Dataset Search Results

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.

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).

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.

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

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.

We studied vegetation metric robustness to environmental (season, interannual, and regional) and methodological (observer) variables, as well as adequate sample size for vegetation metrics across four regions of the United States.

Use of cellulosic biofuels from non-feedstocks are modeled using the BEPAM (Biofuel and Environmental Policy Analysis Model) model to quantifying the uncertainties about induced land use change effects, net greenhouse gas saving potential, and economic costs. The code is in GAMS, general algebraic modeling language. NOTE: Column 3 is titled "BAU" in "merged_BAU.gdx", "merged_RFS.gdx", and "merged_CEM.gdx", but contains "RFS" data in "merged_RFS.gdx" and "CEM" data in "merged_CEM.gdx".

The dataset contains the high-throughput matrix-assisted laser desorption/ionization mass spectrometry XmL files for the atrial gland and red hemiduct of Aplysia californica.

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.

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.

This dataset is associated with a larger manuscript published in 2022 in the Illinois Natural History Survey Bulletin to summarize all known records for nonindigenous aquatic mollusks in Illinois, and full sources are referenced within the manuscript. We examined museum holdings, literature accounts, publicly available databases sponsored by the U.S. Geological Survey (USGS) - Nonindigenous Aquatic Species program (http://nas.er.usgs.gov/.) and InvertEBase (invertebase.org). We also included sporadic field survey data of encounters of nonindigenous aquatic species from colleagues within the Illinois Natural History Survey, Illinois Department of Natural Resources, U.S. Fish and Wildlife Service, county forest preserve districts, and other natural resource agencies about their encounters with nonindigenous aquatic mollusk species. Lastly, we examined the role and utility of citizen-science data to document occurrences of nonindigenous aquatic mollusk species. We queried iNaturalist (www.inaturalist.org) for all available nonindigenous freshwater mollusk data for Illinois. Table heading descriptions (if not intuitive) are: “INHS verified” is whether an INHS staff member verified the record by observing vouchered specimen or photograph; “Source” is where a record was accessed or obtained; “individualCount” is number collected or observed in a record; “MuseumCode” is standard museum abbreviation or acronym; “Institution” is source that housed or reported a record, and this also includes the spelled-out museum code; “Collectors” typically indicates who collected the specimen or voucher; “Lat_Long determined by” denotes whether collection coordinates were stated by the collector or by a curator (using inference from data available); “fieldNumber” typically indicates a unique field number that a collector may have used in the field; “identifiedBy” typically explains who identified a specimen or verified a specimen identification.

Data for the Appendices of Bush et al. article published in Ecology and Evolution. Contains genomic analysis information for a strain of Aspergillus flavus isolated from bee bread in East Central Illinois.

This dataset is for the publication "Do Nearctic hover flies (Diptera: Syrphidae) engage in long-distance migration? An assessment of evidence and mechanisms." It consists of 11 Excel spreadsheets and 4 R scripts which correspond to the analyses which were conducted. Paper abstract: Long-distance insect migration is poorly understood despite its tremendous ecological and economic importance. As a group, Nearctic hover flies (Diptera: Syrphidae: Syrphinae), which are crucial pollinators as adults and biological control agents as larvae, are almost entirely unrecognized as migratory despite examples of highly migratory behavior among several Palearctic species. Here, we examined evidence and mechanisms of migration for four hover fly species (Allograpta obliqua, Eupeodes americanus, Syrphus rectus, and Syrphus ribesii) common throughout eastern North America using stable hydrogen isotope (δ2H) measurements of chitinous tissue, morphological assessments, abundance estimations, and cold-tolerance assays. While further studies are needed, non-local isotopic values obtained from hover fly specimens collected in central Illinois support the existence of long-distance fall migratory behavior in Eu. americanus, and to a lesser extent S. ribesii and S. rectus. Elevated abundance of Eu. americanus during the expected autumn migratory period further supports the existence of such behavior. Moreover, high phenotypic plasticity of morphology associated with dispersal coupled with significant differences between local and non-local specimens suggest that Eu. americanus exhibits a unique suite of morphological traits that decrease costs associated with long-distance flight. Finally, compared to the ostensibly non-migratory A. obliqua, Eu. americanus was less cold tolerant, a factor that may be associated with migratory behavior. Collectively, our findings imply that fall migration occurs in Nearctic hover flies, but we consider methodological limitations of our study in addition to potential ecological and economic consequences of these novel findings.

The following files were used to reconstruct the phylogeny of the leafhopper subfamily Deltocephalinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5. <b>1) taxon_sampling.csv:</b> contains the sequencing ids (1st column) and the taxonomic information (2nd column) of each sample. Sequencing ids were used in the alignment files and partition files. <b>2)concatenated_nt.phy:</b> concatenated nucleotide alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file lists the sequences of 163,365 nucleotide positions from 429 genes in 730 samples. Hyphens are used to represent gaps. <b>3) concatenated_nt_partition.nex:</b> the partitions for the concatenated nucleotide alignment. The file partitions the 163,365 nucleotide characters into 429 character sets, and defines the best substitution model for each character set. <b>4) concatenated_aa.phy:</b> concatenated amino acid alignment used for the maximum likelihood analysis of Deltocephalinae by IQ-TREE v1.6.12. The file gives the sequences of 53,969 amino acids from 429 genes in 730 samples. Hyphens are used to represent gaps. <b>5) concatenated_aa_partition.nex:</b> the partitions for the concatenated amino acid alignment. The file partitions the 53,969 characters into 429 character sets, and defines the best substitution model for each character set. <b>6) concatenated_nt_106taxa.phy:</b> a reduced concatenated nucleotide alignment representing 107 samples x 86 genes. This alignment is used to estimate the divergence times of Deltocephalinae using MCMCTree in PAML v4.9. The file lists the sequences of 79,239 nucleotide positions from 86 genes in 107 samples. Hyphens are used to represent gaps. <b>7) concatenated_nt_106taxa_partition.nex:</b> the partitions for the nucleotide alignment concatenated_nt_106taxa.phy. The file partitions the 79,239 nucleotide characters into 86 character sets, and defines the best substitution model for each character set. <b>8) individual_gene_alignment.zip:</b> contains 429 FAS files, one for each of the partitioned nucleotide character sets in the concatenated_nt_partition.nex file. 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.

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.

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.

The following files were used to reconstruct the phylogeny of the leafhopper subfamily Typhlocybinae, using IQ-TREE v1.6.12 and ASTRAL v 4.10.5. <b>1) Taxon_sampling.csv:</b> contains the sample IDs (1st column) and the taxonomic information (2nd column). Sample IDs were used in the alignment files and partition files. <b>2) concatenated_nt_complete.phy:</b> a complete concatenated nucleotide dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 154,992 nucleotide positions (intron included) from 665 loci. Hyphens are used to represent gaps. <b>3) concatenated_nt_complete_partition.nex:</b> the partitioning schemes for concatenated_nt_complete.phy. The file partitions the 154,992 nucleotide characters into 426 character sets, and defines the best substitution model for each character set. <b>4) concatenated_cds_complete.phy:</b> a complete concatenated coding DNA sequence dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 153,525 nucleotide positions (intron excluded) from 665 loci. Hyphens are used to represent gaps. <b>5) concatenated_cds_complete_partition.nex:</b> the partitioning schemes for concatenated_cds_complete.phy. The file partitions the 153,525 nucleotide characters into 426 character sets, and defines the best substitution model for each character set. <b>6) concatenated_nt_reduced.phy:</b> a reduced concatenated nucleotide dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12. The file lists the sequences of 248 samples with 95,076 nucleotide positions (intron included) from 374 loci. Hyphens are used to represent gaps. <b>7) concatenated_nt_reduced_partition.nex:</b> the partitioning schemes for concatenated_nt_reduced.phy. The file partitions the 95,076 nucleotide characters into 312 character sets, and defines the best substitution model for each character set. <b>8) concatenated_aa_complete.phy:</b> a complete concatenated amino acid dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12, corresponding to concatenated_cds_complete.phy. The file lists the sequences of 248 samples with 51,175 amino acid positions from 665 loci. Hyphens are used to represent gaps. <b>9) concatenated_aa_complete_partition.nex:</b> the partitioning schemes for concatenated_aa_complete.phy. The file partitions the 51,175 amino acid characters into 426 character sets, and defines the best substitution model for each character set. <b>10) concatenated_aa_reduced.phy:</b> a reduced concatenated amino acid dataset used for the maximum likelihood analysis by IQ-TREE v1.6.12, corresponding to concatenated_nt_reduced.phy. The file lists the sequences of 248 samples with 31,384 amino acid positions from 374 loci. Hyphens are used to represent gaps. <b>11) concatenated_aa_reduced_partition.nex:</b> the partitioning schemes for concatenated_aa_reduced.phy. The file partitions the 31,384 amino acid characters into 312 character sets, and defines the best substitution model for each character set. <b>12) Individual_gene_alignment.zip:</b> contains 426 FASTA files, each one is an 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.

The dataset is for a study conducted to understand genome-wide association (GWA) and genomic prediction of biomass yield and 14 yield-components traits in Miscanthus sacchariflorus. We evaluated a diversity panel with 590 accessions of M. sacchariflorus grown across four years in one subtropical and three temperate locations and genotyped with 268,109 single nucleotide polymorphisms (SNPs).