cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.pr318
title: Data from: RAD sequencing and genomic simulations resolve hybrid origins within North American Canis

description: Top predators are disappearing worldwide, significantly changing
 ecosystems that depend on top-down regulation. Conflict with humans
 remains the primary roadblock for large carnivore conservation, but for
 the eastern wolf (Canis lycaon), disagreement over its evolutionary
 origins presents a significant barrier to conservation in Canada and has
 impeded protection for grey wolves (Canis lupus) in the USA. Here, we use
 127 235 single-nucleotide polymorphisms (SNPs) identified from
 restriction-site associated DNA sequencing (RAD-seq) of wolves and
 coyotes, in combination with genomic simulations, to test hypotheses of
 hybrid origins of Canis types in eastern North America. A principal
 components analysis revealed no evidence to support eastern wolves, or any
 other Canis type, as the product of grey wolf × western coyote
 hybridization. In contrast, simulations that included eastern wolves as a
 distinct taxon clarified the hybrid origins of Great Lakes-boreal wolves
 and eastern coyotes. Our results support the eastern wolf as a distinct
 genomic cluster in North America and help resolve hybrid origins of Great
 Lakes wolves and eastern coyotes. The data provide timely information that
 will shed new light on the debate over wolf conservation in eastern North
 America.
description: MetaData_Quality_VCFThis file contains 1) metadata that describes each sample used, 2) quality scores from sequencing on Illumina platform, and 3) an initial VCF file with individual genotypes compiled from the raw sequencing data (refer to methods in publication for a description of genotypes used to generate the PCA in the manuscript).Eastern Wolf Raw DataThis file contains raw Illumina sequence data for the Eastern Wolves (Canis lycaon). Please check the metadata to confirm and cross-reference sample IDs.EasternWolfRawData.zipEastern Coyote Raw DataThis file contains raw Illumina sequence data for the Eastern Coyotes (Canis latrans var.). Please check the metadata to confirm and cross-reference sample IDs.EasternCoyoteRawData.zipGreat Lakes Boreal Wolf Raw DataThis file contains raw Illumina sequence data for the Great Lakes Boeal Wolves (Canis lupus var). Please check the metadata to confirm and cross-reference sample IDs.GreatLakesBorealWolfRawData.zipGrey Wolf Raw DataThis file contains raw Illumina sequence data for the Grey Wolves (Canis lupus) and Dog (Canis lupus familiaris). Please check the metadata to confirm and cross-reference sample IDs.GreyWolfDogRawData.zipWestern Coyote Raw DataThis file contains raw Illumina sequence data for the Western Coyotes (Canis latrans). Please check the metadata to confirm and cross-reference sample IDs.WesternCoyoteRawData.zip
DOI: 10.5061/dryad.2qg01
title: Data from: Adaptive genomic divergence under high gene flow between freshwater and brackish-water ecotypes of prickly sculpin (Cottus asper) revealed by Pool-Seq

description: Understanding the genomic basis of adaptive divergence in the presence of
 gene flow remains a major challenge in evolutionary biology. In prickly
 sculpin (Cottus asper), an abundant euryhaline fish in northwestern North
 America, high genetic connectivity among brackish-water (estuarine) and
 freshwater (tributary) habitats of coastal rivers does not preclude the
 build-up of neutral genetic differentiation and emergence of different
 life history strategies. Because these two habitats present different
 osmotic niches, we predicted high genetic differentiation at known teleost
 candidate genes underlying salinity tolerance and osmoregulation. We
 applied whole-genome sequencing of pooled DNA samples (Pool-Seq) to
 explore adaptive divergence between two estuarine and two tributary
 habitats. Paired-end sequence reads were mapped against genomic contigs of
 European Cottus, and the gene content of candidate regions was explored
 based on comparisons with the threespine stickleback genome. Genes showing
 signals of repeated differentiation among brackish-water and freshwater
 habitats included functions such as ion transport and structural
 permeability in freshwater gills, which suggests that local adaptation to
 different osmotic niches might contribute to genomic divergence among
 habitats. Overall, the presence of both repeated and unique signatures of
 differentiation across many loci scattered throughout the genome is
 consistent with polygenic adaptation from standing genetic variation and
 locally variable selection pressures in the early stages of life history
 divergence.
description: Genomic read data for
 Fraser Estuary in bam formatBam file with genomic
 read data (HiSeq 2000, 100bp paired end reads, sequencing of 44 pooled
 Cottus fishes from Fraser River Estuary)CottusMap_mergedBW1estQ20.bamGenomic read data for Capilano Estuary in bam formatBam file with genomic read data (HiSeq2000, 100bp paired-end reads, pooled sequences of 44 Cottus individuals from Capilano Estuary)CottusMap_mergedBW2capQ20.bamGenomic read data for Hatzic Lake in bam formatBam file with genomic read data (HiSeq2000, 100bp paired-end reads, pooled sequences of 44 Cottus individuals from Hatzic Lake)CottusMap_mergedFW1hatQ20.bamGenomic read data for Pitt lake in bam formatBam file with genomic read data (HiSeq2000, 100bp paired-end reads, pooled sequences of 44 Cottus individuals from Pitt Lake)CottusMap_mergedFW2pittQ20.bam
DOI: 10.5061/dryad.3v39m
title: Data from: Reconstructing the microbial diversity and function of pre-agricultural tallgrass prairie soils in the United States

description: Native tallgrass prairie once dominated much of the midwestern United
 States, but this biome and the soil microbial diversity that once
 sustained this highly productive system have been almost completely
 eradicated by decades of agricultural practices. We reconstructed the soil
 microbial diversity that once existed in this biome by analyzing relict
 prairie soils and found that the biogeographical patterns were largely
 driven by changes in the relative abundance of Verrucomicrobia, a poorly
 studied bacterial phylum that appears to dominate many prairie soils.
 Shotgun metagenomic data suggested that these spatial patterns were
 associated with strong shifts in carbon dynamics. We show that metagenomic
 approaches can be used to reconstruct below-ground biogeochemical and
 diversity gradients in endangered ecosystems; such information could be
 used to improve restoration efforts, given that even small changes in
 below-ground microbial diversity can have important impacts on ecosystem
 processes.
description: fierer_tallgrassAll data pertaining to this study are in this archive.
DOI: 10.5061/dryad.pm0hn
title: Data from: Identification of species in the angiosperm family Apiaceae using DNA barcodes

description: Apiaceae (Umbelliferae) is a large angiosperm family that includes many
 medicinally important species. The ability to identify these species and
 their adulterants is important, yet difficult to do so because of their
 subtle fruit morphological differences and often lack of diagnostic
 features in preserved specimens. Moreover, dried roots are often the
 official medical organs, making visual identification to species almost
 impossible. DNA barcoding has been proposed as a powerful taxonomic tool
 for species identification. The Consortium for the Barcode of Life (CBOL)
 Plant Working Group has recommended the combination of rbcL+matK as the
 core plant barcode. Recently, the China Plant BOL Group proposed that the
 nuclear ribosomal DNA internal transcribed spacer (ITS), as well as a
 subset of this marker (ITS2), be incorporated alongside rbcL+matK into the
 core barcode for seed plants, particularly angiosperms. In this study, we
 assess the effectiveness of these four markers plus psbA-trnH as Apiaceae
 barcodes. A total of 6,032 sequences representing 1,957 species in 385
 diverse genera were sampled, of which 211 sequences from 50 individuals
 (representing 7 species) were newly obtained. Of these five markers, ITS
 and ITS2 showed superior results in intra- and interspecific divergence
 and DNA barcoding gap assessments. For the matched dataset (173 samples
 representing 45 species in 5 genera), the ITS locus had the highest
 identification efficiency (73.3%), yet ITS2 also performed relatively well
 with 66.7% identification efficiency. The identification efficiency
 increased to 82.2% when using an ITS+psbA-trnH marker combination
 (ITS2+psbA-trnH was 80%), which was significantly higher than that of
 rbcL+matK (40%). For the full sample dataset (3,052 ITS sequences, 3,732
 ITS2 sequences, 1,011 psbA-trnH sequences, 567 matK sequences, and 566
 rbcL sequences), ITS, ITS2, psbA-trnH, matK, and rbcL had 70.0%, 64.3%,
 49.5%, 38.6%, and 32.1% discrimination abilities, respectively. These
 results confirm that ITS or its subset ITS2 be incorporated into the core
 barcode for Apiaceae and that the combination of ITS/ITS2+psbA-trnH has
 much potential value as a powerful, standard DNA barcode for Apiaceae
 identification.
description: Apiaceae sequences used
 to evaluate the five DNA barcodes.GenBank accession
 numbers for all of the sequences used in this paper have been listed in
 this file.Table_S1.xlsxApiaceae sequences used to evaluate the five DNA barcodes.All sequences (3,052 ITS sequences, 3,732 ITS2 sequences, 1,011 psbA-trnH sequences, 567 matK sequences, and 566 rbcL sequences) have been used to evaluate the five DNA barcodes.all_sequences.zip
DOI: 10.15482/usda.adc/26956279
title: Data and code from: Mycotoxin contamination & the nutritional content of corn targeted for animal feed

description: This dataset contains raw data (Excel spreadsheet, .xlsx), R statistical code (RMarkdown notebook, .Rmd), and rendered output of the R notebook (HTML). This comprises all raw data and code needed to reproduce the analyses in the manuscript:Pokoo-Aikins, A., C. M. McDonough, T. R. Mitchell, J. A. Hawkins, L. F. Adams, Q. D. Read, X. Li, R. Shanmugasundaram, E. Rodewald, P. Acharya, A. E. Glenn, and S. E. Gold. 2024. Mycotoxin contamination and the nutritional content of corn targeted for animal feed. <i>Poultry Science</i>, 104303. DOI: 10.1016/j.psj.2024.104303.The data consist of the mycotoxin concentration, nutrient content, and color of different samples of corn (maize). We model the effect of mycotoxin concentration on the concentration of several different nutrients in corn. We include main effects of the different mycotoxins as well as two-way interactions between each pair of mycotoxins. We also include analysis of mycotoxin effects on the <i>L</i> variable from the color analysis, because it seems to be the one most important for determining the overall color of the corn. We use AIC to compare the models with and without interaction terms. We find that the models without interaction terms are better so we omit the interactions. We present adjusted R-squared values for each model as well as the p-values associated with the average slopes (effect of each mycotoxin on each nutrient). Finally, we produce the figures that appear in the above cited manuscript.Column metadata can be found in the Excel spreadsheet.Included files<b>Combined LCMS NIR Color data.xlsx</b>: Excel file with all raw data (sheet 1) and column metadata (sheet 2).<b>corn_mycotoxin_analysis_archived.Rmd</b>: RMarkdown notebook with all analysis code<b>corn_mycotoxin_analysis_archived.html</b>: rendered output of R notebook
DOI: 10.15482/usda.adc/26956279.v1
title: Data and code from: Mycotoxin contamination & the nutritional content of corn targeted for animal feed

description: This dataset contains raw data (Excel spreadsheet, .xlsx), R statistical code (RMarkdown notebook, .Rmd), and rendered output of the R notebook (HTML). This comprises all raw data and code needed to reproduce the analyses in the manuscript:Pokoo-Aikins, A., C. M. McDonough, T. R. Mitchell, J. A. Hawkins, L. F. Adams, Q. D. Read, X. Li, R. Shanmugasundaram, E. Rodewald, P. Acharya, A. E. Glenn, and S. E. Gold. 2024. Mycotoxin contamination and the nutritional content of corn targeted for animal feed. <i>Poultry Science</i>, 104303. DOI: 10.1016/j.psj.2024.104303.The data consist of the mycotoxin concentration, nutrient content, and color of different samples of corn (maize). We model the effect of mycotoxin concentration on the concentration of several different nutrients in corn. We include main effects of the different mycotoxins as well as two-way interactions between each pair of mycotoxins. We also include analysis of mycotoxin effects on the <i>L</i> variable from the color analysis, because it seems to be the one most important for determining the overall color of the corn. We use AIC to compare the models with and without interaction terms. We find that the models without interaction terms are better so we omit the interactions. We present adjusted R-squared values for each model as well as the p-values associated with the average slopes (effect of each mycotoxin on each nutrient). Finally, we produce the figures that appear in the above cited manuscript.Column metadata can be found in the Excel spreadsheet.Included files<b>Combined LCMS NIR Color data.xlsx</b>: Excel file with all raw data (sheet 1) and column metadata (sheet 2).<b>corn_mycotoxin_analysis_archived.Rmd</b>: RMarkdown notebook with all analysis code<b>corn_mycotoxin_analysis_archived.html</b>: rendered output of R notebook
DOI: 10.5061/dryad.s6j1822
title: Data from: Fire, grazing, and climate shape plant-grasshopper interactions in a tallgrass prairie

description: 1. Species interactions are integral to ecological community function and
 the structure of species interactions has repercussions for the
 consequences of species extinctions. Few studies have examined the role of
 environmental factors in controlling species interaction networks across
 time. 2. We examined variation in plant-grasshopper network structural
 properties in response to three major grassland drivers: periodic fire,
 ungulate grazing and climate. 3. We sequenced a plant barcoding gene from
 extracted grasshopper gut contents to characterize diets of 26 grasshopper
 species. Resulting grasshopper species’ diets were combined with long-term
 plant and grasshopper surveys to assemble plant-grasshopper networks
 across 13-19 years for 6 watersheds subjected to varying fire and grazing
 treatments. 4. Network modularity, generality, and predicted grasshopper
 community robustness to plant species loss all increased in grazed
 watersheds. Temperature decreased predicted grasshopper community
 robustness to plant species loss. 5. Grasshopper communities were found to
 be vulnerable to climatic warming due to host plant loss. However,
 intermediate disturbance from ungulate grazers may maintain grasshopper
 diversity and buffer community robustness to species loss. Our results
 suggest that climate and disturbance shape the structure of ecological
 interaction networks and thus have many indirect effects on species
 persistence though direct effects on interaction partners.
description: Welti et al. 2018_Online
 data_Network metricsClimate, fire and
 grazing treatment and network metrics for plant-grasshopper
 networks.Welti et al. 2018_Online
 data_Plant-grasshopper networksWeighted
 plant-grasshopper networks for each year and watershed.
DOI: 10.15468/dl.f9yg5s
title: Occurrence Download

description: A dataset containing 69908 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "HasGeospatialIssue is false",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 {
 "not" : {
 "BasisOfRecord" : [
 "is one of (Fossil, Living Specimen)"
 ]
 }
 }
 ]
 },
 "Year is greater than or equal to 2000",
 "Continent is Europe",
 "TaxonKey is Orchis militaris"
 ]
}

 The dataset includes 69908 records from 482 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0000587-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.rc1kv
title: Data from: Size distribution of function-based human gene sets and the split-merge model

description: The sizes of paralogues—gene families produced by ancestral
 duplication—are known to follow a power-law distribution. We examine the
 size distribution of gene sets or gene families where genes are grouped by
 a similar function or share a common property. The size distribution of
 Human Gene Nomenclature Committee (HGNC) gene sets deviate from the
 power-law, and can be fitted much better by a beta rank function. We
 propose a simple mechanism to break a power-law size distribution by a
 combination of splitting and merging operations. The largest gene sets are
 split into two to account for the subfunctional categories, and a small
 proportion of other gene sets are merged into larger sets as new common
 themes might be realized. These operations are not uncommon for a curator
 of gene sets. A simulation shows that iteration of these operations
 changes the size distribution of Ensembl paralogues and could lead to a
 distribution fitted by a rank beta function. We further illustrate
 application of beta rank function by the example of distribution of
 transcription factors and drug target genes among HGNC gene families.
description: ensembl-nov2015data for Fig.1: ensembl-nov2015.txt column 1: Ensembl gene family ID column 2: number of genes in the (Ensembl) gene family column 3: description of the (Ensembl) gene familygf-size-feb2016data for Fig.2: gf-size-feb2016.txt column 1: HGNC gene family ID or name column 2: number of genes in the (HGNC) gene family (possibly including pseudogenes) column 3: number of genes in the (HGNC) gene family (excluding pseudogenes) column 4: description of the (HGNC) gene familygene-fam-with-TFdata for Fig.4: gene-fam-with-TF.txt column 1: HGNC gene family ID or name column 2: number of transcription factors in the (HGNC) gene family column 3: number of genes in the (HGNC) gene family (possibly including pseudogenes) column 4: description of the (HGNC) gene familygene-fam-with-drug-targetdata for Fig.5: gene-fam-with-drug-target.txt column 1: HGNC gene family ID or name column 2: number of drug target genes (gene products) in the (HGNC) gene family column 3: number of genes in the (HGNC) gene family (possibly including pseudogenes) column 4: description of the (HGNC) gene family
DOI: 10.5061/dryad.f431f
title: Data from: Resource availability and roosting ecology shape reproductive phenology of rain forest insectivorous bats

description: Bats in temperate and subtropical regions typically synchronize birth of a
 single young with peaks in resource availability driven by local climate
 patterns. In tropical rain forest, insects are available throughout the
 year, potentially allowing departures from seasonal monoestry. However,
 reproductive energy budgets may be constrained by the cost of commuting to
 foraging grounds from distant roosts. To test these hypotheses, we
 simultaneously tracked female reproductive activity of 11 insectivorous
 bat species, insect biomass, and local weather variables for 20 months in
 a Malaysian rain forest. Five species roost in forest structures and hence
 have low commuting costs, whereas six species depend on caves, which are
 limited in the landscape, and are presumed to incur higher commuting costs
 to foraging sites. Monthly insect biomass was positively correlated with
 monthly rainfall, and there was a significant relationship between insect
 biomass and lactation in cave-roosting but not forest-roosting species.
 Cave-roosting species were seasonally monoestrus, with parturition
 confined to a two-month period, whereas in forest-roosting species,
 pregnancy and lactation were recorded throughout the year. Our results
 suggest that the energetic costs of commuting from roosts to foraging
 grounds shape annual reproductive patterns in tropical rain forest
 insectivorous bats. Ongoing changes in forest landscapes are likely to
 increase these costs for cave-roosting bats, further restricting
 reproductive opportunities. Climate change is projected to influence the
 timing of rainfall events in many tropical habitats, which may disrupt
 relationships between rainfall, insect biomass, and bat reproductive
 timing, further compromising reproductive success.
description: Nurul-Ain et
 al_Reproductive phenology of tropical insectivorous batsRaw data of bats capture
 and insect biomass.
DOI: 10.5061/dryad.36634
title: Data from: Influence of northern limit range on genetic diversity and structure in a widespread North American tree, sugar maple (Acer saccharum Marshall)

description: Due to climate change, the ranges of many North-American tree species are
 expected to shift northward. Sugar maple (Acer saccharum Marshall) reaches
 its northern continuous distributional limit in north-eastern North
 America at the transition between boreal mixed-wood and temperate
 deciduous forests. We hypothesized that marginal fragmented northern
 populations from the boreal mixed-wood would have a distinct pattern of
 genetic structure and diversity. We analyzed 18 microsatellite loci
 variation in 23 populations distributed along three latitudinal transects
 (west, central and east) that encompass the continuous-discontinuous
 species range. Each transect was divided into two zones, continuous
 (temperate deciduous) and discontinuous (boreal mixed-wood), based on
 sugar maple stand abundance. Respective positive and negative
 relationships were found between the distance of each population to the
 northern limit (D north), and allelic richness (AR) and population
 differentiation (FST). These relations were tested for each transect
 separately; the pattern (discontinuous/continuous) remained significant
 only for the western transect. structure analysis revealed the presence of
 four clusters. The most northern populations of each transect were
 assigned to a distinct group. Asymmetrical gene flow occurred from the
 southern into the four northernmost populations. Southern populations in
 Québec may have originated from two different postglacial migration
 routes. No evidence was found to validate the hypothesis that northern
 populations were remnants of a larger population that had migrated further
 north of the species range after the retreat of the ice sheet. The
 northernmost sugar maple populations possibly originated from long
 distance dispersal.
description: AcerSaccharum-18ssr-Lat-23popMicrosatellites data from 18 markers on 23 sugar maple populations across the northern limit of the species in Québec, Canada. Populations are naturals and split into 2 cohorts (sapling and mature).2013-06-24-18ssr-Lat-23pop-PourDryad.xls