cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.17632/xdtfb78cty.1
title: Data for: Apparent Polar Wander Path for East Asia and Implications for Paleomagnetic Low Inclination in Sedimentary Rocks

description: A total of 1487 paleomagnetic directional data (816 for the South China Block; 671 for the North China Block) analyzed in this study were tabulated in Excel format.
DOI: 10.5061/dryad.03g3s3q/1
title: LFMM file for Corymbia calophylla.

description: This data has 263 individuals row wise and 9593 SNPs column wise. 0 = major homozygote, 1 = heterozygote, 2 = minor homozygote.
DOI: 10.5061/dryad.03g3s3q/2
title: File with climate data for LFMM

description: Climate data for LFMM for each individual. column 1 = maximum temperature of the warmest month; column 2 = mean annual precipitation; column 3 = aridity index.
DOI: 10.5061/dryad.03g3s3q/3
title: Baypass file for Corymbia calophylla

description: Rows are SNPs. Columns are population level allele counts. Two columns per locus. In the file, there are 27 populations and 9593 SNPs.
DOI: 10.5061/dryad.03g3s3q/4
title: Environmental data file for Bayenv and BayPass

description: Climate variables for populations. The climate variables are standardised following BayEnv's manual. Row 1 = maximum temperature of the warmest month; Row 2 = mean annual precipitation; Row 3 = aridity index.
DOI: 10.5061/dryad.03g3s3q/5
title: Bayenv data file for Corymbia calophylla

description: Population level allele counts for Bayenv input. Rows are SNPs, two rows per locus. Columns are populations.
DOI: 10.5061/dryad.03g3s3q/6
title: Pairwise FST file for GDM input

description: Pairwise FST for all of the SNPs for GDM analysis.
DOI: 10.5061/dryad.174667c/10
title: S5 Fig
DOI: 10.5061/dryad.174667c/11
title: S6 Fig
DOI: 10.5061/dryad.174667c/12
title: S7 Fig
DOI: 10.5061/dryad.174667c/13
title: S8 Fig
DOI: 10.5061/dryad.174667c/9
title: S4 Fig
DOI: 10.5061/dryad.5c4c6h8/1
title: Data_ChiralMF-20190428
DOI: 10.5061/dryad.5c4c6h8/2
title: Supple-Data_ChiralMF-20190428.2
DOI: 10.5061/dryad.7nf7d35/1
title: Au+ and Au- stability data

description: This data is for nanoparticle stability in various conditions afters 24 hours
DOI: 10.5061/dryad.7nf7d35/2
title: Increased silver concentration

description: Spectra for the synthesis of the nanostars with the increase of silver nitrate concentration
DOI: 10.5061/dryad.8d44d4q/1
title: PhuongSupplementaryFiles

description: All supplementary figures, tables, and supplementary doc on fossil calibration.
DOI: 10.5061/dryad.c04k521/1
title: Foraging bird abundance on canopy trees within shade-coffee farms

description: Abundance of foraging birds of each species for each observation period. country: country data was collected in (Nicaragua or Colombia); year: year data was collected (2015 or 2016); observer: observer initials; date_format: date of observation; juldate: julian calendar date; observation_num: observation number; treeID_format: individual code to identify trees; observationID: unique identifier; treesp: tree species common name (see paper for species names); time_format: time of observation; bird_sp: bird species common name (Colombia) or code (Nicaragua); num_birds: count of individuals; migratory_insectivore: binary dummy variable for primarily insectivorous migratory species; notes: miscellaneous notes; canopy_volume: canopy volume (meters cubed); scale_volume: scaled canopy volume with mean zero
DOI: 10.5061/dryad.c04k521/2
title: bothcountries_data_format_19feb2019_foragingtime_format

description: Foraging times of individual birds on trees. country: country data was collected in (Nicaragua or Colombia); year: year data was collected (2015 or 2016); treesp: common name of tree species (see paper for species names); treeID: unique identifier for individual focal trees; bird.sp: common name (Colombia) or code (Nicaragua) for bird species observed); migratory_insectivore: binary dummy variable indicating if bird species was a primarily insectivorous migratory bird; total_sec: total number of seconds observed foraging in the focal tree; vol: canopy volume of the focal tree (meters cubed); prop_sec: proportion of the total observation period (600 seconds) that the individual bird was observed foraging; scale_vol: scaled canopy volume with mean zero.
DOI: 10.5061/dryad.c04k521/3
title: bothcountries_species_richness_longformat

description: Number of individuals for each bird species on all trees observed including zeros. country: country tree was observed in (Nicaragua or Colombia); year: year of observation (2016); treesp: common name of tree species observed (see paper for species names); bird_sp: common name (Colombia) or code (Nicaragua) for each bird species observed; count: number of individuals observed (including zeros if never observed foraging in a tree species).
DOI: 10.5061/dryad.fj02s0j/57
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part8
DOI: 10.5061/dryad.fj02s0j/58
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part9
DOI: 10.5061/dryad.fj02s0j/59
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part10
DOI: 10.5061/dryad.fj02s0j/60
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part11
DOI: 10.5061/dryad.fj02s0j/61
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part12
DOI: 10.5061/dryad.fj02s0j/62
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part13
DOI: 10.5061/dryad.fj02s0j/63
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part14
DOI: 10.5061/dryad.fj02s0j/64
title: Supplementary data: CR1 retroelement insertions bioinformatic pipeline part15
DOI: 10.5061/dryad.fj02s0j/65
title: Supplementary Figure S1

description: Supplementary Figure S1  Palaeognath phylogenetic relationships inferred with MP-EST (a-d) and ASTRAL (e-h) coalescent-based species tree methods and maximum-likelihood inference of fully partitioned concatenated alignments with ExaML (i-l).  Topologies were inferred from 12,676 conserved non-exonic elements (CNEEs; parts a,e,i), 5,016 introns (parts b,f,j), 3,158 ultraconserved elements (UCEs; parts c,g,k), and the total evidence data set of 20,850 loci combined across marker types (TENT; parts d,h,l).  Bootstrap supports are drawn for clades with &lt; 100% support.
DOI: 10.5061/dryad.g44j6g2/1
title: Data & Code

description: Body mass and fGCM data collected on wild meerkats in the field. R codes for model 1a (body mass in emigrants, returners, and residents), model 1b (fGCM in emigrants, returners, and residents), model 2a (emigrant body mass during dispersal stages), and model 2b (emigrant fGCM during dispersal stages).
DOI: 10.5061/dryad.g5q6g80/1
title: Data from: Extensive allopolyploidy in the Neotropical genus Lachemilla (Rosaceae) revealed by PCR-based target enrichment of the nuclear ribosomal DNA cistron and plastid phylogenomics. AJB

description: This package contains the all the alignments and trees from the phylogenetic analyses from the paper. Also, it includes the demultiplexed reads ready to run Fluidimg2PURC in two separate files.
DOI: 10.5061/dryad.n11h95s/1
title: McNewetal_dryad_nestlingmeasurements

description: Condition and size of nestlings in study. Each row is a nestling. Nestlings were measured multiple times (see methods).
DOI: 10.5061/dryad.n11h95s/2
title: McNewetal_dryad_behavior

description: Data on nestling provisioning used in the study. Each row is a video observation period, recorded at an individual nest.
DOI: 10.5061/dryad.n11h95s/3
title: McNewetal_dryad_allnests

description: Data on reproductive success of nests in the study. Each row is a nest.
DOI: 10.5061/dryad.pp68kp4/1
title: CASA rawdata

description: Computer assisted sperm analysis from Pomatoschistus minutus sperm tested with and without associated sperm duct gland substances.
DOI: 10.5061/dryad.pp68kp4/2
title: Viability rawdata

description: Sperm viability raw data from Pomatoschistus minutus sperm tested with and without associated sperm duct gland substances.
DOI: 10.5061/dryad.ps7jt5b/1
title: Tree species abundance in Georgetown Guyana

description: These data represent the abundance of tree species in Georgetown Guyana. Individual trees with diameter at breast height (1.3 m) greater than 7 cm were counted in 45 transects with dimensions of 200 m in length and 60 m in width (30 m on each side). The Species column represents species identification, Abundance represents counts of each species wihtin each transect, Transect.No. represents a unique identifier for each transect, Transect.Type represents whether transects were commercial or residential, No.of.Buildings represents number of buildings within a transect, total.BA.m2 represents total basal area of all trees in a transect in square meters, total.crownArea.m2 represents the crown area of all tree species in a transect in square meters, Proportion.East.Indian represents proportion of residents of East Indian ancestry in neighborhoods containing transects, Origin.code represents the origin of tree species, Use.Acronym represents use of trees (C=cultivated for edible products, WP=wild plant, OR=ornamental), and Unique.to.Guyana represents whether the species was present in floristic inventories of Brazilian and Venezuelan cities (present in other cities=0, absent from other cities=1).
DOI: 10.5061/dryad.q0ht491/3
title: Alleles in derived populations

description: Alleles in restored/regenerated populations not occurring in wild-origin population samples. Occurrences are expressed by their De Silva frequency.
DOI: 10.5061/dryad.q0ht491/4
title: Allelic capture

description: Alleles occurring in wild origin populations which were also captured in restored/regenerated populations. Occurrences are expressed by their De Silva frequencies.
DOI: 10.5061/dryad.q0ht491/5
title: De Silva Frequencies
DOI: 10.5061/dryad.rg576jq/1
title: Heterozygosity for 100 kb windows

description: The proportion of all genotyped sites that are heterozygous sites per 100 kb window for each individual. Only sites with an individual depth of coverage of 5X were considered.
DOI: 10.5061/dryad.rg576jq/2
title: Depth of coverage

description: For each individual (columns), the number of sites in the genome with a given depth of coverage (rows) is given.
DOI: 10.5061/dryad.rg576jq/3
title: Site frequency spectra (SFS) (14 files)

description: Site requency spectra (SFS) estimated using ANGSD from RAD-seq data mapped to the reference genome.
Four types of files are provided: (1) SFS for the whole genome (with 20 bootstrap replicates), (2) for males only (with 20 bootstrap replicates), (3) for 'normal-recombination' scaffolds only (with 20 bootstrap replicates), (4) for 'normal-recombination' scaffolds with drop-one-out replicates.
DOI: 10.5061/dryad.rg576jq/4
title: Scaffold order and orientation for pseudo-chromosomal assembly

description: Chromosome, start and end position and orientation for each scaffold, based on mummer alignment of the Eurasian skylark scaffolds against the zebra finch genome, with additional manual edits.
DOI: 10.5061/dryad.rg576jq/5
title: Input files and relatedness estimates from NgsRelate (6 files)

description: Input VCF files and output files from NgsRelate. Files of sample names for each individual are also provided.
DOI: 10.5061/dryad.rg576jq/6
title: Input files and relatedness estimates from KGD

description: Input files produced using ANGSD and relatedness matrices  estimated using KGD.
DOI: 10.5061/dryad.rg576jq/7
title: Stairwayplot best model

description: Output from Stairwayplot for the best fitting model of population size over time for Raso lark.
DOI: 10.5061/dryad.rj2gf5j/1
title: Raw data for Hao et al., Ecology and Evolution

description: Raw data for Hao et al., Ecology and evolution. File includes two data tables describing vegetation cover, temperature and precipitation change. Other figures have also been put in the data file.
DOI: 10.5061/dryad.s6s9p58/1
title: Habitat and landuse of rodents in mainland Southeast-Asia

description: The information on presence of each individual of four species of rodents was obtained during the ANR project CERoPath. See:
Morand S, Bordes F, Blasdell K, Pilosof S, Cornu J, Chaisiri K, Chaval Y, Cosson J, Claude J, Feyfant T, Herbreteau V, Dupuy S, Tran A (2015) Assessing the distribution of disease-bearing rodents in human-modified tropical landscapes. Journal of Applied Ecology 52(3): 784–794. https://doi.org/10.1111/1365-2664.12414
And:
Morand S, Bordes F, Blasdell K, Pilosof S, Cornu J, Chaisiri K, Chaval Y, Cosson J, Claude J, Feyfant T, Herbreteau V, Dupuy S, Tran A (2015) Data from: Assessing the distribution of disease-bearing rodents in human-modified tropical landscapes. Dryad Digital Repository. https://doi.org/10.5061/dryad.m0s63. 
If you use the data in this file, please cite the original publication and data package.
DOI: 10.5061/dryad.tp5923t/1
title: Data Files
DOI: 10.17632/by35w43h34.1
title: Data for: Nuclear genome shuffling increases recombinant protein expression in the chloroplast of Chlamydomonas reinhardtii

description: Supplemental data for "Nuclear genome shuffling significantly increases production of chloroplast-based recombinant protein in Chlamydomonas reinhardtii" by Fields et al.
DOI: 10.17632/cn9k4m72cx.1
title: Data for: Antibacterial effects of carbon quantum dots@hematite nanostructures deposited on titanium against Gram-positive and Gram-negative bacteria

description: The bactericidal activity of the prepared Ti/α-Fe2O3 and Ti/CQD@α-Fe2O3 samples against S. aureus and E. coli bacteria strains under dark and illumination conditions.
DOI: 10.17632/j7psz6xstc.1
title: Data for: Joint inversion of ambient noise and earthquake data in the Trans-North China Orogen: on-going lithospheric modification and its impact on the Cenozoic continental rifting

description: The Shear wave velocity model of the TNCO obtained in the present study
DOI: 10.17632/pbmnt6f2mz.1
title: Data for: The Protective role of IL-1 Ra on Intestinal Ischemia Reperfusion Injury by anti-oxidative stressCin Rat
DOI: 10.17632/x59tzy85sj.1
title: Data for: In vivo assessment of the mechanical properties of crystalline lenses in a rabbit model using ultrasound elastography: effects of ultrasound frequency and age
DOI: 10.17632/xrb4k963tt.1
title: Data for: Feasibility Analysis of a Droppable Igniter for In-situ Combustion

description: Calculation results with formulas（1）~（12）
DOI: 10.5061/dryad.03g3s3q/7
title: Climate and geographical information for GDM input

description: Climate and geographical information for GDM input
DOI: 10.5061/dryad.03g3s3q/8
title: Example gdm file for SNP j8105

description: Pairwise FST matrix for GDM input for the SNP j8105.
DOI: 10.5061/dryad.03g3s3q/9
title: R code for gdm analysis

description: Reference data set and SNP j8105 for gdm analysis.
DOI: 10.5061/dryad.1nh544n/1
title: Sim_300BQs_200Loci_025

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/2
title: Sim_300BQs_200Loci_075

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/3
title: Sim_300BQs_400Loci_025

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/4
title: Sim_300BQs_400Loci_075

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/5
title: Sim_1000BQs_200Loci_025_Rep1-3

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/6
title: Sim_1000BQs_200Loci_025_Rep4-6

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/7
title: Sim_1000BQs_200Loci_025_Rep7-10

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.1nh544n/8
title: Sim_1000BQs_200Loci_075_Rep1-3

description: We store output data from stochastic simulation studies on honeybee breeding schemes relying on different genetic models. In particular, the infinitesimal model and the finite locus models are taken into consideration. Output files contain data on true and estimated breeding values, performance tests, inbreeding coefficients and pedigree data. For more information please also consult the README file
DOI: 10.5061/dryad.33jn722/1
title: Gene Annotation

description: Gene annotations, including GO terms, EC codes for each transcript
DOI: 10.5061/dryad.33jn722/2
title: Paml Branch Tests Results

description: Summary of likelihoods, LRT, omega values for all paml branch tests
DOI: 10.5061/dryad.33jn722/3
title: Paml Site Test Results
DOI: 10.5061/dryad.6bm4228/1
title: Ram Mountain data

description: Both sheets contain longitudinal data collected on male and female bighorn sheep at Ram Mountain, Alberta, Canada between 1973 and 2017. The first sheet includes data related to natural mortality, while the second sheet includes data related to overall (natural + hunting) mortality.
DOI: 10.5061/dryad.97np7bt/1
title: Biogeography of Gagea Appendix including TableS1, Figures S1-S4

description: Includes the information on studied material (voucher, origin and references, origin), cpDNA haplotype (HT) and ITS type and Gene bank accession numbers (European
Nucleotide Archive) and additional phylogenetic trees.
DOI: 10.5061/dryad.b24p647/1
title: XRD data

description: The raw data of XRD patterns belong to TiO2 thin films (Fig.3a).
DOI: 10.5061/dryad.b24p647/2
title: Raman Spectroscopy

description: The Raman Spectra of TiO2 films (Fig.3b).
DOI: 10.5061/dryad.b24p647/3
title: UV-VIS spectroscopy

description: Total transmittance spectra for TiO2 thin films (Fig.4a).
DOI: 10.5061/dryad.b24p647/4
title: Band gap Cal.

description: The raw data about band gap calculations of all samples (Fig.4b).
DOI: 10.5061/dryad.b24p647/5
title: XPS

description: The data of oxygen (O1s) core level spectra of the surface of TiO2 films (Fig.5).
DOI: 10.5061/dryad.b24p647/6
title: Degradation of MTBE

description: The data and calculations of the degradation of MTBE in the multi-section plug-flow photocatalytic reactor.
DOI: 10.5061/dryad.c0282c8/1
title: MHC-linked microsatellite genotypes

description: This data file contains genotypes for 14 microsatellite markers linked to major histocompatibility complex (MHC) genes that were genotyped in 105 coyotes (Canis latrans) sampled in New York, New Jersey, and Connecticut. Metadata includes sample identification number and urbanization subgroup. The two subgroups include coyotes sampled within New York City (NYC) and outside of NYC (non-NYC). Please see the map provided in Figure 1 to better visualize sampling locations. Missing genotype data is indicated with zeros.
DOI: 10.5061/dryad.d0q331t/1
title: Data_Files

description: The folder contains files needed perform the analysis described in “Resistance Gene Carriage Predicts Growth of Natural and Clinical Escherichia coli Isolates in the Absence of Antibiotics”. 

As well as the data contained here, several data sets from a previous paper are used. This paper is titled "Associations among Antibiotic and Phage Resistance Phenotypes in Natural and Clinical Escherichia coli Isolates", for which the data are freely available at https://doi.org/10.5061/dryad.gj318. Please see Readme file for more information.
DOI: 10.5061/dryad.d2h629q/1
title: Phylogeny of 33 Ithomiini species

description: Phylogeny of the 33 Ithomiini species used in the study and extracted from the 340 species Ithomiini phylogeny by Chazot et al. (accepted in Global Ecology and Biogeography)
DOI: 10.5061/dryad.d2h629q/2
title: Data of transparency & detectability of 33 Ithomiini species, and PA concentration and measures of unpalatability for 10 of these species

description: 1-Average transparency and detectability by avian predators (chromatic & achromatic contrast in just noticeable difference units [JNDs] for UVS- & VS-vision in large gap & forest shade light conditions) for the 33 Ithomiini species of the study. 2-Data for behavioural experiments with chicks to test unpalatability of 10 Ithomiini taxa (indicated in bold red in the first list) are also provided, including the number (& assigned colour ) of experimental pellets attacked at each trial (for a total of 12 trials per chick) for all 6 chicks tested for each butterfly species. 3-PA concentrations (μg/mg) measured for individual butterflies of the 10 selected taxa are also given.
DOI: 10.5061/dryad.ff18q9d/1
title: Appendix S1 - Pipeline from raw reads to phylogenomics and dating analysis

description: Scripts used to perform the analyses presented in this study.
DOI: 10.5061/dryad.ff18q9d/13
title: Appendix S8 - Gene- and site-concordance and discordance factors

description: Appendix S8. Gene- and site-concordance and discordance factors estimated with the Datasets 1 and 3 (760-gene) and Dataset 2 (6621-gene).
DOI: 10.5061/dryad.ff18q9d/2
title: Appendix S2 - Dataset 1 with 760 genes (amino acids format)

description: Phylogenomic dataset of Papilionoidea including 760 orthologous genes in amino acid format (Dataset 1).
DOI: 10.5061/dryad.ff18q9d/3
title: Appendix S3 - Dataset 2 with 6621 genes (amino acids format)

description: Phylogenomic dataset of Papilionoidea including 6,621 orthologous genes in amino acid format (Dataset 2).
DOI: 10.5061/dryad.ff18q9d/4
title: Appendix S4 - Dataset 3 with 760 genes (nucleotides format with gene partitions)

description: Phylogenomic dataset of Papilionoidea including 760 orthologous genes in nucleotide format (Dataset 3).
DOI: 10.5061/dryad.ff18q9d/5
title: Appendix S5 - Dataset 4 with 6407 genes (nucleotides format with gene partitions)

description: Phylogenomic dataset of Papilionoidea including 6,621 orthologous genes in nucleotide format (Dataset 4).