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published: 2023-09-20
Dataset includes bee trait information and species abundance information for bees collected at 29 forests plots in southern Illinois, USA. Plots are located within three public land sites. Environmental data were also collected for each of the 29 plots.
keywords: wild bees; forest management; functional traits
has sharing link
published: 2023-09-01
An online and paper knowledge, attitudes, and practices survey on ticks and tick-borne diseases (TBD) was distributed to farmers in Illinois during summer 2020 to spring 2022 (paper version titled Final Draft Farmer KAP_v.SoftCopy_Revised.docx). These are the raw data associated with that survey and the survey questions used (FarmerTickKAPdata.csv, data dictionary in Data Description.docx). We have added calculated values (columns 286 to end, code for calculation in FarmerKAPvariableCalculation.R), including: the tick knowledge score, TBD knowledge score, and total knowledge score, which are the sum of the total number of correct answers in each category, and score percent, which are the proportion of correct answers in each category.
keywords: ticks; survey; tick-borne disease; farmer
published: 2023-08-11
This dataset contains leaf photosynthetic and biochemical traits, plant biomass, and yield in five C3 crops (chickpea, rice, snap bean, soybean, wheat) and four C4 crops (sorghum, maize, Miscanthus × giganteus, switchgrass) grown under ambient and elevated O3 concentration ([O3]) in the field at free-air O3 concentration enrichment (O3-FACE) facilities over the past 20 years.
keywords: C3 and C4 crops; elevated O3; FACE; photosynthesis; yield
published: 2023-08-04
Data are provided that are relevant to the rare plant Phlox pilosa ssp. sangamonensis, or Sangamon phlox, and other members of the genus that occur in its native range. Sangamon phlox is a state-endangered subspecies that is only known to occur in two Illinois counties. Data provided come from all known Sangamon phlox populations, which we estimate as 10 separate populations. Data include genetic data from DNA microsatellite loci (allele sizes and basic summaries), flowering population size estimates, rates of fruit set, and rates of seed set. Additionally, genetic data (from microsatellites) are provided for Phlox divaricata ssp. laphamii (three populations), Phlox pilosa ssp. pilosa (two populations), and Phlox pilosa ssp. fulgida (two populations).
keywords: Phlox; conservation genetics; microsatellites; endemism; rare plants
published: 2023-07-27
The text file contains the original aligned DNA nucleotide sequence data used in the phylogenetic analyses of Feng et al. (in review), comprising the 3 protein-coding genes (histone H3, cytochrome oxidase I and 2) and 2 ribosomal genes (28S D8 and 16S). The text file is marked up according to the standard NEXUS format commonly used by various phylogenetic analysis software packages. The file will be parsed automatically by a variety of programs that recognize NEXUS as a standard bioinformatics file format. The first six lines of the file identify the file as NEXUS, indicate that the file contains data for 257 taxa (species) and 2995 characters (nucleotide positions), indicate that the characters are DNA sequence, that gaps inserted into the DNA sequence alignment are indicated by a dash, and that missing data are indicated by a question mark. The remainder of the file contains the aligned nucleotide sequence data for the five genes. Data partitions, representing the individual genes and different codon positions of the protein-coding genes, are indicated by the lines beginning "charset" near the end of the file. Two supplementary tables in the provided PDF file provide additional information on the species in the dataset, including the GenBank accession numbers for the sequence data (Table S1) and the DNA substitution models used for each of the data partitions used for analyses in the phylogenetic analysis program IQ-Tree (version 1.6.8) (Table S3), as described in the Methods section of the paper. The supplemental tables will also be linked to the article upon publication at the journal website.
keywords: Insect; leafhopper; dispersal; vicariance; evolution
published: 2023-07-05
Complete soils dataset for the La Planada forest dynamics plot associated with publication: John et al. (2007) "Soil nutrients influence the spatial distributions of tropical tree species" PNAS 104:864-869 www.pnas.org/cgi/doi/10.1073/pnas.0604666104
keywords: tropical forest soil; montane forest; cation availability; spatial distribution of tree species
published: 2023-07-01
This is the data used in the paper "Assessment of spatiotemporal flood risk due to compound precipitation extremes across the contiguous United States". Code from the Github repository https://github.com/adtonks/precip_extremes can be used with the data here to reproduce the paper's results. v1.0.0 of the code is also archived at https://doi.org/10.5281/zenodo.8104252 This dataset is derived from NOAA-CIRES-DOE 20th Century Reanalysis V3. The NOAA-CIRES-DOE Twentieth Century Reanalysis Project version 3 used resources of the National Energy Research Scientific Computing Center managed by Lawrence Berkeley National Laboratory which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231 and used resources of NOAA's Remotely Deployed High Performance Computing Systems.
keywords: spatiotemporal; CONUS; United States; precipitation; extremes; flooding
planned publication date: 2024-01-01
Supplementary data tables for the dissertation "Hybridization dynamics and population genomics of a Manacus hybrid zone." This work focuses on the dynamics of hybridization over time in two species of tropical birds, the golden-collared manakin (Manacus vitellinus) and white-collared manakin (Manacus candei) comparing data from historical museum samples and contemporary wild-caught birds. Table A1 contains the sample metadata for the Manacus Restriction site-associated DNA sequencing dataset used in the dissertation with associated NCBI Biosample Accession numbers, Smithsonian Museum of Natural History number (where applicable), sample IDs, sampling site locations, and sample information of year the sample was taken, age, and sex. Table A6 contains phenotypic measurements of male plumage traits of manakins used in cline analyses to assess hybrid zone movement over time in historical and contemporary datasets, including beard length (mm), epaulet width (mm), tail length (mm), collar color (nm), and belly color (nm). Table A7 contains a summary of male plumage measurements across the hybrid zone. Table C1 contains a list of annotated protein coding genes in candidate regions of interest in Manacus genomes using outlier regions of genomic divergence, linkage disequilibrium, and enrichment of parental private alleles.
keywords: csv; manacus; manakin; genomics; dissertation
published: 2023-07-28
The dataset is for a study conducted to understand genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus. We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single nucleotide polymorphisms (SNPs).
keywords: Miscanthus sacchariflorus; genome-wide association analysis; genomic prediction; bioenergy; biomass
published: 2023-07-26
This data set contains data used for “Improved Net Carbon Budgets in the US Midwest through Direct Measured Impacts of Enhanced Weathering.” Data include biomass, soil bulk densities, soil respiration measurements, soil lanthanide element analysis, plant tissue analysis for major cations, and eddy covariance fluxes.
keywords: agriculture; bioenergy crop; carbon budget; eddy covariance; net ecosystem carbon balance; net primary production; soil respiration; enhanced weathering; carbon dioxide removal; Illinois
has sharing link
published: 2023-07-14
This dataset includes a total of 300 images of 45 extant species of Podocarpus (Podocarpaceae) and nine images of fossil specimens of the morphogenus Podocarpidites. The goal of this dataset is to capture the diversity of morphology within the genus and create an image database for training machine learning models. The images were taken using Airyscan confocal superresolution microscopy at 630x magnification (63x/NA 1.4 oil DIC). The images are in the CZI file format. They can be opened using Zeiss propriety software (Zen, Zen lite) or open microscopy software, such as ImageJ. More information on how to open CZI files can be found here: [https://www.zeiss.com/microscopy/us/products/microscope-software/zen/czi.html#microscope---image-data]
keywords: superresolution microscopy; Zeiss Airyscan; CZI images; conifer; saccate pollen
published: 2023-05-30
Primary occurrence data for Clem, Hart, & McElrath. 2023. A century of Illinois hover flies (Diptera: Syrphidae): Museum and citizen science data reveal recent range expansions, contractions, and species of potential conservation significance. Included are a license.txt file, the cleaned occurrences from each of the six merged datasets, and a cleaned, merged dataset containing all occurrence records in one spreadsheet, formatted according to Darwin Core standards, with a few extra fields such as GBIF identifiers that were included in some of the original downloads.
keywords: csv; occurrences; syrphidae; hover flies; flies; biodiversity; darwin core; darwin-core; GBIF; citizen science; iNaturalist
published: 2023-02-10
Data and documentation for Ornithological Applications manuscript “Integrating multiple data sources improves prediction and inference for upland game bird occupancy models” by Robert L. Emmet, Thomas J. Benson, Maximilian L. Allen, and Kirk W. Stodola We combined data from the North American Breeding Bird Survey and eBird with a targeted survey (IDNR upland game) to estimate habitat use of northern bobwhite and ring-necked pheasant in Illinois and to document the efficiency and overlap among the various data sources. Data include, eBird, USGS Breeding Bird Survey, National Land Cover Database, Upland game bird surveys, stream data)
keywords: data integration; occupancy; avian population modelling; northern bobwhite;Colinus virginianus; ring-necked pheasant; Phasianus colchicus
published: 2023-07-10
Bee movement between habitat patches in a naturally fragmented ecosystem depended on species, patch, and matrix variables. Using a mark-recapture methodology in the naturally fragmented Ozark glade ecosystem, we assessed the importance of bee size, nesting biology, the distance between patches (e.g., isolation), and nesting and floral resources in habitat patches and the surrounding matrix on bee movement. This dataset includes seven data files, three R code files, and a QGIS tool. Three of the data files include information collected at the study sites with regard to bees and matrix and patch characteristics. The other four data files are spatial files used to quantify the characteristics of the forest canopy between the study sites and the edge-to-edge distances between the study sites. R code in the R Markdown file recreates the analysis and data presentation for the associated publication. R script files contain processes for calculating some of the explanatory variables used in the analysis. The QGIS tool can be used as the first step to obtaining average values from a raster file where the cells are large relative to the areas of interest (AOI) that you would like to characterize. The second step is contained in one of the aforementioned R scripts. Detected effects included: Larger bees were more likely to move between patches. Bee movement was less likely as the distance between patches increased. However, relatively short distances (~50 m) inhibited movement more than our a priori expectations. Bees were unlikely to move away from home patches with abundant and diverse floral and below-ground nesting resources. When home patches were less resource-rich, bee movement depended on the characteristics of the away patch or the matrix. In these cases, bees were more likely to move to away patches with greater below-ground nesting and floral resources. Matrix habitats with more available floral and below-ground nesting resources appear to impede movement to neighboring patches, potentially because they already provide supplemental resources for bees.
keywords: habitat fragmentation; bees; movement; mark-recapture; nesting resources; floral resources; isolation
published: 2023-07-05
This dataset contains all data used in the paper "Impact of genotype-calling methodologies on genome-wide association and genomic prediction in polyploids". The dataset includes genotypes and phenotypic data from two autotetraploid species Miscanthus sacchariflorus and Vaccinium corymbosum that was used used for genome wide association studies and genomic prediction and the scripts used in the analysis. In this V2, 2 files have the raw data are added: "Miscanthus_sacchariflorus_RADSeq.vcf" is the VCF file with the raw SNP calls of the Miscanthus sacchariflorus data used for genotype calling using the 6 genotype calling methods. "Blueberry_data_read_depths.RData" is the a RData file with the read depth data that was used for genotype calling in the Blueberry dataset.
keywords: Polyploid; allelic dosage; Bayesian genotype-calling; Genome-wide association; Genomic prediction
published: 2022-12-21
This dataset is associated with a larger manuscript published in 2022 in the Illinois Natural History Survey Bulletin that summarized the Fishes of Champaign County project from 2012-2015. With data spanning over 120 years, the Fishes of Champaign County is a comprehensive, long-term investigation into the changing fish communities of east-central Illinois. Surveys first occurred in Champaign County in the late 1880s (40 sites), with subsequent surveys in 1928–1929 (125 sites), 1959–1960 (143 sites), and 1987–1988 (141 sites). Between 2012 and 2015, we resampled 122 sites across Champaign County. The combined data from these five surveys have produced a unique perspective into not only the fish communities of the region, but also insight into in-stream habitat changes during the past 120 years. The dataset is in Microsoft Access format, with five data tables, one for each time period surveyed. Field names are self-explanatory, with some variation in data types collected during different surveys as follows: Forbes & Richardson (1880s) collected presence/absence only. Thompson & Hunt (1928-1929) collected abundance only, Larimore & Smith (1959-1960) collected length and weight for some samples, but only presence/absence at others. In some cases, fish of the same species were weighed in bulk, with the fields “LOW” and “HIGH” indicating the lower and upper limits of total length in the batch, and weight indicating the gross weight of all fish in the batch. Larimore and Bayley (1987-1988) collected length and weight for all surveys, and Sherwood and Stein (2012-2015) collected length and weight for all surveys except for cases where extremely abundant single species where subsampled. Lengths are reported in millimeters, and weight in grams. Two lookup tables provide information about species codes used in the data tables and sample site location and notes.
keywords: fishes of Champaign County; streams; anthropogenic disturbances; long-term dataset
published: 2023-06-01
Results of RT-LAMP reactions for influenza A virus diagnostic development.
keywords: swine influenza; LAMP; gBlock
published: 2023-03-08
A stochastic domination analysis model was developed to examine the effect that emerging carbon markets can have on the spatially varying returns and risk profiles of bioenergy crops relative to conventional crops. The code is written in MATLAB, and includes the calculated output. See the README file for instructions to run the code.
keywords: bioenergy crops; economic modeling; stochastic domination analysis model;
published: 2023-05-02
This dataset includes structural MRI head scans of 32 piglets, at 28 days of age, scanned at the University of Illinois. The dataset also includes manually drawn brain masks of each of the piglets. The dataset also includes brain masks that were generated automatically using Region-Based Convolutional Neural Networks (Mask R-CNN), trained on the manually drawn brain masks.
keywords: Brain extraction; Machine learning; MRI; Piglet; neural networks
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