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planned publication date: 2024-12-01
Hohoff, Tara; Rogness, Brittany; Davis, Mark (2024): Forestry Management Survey by the Illinois Bat Conservation Program. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1426397_V1
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
Nowak, Jennifer E.; Sweet, Andrew D.; Weckstein, Jason D.; Johnson, Kevin P. (2019): Data for: A molecular phylogenetic analysis of the genera of fruit doves and their allies using dense taxonomic sampling. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9797270_V1
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
Fraebel, David T.; Kuehn, Seppe (2019): Sequencing data for migration rate selection experiments (0.2% agar, 1mM sugar). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2128477_V1
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
Choi, Sang Hyun; Rao, Vikyath D.; Gernat, Tim; Hamilton, Adam R.; Robinson, Gene E.; Goldenfeld, Nigel (2019): Honeybee F2F event data for The origin of heavy tails in honeybee and human interaction times. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4021786_V1
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
Choi, Sang Hyun; Rao, Vikyath; Gernat, Tim; Hamilton, Adam; Robinson, Gene; Goldenfeld, Nigel (2019): Honeybee trophallaxis event data for The origin of heavy tails in honeybee and human interaction times. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2712449_V1
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
Wang, Yu; Burgess, Steven J. ; de Becker, Elsa ; Long, Stephen P. (2019): Data and code for: Photosynthesis in the fleeting shadows: An overlooked opportunity for increasing crop productivity?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9453481_V1
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: 2024-01-18
Sinaiko, Guy; Cao, Yanghui; Dietrich, Christopher H. (2024): Datasets for phylogenomics of the leafhopper genus Neoaliturus Distant. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8336414_V1
The following files include specimen information, DNA sequence data, and additional information on the analyses used to reconstruct the phylogeny of the leafhopper genus Neoaliturus as described in the Methods section of the original paper: 1. Taxon_sampling.csv: contains data on the individual specimens from which DNA was extracted, including sample code, taxon name, collection data (locality, date and name of collector) and museum unique identifier. 2. Alignments.zip: a ZIP archive containing 432 separate FASTA files representing the aligned nucleotide sequences of individual gene loci used in the analysis. 3. Concatenated_Matrix.fa: is a FASTA file containing the concatenated individual gene alignments used for the maximum likelihood analysis in IQ-TREE. 4. Genes_and_Loci.rtf: identifies the individual genes and loci used in the analysis. The partition name is the same as the name of the individual alignment file in the zipped Alignments folder. 5. Partitions_best_scheme.nex: is a text file in the standard NEXUS format that indicates the names of the individual data partitions and their locations in the concatenated matrix, and also indicates the substitution model for each partition.
keywords:
leafhopper; phylogeny; anchored-hybrid-enrichment; DNA sequence; insect
published: 2023-12-23
Rodriguez-Zas, Sandra (2023): Supplemental File companion to a manuscript to be submitted. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8635710_V1
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
Wuebbles, D; Angel, J; Petersen, K; Lemke, A.M. (2021): An Assessment of the Impacts of Climate Change in Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1260194_V1
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
published: 2023-07-27
Feng, Ling; Takiya, Daniela; Krishnankutty, Sindhu; Dietrich, Christopher; Zhang, Yalin (2023): NEXUS file for Phylogeny and Biogeography of the Sharpshooters (Hemiptera: Cicadellidae: Cicadellinae). University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-0855589_V1
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: 2023-12-08
Preza Fontes, Giovani; Greer, Kristin; Pittelkow, Cameron (2023): Data for Does biochar increase nitrogen use efficiency in maize?. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8987372_V1
A two-year field study was conducted to test the hypothesis that biochar application increases inorganic soil N availability during maize growth, leading to higher grain yields and N recovery efficiency while reducing the risk of N leaching following harvest. Four N fertilizer rates (0, 90, 179, and 269 kg ha-1 as urea ammonium nitrate solution) were applied with or without biochar (10 Mg ha-1) before maize planting each year. This dataset contains selected summary statistics (average and standard deviation) on soil and plant measurements. This file package also includes a readme.txt file that describes the data in detail, including attribute descriptions.
keywords:
biochar; nitrogen fertilizer; nitrogen use efficiency; corn yield, soil inorganic nitrogen; nitrate leaching
published: 2023-12-18
Edmonds, Devin; Adamovicz, Laura; Allender, Matthew; Colton, Andrea; Randy, Nyboer; Michael, Dreslik (2023): Data for Evaluating Population Persistence of Ornate Box Turtles. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6384815_V1
We conducted long-term capture-mark-recapture surveys on two isolated ornate box turtle (Terrapene ornata) populations in northern Illinois, USA. This dataset provides the capture history strings and additional demographic information used for estimating population vital rates with robust design capture-mark-recapture models. The vital rates were then used in a stage-based population projection matrix model for each population.
keywords:
demography; capture-mark-recapture; vital rates; conservation; wildlife ecology
published: 2023-07-05
Dalling, James William; Norden, Natalia (2023): La Planada Forest Dynamics Plot soils dataset. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6140727_V1
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: 2024-01-01
Long, Kira (2024): Supplementary files for dissertation "Hybridization dynamics and population genomics of a Manacus hybrid zone". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-6588343_V1
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: 2023-12-18
Johnson, Claire A.; Benson, Thomas J. (2023): Data from: Dynamic, multi-scale analyses indicate site- and landscape-level forest cover drive Yellow-billed and Black-billed Cuckoo interannual turnover. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2905024_V1
Data in this publication were used to examine the effects of habitat and landscape-level covariates on occupancy and interannual dynamics and the effects of environmental factors on detection of Black-billed Cuckoos and Yellow-billed Cuckoos. Data were collected between 2019-2020 in northern Illinois, USA. Procedures were approved by the Illinois Institutional Animal Care and Use Committee (IACUC), protocol no. 19086.
keywords:
Black-billed Cuckoo; habitat use; multi-scale; occupancy dynamics; turnover; Yellow-billed Cuckoo
published: 2023-12-15
Abidi, Syeda Nayab; Hsu, Felicity; Smith-Bolton, Rachel (2023): Data for Regenerative growth is constrained by brain tumor to ensure proper patterning in Drosophila. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9119268_V1
This page contains the data for the publication "Regenerative growth is constrained by brain tumor to ensure proper patterning in Drosophila" published in PLOS Genetics in 2023.
published: 2023-12-13
Tiemann, Jeremy (2023): Distribution of nonindigenous Basket Clams (Corbicula spp.) in Mexico. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9221608_V1
Corbicula spp. are one of the most prolific aquatic invasive species in the world and can have negative effects on aquatic ecosystems. We performed qualitative field surveys, examined literature accounts and natural history museum holdings, and accessed citizen science data sources to document the distribution of Corbicula in Mexico and shared drainages. Through 26 publications (N = 127 records), 312 museum holdings, and 446 iNaturalist records, we documented 885 records pertaining to Corbicula in Mexico and shared drainages. The first record of the species in Mexico was in 1969, and it has since been reported from 26 of the 32 Mexican states and most of the major river basins throughout the country. However, we suggest Corbicula is more prevalent in Mexico than we report in this work as it is often under sampled / under reported.
keywords:
Corbicula; exotic species; invasive species; Asian Clams; Bivalvia; freshwater systems
published: 2023-12-06
Starbuck, Clarissa; DeSchepper, Logan; Hoggatt, Meredith; O'Keefe, Joy (2023): Data for Tradeoffs in sound quality and cost for passive acoustic devices. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4200947_V1
This dataset accompanies an article published in the journal Bioacoustics: "Tradeoffs in sound quality and cost for passive acoustic devices", https://doi.org/10.1080/09524622.2023.2290715. The dataset contains measurements for acoustic call files for free-flying bats simultaneously recorded on both Audiomoth and Anabat Swift passive acoustic recording devices in a conservation area in northeastern Missouri, USA. We paired calls from the two devices and compared indicators of recording quality measured in a proprietary program (Bat Call Identification Software). The dataset also contains a file enumerating the proportions of calls classified as low frequency, mid frequency, or Myotis (three phonic groups) for each type of recording device. The data were used to compare the quality and sensitivity of the two devices. The scripts for modeling procedures and figures are included in the dataset.
keywords:
Bats; echolocation; passive acoustic monitoring; sensors
published: 2023-10-26
Louie, Allison Y.; Rund, Laurie A.; Komiyama-Kasai, Karin A.; Weisenberger, Kelsie E.; Stanke, Kayla L.; Larsen, Ryan J.; Leyshon, Brian J.; Kuchan, Matthew J.; Das, Tapas; Steelman, Andrew J. (2023): Data for "A hydrolyzed lipid blend diet promotes myelination in neonatal piglets in a region and concentration-dependent manner.". University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-4218705_V1
This dataset contains MRI data and Imaris modeling analysis of CLARITY-cleared, immunostained tissue associated with a study that assessed the effects of lipid blends containing various levels of a hydrolyzed fat system on myelin development in healthy neonatal piglets. Data are from thirty-two piglets of mixed sexes across four diet treatment groups and includes a sow-fed reference group. MRI data (presented in Figure 2 of the associated article) consists of volumetric data from Voxel-Based Morphometry analysis in brain grey matter and white matter, as well as mean fractional anisotropy and mean orientation dispersion index data from Tract-Based Spatial Statistics analysis. Imaris data (presented in Figure 3 of the associated article) consists of twenty-one select output measures from 3D modeling analysis of PLP-stained prefrontal cortex tissue. All methods used for collection/generation/processing of data are described in the associated article: Louie AY, Rund LA, Komiyama-Kasai KA, Weisenberger KE, Stanke KL, Larsen RJ, Leyshon BJ, Kuchan MJ, Das T, Steelman AJ. A hydrolyzed lipid blend diet promotes myelination in neonatal piglets in a region and concentration-dependent manner. J Neurosci Res. 2023.
keywords:
myelin; dietary lipid; white matter; CLARITY; Imaris; voxel-based morphometry; diffusion tensor imaging
published: 2023-10-16
Rasoarimanana, Tantely; Edmonds, Devin; Marquis, Olivier (2023): Data for Mantella baroni Habitat Preference and Abundance. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-2234820_V1
This dataset provides microhabitat and environmental variables collected in the habitat of the poison frog Mantella baroni from 155 1-meter square quadrats in Vohimana Reserve along forest valleys, on slopes, and on ridgelines. We also provide data from photographic capture-recapture surveys used for estimating abundance.
keywords:
occupancy; abundance; amphibian; Madagascar; microhabitat; capture-recapture
published: 2019-07-11
Daniels, Melissa; Larson, Eric (2019): Data for Effects of forest windstorm disturbance on invasive plants in protected areas of southern Illinois, USA. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-1401121_V1
We studied the effect of windstorm disturbance on forest invasive plants in southern Illinois. This data includes raw data on plant abundance at survey points, compiled data used in statistical analyses, and spatial data for surveyed plots and units. This file package also includes a readme.doc file that describes the data in detail, including attribute descriptions.
keywords:
tornado, blowdowns, derecho, invasive plants, Shawnee National Forest, southern Illinois
published: 2023-09-20
Chase, Marissa H. ; Charles, Brian; Harmon-Threatt, Alexandra; Fraterrigo, Jennifer (2023): Diverse forest management strategies support functionally and temporally distinct bee communities. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-8891496_V1
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
published: 2023-09-01
Chakraborty, Sulagna; Steckler, Teresa; Gronemeyer, Peg; Mateus-Pinilla, Nohra; Smith, Rebecca (2023): Farmers’ knowledge, attitudes, and prevention practices regarding ticks and tickborne diseases in Illinois. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-3988796_V1
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
Li, Shuai; Leakey, Andrew D.B.; Moller, Christopher A.; Montes, Christopher M.; Sacks, Erik J.; DeKyoung, Lee; Ainsworth, Elizabeth A. (2023): Similar photosynthetic, but different yield responses of C3 and C4 crops to elevated O3. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-9446886_V1
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
Zinnen, Jack; Matthews, Jeffrey W.; Zaya, David N. (2023): Genetic, demographic, and spatial information for a study of Phlox pilosa ssp. sangamonensis, and congeners. University of Illinois at Urbana-Champaign. https://doi.org/10.13012/B2IDB-5376622_V1
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