cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.71b5t/4
title: Data and Analysis Scripts for Selection Analyses of Paired HIV-1 gag and gp41 Sequences Obtained Before and After Antiretroviral Therapy

description: This file contains all data and analysis scripts for the selection analyses of paired HIV-1 gag and gp41 sequences. It is a snapshot of the Github repository github.com/hivdb/gag-gp41. The exact version of this snapshot is 59951f0. A README.md file is included in this zip file.
DOI: 10.5061/dryad.77h8fd8/1
title: Phocoena_CR_sequences_Dryad_040418

description: Control region sequences resolved from Alaska harbor porpoise.
DOI: 10.5061/dryad.77v1s92/8
title: Gibsonetal2018_analysis-codes_field-data

description: codes for analysis and graphing of all field data
DOI: 10.5061/dryad.77v1s92/9
title: Gibsonetal2018_analysis-codes_experimental-data

description: codes for analysis and graphing of all experimental data
DOI: 10.5061/dryad.7kj7t1q/2
title: Diplostoloidea_archive_UCE

description: UCE loci fasta files extracted from draft genomes via the PHYLUCE pipeline.
DOI: 10.5061/dryad.82fm72s/1
title: Data from Experiments 1-3

description: Matlab m-file containing data from Experiments 1-3 and plotting code
DOI: 10.5061/dryad.9jj4f50/1
title: Data_Nutrient_Fluctuations_plant_invasion

description: Data in the table is self-explanatory. If you want to know more detials, please contact me by ecoyj.liu@gmail.com
DOI: 10.5061/dryad.b4vg0.1/12.1
title: Figure S4 data

description: Ingoing links probabilities of each cluster (matrix 14x14)
DOI: 10.5061/dryad.b56tm0t/1
title: FinalMAF01_Pruned103_5354

description: VCF file of LD pruned SNPs. The file contains 5354 diallelic SNPs from 103 Q. rugosa individuals used in all further statistical analyses, including Genepop, Strucuture, LFMM, Bayescan, Gradient Forests.
Details of geographic location of sampling sites, climate data and sample sizes per population are provided in Supporting Information (Table S1).
DOI: 10.5061/dryad.b56tm0t/2
title: gradient_forests

description: The directory gradient_forests contains the readme of gradient forests analyses in R format (named GradientForests_commands.R) and all the necessary input files
DOI: 10.5061/dryad.b8p41t8/1
title: ForagingChoice_different_diets

description: Data for the foraging experiment where larvae had to choose between different diets.
DOI: 10.5061/dryad.b8p41t8/2
title: ForagingChoice_aggregation

description: Data for the foraging experiment to evaluate aggregation. Note that to upload this file in R, please use read.table with sep argument = "\t".
DOI: 10.5061/dryad.b8p41t8/3
title: Larval_body_mass

description: Data for larval body mass.
DOI: 10.5061/dryad.d9j09bm/2
title: Data Table A

description: Summary statistics derived for 30 empirical datasets used for estimating speciation mode.
DOI: 10.5061/dryad.d9j09bm/3
title: Data Table B

description: Model parameters and derived summary statistics for simulated dataset
DOI: 10.5061/dryad.f3g1r32/1
title: NORLIM_occurrence

description: Occurrence data and site covariates for Norops limifrons; p indicates survey period; pasture sites coded with "POT" secondary sites are P7 (bej), P10(sat), P14(sr), old-growth sites are P8(sv), P5, and TIR
DOI: 10.5061/dryad.gg6n17s/1
title: Tokpelaia Tpnig genome assembly and annotations

description: Tpnig genome assembly obtained through metagenomic techniques and annotated using the RAST server.
DOI: 10.5061/dryad.j8d54fn/1
title: README

description: This file explains all of the variables in each of the datasets that accompany: Karniski C, Krzyszczyk E, Mann J. 2018ms. Senescence impacts reproduction and maternal investment in bottlenose dolphins.
DOI: 10.5061/dryad.j8d54fn/2
title: maternal_age_calf_survival_Karniski_2018

description: Dataset used for modeling the effects of maternal age on calf survival
DOI: 10.5061/dryad.j8d54fn/3
title: IBI_Karniski_2018

description: Dataset used for modeling effects of maternal age and calf mortality on interbirth intervals
DOI: 10.5061/dryad.j8d54fn/4
title: weaning_Karniski_2018

description: Dataset used for modeling the effect of maternal age on calf age at weaning
DOI: 10.5061/dryad.kj2d3/1
title: Experimental Results

description: The Monte Carlo experimental results of spreading time in different complex networks.
DOI: 10.5061/dryad.kt14vq3/1
title: Figure 1
DOI: 10.5061/dryad.mn0254p/1
title: Occurrence records of Drosophila suzukii

description: Microsoft Excel spreadsheet with two worksheets (tabs). First sheet: Information about all 517 occurrence records used in the study, as obtained through extensive literature review and through mining online databases, e.g. Taxodros (http://www.taxodros.uzh.ch) and European and Mediterranean Plant Protection Organization (EPPO - https://www.eppo.int). Columns describe: country, state or region (if applicable), latitude, longitude, the year of the first observation at the specific site (if available), status, and references. Regarding the status we distinguish between: widespread, present, restricted distribution, and few occurrences similar to the EPPO and the National Plant Protection Organizations (NPPOs) of the International Plant Protection Convention (IPPC: https://www.ippc.int/en/news/tag/nppo/). In most information sources, GPS coordinates of occurrences were given, but in the cases where direct coordinates could not be obtained, the GPS coordinates were identified from geographic sites, e.g. cities, lakes, etc. outlined in the studies. Some recent occurrences were only listed as a rather imprecise geographic location such as a country in some databases (e.g. Toxodros). In all cases, the original literature was mined for precise information on the distributions of individual occurrences. Second sheet: Reference list of all occurrence data
DOI: 10.5061/dryad.mr00v92/1
title: Cumulative zooplankton occurrence and fish introduction records

description: Compilation of historical zooplankton occurrence records for lakes and ponds across western North America (see Appendix 1 in Supplementary Material for details of zooplankton data handling and detailed references). FISH_STOCKING refers to introduced fish status (present/absent) at time of sampling (see Appendix 3 for details/data sources). RECENT_DATE, RECENT_REF, RESEARCH_GROUP, and #_YEARS_SAMPLED refer to the most recent confirmed zooplankton sampling date, abbreviated zooplankton sampling reference, research group or taxonomist, and number of sampling years integrated for species occurrence estimates, respectively (see Appendix 5 for further details).
DOI: 10.5061/dryad.n8h5147/1
title: sex reversal of tongue sole

description: supplementary data description
File_S1_phenotypes.txt contains fish ID, genotypic sex, phenotypic sex, allele at SNP Cyn_Z_6676874, incidence of sex reversal.
File_S2_genotypes.txt contains ID and genotypes of 33410 markers, which are expressed as 012, 0 and 2 stand for homozygotes of each alleles, and 1 for heterozygote. 
File_S3_SNP_info.txt contains three columns, they are marker name, chromosome, and position in order.
DOI: 10.5061/dryad.s156m7r/1
title: Kempel_dataset-Malecore_et_al._2018

description: Data on emergence and survival collected in the field (Kempel et al. 2013, Malecore et al. 2018). Columns: Abbreviation (species name abbreviation), Species (Genus_species), Family (family), Plot.NR(plot nr. within site), plotunique (unique plot identifier), total.spring.2008 (nr. of seedlings in spring 2008), presence.spring.2008 (presence of seedling in spring 2008), total.late.2008 (nr. of seedlings in summer 2008), presence.late.2008 (presence of seedling in late 2008), total.spring.2009 (nr. of seedlings in spring 2009), presence.spring.2009 (presence of seedling in spring 2009), total.late.2009 (nr. of seedlings in summer 2009), presence.late.2009 (presence of seedling in late 2009), total.spring.2010 (nr. of seedlings in spring 2010), presence.spring.2010 (presence of seedling in spring 2010), total.late.2010 (nr. of seedlings in summer 2010), presence.late.2010 (presence of seedling in late 2010), Status (alien/native), Site_ID (identifier of site), Disturbance (yes/no), Density (nr. of seeds sown in plot:1, 5, 50 or 500)
DOI: 10.5061/dryad.s156m7r/2
title: Kempel_abundance_matrix-Malecore_et_al._2018

description: Data on vegetation survey in Kempel et al. (2013) sites, using the Braun-Blanquet scale. Columns: Sites. Rows: Species (Genus_species)
DOI: 10.5061/dryad.s156m7r/3
title: Mueller_pin_quadrat_survey-Malecore_et.al._2018

description: Data on vegetation survey in Mueller et al. (2016) sites. Survey carried out using a 12-point frame, consisted of a rod with twelve 2-mm diameter pins 5 cm apart. The frame was positioned at random within each plot, and all plants touching the 12 pins were identified and counted as "hits" for those species . Six replicates per plot. Columns: Date (date of survey), Site (site identifier), Plot (plot within site identifier), PlotID (unique plot identifier site+plot), Planted (seeds or seedlings), Cage_type (closed or open herbivory exclosure cage),  Fungicide (yes/no: F/NF), Disturbance (high/low: H/L), Replicate (replicate number: 1-6), Pin_number (pin number: 1-12), ID (unique pin identifier, site+plot+replicate+pin.number), Species (Genus_species, GRASS for all grass species, SOIL when no plant touching the pin)
DOI: 10.17632/22mytz7m4s.1
title: Data for: The Molecular Communications Markup Language (MolComML)

description: The XML files made available are those used to set up the molecular communications simulators to simulate the case studies described in the paper "The Molecular Communications Markup Language (MolComML". All details about the simulations are reported in the paper. The first XML file, case_study_1_DiffusionBased.xml, is used to set up the simulation of a simple diffusion scenario (a punctiform transmitter and a spherical, absorbing receiver), and it is used by both BiNS2 and N3SIM simulators, producing the same results. The second XML file, case_study_2_BloodCTC.xml, is used to set up the simulation of a section of a blood vessel to detect circulating cancer cells (CTCs) by a fixed transparent receiver, and it is used by the BiNS2 simulator. The third XML file, case_study_3_combined_simulators_size_20.xml, is used to set up the simulation of the communication via diffusion of neurotransmitters in a synaptic cleft, from the axon terminal to the dendrite. The uploaded file is that generated as output by BiNS2 and used to configure the simulation in N3SIM.
DOI: 10.17632/6yw2db7hdg.4
title: Data for: ENDOSCOPIC TRANSCANAL MYRINGOPLASTY : IS LEARNING CURVE A MYTH ?

description: Endoscopic transcanal Myringoplasty : Is Learning Curve a myth
DOI: 10.17632/nmfkyzj2jd.1
title: Data for: Characteristics of TiO2 Thin Films Surfaces Treated by O2 Plasma in Dielectric Barrier Discharge with the Assistance of External Heating
DOI: 10.17632/v2nn6m6b2x.1
title: Data for: The timing and cause of glacial activity during the last glacial in central Tibet based on 10Be surface exposure dating east of Mount Jaggang, the Xainza Range

description: Supplementary materials
DOI: 10.5061/dryad.12cm083/1
title: Supplementary File1_phenotypes

description: The txt file contains the phenotypes assessed in our study for all mice under control (CTRL) or enriched (conditions). The file is a txt file, comma delimited. Eache mouse is one line. All abbreviations and the phenotypes are explained in the article.
DOI: 10.5061/dryad.2350931/1
title: ResultsFINALJune202016

description: This is a CSV database containing the results of parameter sweeps with the model described above.  It contains 13 columns and 48,001 rows (1 header row plus 48,000 rows of data).

Descriptions of Column Headings:

Replicate = the number of the particular simulation run
Strategy = female mate choice strategy; may be BestOfN, MinThresh, or Random
Parameter = the particular setting for a strategy parameter; the n in the BestOfN strategy or the threshold theta in the MinThresh strategy; the Random strategy has no additional parameter values
NumFemales = number of female agents in the simulation; varied from 5 to 20 in increments of 5
MalePulses = the mean of the normally distributed population of pulse numbers from which the individual male agent pulse numbers are drawn
MaleDistribution = the type of spatial distribution of male agents used in the particular simulation run; may be random, Gaussian, or inverse Gaussian
NumMated = the number of female agents that mate before the end of the simulation run
AvgMatedPulsesPerCall = the average number of pulses per call across all male agents that mated 
AvgMateTime = the average time to mating for female agents that mate (search time for those that do not mate is not included)
AvgDistanceTraveled = the average distance traveled by all female agents in the simulation, including those that mate and those that do not
AvgFemalesSwitches = the average number of times each female agent switched from one target male to another
AvgPulseNumber = the average number of pulses per call across all male agents in the simulation, including those that mate and those that do not
LastCycle = the time step at which the simulation run came to an end
DOI: 10.5061/dryad.341kj02/1
title: Raw data for 2289 individuals of songbird

description: Individual data points for each sperm cell (used to create the species mean values), as well as accession numbers for the sperm bank at the Natural History Museum in Oslo.
DOI: 10.5061/dryad.341kj02/2
title: R code

description: R code for all analyses
DOI: 10.5061/dryad.368n7d9/1
title: Cerci SPHARM models of male Enallagma Damselflies

description: This zip file contains raw and spherical harmonics representations of morphological structures used by Enallagma damselfly males to grasp females during mating, and principal components scores extracted from these models.
DOI: 10.5061/dryad.369417f/1
title: Description of cases - Appendix 1
DOI: 10.5061/dryad.4006fm8/3
title: Table S3

description: Trees and trait data files used to calculate species-specific rates of evolution (data used to obtain the results in table S3).
DOI: 10.5061/dryad.4006fm8/4
title: Table S5

description: Trees and trait data files used to calculate species-specific rates of evolution, as well as data for candidate predictor variables (data used to obtain the results in Table S5).
DOI: 10.5061/dryad.4006fm8/5
title: Table S6

description: Trees and trait data files used to calculate clade rates of evolution, as well as data for candidate predictor variables (data used to obtain the results in table S6).
DOI: 10.5061/dryad.4006fm8/6
title: Table S7

description: Tree and trait data file used to calculate clade rates of evolution, as well as data for candidate predictor variables (data used to obtain the results in table S7).
DOI: 10.5061/dryad.4fq5vr6/1
title: Carbon flux data

description: Carbon flux data. All the abbreviation and the unit can be observed in the manuscript.
DOI: 10.5061/dryad.4fq5vr6/2
title: Rainfall and soil water content data

description: Rainfall and soil water content data. All the abbreviation and the unit can be observed in the manuscript.
DOI: 10.5061/dryad.4fq5vr6/3
title: Root surface area of A. scoparia and G. uralensis

description: Root surface area of A. scoparia and G. uralensis. All the abbreviation and the unit can be observed in the manuscript.
DOI: 10.5061/dryad.50r4t2p/1
title: Stegastes behavior and coral performance
DOI: 10.5061/dryad.59185/1
title: Data S1

description: Genes differentially expressed in wild type and wsl5.
DOI: 10.5061/dryad.59185/2
title: Data S2

description: Genes differentially expressed in wild type and wsl5 under different temperature conditions.
DOI: 10.5061/dryad.59185/3
title: Supplementary information

description: Table S1, S2 and Fig. S1-S10
DOI: 10.5061/dryad.5d9s571/1
title: qPCR data from junco hypothalami and testes

description: *The first six tabs each display values for hypothalamic genes
*The last four tabs each display values for testicular genes
*Band # refers to the USFWS silver, metal band that each, individual bird was banded with
*Population refers to residents (Junco hyemalis carolinensis) and migrants (Junco hyemalis hyemalis)
*Hypothalamus reference genes were PPIA and GAPDH
*The testicular reference gene was RPL4
*For details on how qPCR assays were run, assay variation, etc. please see main text and supplementary materials
*Note: Hypothalamic genes were run so all individuals were on the same plate. Testicular genes were run so one plate had all genes from the same individual.
DOI: 10.5061/dryad.7f25j43/1
title: Participant scores and projections

description: Demographic data, recall data, recognition data, and projections.
DOI: 10.5061/dryad.7h41b81/1
title: dataset_1

description: Variables associated with salt-sensitive blood pressure phenotype and clinical conditions associated with a low salt requirement. Investigation and quantification of the drug associated sodium intake in the last 30 days.
DOI: 10.5061/dryad.7h41b81/2
title: dataset_2

description: Serum sodium and potassium of each participant, and comedications eventually taken.
DOI: 10.5061/dryad.7h41b81/3
title: dataset_3

description: Exploratory variables.
DOI: 10.5061/dryad.7kj7t1q/3
title: Diplostomoidea_alignment_archive

description: Phylip file and associated characters sets used in the phylogenomic analyses.
DOI: 10.5061/dryad.941r8h0/1
title: Muth data for Dryad

description: Data for Muth et al A pollen fatty acid enhances learning and survival in bumblebees. Each tab relates to each experiment in the manuscript (as labelled).
DOI: 10.5061/dryad.9s6f82f/1
title: Size-specific residuals of size spectra

description: Data representing the residuals of each of the size classes (columns) from fish size spectra of 74 German lakes (rows).
DOI: 10.5061/dryad.9s6f82f/2
title: R code to generate random residual x lake matrix

description: An example by using simulated data to generate 100 random residual x lake matrices from an observed matrix.
DOI: 10.5061/dryad.bq201/1
title: American Mink _dryad

description: This file contains the readings of microsatellites with which it was carried out in this article. (11 microsatellite loci)
DOI: 10.5061/dryad.c6p8q62/1
title: All summer flounder SNPs following bioinformatics filters

description: VCF file containing ddRADseq data for summer flounder. This file contains all SNPs remaining following bioinformatics filters.
DOI: 10.5061/dryad.c6p8q62/2
title: 1137 summer flounder SNPs

description: VCF file containing ddRADseq data for summer flounder. This file contains the first SNP on each contig, resulting in 1137 SNPs. These SNPs were used in the main analyses.
DOI: 10.5061/dryad.c6p8q62/3
title: Structure formatted file made from SNP.DP3g95maf05.FIL.FIL.recode.updated.onesnp.vcf

description: This file is formatted for input in the program STRUCTURE. It contains 1137 SNPs across 241 summer flounder. The first column identifies an individual fish. There are two rows for every fish. The second column is a population identifier. Columns 3-1139 are SNPs. Values of 1-4 indicate nucleotides (A = 1, T = 2, G = 3, C = 4). Missing data are indicated by -9.
DOI: 10.5061/dryad.c6p8q62/4
title: Summer flounder metadata

description: This files contains metadata for the 232 summer flounder used in the main analyses. Data include the individual ID used for sequencing, capture date, sex, total length (cm), maturity status, collecting agency, latitude, longitude, calculated distance from a southern point, depth of capture, bottom temperature at capture, bottom salinity at capture and population grouping for BayEnv2 analysis.
DOI: 10.5061/dryad.f3g1r32/2
title: NORHUM_occurrence

description: Occurrence data and site covariates for N. limifrons ; p indicates survey period; pasture sites coded with "POT" secondary sites are P7 (bej), P10(sat), P14(sr), old-growth sites are P8(sv), P5, and TIR
DOI: 10.5061/dryad.f3g1r32/3
title: 2016_2017_Temperature_SecondaryForest

description: Operative Temperature by site in secondary forests; pasture sites coded with "POT" secondary sites are P7 (bej), P10(sat), P14(sr), old-growth sites are P8(sv), P5, and TIR
DOI: 10.5061/dryad.f3g1r32/4
title: 2016_2017_Temperature_Pasture

description: Operative temperature by site in pasture; pasture sites coded with "POT" secondary sites are P7 (bej), P10(sat), P14(sr), old-growth sites are P8(sv), P5, and TIR
DOI: 10.5061/dryad.f3g1r32/5
title: 2016_2017_Temperature_OG

description: Operative temperatures for old growth sites; pasture sites coded with "POT" secondary sites are P7 (bej), P10(sat), P14(sr), old-growth sites are P8(sv), P5, and TIR
DOI: 10.5061/dryad.fk5k3vs/1
title: Crown colouration

description: Data set on crown colouration and infection status of blue tits (Cyanistes caeruleus) from the nest-box population on the island of Gotland (Sweden; 57°01'N 18°16'E). The table contain details on identity, sex, age, mass, tarsus length, status of parasitic infection and six colour metrics. All colour metrics were calculated using package pavo, in R software.
DOI: 10.5061/dryad.fk5k3vs/2
title: Breast colouration

description: Data set on breast colouration and infection status of blue tits (Cyanistes caeruleus) from the nest-box population on the island of Gotland (Sweden; 57°01'N 18°16'E). The table contain details on identity, sex, age, status of parasitic infection and six colour metrics. All colour metrics were calculated using package pavo, in R software.
DOI: 10.5061/dryad.gg6n17s/2
title: Frischella Fpnig genome assembly and annotation

description: Fpnig genome assembly obtained through metagenomic techniques and annotated using the RAST server.
DOI: 10.5061/dryad.gg6n17s/3
title: Representative sequences for ZOTUs

description: Representative bacterial 16S rRNA gene sequences for zero-radius OTUs identified in this study. These sequences were identified using the UNOISE pipeline.
DOI: 10.5061/dryad.gg6n17s/4
title: Contaminant-filtered sequences

description: These are all sequences that passed filtering using blank samples to identify likely contaminants.
DOI: 10.5061/dryad.gg6n17s/5
title: Pseudomyrmex flavicornis adult metagenome assembly

description: Assembly of the metagenome obtained from dissected guts of adult Pseudomyrmex flavicornis from colony BER0517. Scaffolds classified as Acetobacteraceae are marked as such.
DOI: 10.5061/dryad.gg6n17s/6
title: Pseudomyrmex nigropilosus larval metagenome assembly

description: Assembly of the metagenome obtained from dissected meconia of Pseudomyrmex nigropilosus larvae from colony BER0554. Scaffolds classified as Alphaproteobacteria and Gammaproteobacteria are marked as such.
DOI: 10.5061/dryad.gg6n17s/7
title: OTU table

description: The full OTU table produced in this study.
DOI: 10.5061/dryad.gg6n17s/8
title: SUPERSEDED - Nitrogen isotope ratios

description: Nitrogen isotope ratio data for all ant and plant samples used in this study.
DOI: 10.5061/dryad.gg6n17s/9
title: Nitrogen isotope data

description: Nitrogen isotope raw and standardized data for all samples included in this study.
DOI: 10.5061/dryad.hm043k3/1
title: All data for captive birds

description: This data file includes all isotope enrichments values for every blood and faecal sample collected from each bird in the captive birds component of our study.  It also includes the calculations used to determine DEE and all formulas link to the samples used so that readers can review the data used in detail.
DOI: 10.5061/dryad.j8d54fn/5
title: birth_order_weaning_Karniski_2018

description: Dataset used for modeling the effects of birth order on weaning age
DOI: 10.5061/dryad.r4v7623/1
title: COI

description: A fas file containing the aligned COI sequences from 406 Matrona basilaris.
DOI: 10.5061/dryad.r4v7623/2
title: COII

description: A fas file containing the aligned COII sequences from 406 Matrona basilaris.
DOI: 10.5061/dryad.r4v7623/3
title: ND1

description: A fas file containing the aligned ND1 sequences from 406 Matrona basilaris.