were no significant differences detected by qRT-PCR between the IB4+ and IB4- cells. However, both groups showed upregulation of Itgβ1 and Plaur after 24 hr on LN, the IB4+ group also had increased Plat, and the IB4- cells showed decreased Lamb1, Icam1 and AdamTs1. Further, the array screen also detected a number of genes (not subjected to qRT-PCR) expressed similarly by both populations in relatively high levels but not detectably influenced by time in culture (Bsg, Cst3, Ctsb, Ctsd, Ctsl, Mmp14, Mmp19, Sparc. We carried out immunohistochemistry to confirm expression of proteins encoded by a number of these genes. Conclusions:Our results show that 1B4+ and IB4- neurons differ in the expression of several genes that are associated with responsiveness to the ECM prior to culturing (AdamTs1, FN, Icam1, Lamb1, Plat, Plaur). The data suggest that the genes expressed at higher levels in the IB4- neurons could contribute to the initial growth response of these cells in a permissive environment and could also represent a common injury response that subsequently promotes axon regeneration. The differential expression of several extracellular matrix molecules (FN, Lamb1, Icam) may suggest that the IB4- neurons are capable of maintaining /secreting their local extracellular environment which could aid in the regenerative process. Overall, these data provide new information on potential targets that could be manipulated to enhance axonal regeneration in the mature nervous system.

  • Open Access English
    Authors: 
    Lamaze, Fabien C.; Pavey, Scott A.; Normandeau, Eric; Roy, Gabriel; Garant, Dany; Bernatchez, Louis;
    Publisher: Dryad
    Project: NSERC

    2009 dataThis dataset contains: gene expression values, physiological parameters, Q_values, Minisatellites length, MHCIIb alleles, parasitological parameters.data_2009_MEC-13-1125.xlsx2008-2009_parasites_dataThis dataset contains parasitological informations for the individuals sampled in 2008 and 2009. The lakes, refere to Amanites (AMA), Belles de jour (BEL), Caribou (Car), Méthot (MET), Main de fer (MAI) and Petit Saint-Bernard (BER).data_2008-2009_parasites_MEC-13-1125.xlsxMHCIIb_genotypes_dataThis dataset was generated with the genotyping pipeline described in the manuscript. It contains MHCIIb genotypes for all populations. Lakes refere to : Amanites (AMA), Belles-de-Jour (BEL), Methot (MET), Arcand (ARC), Rivard (RIV), Veillette (VEI), Caribou (CAR), Main de fer (MAI), Sorbier (SOR) and Petit saint Bernard (BER).data_genotype_2008_MHCII.xlsxData of the laboratory experimentThis dataset contains the following variables: MHCIIb gene expression values, physiological parameters (weight, length and Fulton condition index), Minisatellites groups (either long or short based on the number of repeat), family and temperature.data_laboratory-experiment.xlsx454 raw MHC2b sequencesThis file contains raw 454 sequences of the MHC2b gene.454_seq_2011090210000039.zipMHC_alleles_sequencesSequences of the 29 MHC2b alleles described in the study. These sequences were aligned with muscle, using MEGAv5 and are in the fasta format.MHC_alleles_aligned_10-04-2012.fasta The capacity of an individual to battle infection is an important fitness determinant in wild vertebrate populations. The major histocompatibility complex (MHC) genes are crucial for a host’s adaptive immune system to detect pathogens. However, anthropogenic activities may disrupt natural cycles of co-evolution between hosts and pathogens. In this study we investigated the dynamic sequence and expression variation of host parasite interactions in brook charr (Salvelinus fontinalis) in a context of past human disturbance via population supplementation from domestic individuals. To do so, we developed a new method to examine selection shaping MHC diversity within and between populations and found a complex interplay between neutral and selective processes that varied among lakes that were investigated. We provided evidence for a lower introgression rate of domestic alleles and found that parasite infection increased with domestic genomic background of individuals. We also documented an association between individual MHC alleles and parasite taxa. Finally, longer cis regulatory minisatellites were positively correlated with MHC II down-regulation and domestic admixture, suggesting that inadvertent selection during domestication resulted in a lower immune response capacity, through a trade-off between growth and immunity, which explained the negative selection of domestic alleles at least under certain circumstances.

  • Open Access
    Authors: 
    Chu, Jackson W. F.; Gale, Katie S. P.;
    Project: NSERC

    Expansion of oxygen deficient waters (hypoxia) in the northeast Pacific Ocean (NEP) will have marked impacts on marine life. The response of the resident communities will be a function of their ecophysiological constraints in low oxygen, although this remains untested in the NEP due to a lack of integrative studies. Here, we combine in situ surveys and lab-based respirometry experiments were conducted on three indicator species (spot prawn Pandalus platyceros, slender sole Lyopsetta exilis, squat lobster Munida quadrispina) of seasonally hypoxic systems in the NEP to test if metabolic constraints determine distributions and energy sequestration in a hypoxic setting. These experiments were integrated with a global review of critical oxygen levels ( math formula; lower threshold of aerobic metabolism) for crustaceans to determine if math formula-based hypoxia thresholds are different among ocean basins. Our results show that species-specific differences in math formula and standard metabolic rates (1) determine the lowest environmental oxygen ([O2]env) at which in situ populations occur, (2) result in disproportionate shifts in distributions among co-occurring species during summer hypoxia expansion events, and (3) characterize shifts in megafaunal community respiration rates due to marked spatio-temporal variability in [O2]env. Our results show that math formula-based hypoxia thresholds are significantly lower in the East Pacific Ocean relative to other major ocean basins, which suggests that the physiological response of local fauna to deoxygenation can be determined by the natural variability and oxygen exposure in a region. In order to establish realistic predictions on the biological consequences of marine deoxygenation, we suggest integrating metabolism-based traits to calculate hypoxia thresholds for marine ecosystems. CHONe_EF-13_ChuJ_Data_LnO2016Data are from lab-based respirometry experiments designed to measure metabolic rates (oxygen consumption) and critical oxygen tensions (O2crit or Pcrit) for slender sole, spot prawn, and squat lobster. Data was collected as part of a PhD thesis (J.W.F. Chu).

  • Open Access
    Authors: 
    Schott, Ryan K.; Panesar, Bhawandeep; Card, Daren C.; Preston, Matthew; Castoe, Todd A.; Chang, Belinda S. W.;
    Project: NSERC

    Despite continued advances in sequencing technologies, there is a need for methods that can efficiently sequence large numbers of genes from diverse species. One approach to accomplish this is targeted capture (hybrid enrichment). While these methods are well established for genome resequencing projects, cross-species capture strategies are still being developed and generally focus on the capture of conserved regions, rather than complete coding regions from specific genes of interest. The resulting data is thus useful for phylogenetic studies, but the wealth of comparative data that could be used for evolutionary and functional studies is lost. Here we design and implement a targeted capture method that enables recovery of complete coding regions across broad taxonomic scales. Capture probes were designed from multiple reference species and extensively tiled in order to facilitate cross-species capture. Using novel bioinformatics pipelines we were able to recover nearly all of the targeted genes with high completeness from species that were up to 200 myr divergent. Increased probe diversity and tiling for a subset of genes had a large positive effect on both recovery and completeness. The resulting data produced an accurate species tree, but importantly this same data can also be applied to studies of molecular evolution and function that will allow researchers to ask larger questions in broader phylogenetic contexts. Our method demonstrates the utility of cross-species approaches for the capture of full length coding sequences, and will substantially improve the ability for researchers to conduct large-scale comparative studies of molecular evolution and function. Supplementary File 2 - Probe Design and SequencesComplete set of probes used for cross-species targeted capture and associated dataSupplementary File 3 - Assembly and Analysis Pipelines and ScriptsCustom pipelines and scripts for the assembly and analysis of cross-species targeted capture dataSupplementary File 4 - Anolis ReferenceReference file used for assemblySupplementary File 5 - Snake ReferenceReference file used for assemblySupplementary File 6 - Gekko ReferenceReference file used for assembly

  • Open Access English
    Authors: 
    Shahsavarifard, Mohammad; Bibeau, Eric Louis;
    Country: Canada

    Dataset includes power and thrust coefficients of a 19.8 cm diameter horizontal axis hydrokinetic model turbine measured experimentally in a water tunnel. Tests are done at 0.7, 0.9, and 1.1 m/s water speeds for three turbine configurations: turbine blade alone and then with two shrouds. Output power of the turbine and its thrust force are measured experimentally. Results are corrected using a theoretical model that accounts for free surface proximity and blockage effects of the water tunnel. Please see the description file on details of the experiment.

  • Open Access
    Authors: 
    Moore, Kayla; Holländer, Hartmut;
    Country: Canada

    The data was collected during laboratory experiments in a 2-D porous media, in a 0.9 m x 0.3 m x 0.12 m box. Sand hydraulic conductivity was 2.3E-3 m/s. A salt core was placed along the bottom third of the tank. A constant head boundary was applied at the top left and top right corners of the tank. Gradients of 2%, 5% and 10% were used. Salt concentrations were collected using resistance measurements which were calibrated against standards.

  • Open Access
    Authors: 
    Martin, Paul R.; Bonier, Frances;
    Project: NSERC

    Urbanization represents an extreme transformation of more natural systems. Populations of most species decline or disappear with urbanization, and yet some species persist and even thrive in cities. What determines which species persist or thrive in urban habitats? Direct competitive interactions among species can influence their distributions and resource use, particularly along gradients of environmental challenge. Given the challenges of urbanization, similar interactions may be important for determining which species persist or thrive in cities; however, their role remains poorly understood. Here we use a global dataset to test among three alternative hypotheses for how direct competitive interactions and behavioral dominance may influence the breeding occurrence of birds in cities. We find evidence to support the Competitive Interference Hypothesis: behaviorally dominant species were more widespread in urban habitats than closely-related subordinate species, but only in taxa that thrive in urban environments (hereafter, urban-adapted), and only when dominant and subordinate species overlapped their geographic ranges. This result was evident across diverse phylogenetic groups, but varied significantly with a country’s level of economic development. Urban-adapted, dominant species were more widespread than closely-related subordinate species in cities in developed, but not developing, countries; countries in economic transition showed an intermediate pattern. Our results provide evidence that competitive interactions broadly influence species responses to urbanization, and that these interactions have asymmetric effects on subordinate species that otherwise could be widespread in urban environments. Results further suggest that economic development might accentuate the consequences of competitive interactions, thereby reducing local diversity in cities. Behavioural dominance dataDetails of behavioural dominance relationships among focal species pairs.urban.data.dominance.txtDataset used in analysisDataset used in analysis, corresponding to the R code.urban.data.for.analysis.csvFull raw datasetRaw dataset including all responses entered separately.urban.data.raw.responses.csvSubset of dataset for species pairs with quantitative dominance dataSubset of dataset for species pairs with either accessible, quantitative data on dominance relationships, or whose dominance relationships are based on the results of experiments. Dataset corresponds to a supplemental analysis (see R code line 2344).subset.quant.urban.data.for.analysis.csvR code for analysisR code for all analyses and figures.urban.analysis.RPhylogenyPhylogeny of focal species used in analyses, in Newick formaturban.tree.final

  • Open Access
    Authors: 
    Gonsamo, Alemu; Sothe, Camile; Snider, James; Finkelstein, Sarah; Arabian, Joyce; Kurz, Werner;
    Publisher: 4TU.ResearchData
    Country: Netherlands
    Project: NSERC

    *** Carbon storage and distribution in terrestrial ecosystems of Canada *** Authors: C. Sothe,1* A. Gonsamo,1 J. Arabian,2 W. A. Kurz,3 S. A. Finkelstein,4 J. Snider2 1School of Earth, Environment & Society, McMaster University, Hamilton, Ontario, Canada. 2World Wildlife Fund Canada, Toronto, Ontario, Canada. 3Canadian Forest Service, Natural Resources Canada, Victoria, British Columbia, Canada. 4Department of Earth Sciences, University of Toronto, Toronto, Ontario, Canada. Corresponding author: Camile Sothe (sothec@mcmaster.ca) ***General Introduction*** This dataset contains the updated version of maps with the spatial distribution of soil carbon stock in Canada and associated uncertainties. It is being made public to act as supplementary data for the publication 'Large soil carbon storage in terrestrial ecosystems of Canada'. The maps were produced in the Remote Sensing Lab, McMaster University, between January 2020 and October 2021. This research project was made possible by a grant from the World Wildlife Fund (WWF)- Canada ***Purpose of the project*** This project aimed to produce the first wall-to-wall estimate of carbon stocks in plants and soils of Canada at 250 m spatial resolution using multisource satellite, climate and topographic data and a machine-learning algorithm. ***Methods*** To generate the soil carbon stock map, we used 39,323 ground samples of soil organic carbon concentration (g/kg) distributed in 6,533 sites, 11,068 ground samples of bulk density (kg/dm3) distributed in 2,157 sites, long-term climate data, multisource remote sensing data, topographic information, soil type, depth, and a 3D random forest regression model. The uncertainty map was generated using the random forest quantile regression approach difference between 95th and 5th quantiles (90% confidence interval) of soil organic carbon and bulk density predictions. ***Description of the data*** -250m spatial resolution -WGS-84 projection -Area= 8.4 million km² -Units= kg/m² -0-30cm and 0-1m soil depth -water and ice/snow areas were masked based on the 2015 Land Cover of Canada (https://open.canada.ca/data/en/dataset/4e615eae-b90c-420b-adee-2ca35896caf6) -SOC stock in permafrost areas was discounted according to ice abundance using the 'Ground ice map of Canada' (O'Neill et al., 2020 - https://doi.org/10.4095/326885) -shallow soils were discounted using the rooting depth fraction from the National Soil Database (http://sis.agr.gc.ca/cansis/nsdb/slc/index.html) This project aimed to produce the first wall-to-wall estimate of C stocks in plants and soils of Canada at 250 m spatial resolution. This dataset contains the map with the soil organic carbon (SOC) in kg/m² for entire Canada in 30cm and 1m depth, and the uncertainty in SOC predictions. The SOC stock map was produced using 39,323 ground samples of soil organic carbon concentration (g/kg) distributed in 6,533 sites, 11,068 ground samples of bulk density (kg/dm3) distributed in 2,157 sites, long-term climate data, remote sensing observations and a machine learning model. The soil samples containing the x and y coordinates, depth and SOC (in g/kg) information were overlaid with the stacked covariates (soil forming factors) to compose the regression matrix. Random forest models were trained using a recursive feature elimination scheme and a cross-validation assessment. The best model was used for spatial prediction of SOC over Canada in intermediate depths between 0 and 1 m (0cm, 5cm, 15cm, 30cm, 60cm, 100cm). Afterwards, the SOC stock of each depth increment was computed using SOC concentration and bulk density maps, and corrected with coarse fragment information. The depth increments have been added to compose the 0-30cm and 0-1m depth intervals multiplied by rooting depths fraction to discount shallow soils. Water and ice/snow areas were removed using a mask based on the Land Cover of Canada map. Ground ice in permafrost areas was discounted according to ice abundance using the ground ice map of Canada. The SOC stock uncertainty map is the difference between the first and third quantiles of a quantile regression forest approach of SOC concentration and bulk density prediction (90% confidence interval).

  • Open Access
    Authors: 
    Kay, Sharon; Gehman, Alyssa-Lois; Harley, Christopher;
    Publisher: Data Archiving and Networked Services (DANS)
    Project: NSERC

    EvasteriasPisasterSurvey_Table_2_Fig_1_dataLong term Evasterias and Pisaster population data in Burrard Inlet, British Columbia, Canada. Percent of maximum abundance (denoted as “percent_max”) for each species and proportion of each species within the sea star community (denoted as “prop_sp”), during winter surveys from 2008 to 2017. Each survey’s percent of maximum abundance was calculated using the maximum abundance recorded for that site during our surveys from 2008 to 2017. Data are split into “pre” and “post” estimated time of outbreak of wasting disease, n = 9 surveys for years before wasting and n = 40 surveys for years after wasting. Surveys are from 5 sites, and estimates of area surveyed at each site are provided. Salinity is opportunistically reported.Table_2_Fig_1_data.csvTable3_Fig_2_dataBreakdown of disease progression in Evasterias and Pisaster over 28 days, in terms of number of asymptomatic (“num_healthy”) and the number of surviving individuals remaining in a tank “(num_alive”), after experimental exposure to conspecifics with signs of SSWD. “Day” indicates the duration of experiment and “tank” indicates the replicate tanks of initially uninfected sea stars. “Census_sick” and “census_dead” indicates a binary assignment of 0 or 1, where 0 denotes more than half the population of 5 sea stars is healthy/alive and 1 denotes more than half the population is sick/dead. See supplement S1.2 for more details on the methods of the experiments.TableS3_FigS3_dataMean percent change in wet weight (grams) across competition treatments, from all three experiment rounds. Competition treatments are labeled by the number of sea stars held in a tank, and of what species. Evasterias is abbreviated with “Eva” and Pisaster is abbreviated with “Pi”. The interspecific treatment for Evasterias response was “Eva (2 Eva + 2 Pi)” and for Pisaster response was “Pi (2 Eva + 2 Pi)”. Each treatment was replicated three times per experiment (denoted as “tank” number), with the exception of experiment three, where the interspecific treatment was replicated four times, for a total of 9 replications and 10 replications respectively across all three experiments. Sample size varied per treatment as some sea stars developed signs of SSWD and thus were removed and replaced with uninfected sea stars. Replacement sea star weights were not included in the data set or growth analysis. For more details on the methods see supplement section S1.3.Fig_S4_dataSeasonal abundance data for Pisaster and Evasterias for April 2016 to March 2017. Mean percent of maximum abundance (denoted as “percent_max”) and mean proportion of species in community (denoted as “prop_sp”), over the months of one year. Each survey’s percent of maximum abundance was calculated using the maximum abundance recorded for that site during our surveys in 2016/2017.Surveys are from 5 sites, and estimates of area surveyed at each site are provided. Salinity is opportunistically reported. See supplement section S1.1 for more details on the methods. Disease emergence occurs within the context of ecological communities, and disease driven declines in host populations can lead to complex direct and indirect ecological effects. Varying effects of a single disease among multiple susceptible hosts could benefit relatively resistant species. Beginning in 2013, an outbreak of sea star wasting disease (SSWD) led to population declines of many sea star species along the west coast of North America. Through field surveys and laboratory experiments, we investigated how and why the relative abundances of two co-occurring sea star species, Evasterias troschelii and Pisaster ochraceus, shifted during the ongoing wasting epidemic in Burrard Inlet, British Columbia, Canada. We hypothesized that Evasterias is competitively inferior to Pisaster but more resistant to SSWD. Thus, we predicted that SSWD-induced declines of Pisaster could mitigate the negative effects of SSWD on Evasterias, as the latter would experience competitive release. We document shifts in sea star abundance from 2007-2017: Pisaster abundance and mean size declined during the outbreak, while Evasterias abundance increased from relatively rare to numerically dominant within the intertidal. When exposed to symptomatic sea stars, Pisaster and Evasterias both showed signs of SSWD, but transmission and susceptibility was lower in Evasterias. Despite diet overlap documented in our field surveys, Evasterias was not outcompeted by Pisaster in laboratory trails conducted with the relatively small Pisaster available after the outbreak. Interference competition with larger Pisaster, or prey exploitation by Pisaster during summer when Evasterias is primarily subtidal, may explain the rarity of Evasterias prior to Pisaster declines. Our results suggest that indirect effects mediated by competition can mask some of the direct effects of disease outbreaks, and the combination of direct and indirect effects will determine the restructuring of a community after disturbance.

  • Research data . 2012
    Open Access English
    Authors: 
    Bibeau, Eric;
    Publisher: MSpace University of Manitoba Institutional Repository
    Country: Canada

    Dataset of driving behaviour within the perimeter of Winnipeg collected from May 2009 to May 2010.