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Datasets

published: 2023-12-01
 
Mist netting data for little brown bats (Myotis lucifugus) in McHenry County, Illinois and output of acoustic data processed using Kaleidoscope (Version 5.1.9, Bats of North America 5.1.0; Wildlife Acoustics) auto-identification software. Associated survey metadata and landcover metrics calculated using Fragstats included.
keywords: little brown bats; mist netting; acoustics
published: 2024-02-08
 
This dataset contains transcribed entries from the "Prairie Directory of North America" (Adelman and Schwartz 2013) for the Tallgrass, Mixed Grass, and Shortgrass prairie regions of the united states. We identified the historical spatial extent of the Tallgrass, Mixed Grass, and Shortgrass prairie regions using Ricketts et al. (1999), Olson et al. (2001), and Dixon et al. (2014) and selected the counties entirely or partially within these boundaries from the USDA Forest Service (2022) file. The resulting lists of counties are included as separate files. The dataset contains information on publicly accessible grasslands and prairies in these regions including acreage and amenities like hunting access, restrooms, parking, and trails.
keywords: grasslands; prairies; prairie directory of north america; site amenities; site attributes
published: 2019-02-07
 
This dataset contains all data used in the two studies included in "PICAN-PI..." by Nute, et al, other than the original raw sequences. That includes: 1) Supplementary information for the Manuscript, including all the graphics that were created, 2) 16S Reference Alignment, Phylogeny and Taxonomic Annotation used by SEPP, and 3) Data used in the manuscript as input for the graphics generation (namely, SEPP outputs and sequence multiplicities).
keywords: microbiome; data visualization; graphics; phylogenetics; 16S
published: 2019-03-06
 
This dataset is provided to support the statements in Tarokh, A., and R.Y. Makhnenko. 2019. Remarks on the solid and bulk responses of fluid-filled porous rock, Geophysics. The unjacketed bulk modulus is a poroelastic parameter that can be directly measured in a laboratory test under a loading that preserves the difference between the mean stress and pore pressure constant. For a monomineralic rock, the measurement of the unjacketed bulk modulus is ignored because it is assumed to be equal to the bulk modulus of the solid phase. To examine this assumption, we tested porous sandstones (Berea and Dunnville) and limestones (Apulian and Indiana) mainly composed of quartz and calcite, respectively, under the unjacketed condition. The presence of microscale inhomogeneities, in the form of non-connected (occluded) pores, was shown to cause a considerable difference between the unjacketed bulk modulus and the bulk modulus of the solid phase. Furthermore, we found the unjacketed bulk modulus to be independent of the unjacketed pressure and Terzaghi effective pressure and therefore a constant.
keywords: Poroelasticity; anisotropic solid skeleton; unjacketed bulk modulus; non-connected porosity
published: 2019-03-22
 
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>)
keywords: songbirds; flight ability; wing development; wing length; wing emergence; nestling development; post-fledging
published: 2019-03-19
 
This repository includes scripts and datasets for the paper, "TreeMerge: A new method for improving the scalability of species tree estimation methods." The latest version of TreeMerge can be downloaded from Github (https://github.com/ekmolloy/treemerge).
keywords: divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-16
 
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>
keywords: divide-and-conquer; statistical consistency; species trees; incomplete lineage sorting; phylogenomics
published: 2019-05-10
 
Data necessary for production of figures presented in "Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models" by Pradhan et al.
keywords: Efficient enzyme coupling algorithms identify functional pathways in genome-scale metabolic models;
published: 2019-05-31
 
This dataset includes all data presented in the manuscript entitled: "Dynamic controls on field-scale soil nitrous oxide hot spots and hot moments across a microtopographic gradient"
keywords: denitrification; depressions; microtopography; nitrous oxide; soil oxygen; soil temperature
published: 2019-06-03
 
This dataset contains raw data associated with the red fox Y-chromosome assembly (see https://doi.org/10.3390/genes10060409). It includes a fasta file of the 171 scaffolds from the red fox reference genome assembly identified as likely to contain Y-chromosome sequence, the raw BLAST results, and the ABySS assemblies described in the manuscript.
keywords: Y-chromosome; carnivore; Vulpes vulpes; sex chromosomes; MSY; Y-chromosome genes; copy-number variation; BCORY2; UBE1Y; next-generation sequencing
published: 2019-06-22
 
keywords: conspecific attraction; fruit-eating bird; Hawaiian flora; playback experiment; seed dispersal; social information; Zosterops japonicas
published: 2018-01-03
 
Concatenated sequence alignment, phylogenetic analysis files, and relevant software parameter files from a cophylogenetic study of Brueelia-complex lice and their avian hosts. The sequence alignment file includes a list of character blocks for each gene alignment and the parameters used for the MrBayes phylogenetic analysis. 1) Files from the MrBayes analyses: a) a file with 100 random post-burnin trees (50% burnin) used in the cophylogenetic analysis - analysisrandom100_trees_brueelia.tre b) a majority rule consensus tree - treeconsensus_tree_brueelia.tre c) a maximum clade credibility tree - mcc_tree_brueelia.tre The tree tips are labeled with louse voucher names, and can be referenced in Supplementary Table 1 of the associated publication. 2) Files related to a BEAST analysis with COI data: a) the XML file used as input for the BEAST run, including model parameters, MCMC chain length, and priors - beast_parameters_coi_brueelia.xml b) a file with 100 random post-burnin trees (10% burnin) from the BEAST posterior distribution of trees; used in OTU analysis - beast_100random_trees_brueelia.tre c) an ultrametric maximum clade credibility tree - mcc_tree_beast_brueelia.tre 3) A maximum clade credibility tree of Brueelia-complex host species generated from a distribution of trees downloaded from https://birdtree.org/subsets/ - mcc_tree_brueelia_hosts.tre 4) Concatenated sequence alignment - concatenated_alignment_brueelia.nex
keywords: bird lice; Brueelia-complex; passerines; multiple sequence alignment; phylogenetic tree; Bayesian phylogenetic analysis; MrBayes; BEAST
published: 2018-04-05
 
GBS data from Phaseolus accessions, for a study led by Dr. Glen Hartman, UIUC. <br />The (zipped) fastq file can be processed with the TASSEL GBS pipeline or other pipelines for SNP calling. The related article has been submitted and the methods section describes the data processing in detail.
published: 2018-08-01
 
This set of scripts accompanies the manuscript describing the R package polyRAD, which uses DNA sequence read depth to estimate allele dosage in diploids and polyploids. Using several high-confidence SNP datasets from various species, allelic read depth from a typical RAD-seq dataset was simulated, then genotypes were estimated with polyRAD and other software and compared to the true genotypes, yielding error estimates.
keywords: R programming language; genotyping-by-sequencing (GBS); restriction site-associated DNA sequencing (RAD-seq); polyploidy; single nucleotide polymorphism (SNP); Bayesian genotype calling; simulation
published: 2018-08-03
 
These data include information on a field experiment on Castilleja coccinea (L.) Spreng., scarlet Indian paintbrush (Orobanchaceae). There is intraspecific variation in scarlet Indian paintbrush in the color of the bracts surrounding the flowers. Two bract color morphs were included in this study, the scarlet and yellow morphs. The experiment was conducted at Illinois Beach State Park in 2012. The aim of the work was to compare the color morphs with regard to 1) self-compatibility, 2) response to pollinator exclusion, 3) cross-compatibility between the color morphs, and 4) relative female fertility and male fitness. Three files are attached with this record. The raw data are in "fruitSet.csv" and "seedSet.csv", while "readme.txt" has detailed explanations of the raw data files.
keywords: Castilleja coccinea; Orobanchaceae; floral color polymorphism; bract color polymorphism; breeding system; hand-pollination; self-compatibility; reproductive assurance
published: 2018-11-21
 
This set of scripts accompanies the manuscript describing the R package polyRAD, which uses DNA sequence read depth to estimate allele dosage in diploids and polyploids. Using several high-confidence SNP datasets from various species, allelic read depth from a typical RAD-seq dataset was simulated, then genotypes were estimated with polyRAD and other software and compared to the true genotypes, yielding error estimates.
keywords: R programming language; genotyping-by-sequencing (GBS); restriction site-associated DNA sequencing (RAD-seq); polyploidy; single nucleotide polymorphism (SNP); Bayesian genotype calling; simulation
planned publication date: 2024-12-01
 
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.
keywords: forestry management; online survey; wildlife
published: 2019-08-13
 
Multiple sequence alignments from concatenated nuclear and mitochondrial genes and resulting phylogenetic tree files of fruit doves and their close relatives. Files include: BEAST input XML file (fruit_dove_beast_input.xml); a maximum clade credibility tree from a BEAST analysis (fruit_dove_beast_mcc.tre); concatenated multiple sequence alignment NEXUS files for the novel dataset (fruit_dove_concatenated_alignment.nex, 76 taxa, 4,277 characters) and the dataset with additional sequences (fruit_dove_plus_cibois_data_concatenated_alignment.nex, 204 taxa, 4,277 characters), both of which contain a MrBayes block including partition information; and 50% majority-rule consensus trees generated from MrBayes analyses, using the NEXUS alignment files as inputs (fruit_dove_mrbayes_consensus.tre, fruit_dove_plus_cibois_data_mrbayes_consensus.tre).
keywords: fruit doves; multiple sequence alignment; phylogeny; Aves: Columbidae
published: 2019-09-17
 
BAM files for evolved strains from migration rate selection experiments conducted in low viscosity (0.2% w/v) agar plates containing M63 minimal medium with 1mM of mannose, melibiose, N-acetylglucosamine or galactose
published: 2019-10-03
 
Dataset for F2F events of honeybees. F2F events are defined as face-to-face encounters of two honeybees that are close in distance and facing each other but not connected by the proboscis, thus not engaging in trophallaxis. The first and the second columns show the unique id's of honeybees participating in F2F events. The third column shows the time at which the F2F event started while the fourth column shows the time at which it ended. Each time is in the Unix epoch timestamp in milliseconds.
keywords: honeybee;face-to-face interaction
published: 2019-10-15
 
Filtered trophallaxis interactions for two honeybee colonies, each containing 800 worker bees and one queen. Each colony consists of bees that were administered a juvenile hormone analogy, a vehicle treatment, or a sham treatment to determine the effect of colony perturbation on the duration of trophallaxis interactions. Columns one and two display the unique identifiers for each bee involved in a particular trophallaxis exchange, and columns three and four display the Unix timestamp of the beginning/end of the interaction (in milliseconds), respectively.<br /><b>Note</b>: the queen interactions were omitted from the uploaded dataset for reasons that are described in submitted manuscript. Those bees that performed poorly are also omitted from the final dataset.
keywords: honey bee; trophallaxis; social network
published: 2019-12-20
 
This dynamic photosynthesis model of soybean canopy is developed by Yu Wang (yuwangcn@illinois.edu), IGB, University of Illinois. If you want to know more details, please check the following publication Yu Wang, Steven J. Burgess, Elsa de Becker, Stephen P. Long. Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity? The Plant Journal.
keywords: Matlab; Soybean canopy; photosynthesis model
published: 2023-12-23
 
Supplemental document corresponding to a submission to Physiological Genomics (Data supplements and source materials must now be deposited in a community-recognized data repository or to a generalist public access repository if no community resource is available. See "Author/Production Requirements" for more information.) https://pg.msubmit.net/
keywords: Supplemental, Physiological Genomics
published: 2021-05-17
 
Please cite as: Wuebbles, D., J. Angel, K. Petersen, and A.M. Lemke, (Eds.), 2021: An Assessment of the Impacts of Climate Change in Illinois. The Nature Conservancy, Illinois, USA. https://doi.org/10.13012/B2IDB-1260194_V1 Climate change is a major environmental challenge that is likely to affect many aspects of life in Illinois, ranging from human and environmental health to the economy. Illinois is already experiencing impacts from the changing climate and, as climate change progresses and temperatures continue to rise, these impacts are expected to increase over time. This assessment takes an in-depth look at how the climate is changing now in Illinois, and how it is projected to change in the future, to provide greater clarity on how climate change could affect urban and rural communities in the state. Beyond providing an overview of anticipated climate changes, the report explores predicted effects on hydrology, agriculture, human health, and native ecosystems.
keywords: Climate change; Illinois; Public health; Agriculture; Environment; Water; Hydrology; Ecosystems