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Carrying capacity in a heterogeneous environment with habitat connectivity
The data are population sizes of yeast Saccharaomyces cerevisiae growth in laboratory cultures over a period of several days with different levels of growth inhibitor cycloheximide. Our results provide rigorous experimental tests of new and old theory, demonstrating how the traditional notion of carrying capacity is ambiguous for populations diffusing in spatially heterogeneous environments.
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Scaling antibiotic efficacy from cells to metapopulations
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The data are population sizes of yeast Saccharaomyces cerevisiae growth in laboratory cultures over a period of several days with different levels of growth inhibitor cycloheximide and of nutrient levels.
Demographic analysis demonstrates systematic but independent spatial variation in abiotic and biotic stressors across 59 percent of a global species range
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Five figures and four tables associated with: "Katharine J. Ruskin, Matthew A. Etterson, Thomas P. Hodgman, Alyssa C. Borowske, Jonathan B. Cohen, Chris S. Elphick, Christopher R. Field, Rebecca A. Longenecker, Erin King, Alison R. Kocek, Adrienne I. Kovach, Kathleen M. O'Brien, Nancy Pau, W. Gregory Shriver, Jennifer Walsh, Brian J. Olsen, Demographic analysis demonstrates systematic but independent spatial variation in abiotic and biotic stressors across 59 percent of a global species range, The Auk, Volume 134, Issue 4, 1 October 2017, Pages 903–916, https://doi.org/10.1642/AUK-16-230.1". Portions of this dataset are inaccessible because: The formats, pptx and jpeg, are incompatible. They can be accessed through the following means: Open access journal article. Format: PowerPoint of five figures, and four tables. This dataset is associated with the following publication: Ruskin, K., M. Etterson, T. Hodgman, A. Borowske, J. Cohen, C. Elphick, C. Field, R. Longenecker, E. King, A. Kocek, A. Kovach, K. O'Brien, N. Pau, G. Shriver, J. Walsh, and B. Olsen. Demographic analysis demonstrates systematic but independent spatial variation in abiotic and biotic stressors across 59 percent of a global species range.. The Auk. American Ornithologists' Union, Shipman, VA, USA, 134(4): 903-916, (2017).
Transcription profiling of S. cerevisiae cultures grown under low shear-modeled microgravity
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The goal of this study was to assess whether low shear-modeled microgravity (LSMMG) affects yeast genomic expression patterns using the powerful tool of whole genome microarray hybridization. We determined changes in the yeast model organism, Saccharomyces cerevisisae, when grown in LSMMG using the rotating High Aspect Ratio Vessel (HARV). A significant number of genes were up- or down-regulated by at least two fold in cells that were grown for 5 generations or 25 generations in HARVs. We identified genes in cell wall integrity signaling pathways containing MAP kinase cascades that may provide clues to novel physiological responses of eukaryotic cells to the external stress of a low-shear modeled microgravity environment. A comparison of the microgravity response to other environmental stress response (ESR) genes showed that 26% of the genes that respond ,significantly to LSMMG are involved in a general environmental stress response, while 74% of the genes may represent a unique transcriptional response to microgravity. In addition, we found changes in genes involved in budding, cell polarity establishment, and cell separation that confirm our hypothesis that exposure to LSMMG causes changes in gene transcription resulting in a phenotypic response. The results of the study provide interesting clues to potential mechanisms involved in the response to, adaptation to, and survival of eukaryotic cells in a microgravity environment and our findings may have important health implications for human spaceflight. Experiment Overall Design: Four conditions are compared with three replicates each: yeast grown in low-shear modeled microgravity (HARV bioreactor) for 5 and 25 generations; yeast grown in a horizontal (non-LSMMG) HARV bioreactor for 5 and 25 generations.
Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment
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The data is in the form of genomic sequences deposited in a public database, growth curves, and bioinformatic analysis of sequences. This dataset is associated with the following publication: Henson, M., J. Santodomingo , P. Kourtev, R. Jensen, and D. Learman. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment. PeerJ. PeerJ Inc., Corte Madera, CA, USA, e1395, (2015).
Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment
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The data is in the form of genomic sequences deposited in a public database, growth curves, and bioinformatic analysis of sequences. This dataset is associated with the following publication: Henson, M., J. Santodomingo , P. Kourtev, R. Jensen, and D. Learman. Metabolic and genomic analysis elucidates strain-level variation in Microbacterium spp. isolated from chromate contaminated sediment. PeerJ. PeerJ Inc., Corte Madera, CA, USA, e1395, (2015).
Glucose Suppressed Cyanobacterial Abundance
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Data shows that prophylactic addition of glucose to Harsha Lake water samples could inhibit cyanobacteria growth based on metagenomic sequencing data used to examine differences in the composition of bacterial communities between Treated and Control containers. The sequencing data shows that the addition of glucose to a container receiving weekly additions of Lake water suppressed the cyanobacterial populations during the entire summer bloom season. This dataset is associated with the following publication: Linz, D., I. Struewing, N. Sienkiewicz, A.D. Steinman, C.G. Partridge, K. McIntosh, J. Lu, and S. Vesper. Periodic Addition of Glucose Suppressed Cyanobacterial Abundance in Additive Lake Water Samples during the Entire Bloom Season. Journal of Water Resource and Protection. Scientific Research Publishing, Inc., Irvine, CA, USA, 16: 140-15, (2024).
Data for: Ignoring species availability biases occupancy estimates in single-scale occupancy models
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We simulate over 28,000 datasets and saved their model outputs to answer the following three questions: (1) what is an adequate sampling design for the multi-scale occupancy model when there are a priori expectations of parameter estimates?, (2) what is an adequate sampling design when we have no expectations of parameter estimates?, and (3) what is the cost (in terms of bias, accuracy, precision and coverage) in occupancy estimates) if availability is not accounted for? Specifically, we simulated data under four scenarios: Scenario 1 (n = 10,000): Species availability is constant across sites (but less than one), Scenario 2 (n = 9,358): Species availability is heterogenous across sites, Scenario 3 (n = 2,815): Species availability is heterogenous across years, and Scenario 4 (n = 5,942): Species availability is correlated to their detection probability. Then, for each scenario except the first, we analyzed the data using four different estimators: (i) constant multi-scale occupancy model, (ii) multi-scale occupancy model with a random-effects term in the availability part of the model, (iii) constant single-scale occupancy model, and (iv) single-scale occupancy model with a random-effects term in the detection part of the model. Note the formulation of the random-effects terms included in the models mimicked the way that data were simulated (e.g., if species availability was heterogenous across sites, then a site random-effects term was included in the models). The first scenario was analyzed using models (i) and (iii) only. For simplicity, we refer to models (i) and (iii) as ‘constant’ models or 'fixed-effects' models. We refer to models (ii) and (iv) as ‘random-effects’ models. The summary of simulated data and model estimates are located in four folders, each corresponding to a different simulated scenario: Scenario 1 (n = 10,000): Folder ModelOutput_Scen1_TwolevelSim = csv files holding data are named Results_TwoLevelAvail_2lev_x.csv Scenario 2 (n = 9,358): Folder ModelOutput_Scen2_HeteroSite = csv files holding data are named Results_TwoLevelAvail_Hetero_x.csv Scenario 3 (n = 2,815): Folder ModelOutput_Scen3_HeteroYear = csv files holding data are named Results_TwoLevelAvail_HeteroSeason_x.csv Scenario 4 (n = 5,942): Folder ModelOutput_Scen4_Cor = csv files holding data are named Results_TwoLevelAvail_Cor_x.csv Each row in each of the csv files contains information related to a different simulated dataset and includes information related to: sampling design, true parameter values, and model estimates. Other files in the folder correspond to the entire model output (.rda files), time for model run to complete (time_..csv), and a file indicating whether or not the model run finished (nsim...csv). For more information related to those files, we point the user to the code that generated them: Scenario 1 (n = 10,000): Scen1_Constant.R Scenario 2 (n = 9,358): Scen2_HeteroSite.R Scenario 3 (n = 2,815): Scen3_HeteroYear.R Scenario 4 (n = 5,942): Scen4_Corr.R
INHABIT species potential distribution across the contiguous United States (ver. 4.0, June 2024)
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This is a dataset containing the potential distribution of 259 invasive terrestrial plant species. We developed habitat suitability models for invasive plant species selected by Department of Interior land management agencies and other managers. We applied the modeling workflow developed in Young et al. (2020, https://doi.org/10.1371/journal.pone.0229253) and adapted by Jarnevich et al. (2023, https://doi.org/10.1016/j.ecoinf.2023.101997). We developed a national library of environmental variables known to physiologically limit plant distributions (Engelstad et al. 2022 Table S1: https://doi.org/10.1371/journal.pone.0263056) and relied on human input based on natural history knowledge to narrow the variable set for each species before developing habitat suitability models. We developed models using five algorithms with VisTrails: Software for Assisted Habitat Modeling (SAHM 2.2.2, Morisette et al., 2013). For each species, we generated up to three groups of models reflecting various levels of suitability including suitability for occurrence, suitability for abundance (>5% cover), and suitability for high abundance (>25% cover), where there were enough data available to create models. For occurrence, we accounted for uncertainty related to sampling bias by using two alternative sources of background samples. For all three groups of models, we constructed weighted ensembles using up to 20 models (occurrence) or 10 models (abundance) for each species. We also combined the three ensembles using three different thresholds converting the continuous values to suitable/unsuitable, ranging from inclusive to restrictive. This data bundle contains a single file of tabular summaries by management unit (including each species/ensemble type/abundance level combination), a file describing the changes from version 3, and a species metadata file. There is also a subfolder for each species that contains the merged data sets used to create models, up to 9 raster files associated with the species, and tabular outputs including response curve data, variable importance information, and model assessment metrics. The potential nine rasters included in each species subfolders represent the following: 1) Occurrence suitability - Continuous value ensemble 2) Abundance suitability - Continuous value ensemble 3) High abundance suitability - Continuous value ensemble 4) Restricted occurrence suitability - Continuous value ensemble with restricted environmental conditions* 5) Restricted abundance suitability - Continuous value ensemble with restricted environmental conditions* 6) Restricted high abundance suitability - Continuous value ensemble with restricted environmental conditions* 7) 0.01 – first percentile threshold applied to model group ensemble 8) 0.05 – fifth percentile threshold applied to model group ensemble 9) 0.1 – tenth percentile threshold applied to model group ensemble *Restricted environmental conditions = only display areas where environmental characteristics are inside the range of the values used to develop the model. For example, a location with a minimum winter temperature of 12 C would be outside the range of -10 to 10 C used in model development. The bundle documentation files are: 1) 'project_metadata_INHABIT_V4.xml' (this file) which contains the project-level metadata. 2) managementSummaries.csv is the tabular summaries by management unit. 3) 'INHABIT_VersionHistory.txt' contains information on the methodological changes incurred between this release and the previous data release. 4) 'species_metadata.csv' contains information on specific model changes of each species from tuning algorithm parameters to ensure model quality. 5) 'mergedDataset.csv' contains the merged data set used to create the models, including location and associated environmental data, for each species. 6) XX.tif where XX is the raster type explained above. 7) 'responseCurves.csv' is the tabular information need to produce response curves for each predictor
INHABIT species potential distribution across the contiguous United States (ver. 3.0, February 2023)
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We developed habitat suitability models for invasive plant species selected by Department of Interior land management agencies. We applied the modeling workflow developed in Young et al. 2020 to species not included in the original case studies. Our methodology balanced trade-offs between developing highly customized models for a few species versus fitting non-specific and generic models for numerous species. We developed a national library of environmental variables known to physiologically limit plant distributions (Engelstad et al. 2022 Table S1: https://doi.org/10.1371/journal.pone.0263056) and relied on human input based on natural history knowledge to further narrow the variable set for each species before developing habitat suitability models. We developed models using five algorithms with VisTrails: Software for Assisted Habitat Modeling [SAHM 2.1.2]. We accounted for uncertainty related to sampling bias by using two alternative sources of background samples, and constructed model ensembles using the 10 models for each species (five algorithms by two background methods) for three different thresholds (conservative to targeted). This data bundle contains a single file of tabular summaries by management unit (including each species/ ensemble type combination) and a subfolder for each species that contains the merged data sets used to create models, the six raster files associated with the species, and tabular outputs including response curve data, variable importance information, and model assessment metrics. Each of the six rasters represent the following: 1) 0.01 - one percentile threshold 2) 0.1 - ten percentile threshold 3) MaxSS - maximum sensitivity plus specificity threshold 4) 0.01 - one percentile threshold with Restricted Environmental Conditions 5) 0.1 - ten percentile threshold with Restricted Environmental Conditions 6) MaxSS - maximum sensitivity plus specificity threshold with Restricted Environmental Conditions The bundle documentation files are: 1) 'INHABIT_V3_metdata.xml' (this file) which contains the project-level metadata 2) managementSummaries.csv is the tabular summaries by management unit. 3) 'mergedDataset.csv' contains the merged data set used to create the models, including location and associated environmental data, for each species. 4) XX.tif where XX is the raster type explained above (threshold; masked or not). 5) responseCurves.csv is the tabular information need to produce response curves for each predictor retained in each of the 10 models produced for each species. 6) variableImportance.csv is the tabular summaries indicating predictor importance for each of the 10 models produced for each species. 7) assessmentMetrics.csv is the tabular summaries of assessment metrics for each model or ensemble for each species. These data will be integrated into the third version of the Invasive Species Habitat Tool (INHABIT), a web application displaying visual and statistical summaries of nationwide habitat suitability models for manager identified invasive plant species. These species include: African rue (Peganum harmala), Air potato (Dioscorea bulbifera), Alkali swainsonpea (Sphaerophysa salsula), Amur honeysuckle (Lonicera maackii), Amur maple (Acer ginnala), Amur peppervine (Ampelopsis brevipedunculata), Annual bluegrass (Poa annua), Annual rye (Lolium multiflorum), Asian mustard (Brassica tournefortii), Autumn olive (Elaeagnus umbellata), Balloon vine (Cardiospermum halicacabum), Beefsteak mint (Perilla frutescens), Bermudagrass (Cynodon dactylon), Bigleaf periwinkle (Vinca major), Bird vetch (Vicia cracca), Bishop's goutweed (Aegopodium podagraria), Black henbane (Hyoscyamus niger), Bohemian knotweed (Fallopia bohemica), Bradford pear (Pyrus calleryana), Brazilian peppertree (Schinus terebinthifolius), Briton's wild petunia (Ruellia simplex), Broad leaved helleborine (Epipactis helleborine), Buffelgrass (Cenchrus ciliaris), Bulbous bluegrass (Poa bulbosa), Bull thistle (Cirsium vulgare), Bur