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published: 2023-05-08
This dataset includes microclimate species distribution models at a ~3 m2 spatial resolution and free-air temperature species distribution models at ~0.85 km2 spatial resolution for three plethodontid salamander species (Demognathus wrighti, Desmognathus ocoee, and Plethodon jordani) across Great Smoky Mountains National Park. We also include heatmaps representing the differences between microclimate and free-air species distribution models and polygon layers representing the fragmented habitat for each species' predicted range. All datasets include predictions for 2010, 2030, and 2050.
keywords: Ecological niche modeling, microclimate, species distribution model, spatial resolution, range loss, suitable habitat, plethodontid salamanders, montane ecosystems
published: 2023-04-19
Supplemental data sets for the Manuscript entitled " Assembly of wood-inhabiting archaeal, bacterial and fungal communities along a salinity gradient: common taxa are broadly distributed but locally abundant in preferred habitats"
keywords: wood decomposition; aquatic fungi; aquatic bacteria; aquatic archaea; microbial succession; microbial life-history
published: 2023-04-05
Data associated with the manuscript "Eastern banded killifish (Fundulus diaphanus diaphanus) in Lake Michigan and connected watersheds: the invasion of a non-native subspecies" by Jordan H. Hartman, Jeremy S. Tiemann, Joshua L. Sherwood, Philip W. Willink, Kurt T. Ash, Mark A. Davis, and Eric R. Larson. For this project, we sampled 109 locations in Lake Michigan and connected waters and found 821 total banded killifish. Using mitochondrial DNA analysis, we found 31 eastern and 25 western haplotypes which split our banded killifish into 422 eastern banded killifish and 398 western banded killifish. This dataset provides the sampling locations, banded killifish haplotypes, frequency of those haplotypes per location, accession numbers in GenBank, and the associated mitochondrial DNA sequences.
keywords: intraspecific invasion; Lake Michigan; mtDNA; native transplant
published: 2023-04-02
Use of cellulosic biofuels from non-feedstocks are modeled using the BEPAM (Biofuel and Environmental Policy Analysis Model) model to quantifying the uncertainties about induced land use change effects, net greenhouse gas saving potential, and economic costs. The code is in GAMS, general algebraic modeling language. NOTE: Column 3 is titled "BAU" in "merged_BAU.gdx", "merged_RFS.gdx", and "merged_CEM.gdx", but contains "RFS" data in "merged_RFS.gdx" and "CEM" data in "merged_CEM.gdx".
keywords: cellulosic biomass; BEPAM; economic modeling
published: 2023-03-15
This data set is related to the SoyFACE experiments, which are open-air agricultural climate change experiments that have been conducted since 2001. The fumigation experiments take place at the SoyFACE farm and facility in Champaign County, Illinois during the growing season of each year, typically between June and October. - The <i>"SoyFACE Plot Information 2001 to 2021"</i> file contains information about each year of the SoyFACE experiments, including the fumigation treatment type (CO2, O3, or a combination treatment), the crop species, the plots (also referred to as 'rings' and labeled with numbers between 2 and 31) used in each experiment, important experiment dates, and the target concentration levels or 'setpoints' for CO2 and O3 in each experiment. - This data set includes files with minute readings of the fumigation levels (<i>"SoyFACE 1-Minute Fumigation Data Files"</i> folder) from the SoyFACE experiments. The <i>"Soyface 1-Minute Fumigation Data Files"</i> folder contains sub-folders for each year of the experiments, each of which contains sub-folders for each ring used in that year's experiments. This data set also includes hourly data files for the fumigation experiments (<i>"SoyFACE Hourly Fumigation Data Files"</i> folder) created from the 1-minute files, and hourly ambient/weather data files for each year of the experiments (<i>"Hourly Weather and Ambient Data Files"</i> folder). The ambient CO2 and O3 data are collected at SoyFACE, and the weather data are collected from the SURFRAD and WARM weather stations located near the SoyFACE farm. - The <i>"Fumigation Target Percentages"</i> file shows how much of the time the CO2 and O3 fumigation levels are within a 10 or 20 percent margin of the target levels when the fumigation system is turned on. - The <i>"Matlab Files"</i> folder contains custom code (Aspray, E.K.) that was used to clean the <i>"SoyFACE 1-Minute Fumigation Data"</i> files and to generate the <i>"SoyFACE Hourly Fumigation Data"</i> and <i>"Fumigation Target Percentages"</i> files. Code information can be found in the <i>"SoyFACE Hourly Fumigation Data Explanation"</i> file. - Finally, the <i>" * Explanation"</i> files contain information about the column names, units of measurement, and other pertinent information for each data file. *<b>NOTE:</b> We have identified some files in the “SoyFACE 1-Minute Fumigation Data Files” folder in our SoyFACE data set submission that were not downloaded properly - the files were present in the folder, but the actual files were empty. V3 ensures that there are no longer any empty files in the data set.
keywords: SoyFACE; agriculture; agricultural; climate; climate change; atmosphere; atmospheric change; CO2; carbon dioxide; O3; ozone; soybean; fumigation; treatment
published: 2023-03-04
These data represent the raw data from the paper “Evaluating the ability of wetland mitigation banks to replace plant species lost from destroyed wetlands” published in Journal of Applied Ecology in 2023 by Stephen C. Tillman and Jeffrey W. Matthews.
published: 2023-03-06
This dataset includes mass spectrometry, library screening, and gas chromatography data used for creating a high-throughput screening in metabolic engineering.
keywords: mass spectrometry; gas chromatography
published: 2023-02-07
This dataset includes supporting data for our article 'Assessing long-term impacts of cover crops on soil organic carbon in the central U.S. Midwestern agroecosystems'. The dataset contains carbon fluxes and SOC benefits from cover crops at six cover crop experiment sites in Illinois with three rotation systems: (1) without-cover-crop (maize-soybean rotations), (2) non-legume-preceding-maize (maize-annual ryegrass-soybean-annual ryegrass rotations), and (3) legume-preceding-maize (maize-cereal rye-soybean-hairy vetch rotations). <b>*NOTE:</b> there should be 13 files + 1 readme file, instead of 15 files as mentioned in readme.
keywords: Soil organic carbon; cover crops
published: 2021-05-13
Data files and R code to replicate the econometric analysis in the journal article: B Chen, BM Gramig and SD Yun. “Conservation Tillage Mitigates Drought Induced Soybean Yield Losses in the US Corn Belt.” Q Open. https://doi.org/10.1093/qopen/qoab007
keywords: R, Conservation Tillage, Drought, Yield, Corn, Soybeans, Resilience, Climate Change
published: 2022-03-31
This dataset contains our bi-hourly temperature recordings from 40 rocket box style artificial roosts of 5 designs deployed in Indiana and Kentucky, USA from April through September 2019. This dataset also includes our endothermic and faculatively heterothermic daily energy expenditure datasets used in our bioenergetic analysis, which were calculated from the bi-hourly rocket box temperature data. Lastly, we include our overheating counts dataset which summarizes daily overheating events (i.e., temperatures > 40 Celsius) in each rocket box style bat box over the course of the study period, these daily summaries were also calculated from the bi-hourly rocket box temperature recordings.
keywords: artificial roost; bat box; microcllimate; temperature
published: 2022-03-30
This dataset is associated with a larger manuscript published in 2022 in the Illinois Natural History Survey Bulletin to summarize all known records for nonindigenous aquatic mollusks in Illinois, and full sources are referenced within the manuscript. We examined museum holdings, literature accounts, publicly available databases sponsored by the U.S. Geological Survey (USGS) - Nonindigenous Aquatic Species program (http://nas.er.usgs.gov/.) and InvertEBase (invertebase.org). We also included sporadic field survey data of encounters of nonindigenous aquatic species from colleagues within the Illinois Natural History Survey, Illinois Department of Natural Resources, U.S. Fish and Wildlife Service, county forest preserve districts, and other natural resource agencies about their encounters with nonindigenous aquatic mollusk species. Lastly, we examined the role and utility of citizen-science data to document occurrences of nonindigenous aquatic mollusk species. We queried iNaturalist (www.inaturalist.org) for all available nonindigenous freshwater mollusk data for Illinois. Table heading descriptions (if not intuitive) are: “INHS verified” is whether an INHS staff member verified the record by observing vouchered specimen or photograph; “Source” is where a record was accessed or obtained; “individualCount” is number collected or observed in a record; “MuseumCode” is standard museum abbreviation or acronym; “Institution” is source that housed or reported a record, and this also includes the spelled-out museum code; “Collectors” typically indicates who collected the specimen or voucher; “Lat_Long determined by” denotes whether collection coordinates were stated by the collector or by a curator (using inference from data available); “fieldNumber” typically indicates a unique field number that a collector may have used in the field; “identifiedBy” typically explains who identified a specimen or verified a specimen identification.
keywords: Illinois; Exotic species; Non-native aquatic species; NAS; Aquatic Invasive Species; AIS; Mollusk
published: 2023-01-01
The following files were used to reconstruct the phylogeny of the leafhopper subfamily Typhlocybinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5. <b>1) Taxon_sampling.csv:</b> contains the sample IDs (1st column) and the taxonomic information (2nd column). Sample IDs were used in the alignment files and partition files. <b>2) concatenated_nt_complete.phy:</b> a complete concatenated nucleotide dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 154,992 nucleotide positions (intron included) from 665 loci. Hyphens are used to represent gaps. <b>3) concatenated_nt_complete_partition.nex:</b> the partitioning schemes for concatenated_nt_complete.phy. The file partitions the 154,992 nucleotide characters into 426 character sets, and defines the best substitution model for each character set. <b>4) concatenated_cds_complete.phy:</b> a complete concatenated coding DNA sequence dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 153,525 nucleotide positions (intron excluded) from 665 loci. Hyphens are used to represent gaps. <b>5) concatenated_cds_complete_partition.nex:</b> the partitioning schemes for concatenated_cds_complete.phy. The file partitions the 153,525 nucleotide characters into 426 character sets, and defines the best substitution model for each character set. <b>6) concatenated_nt_reduced.phy:</b> a reduced concatenated nucleotide dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 95,076 nucleotide positions (intron included) from 374 loci. Hyphens are used to represent gaps. <b>7) concatenated_nt_reduced_partition.nex:</b> the partitioning schemes for concatenated_nt_reduced.phy. The file partitions the 95,076 nucleotide characters into 312 character sets, and defines the best substitution model for each character set. <b>8) concatenated_aa_complete.phy:</b> a complete concatenated amino acid dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12, corresponding to concatenated_cds_complete.phy. The file lists the sequences of 248 samples with 51,175 amino acid positions from 665 loci. Hyphens are used to represent gaps. <b>9) concatenated_aa_complete_partition.nex:</b> the partitioning schemes for concatenated_aa_complete.phy. The file partitions the 51,175 amino acid characters into 426 character sets, and defines the best substitution model for each character set. <b>10) concatenated_aa_reduced.phy:</b> a reduced concatenated amino acid dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12, corresponding to concatenated_nt_reduced.phy. The file lists the sequences of 248 samples with 31,384 amino acid positions from 374 loci. Hyphens are used to represent gaps. <b>11) concatenated_aa_reduced_partition.nex:</b> the partitioning schemes for concatenated_aa_reduced.phy. The file partitions the 31,384 amino acid characters into 312 character sets, and defines the best substitution model for each character set. <b>12) Individual_gene_alignment.zip:</b> contains 426 FASTA files, each one is an alignment for a gene. Hyphens are used to represent gaps. These files were used to construct gene trees using IQ-TREE v1.6.12, followed by multispecies coalescent analysis using ASTRAL v 4.10.5 based the consensus trees with a minimum average bootstrap value of 70.
keywords: Auchenorrhyncha, Cicadomorpha, Membracoidea, anchored hybrid enrichment
published: 2020-11-25
Video recorded by Louise Barker using a Cannon Powershot camera documents late-season combat behavior in Agkistrodon contortrix. Recorded in Beaufort County, North Carolina, 11.1 km SE of downtown Washington on 21 October 2020.
keywords: Agkistrodon contortrix; combat; mating; reproduction; copperhead; pit viper; Viperidae;
published: 2020-11-06
This data contains bam files and transcripts in the simulated instances generated for the paper 'JUMPER: Discontinuous Transcript Assembly in SARS-CoV-2' submitted for RECOMB 2021. The folder 'bam' contained the simulated bam files aligned using STAR wile the reads were generated using the method polyester Note: in the readme file, close to the end of the document, please ignore this sentence: 'Those files can be opened by using [name of software].'
keywords: transcript assembly; SARS-CoV-2; discontinuous transcription; coronaviruses
published: 2020-10-30
Supporting information for "Urinary Phthalate Metabolite Concentrations and Hot Flashes in Pre- and Perimenopausal Women from the Midlife Women’s Health Study." This file contains tables of the results of stratified analyses of the associations of hot flash outcomes with urinary phthalates metabolites by menopause status, race/ethnicity, body mass index, and depressive status. This file also contains supplementary HPLC methods for the analysis of phthalate metabolites.
keywords: Hot flashes; menopause; phthalates; women
published: 2020-11-05
This version 2 dataset contains 34 files in total with one (1) additional file, called "Culture-dependent Isolate table with taxonomic determination and sequence data.csv". The remaining files (33) are identical to version 1. The following is the information about the new file and its variables: <b>Culture-dependent Isolate table with taxonomic determination and sequence data.csv</b>: Culture table with assigned taxonomy from NCBI. Single direction sequence for each isolate is include if one could be obtained. Sequence is derived from ITS1F-ITS4 PCR amplicons, with Sanger sequencing in one direction using ITS5. The files contains 20 variables with explanation as below: IsolateNumber : unique number identify each isolate cultured Time: season in which the sample was collected Location: the specific name of the location Habitat: type of habitat : either stream or peatland State: state in the USA in which the specific location is located Incubation_pH ID: pH of the medium during isolation of fungal cultures Genus: phylogenetic genus of the fungal isolates (determined by sequence similarity) Sequence_quality: base call quality of the entire sequence used for blast analysis, if known %_coverage: sequence coverage reported from GenBank %_ID: sequence similarity reported from GenBank Life_style : ecological life style if known Phylum: phylogenetic phylum as indicated by Index Fungorum Subphylum: phylogenetic subphylum as indicated by Index Fungorum Class: phylogenetic class as indicated by Index Fungorum Subclass: phylogenetic subclass as indicated by Index Fungorum Order: phylogenetic order as indicated by Index Fungorum Family: phylogenetic Family as indicated by Index Fungorum ITS5_Sequence: single direction sequence used for sequence similarity match using blastn. Primer ITS5 Fasta: sequence with nomenclature in a fasta format for easy cut and paste into phylogenetic software Note: blank cells mean no data is available or unknown.
keywords: ITS1 forward reads; Illumina; peatlands; streams; bogs; fens
published: 2020-12-31
This dataset contains the amino acid and nucleotide alignments corresponding to the phylogenetic analyses of South et al. 2020 in Systematic Entomology. This dataset also includes the gene trees that were used as input for coalescent analysis in ASTRAL.
keywords: Plecoptera; stoneflies; phylogeny; insects
published: 2020-10-27
The data file contains detailed information of the Cochrane reviews that were used in a project associated with the manuscript (working title) "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".
keywords: Cochrane reviews; systematic reviews; randomized control trial; RCT; automation
published: 2020-10-28
We studied we examined the role of stream flow on environmental DNA (eDNA) concentrations and detectability of an invasive clam (Corbicula fluminea), while also accounting for other abiotic and biotic variables. This data includes the eDNA concentrations, quadrat estimates of clam density, and abiotic variables.
keywords: Corbicula; detection probability; eDNA; invasive species; lotic; occupancy modeling
published: 2020-10-27
The data file contains a list of included studies with their detailed metadata, taken from Cochrane reviews which were used in a project associated with the manuscript "Evaluation of an automated probabilistic RCT Tagger applied to published Cochrane reviews".
keywords: Cochrane reviews; automation; randomized controlled trial; RCT; systematic review
published: 2022-12-28
The effect of pesticide contamination on arthropod biomass and diversity in simulated prairie restorations depended on arthropod feeding guild (e.g., predator, herbivore, or pollinator). The pesticides used in this study were the neonicotinoid insecticide clothianidin and the phthalimide fungicide captan. This dataset includes two data files. The first contains information about the study sites ("plots") and pesticide treatments. The second contains information about arthropod biomass and morphospecies richness separated by feeding guild for each month-plot combination. R code in an R Markdown file for the analysis and data presentation in the associated publication is also provided. Detected effects included: predator biomass was 66% lower in plots treated with clothianidin, and this effect persisted across the growing season; the impact on herbivore biomass appeared to be inconsistent, with biomass being 51% lower with clothianidin in June but no detected difference in July or August; herbivore morphospecies richness was 12% lower in plots treated with both clothianidin and captain; pollinators appeared to be unaffected by clothianidin; and pollinator biomass increased by 71% when captan was applied to a plot.
keywords: Arthropod decline; pesticide; clothianidin; captan; habitat restoration; trophic effects; insects
published: 2022-12-11
The data are original electron micrographs from the lab of the late Dr. Burt Endo of the USDA. These data were digitized from photographic prints and glass plate negatives at 600 DPI as 16 bit TIFF files. This fourth version added 6 new ZIP files from the Endo data collection. "Endo folder database.xlsx" is updated to reflect the addition. Information in "Readme_FileNameFormatting.docx" remains the same as in V3.
keywords: Heterodera glycines; Meloidogyne incognita; Burt Endo; nematode
published: 2022-12-07
The Morrow Plots at the University of Illinois at Urbana-Champaign are the longest-running continuous experimental plots in the Americas. In continuous operation since 1876, the plots were established to explore the impact of crop rotation and soil treatment on corn crop yields. In 2018, The Morrow Plots Data Curation Working Group began to identify, collect and curate the various data records created over the history of the experiment. The resulting data table published here includes planting, treatment and yield data for the Morrow Plots since 1888. Please see the included codebook for a detailed explanation of the data sources and their content. This dataset will be updated as new yield data becomes available. *NOTE: While digitized and accessed through IDEALS, the physical copy of the field notebook: <a href="https://archon.library.illinois.edu/archives/index.php?p=collections/controlcard&id=11846">Morrow Plots Notebook, 1876-1913, 1967</a> is also held at the University of Illinois Archives.
keywords: Corn; Crop Science; Experimental Fields; Crop Yields; Agriculture; Illinois; Morrow Plots
published: 2022-11-28
The compiled datasets include county-level variables used for simulating miscanthus and switchgrass production in 2287 counties across the rainfed US including 5-year (2012-2016) averaged growing season degree days (GDD), 5-year (2012-2016) averaged growing season cumulative precipitation, National Commodity Crop Productivity Index (NCCPI) values, regional dummies (only for miscanthus), the regional-level random effect of the yield response function, N price, land cash rent, the first year fixed cost (only for switchgrass), and separate datasets for simulating an alternative model assuming a constant N rate. The GAMS codes are used to run the simulation to obtain the main results including the age-varying profit-maximizing N rate, biomass yields, and annual profits for miscanthus and switchgrass production across counties in the rainfed US. The STATA codes are used to merge and analyze simulation results and create summary statistics tables and key figures.
keywords: Age; Miscanthus; Net present value; Nitrogen; Optimal lifespan; Profit maximization; Switchgrass; Yield; Center for Advanced Bioenergy and Bioproducts Innovation
published: 2022-11-28
Detection data of carnivores and their prey species from camera traps in Fort Hood, Texas and Santa Cruz, California, USA. Non-carnivore and non-prey species (humans, domestic species, avian species, etc.) were excluded from this dataset. All detections of each species at a camera within 30 minutes have been combined to 1 detection (only first detection within that 30 minutes kept) to avoid pseudoreplication. Variable Description: Site= Study area data were collected MonitoringPeriod= year in which data was collected (data were collected at each location over multiple monitoring periods) CameraName= Unique name for each camera location Date= calendar date of detection Time= time of detection -Fort Hood= Central Time USA -Santa Cruz= Pacific Time USA Species= Common name of species detected
keywords: carnivore; community ecology; competition; interspecific interactions; keystone species; mesopredator; predation; trophic cascade