Datasets

This dataset contains BEPAM model code and input data to the replicate the results for "Assessing the Returns to Land and Greenhouse Gas Savings from Producing Energy Crops on Conservation Reserve Program Land." The dataset consists of: (1) The replication codes and data for the BEPAM model. The code file is named as output_0213-2020_Complete_daycent-agversion-[rental payment level]%_[biomass price].gms. (BEPAM-CRP model-Sep2020.zip) (2) Simulation results from the BEPAM model (BEPAM_Simulation_Results.csv) * Item (1) is in GAMS format. Item (2) is in text format.

Datasets that accompany Beilke, Blakey, and O'Keefe 2021 publication (Title: Bats partition activity in space and time in a large, heterogeneous landscape; Journal: Ecology and Evolution).

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

This dataset includes five files developed using the procedures described in the article 'Developing County-level Data of Nitrogen Fertilizer and Manure Inputs for Corn Production in the United States' and Supplemental Information published in the Journal of Cleaner Production in 2021. Citation: Xia, Yushu, Hoyoung Kwon, and Michelle Wander. "Developing county-level data of nitrogen fertilizer and manure inputs for corn production in the United States." Journal of Cleaner Production 309 (2021): e126957. Brief method: The fertilizer and manure inputs for corn were generated with a top-down approach by assigning county-level total N inputs reported by USGS to different crops using state- and county-level survey data. The corn N needs were estimated using empirical extension-based equations coupled with soil and environmental covariates. The estimates of fertilizer N inputs were further refined for corn grain and silage production at the county level and gap-filling (using state-level averages) was carried out to generate final files for U.S. county-level N inputs. The dataset is provided in an alternative format in Google Earth Engine: https://code.earthengine.google.com/13a0078e7ee727bc001e045ad0e8c6fc

Survey questions and data collected from Illinois land managers on practices and knowledge relating to impacts to wildlife. 0s indicated non-selection, 1s indicate selection of answer.

The data provided in this submission are the gene annotations for the Illinois EBP pilot project samples, as well as the predicted proteins for each sample in FASTA format.

Photographs and video of two Lesser Chameleons (Furcifer minor) nesting together at the same time near Itremo, Madagascar.

Photographs and video of the snake Compsophis infralineatus predating upon the chameleons Calumma crypticum and Calumma gastrotaenia near Mandraka, Madagascar.

These data were used to make a predictive model of when ornate box turtles (Terrapene ornata) are likely to be above ground and at risk from fire. The data were generated using shell temperatures, soil temperatures at 0.35 m deep from known overwintering sites, and the spring and fall soil temperature inversion dates during 2019–2022 to infer if 26 individual radio-tracked turtles were above or below ground at three sites in Illinois.

This dataset contains: field study design parameters, plant performance metrics, and nitrogen cycling rates associated with a field experiment that compared nitrification rates between maize lines with and without nitrification inhibition loci nitrogen fixation rates with with and without a nitrogen fixing inoculant product. The overarching goal was to evaluate nitrogen fixation by a diazotroph inoculant and retention of nitrogen in the rhizosphere via a novel nitrification inhibition phenotype of maize.

These data are the result of analyses of the metagenome of North American bats, including 18s and 16s barcode genes designed to target microorganisms of the gut. These files are Phyloseq import files created by the DADA2 program. Each barcode gene is uploaded separately as the four files required to build a phyloseq object. For each barcode gene, the files include amplicon sequence variant (ASV) sequences, sequence tables (seqtab) which connect individual samples to the ASVs, tax tables (taxtab) which identify the taxa present as determined by a Bayesian RDP classifier, and rooted phylogenetic trees for the ASVs. Additionally, we have included a "sample_data" file which is necessary for sorting of samples across all four sequence analysis data sets by study and species. Some sample information which could identify the location of endangered species has been restricted. Multiple studies are represented in the data which can be accessed using standard methods in the Phyloseq program (e.g. For a study of bats, parasites, and gut microbiome dysregulation by Bennett, Suski, and OKeefe 2024 [in prep March 2024], study specific data can be accessed using the Study variable "DYSBIOMICS." File names include reference to the primer set used to generate them (18s primer sets: G3, G4, G6; 16s primer set: 341F3_806R5).

The following files were used to reconstruct the phylogeny of the Megophthalmidae and Ulopidae. Taxon_sampling.csv: contains the sample IDs (1st column) which were used in the alignments and the taxonomic information (2nd to 6th columns). concatenated_aa_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_aa.phy. This file partitions the 52,474 amino acid positions into 427 character sets. concatenated_aa_.phy: a concatenated amino acid dataset with 52,474 amino acid positions. This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps. concatenated_nt_partition.nex: the partitioning schemes for the maximum likelihood analysis using concatenated_nt.phy. This file partitions the 158,364 nucleotide positions into 427 character sets. concatenated_nt_.phy: a concatenated nucleotide dataset with 158,364 nucleotide positions. This dataset was used for the maximum likelihood analysis by IQ-TREE v1.6.12. Hyphens are used to represent gaps. Individual_gene_alignment.zip: contains 427 FASTA files, each one represents the nucleotide 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.

This file contains the delta 15N values for leaf material collected from Cyathea rojasiana tree ferns before and after fertilization using ammonium -15N chloride solution to determine whether 15N update is possible from senescent leaves. Details of the experiment are provided in the online supplement to the published paper. Briefly, In February 2022 we selected three mature C. rojasiana individuals 1-1.5m in height that had leaves rooted in the soil and one new developing (but unexpanded) leaf. For each fern, two plastic pots (10 x 10 x 12 cm) were filled with a 50:50 mixture of washed river sand and soil from the Chorro watershed. For each pot, one senescent leaf that was rooted in the soil was carefully excavated and its roots transplanted into the pot. Pots were then fertilized by adding 30 ml of a 0.02 M 15N solution of ammonium-15N chloride (98% 15N; Sigma-Aldrich 299251; St Louis, MO) to yield a target concentration of 2 µg15N cm-3 of soil. After fertilization pots were carefully enclosed within thick plastic bags, and sealed around the senescent leaf rachis to prevent leaching any of 15N from the pot to the surrounding soil. At the time of N fertilization, pinnae of the youngest fully expanded leaf were collected from each fern. One pinna was collected from the base of the leaf and one from the distal end of the leaf. In March 2022, after 28 days the roots were removed from pots and two additional leaf pinnae sampled from each fern: one from the base and one from the distal end of the youngest (now fully expanded) leaf. Leaf samples were dried for 72 hours at 60 C and then leaf lamina tissue finely ground with a bead beater. The delta 15N for each leaf sample determined at the University of Illinois, Urbana-Champaign using a Thermo Delta V Advantage IRMS run in combination with a Costech 4010 Elemental Analyzer. Samples were run in continuous flow relative to laboratory standards that were calibrated with USGS 40, 41, and NBS 19 reference materials.

Data associated with the manuscript "Stable isotopes and diet metabarcoding reveal trophic overlap between native and invasive Banded Killifish (Fundulus diaphanus) subspecies." by Jordan H. Hartman, Mark A. Davis, Nicholas J. Iacaruso, Jeremy S. Tiemann, Eric R. Larson. For this project, we sampled six locations in Michigan and Illinois for Eastern and Western Banded Killifish and primary consumers. Using stable isotope analysis we found that Eastern Banded Killifish had higher variance in littoral dependence and trophic position than Western Banded Killifish, but both stable isotope and gut content metabarcoding analyses revealed an overlap in the diet composition and trophic position between the subspecies. This dataset provides the sampling locations, accession numbers for gut content metabarcoding data from the National Center for Biotechnology Information Sequence Read Archive, the assignment of each family used in the gut content metabarcoding analysis as littoral, pelagic, terrestrial, or parasite. and the raw stable isotope data from University of California Davis.

These are the responses to an open, convenience sample survey of residents of Illinois to understand their interactions with wild deer. The survey was available on REDCap between December 19, 2022 and December 19, 2023, and was publicized through listserves, Facebook groups, and media reporting. The file "COVID Deer Survey _ REDCap.pdf" contains the codebook for the survey, including the questions; all factor variables have ".factor" added to their name in the dataset. The file "DeerSurveyData.csv" contains the dataset. The file "Score_calculation_for_sharing.R" is the code to create the cleaned dataset used for analysis from the raw survey responses. Throughout, NA is used to represent null/not available/not applicable; this is most likely either a failure to answer the question or, in some cases, a question that was not presented as it is not relevant based on answers to previous questions.

These are the datasets underlying the figures in the manuscript "Methods of active surveillance for hard ticks and associated tick-borne pathogens of public health importance in the contiguous United States: A Comprehensive Systematic Review". The review considered only publications reporting on active tick or tick-borne pathogen surveillance in the contiguous United States published between 1944 and 2018. For the purposes of this review, we were only concerned with studies of Ixodidae (hard ticks) and/or studies of tick-borne pathogens (in humans, animals, or hard ticks) of public health importance to humans. Study designs included cross-sectional, serological, epidemiological, ecological, or observational studies. Only peer-reviewed publications published in the English language were included. Studies were excluded if they focused on a tick that is not a vector of a human pathogen or on a pathogen that does not cause disease in humans, if the tick or tick-borne pathogen findings were incidental, or if they did not include quantitative surveillance data. For the purpose of this study, we defined surveillance data as information on ticks or pathogens provided through active sampling in natural areas; it should be noted that this does not match the strict definition used by the CDC, which requires sustained sampling efforts across time. Studies were also excluded if they: explored regions other than the contiguous US; focused on treatment, vaccine, or therapeutics development and/or diagnostics of human disease; focused on tick or pathogen genetics; focused on experimental studies with ticks or hosts; were tick control and/or management studies; performed only passive surveillance; were review articles; were not peer reviewed; were in a language other than English; the full text was not available; and if the disease was not a risk to the general public. In addition, for articles which reported data that had previously been published, we only included previously unreported information collected by the authors, and we referenced the specific period of collection for these data to ensure we were not double-recording data. Due to publication delays, we also performed a non-systematic review of the literature of articles published between 2019 – 2023 on tick and tickborne pathogen surveillance methods conducted in the contiguous United States. Keyword search was performed in PubMed Central and Web of Science Core Collection databases. The search algorithm keywords included tick(s), Amblyomma, Dermacentor, Ixodes, Rhipicephalus, Acari Ixodidea, tick host(s), Lyme disease, Rocky Mountain Spotted Fever, Spotted Fever Group, Rickettsiosis, Ehrlichiosis, Anaplasmosis, Borreliosis, Tularemia, Babesiosis, tick-borne pathogen, Powassan, Heartland, Bourbon, Colorado tick fever, Pacific Coast tick fever, tick surveillance, surveillance, (sero)epidemiology, prevalence, distribution, ecology, United States. The search algorithm utilized is provided as follows: TI= ((ticks OR Ixodes OR Amblyomma OR Dermacentor OR Rhipicephalus OR "Acari Ixodidi" OR "tick hosts" OR "tick host") OR ("Lyme Disease" OR "Rocky Mountain Spotted Fever" OR "Spotted Fever Group" OR Rickettsiosis OR Rickettsial OR Ehrlichiosis OR Anaplasmosis OR Borreliosis OR Tularemia OR Babesiosis OR Borrelia OR Ehrlichia OR Anaplasma OR Rickettsia OR Babesia OR "tick-borne pathogen" OR "tick borne pathogen")) AND TS= ("tick surveillance" OR surveillance OR epidemiology OR seroepidemiology OR ecology) AND CU=("United States of America" OR "USA" OR "United States" OR United-States). These datasets are the collated data underlying the figures in the manuscript. For more details, please see the publication. The following are explanations for variables used in all the CSV files: Tick: Species of tick collected Tick_Method: Method of collecting ticks Pathogen: Species of pathogen tested for Path_Method: Method of testing for pathogens Decade: Decade of publication n: Number of publications STATE: state in which study was conducted COUNTY: county in which study was conducted 1944 - 2018 (Was surveillance performed?): was there at least one publication included with a publication date within the 1944-2018 period in this geographic region? 2019 - 2023 (Was surveillance performed?): was there at least one publication included with a publication date within the 2019-2023 period in this geographic region?

This accompanying study is published under the title "Estimating soil N2O emissions induced by organic and inorganic fertilizer inputs using a Tier-2, regression-based meta-analytic approach for U.S. agricultural lands" at Science of the Total Environment. The study is authored by Dr. Yushu Xia, Dr. Hoyoung Kwon, and Dr. Michelle Wander. The DOI for this study is <a href="https://doi.org/10.1016/j.scitotenv.2024.171930">https://doi.org/10.1016/j.scitotenv.2024.171930</a>.

This data publication provides example video clips related to research on association among flight ability of juvenile songbirds at fledging and juvenile morphological traits (wing emergence, wing length, body condition, mass, and tarsus length. File names reflect the species dropped in each video. These videos are supplemental material for scientific publications by the authors and reflect an example subset of all videos collected form 2017-2018 as part of a larger study on the post-fledging ecology of grassland and shrubland birds in east-Central Illinois, USA. No birds were harmed/injured in the production of these videos and procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 18221. Individuals depicted in the videos have given consent for the videos to be shared (talent/model release form; <a href="https://publicaffairs.illinois.edu/resources/release/">https://publicaffairs.illinois.edu/resources/release/</a>)

The text file contains the original DNA nucleotide sequence data used in the phylogenetic analyses of Xue et al. (in review), comprising the 13 protein-coding genes and 2 ribosomal gene subunits of the mitochondrial genome. 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 30 taxa (species) and 13078 characters, 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 positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes (version 3.2.6) beginning near the end of the file. The mrbayes block also contains instructions for MrBayes on various non-default settings for that program. These are explained in the Methods section of the submitted manuscript. 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 individual mitochondrial genes and for different codon positions of the protein-coding genes used for analyses in the programs MrBayes and IQ-Tree (version 1.6.8) (Table S2). Full citations for references listed in Table S1 can be found by searching GenBank using the corresponding accession number. The supplemental tables will also be linked to the article upon publication at the journal website.

Aerial imagery utilized as input in the manuscript "Deep convolutional neural networks exploit high spatial and temporal resolution aerial imagery to predict key traits in miscanthus" . Data was collected over M. Sacchariflorus and Sinensis breeding trials at the Energy Farm, UIUC in 2020. Flights were performed using a DJI M600 mounted with a Micasense Rededge multispectral sensor at 20 m altitude around solar noon. Imagery is available as tif file by field trial and date (10). The post-processing of raw images into orthophoto was performed in Agisoft Metashape software. Each crop surface model and multispectral orthophoto was stacked into an unique raster stack by date and uploaded here. Each raster stack includes 6 layers in the following order: Layer 1 = crop surface model, Layer 2 = Blue, Layer 3 = Green, Layer 4 = Red, Layer 5 = Rededge, and Layer 6 = NIR multispectral bands. Msa raster stacks were resampled to 1.67 cm spatial resolution and Msi raster stacks were resampled to 1.41 cm spatial resolution to ease their integration into further analysis. 'MMDDYYYY' is the date of data collection, 'MSA' is M. Sacchariflorus trial, 'MSI' is Miscanthus Sinensis trial, 'CSM' is crop surface model layer, and 'MULTSP' are the five multispectral bands.

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.

This repository includes scripts and datasets for the paper, "Statistically consistent divide-and-conquer pipelines for phylogeny estimation using NJMerge." All data files in this repository are for analyses using the logdet distance matrix computed on the concatenated alignment. Data files for analyses using the average gene-tree internode distance matrix can be downloaded from the Illinois Data Bank (https://doi.org/10.13012/B2IDB-1424746_V1). The latest version of NJMerge can be downloaded from Github (https://github.com/ekmolloy/njmerge).<br /> <strong>List of Changes:</strong> &bull; Updated timings for NJMerge pipelines to include the time required to estimate distance matrices; this impacted files in the following folder: <strong>data.zip</strong> &bull; Replaced "Robinson-Foulds" distance with "Symmetric Difference"; this impacted files in the following folders: <strong> tools.zip; data.zip; scripts.zip</strong> &bull; Added some additional information about the java command used to run ASTRAL-III; this impacted files in the following folders: <strong>data.zip; astral64-trees.tar.gz (new)</strong>

Data associated with the manuscript "Niche conservatism and spread explain hybridization and introgression between native and invasive fish" by Jordan H. Hartman, Joel B. Corush, Eric R. Larson, Jeremy S. Tiemann, Philip Willink, and Mark A. Davis. For this project, we combined results of ecological niche models (ENMs) and next-generation restriction site-associated DNA sequencing (RADseq) to test theories of niche conservatism and biotic resistance on the success of invasion, hybridization, and extent of introgression between native Western Banded Killifish and non-native Eastern Banded Killifish. This dataset provides the sampling locations and number of Banded Killifish in each population, accession numbers for RADseq from the National Center for Biotechnology Information Sequence Read Archive and the assignment of each Banded Killifish, the habitat associations of each population from the ENMs, and the occurrence points used to build the ENMs.

This is the dataset for the manuscript titled, "Differing physiological performance of coexisting cool- and warmwater fish species under heatwaves in the Midwestern United States"

This data set is related to a SoyFACE experiment conducted in 2004, 2006, 2007, and 2008 with the soybean cultivars Loda and HS93-4118. The experiment looked at how seed elements were affected by elevated CO2 and yield. In this V2, 2 new files were added per journal requirement. Total there are 5 data files in text format within the digrado_et_al_gcb_data_V2 and 1 readme file. The name of files are listed below. Details about headers are explained in the readme.txt file. <b>1. ionomic_data.txt file</b> contains the ionomic data (mg/kg) for the two cultivars. The file contains all six technical replicates for each plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>2. yield_data.txt file</b> contains the yield data for the two cultivars (seed yield in kg/ha, seed yield in bu/a, Protein (%), Oil (%)). The file contains yield data for every plot. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>3. mineral_pro_oil_yield.txt file</b> contains the yield per hectare for each mineral (g/ha) along with the yield per hectare for protein and oil (t/ha). This was obtained by multiplying the seed content of each element (minerals, protein, and oil) by the total seed yield. The file contains yield data for every plots. The cultivar, year, treatment, and the plot from which the samples were collected are given for each entry. <b>4. economic_assessment.txt file</b> contains data used to assess the financial impact of altered seed oil content on soybean oil production. <b>5. meteorological_data.txt file</b> contains the meteorological data recorded by a weather station located ~ 3km from the experimental site (Willard Airport Champaign). Data covering the period between May 28 and September 24 were used for 2004; between May 25 and September 24 were used in 2006; between May 23 and September 17 in 2007; and between June 16 and October 24 in 2008.