Dataset Search Results

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).

This data set contains data used for “Improved Net Carbon Budgets in the US Midwest through Direct Measured Impacts of Enhanced Weathering.” Data include biomass, soil bulk densities, soil respiration measurements, soil lanthanide element analysis, plant tissue analysis for major cations, and eddy covariance fluxes.

The data are original electron micrographs from the lab of the late Dr. Burt Endo of the USDA. These data were digitized from photographic prints and glass plate negatives at 600 DPI as 16 bit TIFF files. This fourth version added 6 new ZIP files from the Endo data collection. "Endo folder database.xlsx" is updated to reflect the addition. Information in "Readme_FileNameFormatting.docx" remains the same as in V3.

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.

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.

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

Simulation trajectory data and scripts for Nature manuscript "The structure and physical properties of a packaged bacteriophage particle" that reports the all-atom structure of a complete HK97 virion, including its entire 39,732 base pair genome, obtained through multi-resolution simulations.

The included files were used to reconstruct the phylogeny of Coelidiinae using combined morphological and molecular data, estimate divergence times and reconstruct ancestral biogeographic areas as described in the manuscript submitted for publication. The file “Coelidiinae_dna_morph_combined.nex” is a text file in standard NEXUS format used by various phylogenetic analysis programs. This file includes the aligned and concatenated nucleotide sequences or five gene regions (mitochondrial COI and 16S, and nuclear 28S D-2, histone H3, histone H2A and wingless) indicated by standard “ACGT” nucleotide symbols with missing data indicated by “?”, and morphological character data as defined in Table S3 used in the analyses. The data partitions are indicated toward the end of the file by ranges of numbers (“charset Subset 1 – 4” for the DNA data and “charset morph” for the morphological characters) followed by commands for the phylogenetic analysis program MrBayes that specify the model settings for each data partition. Detailed data on species included (as rows) in the dataset, including collection localities and GenBank accession numbers are provided in the Table_S1_Specimen_information.csv file. The file "TablesS2-S4.pdf" lists the primers used for polymerase chain reaction amplification, the list of morphological character definitions, and the morphological character matrix. The file “RASP_Distribution.csv” contains a list of the species included in the phylogenetic dataset (first column) and a code (second column) indicating their distributions as follows: (A) Oriental, (B) Palaearctic, (C) Australian, (D) Afrotropical, (E) Neotropical, and (F) Nearctic. More than one letter indicates that the species occurs in more than one region. The file "infile_for_BEAST.txt" is the input file in XML format used for the molecular divergence time analysis using the program BEAST (Bayesian Evolutionary Analysis by Sampling Trees) as described in the Methods section of the manuscript. This file includes comments that document the steps of the analysis.

Three datasets: species_abundance_data, species_traits, and environmental_data. The three datasets were collected in the Fortuna Forest Reserve (8°45′ N, 82°15′ W) and Palo Seco Protected Forest (8°45′ N, 82°13′ W) located in western Panama. The two reserves support humid to super-humid rainforests, according to Holdridge (1947). The species_abundance_data and species_traits datasets were collected across 15 subplots of 25 m2 in 12 one-hectare permanent plots distributed across the two reserves. The subplots were spaced 20 m apart along three 5 m wide transects, each 30 m apart. Please read Prada et al. (2017) for details on the environmental characteristics of the study area. Prada CM, Morris A, Andersen KM, et al (2017) Soils and rainfall drive landscape-scale changes in the diversity and functional composition of tree communities in a premontane tropical forest. J Veg Sci 28:859–870. https://doi.org/10.1111/jvs.12540