cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.mq9qzu
title: Occurrence Download

description: A dataset containing 1459 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Lema daturaphila Kogan & Goeden, 1970",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 1459 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082670-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hcpy73
title: Occurrence Download

description: A dataset containing 12697 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-103.93764 55.86938,-114.79259 61.29686,-125.26888 52.20899,-130.69636 38.95585,-123.88046 25.95516,-104.06386 12.5758,-95.6071 15.85753,-93.58758 25.45027,-93.84001 38.95585,-96.74309 50.31568,-103.93764 55.86938))",
 "TaxonKey is Antilocapra americana (Ord, 1815)"
 ]
}

 The dataset includes 12697 records from 67 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082671-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.d37vka
title: Occurrence Download

description: A dataset containing 419 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Hypulus quercinus (Quensel, 1790)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 419 records from 73 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082672-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7nq6bz
title: Occurrence Download

description: A dataset containing 29824 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Leptinotarsa decemlineata (Say, 1824)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 29824 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082674-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dk3dde
title: Occurrence Download

description: A dataset containing 79889 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Acer saccharinum L."
 ]
}

 The dataset includes 79889 records from 546 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082673-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ewm5xm
title: Occurrence Download

description: A dataset containing 310 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Anisoxya fuscula (Illiger, 1798)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 310 records from 68 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082676-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.79n2cm
title: Occurrence Download

description: A dataset containing 798 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Dendropsophus labialis (Peters, 1863)"
 ]
}

 The dataset includes 798 records from 30 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082675-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hryqxn
title: Occurrence Download

description: A dataset containing 29824 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)"
 ]
 }
 }
 ]
 },
 "SpeciesKey is Leptinotarsa decemlineata (Say, 1824)",
 "Year is greater than or equal to 2004",
 "Year is less than or equal to 2023"
 ]
}

 The dataset includes 29824 records from 222 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0082677-240626123714530/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.19342/1
title: Vertical distribution measurements of Meroplanktonic gastropod larvae and the environment. A Canadian Healthy Oceans Network Population Connectivity project, PC-06

description: This dataset was collected in the field (using a plankton pump, CTD, fluorometer and ADCP) for a MSc Thesis and 1 publication. This dataset contains the standardized abundance (count m-3) of meroplanktonic larvae (Margarites spp., Crepidula spp., Astyris lunata, Diaphana minuta, Littorinimorpha,  Arrhoges occidentalis, lyanassa spp., Bittiolum  alternatum, Nudibranchia), temperature, salinity, density, fluorescence, calculated Richardson number and current velocities (north-south, east-west, and vertical velocities) at 6 (3, 6, 9, 12, 18 and 24 m) depths, every 2 h over a 36- and 26-h sampling period, in St. George’s Bay, Nova Scotia, Canada. The dataset also included lunar cycle, diel period, tidal state, date, time, sampling depth, sampling depth range, and more.
DOI: 10.5061/dryad.1pg48/2
title: Survivorship & Fecundity Data from assays conducted on cadmium-supplemented media

description: This data file  contains data used in the study “The effects of selective history and environmental heterogeneity on inbreeding depression in experimental populations of Drosophila melanogaster” by Tristan A.F. Long, Locke Rowe and Aneil Agrawal. For details on how these data were obtained, please consult original article. The data consist of data collected from females obtained from experimentally evolved populations of fruit flies that had been cultured under protocols differing in their amount and type of environmental homogeneity. The  file contains data from individuals assayed on cadmium-supplemented media.
DOI: 10.5061/dryad.266qs/5
title: ConcatenatedAlignmentPositions_gyrB_lepA

description: This file provides locus positions in the alignment in the file ‘Concatenated_gyrB_lepA_PhylotypingTree.nex’ for the gyrB and lepA loci used by the phylotyping analysis. This file includes the gyrB and lepA sequences of the cultured microbiota samples from Othnophagus taurus.
DOI: 10.5061/dryad.266qs/6
title: Analysis

description: This text file contains commands to carry out the RaxML analyses of the matrices contained in BacterialGenomesConcatenated.ConstraintTree.nex and Concatenated_gyrB_lepA_PhylotypingTree.nex. Please note that the data matrices of the NEXUS files must be converted to the Phylip format for use with RAxML. The matrices can be exported using the program Mesquite.
DOI: 10.5061/dryad.2rm60/1
title: Cymbidieae matK/ycf1 combined matrix

description: Aligned matK/ycf1 matrix for 288 individuals of Cymbidieae plus one outgroup; NEXUS file.
DOI: 10.5061/dryad.504636cd/1
title: ALN1

description: Alignment that contains 41 complete nucleotide sequences of Tick-borne encephalitis virus and three out-groups selected among LGTV and OHFV, retrieved from Genbank in January 2011.
DOI: 10.5061/dryad.504636cd/2
title: ALN2

description: Alignment that contains 28 sequences from ALN1 of known collection dates (from 1937 to 2008), with the deletion of out-groups and strains with unusual sampling locations. Non coding flanking regions and gap columns were removed.
DOI: 10.5061/dryad.504636cd/3
title: ALN2_1

description: Alignment derived from ALN2.fas that corresponds to the putative recombinant region (204nt).
DOI: 10.5061/dryad.504636cd/4
title: ALN2_2

description: Alignment derived from ALN2.fas with the deletion of the putative recombinant region.
DOI: 10.5061/dryad.504636cd/5
title: ALN2_C

description: Alignment derived from ALN2.fas that corresponds to the C-gene region.
DOI: 10.5061/dryad.504636cd/6
title: ALN2_E

description: Alignment derived from ALN2.fas that corresponds to the E-gene region.
DOI: 10.5061/dryad.504636cd/7
title: ALN2_NS1

description: Alignment derived from ALN2.fas that corresponds to the NS1-gene region.
DOI: 10.5061/dryad.57r3c/1
title: Supplemental Data

description: Supplemental Data
DOI: 10.5061/dryad.5pc00/1
title: Data for Evans et al. 2013

description: Contains raw data used to test for interacting sperm-ovarian fluid interactions on sperm motility (sheet 1) and for partitioning variance in sperm competitiveness (sheet 2)
DOI: 10.5061/dryad.616n0/1
title: Archived stickleback data raw

description: This file contains data in spreadsheet form on standard length at 150 days post fertilization of stickleback from nine replicate Icelandic populations classified into three types of population: marine populations, old freshwater lake populations and young freshwater lake populations. Full-sib families were split with half the progeny reared exclusively at low (5ppt) and half at high (35 ppt) salinity.  Please see the readme file for details of the data structure.
DOI: 10.5061/dryad.6c45t/1
title: body temperature files

description: Text files containing the body temperature recordings from individual Syrian hamsters co-housed in pairs or single-housed as 'virtual pairs' in laboratory cages.  Temperature is in Celsius (C = Celsius) and was recorded using iButton temperature dataloggers.  Each line contains the date and time of the body temperature recording.  The first number in the filename represents the hamster ID for that file.  Co-housed hamster pairs: 47 with 51, 45 with 53, 42 with 50, 41 with 52, 49 with 44, 46 with 43, 54 with 48, 124 with 98, 75 with 127, 118 with 102, 89 with 116, 113 with 108, 76 with 122, 101 with 81, 117 with 74, 94 with 99, 111 with 84, 93 with 86, 91 with 82.  Virtually-paired hamsters: 112 with 73, 126 with 106, 78 with 104, 110 with 103, 114 with 128, 105 with 100, 129 with 96, 80 with 107, 87 with 95, 88 with 123, 90 with 83, 77 with 92.
DOI: 10.5061/dryad.703s1/1
title: fuel load and Zugunruhe

description: An excel sheet containing data collected on wild caught migrating northern wheatears on Helgoland, Germany. Zugunruhe is expressed as the number of 15 min. periods in a 10 hr. night during which a bird showed at least five activity counts.
DOI: 10.5061/dryad.73f23/1
title: Anti-PA Titers for Equus quagga

description: Anti-anthrax (anti-protective antigen toxin) antibody titers for wild plains zebra immobilized and sampled over 1-5 seasons in Etosha National Park, Namibia. id=animal capture ID. titer=anti-PA titer; the titer is the highest dilution in the titration series for which the mean sample optical density (OD) for that dilution is greater than the mean negative control OD titration curve from all plates (dilution is as 1:dilution; e.g. 1024 is a 1:1024 dilution). titerDUP=anti-PA titer for which the titer is the last dilution at which the mean sample OD is greater than the mean negative control OD buffered by a 95% confidence interval determined by the inter-duplicate error at that dilution, across all samples. titerNCONT=anti-PA titer for which the titer is the last dilution at which the mean sample OD is greater than the mean negative control OD buffered by a 95% confidence interval determined by the inter-negative control error at that dilution, across all samples. plate=plate identifier (date and plate number on that day). ncont=identifier of the negative control sample used.
DOI: 10.5061/dryad.73f23/2
title: Anti-PA Titers for Antidorcas marsupialis

description: Anti-anthrax (anti-protective antigen toxin) antibody titers for wild springbok immobilized and sampled over 1-2 seasons in Etosha National Park, Namibia. id=animal capture ID. titer=anti-PA titer; the titer is the highest dilution in the titration series for which the mean sample optical density (OD) for that dilution is greater than the mean negative control OD titration curve from all plates (dilution is as 1:dilution; e.g. 1024 is a 1:1024 dilution). titerDUP=anti-PA titer for which the titer is the last dilution at which the mean sample OD is greater than the mean negative control OD buffered by a 95% confidence interval determined by the inter-duplicate error at that dilution, across all samples. titerNCONT=anti-PA titer for which the titer is the last dilution at which the mean sample OD is greater than the mean negative control OD buffered by a 95% confidence interval determined by the inter-negative control error at that dilution, across all samples. plate=plate identifier (date and plate number on that day). ncont=identifier of the negative control sample used.
DOI: 10.5061/dryad.73f23/3
title: Anti-PA Titers for Loxodonta africana

description: Anti-anthrax (anti-protective antigen toxin) antibody titers for wild African elephants immobilized and sampled over 1-2 seasons in Etosha National Park, Namibia. id=animal capture ID. titer=anti-PA titer; the titer is the highest dilution in the titration series for which the mean sample optical density (OD) for that dilution is greater than the mean negative control OD titration curve from all plates (dilution is as 1:dilution; e.g. 1024 is a 1:1024 dilution). titerDUP=anti-PA titer for which the titer is the last dilution at which the mean sample OD is greater than the mean negative control OD buffered by a 95% confidence interval determined by the inter-duplicate error at that dilution, across all samples. titerNCONT=anti-PA titer for which the titer is the last dilution at which the mean sample OD is greater than the mean negative control OD buffered by a 95% confidence interval determined by the inter-negative control error at that dilution, across all samples. plate=plate identifier (date and plate number on that day). ncont=identifier of the negative control sample used.
DOI: 10.5061/dryad.7455b/10
title: 10. Table 2 t data

description: Please see the READ ME file associated with this data deposit.
DOI: 10.5061/dryad.7r0d5/1
title: SNP-bis
DOI: 10.5061/dryad.f4392/1
title: California ngaio plant damage survey data

description: This file contains the health status of ngaio plants (Myoporum laetum) in various stages of defoliation by the invasive thrips, Klambothrips myopori in coastal southern California. The data are a mix of field observations and earlier satellite image information of the same plants between 2004 and 2011. The field observations include two levels of rapid data collection. At a minimum the rows contain whether or not the plant was alive and the extent of defoliation and thrips infested shoots. In some years at some sites, plant size was also recorded. See the ReadMe file for more details.
DOI: 10.5061/dryad.f4392/2
title: Drive-by transect observations of planted Myoporum laetum

description: The presence (or coarse abundance) of New Zealand ngaio (Myoporum laetum) and whether or not there is obvious damage from Klambothrips myopori herbivory, recorded per mile using a car odometer while a passenger through various Southern California routes. The routes are described in this text file and provided in a kmz (Google Earth file) in the subsequent file. Klambothrips myopori is a recent arrival to California and has reached high densities where it causes prominent crown dieback, easily visible from a car.
DOI: 10.5061/dryad.f4392/3
title: Drive-by transect routes

description: A Google Earth kmz file containing vectors of the three Southern California routes along which I surveyed for New Zealand ngaio (Myoporum laetum) and visible damage by the recenly arrived and outbreaking herbivore, Klambothrips myopori. See the associated csv file for the observations.
DOI: 10.5061/dryad.fn2rg/14
title: PHY_ML_tree_codonPhyML

description: The maximum likelihood tree inferred from "PHY_alignment.fas", using CodonPhyML. We used the GY model with four categories of non-synonymous/synonymous substitution rate ratios drawn from the discrete gamma distribution, and codon frequencies were estimated from the data under the F3X4 model. The tree topology search was done using the NNI approach, and branch support was estimated using the SH-like aLRT method. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/18
title: NEO_ML_tree_garil

description: The maximum likelihood tree inferred from "NEO_alignment.fas", using Garli with genthreshfortopoterm set to 1,000,000 and 8 independent runs. We partitioned the data by codon position, and GTR+Γ+I, GTR+Γ+I, GTR+I models were applied to each codon position respectively. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/19
title: NEO_ML_tree_pos12_garli

description: The maximum likelihood tree inferred from "NEO_alignment.fas" (third codon excluded), using Garli with genthreshfortopoterm set to 1,000,000 and 8 independent runs. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/20
title: NEO_ML_tree_pos3_garli

description: The maximum likelihood tree inferred from "NEO_alignment.fas" (first and second codon excluded), using Garli with genthreshfortopoterm set to 1,000,000 and 8 independent runs. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/21
title: NEO_ML_tree_codonPhyML

description: The maximum likelihood tree inferred from "NEO_alignment.fas", using CodonPhyML. We used the GY model with four categories of non-synonymous/synonymous substitution rate ratios drawn from the discrete gamma distribution, and codon frequencies were estimated from the data under the F3X4 model. The tree topology search was done using the NNI approach, and branch support was estimated using the SH-like aLRT method. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/22
title: NEO_MLBS_tree_pos12_raxml

description: The maximum likelihood bootstrapping trees from "NEO_alignment.fas", using RAxML (1000 replicates; third codon excluded). Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/23
title: NEO_MLBS_tree_pos3_raxml

description: The maximum likelihood bootstrapping trees from "NEO_alignment.fas", using RAxML (1000 replicates; first and second codon excluded). Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/24
title: NEO_BI_con_tree_MrBayes

description: The 50% majority consensus tree from MrBayes run (25% of the total generations were discarded as burn-in), based on "NEO_alignment.fas". The analysis was carried out with two independent MCMC runs, four chains each, and trees sampled every 1000 generations. We partitioned the data by codon position, and GTR+Γ+I, GTR+Γ+I, GTR+I models were applied to each codon position respectively. Substitution parameters were unlinked and the rate prior was set to vary among partitions. Alphanumeric codes following species names are the four-letter 1KP transcriptome identifiers, Genbank accessions or both.
DOI: 10.5061/dryad.fn2rg/25
title: BlueDevil

description: A Python scripts to extract gene homologs from 1KP transcriptomes. Sequences for gene-of-interest are queried by tBLASTn and the significant hits to transcriptome scaffolds are extracted. For each scaffold, the best open reading frame is identified, and the sequence is translated into amino acids and then BLASTp queried against the NCBI non-redundant protein database (nr). The scaffolds is discarded if they did not match the homologs in the nr database with an e-value threshold of &lt;0.001. The filtered scaffolds from SOAP de novo and SOAP de novo trans assemblies are then merged using CAP3.
DOI: 10.5061/dryad.g4sh8/1
title: Occurrence data for the coffee white stem borer in Zimbabwe obtained from biological surveys

description: Data collected from biological field surveys done in 2003. The data shows the XY cordinates of coffee farms surveyed and the occurrence of CWB (1 present, 0 absent) The data is in decimal degrees format (WGS84) and unprojected.
DOI: 10.5061/dryad.hd31m/1
title: Castaneus_Morphometric_Data

description: Microsoft Excel file with individual measurements of all specimens used in the publication.  For abbreviations, see text of the paper.
DOI: 10.5061/dryad.kc4j4/1
title: Survey data for Dryad

description: Tables of analysed data some of which were used in the paper
DOI: 10.5061/dryad.kg45v/1
title: number of larvae, pupae and adults (figure 2 from paper)

description: In this file are numbers of larvae, pupae and adults shown from one forward simulation. There are 10 columns. The first indicates time in days. Then three columns indicate total number of larvae, pupae and adults followed by number of larvae, pupae and adults in good patches (g_) and bad patches (b_).
DOI: 10.5061/dryad.kg45v/2
title: behavior

description: This file lists the number of individuals that feeding, flying or reproducing in good patch (g_) and bad patches (b_) dependent on time in the year. This data is used to produce figure 3A, 3B and 3C in the paper
DOI: 10.5061/dryad.kg45v/3
title: traits

description: This file lists the average fat (fat), abdomen (abd) and thorax (tho) weight and biological age (age) in good (g_) and bad pacthes (b_) of model simulations dependent on time. This data is used to create figure 3D, 3E and 3F.
DOI: 10.5061/dryad.nc866/1
title: Supplementary Information for Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit

description: Supplementary tables and figures.
DOI: 10.5061/dryad.r0056/56
title: TuRE_metaphlan

description: MetaPhlAn microbial profile for sample TuRE.
DOI: 10.5061/dryad.r0056/57
title: Ty_metaphlan

description: MetaPhlAn microbial profile for sample Ty.
DOI: 10.5061/dryad.r0056/58
title: TyRE_metaphlan

description: MetaPhlAn microbial profile for sample TyRE.
DOI: 10.5061/dryad.r0056/59
title: Ya_metaphlan

description: MetaPhlAn microbial profile for sample Ya.
DOI: 10.5061/dryad.r0056/60
title: YaRE_metaphlan

description: MetaPhlAn microbial profile for sample YaRE.
DOI: 10.5061/dryad.r0056/61
title: Ancient_Horse_Metagenomics_RScript

description: R script for analysing microbial profiles generated by MetaPhlAn.
DOI: 10.5061/dryad.r0056/62
title: plots_horses_MapDamage

description: map Damage profile of endogenous DNA