Datasets

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>

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 (TBD). Please refer to the study for detailed data extraction and processing methods.

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.

BAM files for founding strain (MG1655-motile) as well as evolved strains from replicate motility selection experiments in low-viscosity agar plates containing either rich medium (LB) or minimal medium (M63+0.18mM galactose)

This deposit contains all raw data and analysis from the paper "In-cell titration of small solutes controls protein stability and aggregation". Data is collected into several types: 1) analysis*.tar.gz are the analysis scripts and the resulting data for each cell. The numbers correspond to the numbers shown in Fig.S1. (in publication) 2) scripts.tar.gz contains helper scripts to create the dataset in bash format. 3) input.tar.gz contains headers and other information that is fed into bash scripts to create the dataset. 4) All rawData*.tar.gz are tarballs of the data of cells in different solutes in .mat files readable by matlab, as follows: - Each experiment included in the publication is represented by two matlab files: (1) a calibration jump under amber illumination (_calib.mat suffix) (2) a full jump under blue illumination (FRET data) - Each file contains the following fields: &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;coordleft - coordinates of cropped and aligned acceptor channel on the original image &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;coordright - coordinates of cropped and aligned donor channel on the original image] &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataleft - a 3d 12-bit integer matrix containing acceptor channel flourescence for each pixel and time step. Not available in _calib files &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;dataright - a 3d 12-bit integer matrix containing donor channel flourescence for each pixel and time step. This will be mCherry in _calib files and AcGFP in data files. &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;frame1 - original image size &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;imgstd - cropped dimensions &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;numFrames - number of frames in dataleft and dataright &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;videos - a structure file containing camera data. Specifically, videos.TimeStamp includes the time from each frame.

The files are plain text and contain the original data used in phylogenetic analyses of of Typhlocybinae (Bin, Dietrich, Yu, Meng, Dai and Yang 2022: Ecology & Evolution, in press). The three files with extension .phy are text files with aligned DNA sequences in the standard PHYLIP format and correspond to Matrix 1 (amino acid alignment), Matrix 2 (nucleotide alignment of first two codon positions of protein-coding genes) and Matrix 3 (nucleotide alignment of protein-coding genes plus 2 ribosomal genes) described in the Methods section. An additional text file in NEXUS format (.nex extension) contains the morphological character data used in the ancestral state reconstruction (ASCR) analysis described in the Methods. NEXUS is a standard format used by various phylogenetic analysis software. For more information on data file content, see the included "readme" files.

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.

This dataset provides files for use in analysis of human land preference across Australasia, and in a localized analysis of land preference in Laos and Vietnam. All files can be imported into ArcGIS for visualization, and re-analyzed using the open source Maxent species distribution modeling program. CSV files contain known human presence sites for model validation. ASC files contain geographically coded environmental data for mean annual temperature and mean annual precipitation during the Last Glacial Maximum, as well as downward slope data. All ASC files are in the WGS 1984 Mercator map projection for visualization in ArcGIS and can be opened as text files in text editors supporting large file sizes.

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).

This repository includes scripts and datasets for the paper, "FastMulRFS: Fast and accurate species tree estimation under generic gene duplication and loss models." Note: The results from estimating species trees with ASTRID-multi (included in this repository) are *not* included in the FastMulRFS paper. We estimated species trees with ASTRID-multi in the fall of 2019, but ASTRID-multi had an important bug fix in January 2020. Therefore, the ASTRID-multi species trees in this repository should be ignored.

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).

Shared dataset consists of 16S sequencing data of microbial communities. Each community is composed of heterotrophic bacteria derived from one of two soil samples and the model algae Chlamydomonas reinhardtii. Each comunity was placed in a materially closed environment with an initial supply of carbon in the media and subjected to light-dark cycles. The closed microbial ecosystems (CES) survived via carbon cycling. Each CES was subjected to rounds of dilution, after which the community was sequenced (data provided here). The shared dataset allowed us to conclude that CES consistently self-assembled to cycle carbon (data not provided) via conserved metabolic capabilites (data not provided) dispite differences in taxonomic composition (data provided). --------------------------- Naming convention: [soil sample = A or B][CES replicate = 1,2,3, or 4]_[round number = 1,2,3,or 4]_[reverse read = R or forward read = F]_filt.fastq Example -- A1_r1_F_filt.fastq means soil sample A, CES replicate 1, end of round1, forward read

The text file contains the original data used in the phylogenetic analyses of Xue et al. (2020: Systematic Entomology, in press). 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 89 taxa (species) and 2676 characters, indicate that the first 2590 characters are DNA sequence and the last 86 are morphological, that gaps inserted into the DNA sequence alignment and inapplicable morphological characters are indicated by a dash, and that missing data are indicated by a question mark. The file contains aligned nucleotide sequence data for 5 gene regions and 86 morphological characters. The positions of data partitions are indicated in the mrbayes block of commands for the phylogenetic program MrBayes at the end of the file (Subset1 = 16S gene; Subset2 = 28S gene; Subset3 = COI gene; Subset 4 = Histone H3 and H2A genes). The mrbayes block also contains instructions for MrBayes on various non-default settings for that program. These are explained in the original publication. Descriptions of the morphological characters and more details on the species and specimens included in the dataset are provided in the supplementary document included as a separate pdf, also available from the journal website. The original raw DNA sequence data are available from NCBI GenBank under the accession numbers indicated in the supplementary file.

This repository includes scripts, datasets, and supplementary materials for the study, "NJMerge: A generic technique for scaling phylogeny estimation methods and its application to species trees", presented at RECOMB-CG 2018. The supplementary figures and tables referenced in the main paper can be found in njmerge-supplementary-materials.pdf. The latest version of NJMerge can be downloaded from Github: https://github.com/ekmolloy/njmerge. ***When downloading datasets, please note that the following errors.*** In README.txt, lines 37 and 38 should read: + fasttree-exon.tre contains lines 1-25, 1-100, or 1-1000 of fasttree-total.tre + fasttree-intron.tre contains lines 26-50, 101-200, or 1001-2000 of fasttree-total.tre Note that the file names (fasttree-exon.tre and fasttree-intron.tre) are swapped. In tools.zip, the compare_trees.py and the compare_tree_lists.py scripts incorrectly refer to the "symmetric difference error rate" as the "Robinson-Foulds error rate". Because the normalized symmetric difference and the normalized Robinson-Foulds distance are equal for binary trees, this does not impact the species tree error rates reported in the study. This could impact the gene tree error rates reported in the study (see data-gene-trees.csv in data.zip), as FastTree-2 returns trees with polytomies whenever 3 or more sequences in the input alignment are identical. Note that the normalized symmetric difference is always greater than or equal to the normalized Robinson-Foulds distance, so the gene tree error rates reported in the study are more conservative. In njmerge-supplementary-materials.pdf, the alpha parameter shown in Supplementary Table S2 is actually the divisor D, which is used to compute alpha for each gene as follows. 1. For each gene, a random value X between 0 and 1 is drawn from a uniform distribution. 2. Alpha is computed as -log(X) / D, where D is 4.2 for exons, 1.0 for UCEs, and 0.4 for introns (as stated in Table S2). Note that because the mean of the uniform distribution (between 0 and 1) is 0.5, the mean alpha value is -log(0.5) / 4.2 = 0.16 for exons, -log(0.5) / 1.0 = 0.69 for UCEs, and -log(0.5) / 0.4 = 1.73 for introns.

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.

This dataset contains genotypic and phenotypic data, R scripts, and the results of analysis pertaining to a multi-location field trial of Miscanthus sinensis. Genome-wide association and genomic prediction were performed for biomass yield and 14 yield-component traits across six field trial locations in Asia and North America, using 46,177 single-nucleotide polymorphism (SNP) markers mined from restriction site-associated DNA sequencing (RAD-seq) and 568 M. sinensis accessions. Genomic regions and candidate genes were identified that can be used for breeding improved varieties of M. sinensis, which in turn will be used to generate new M. xgiganteus clones for biomass.

Dataset includes the dataset for estimating bat density from acoustic data and the R code. The data support a publication by Meredith L. Hoggatt, Clarissa A. Starbuck, and Joy M. O'Keefe entitled Acoustic monitoring yields informative bat population density estimates.

Upon treatment removal, spontaneous and random reactivation of latently infected T cells remains a major barrier toward curing HIV. Due to its stochastic nature, fluctuations in gene expression (or “noise”) can bias HIV reactivation from latency, and conventional drug screens for mean gene expression neglect compounds that modulate noise. Here we present a time-lapse fluorescence microscopy image set obtained from a Jurkat T-cell line, infected with a minimal HIV gene circuit, treated with 1,806 small molecule compounds, and imaged for 48 hours. In addition, the single-cell time-dependent reporter dynamics (single-cell gene expression intensity and noise trajectories) extracted from the image dataset are included. Based on this dataset, a total of 5 latency promoting agents of HIV was found through further experimentation in Lu et al., PNAS 2021 (doi: 10.1073/pnas.2012191118). For a detailed description of the dataset, please refer to the readme file.

Data sets relating to the manuscript “Long-term yields in annual and perennial bioenergy crops in the Midwestern USA” published in Global Change Biology Bioenergy. Field data, including annual peak biomass and harvest yields from maize/soy, miscanthus, switchgrass, and prairie field trials from 2008-2018 are included. Peak and harvest biomass for fertilized and unfertilized miscanthus are included from 2014-2018.