cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s11f216/13
title: Phylogeny inferred using coalescent method

description: Contains tree with local posterior probabilities in Newick format. Obtained using ASTRAL-II using trees in file 'all_gene_trees_no_arba.tre'.
DOI: 10.5061/dryad.s11f216/14
title: 345 gene trees selected for coalescent inference

description: Subsampling of 345 gene trees from file 'all_gene_trees.tre' with the lowest branch-length heterogeneity and saturation levels. Individual gene sequences come from file 'echinoids70_noarba.fa'.
DOI: 10.5061/dryad.s11f216/15
title: Phylogeny inferred using coalescent method using 345 trees

description: Contains tree with local posterior probabilities in Newick format. Obtained using ASTRAL-II using trees in file '354trees_for_ASTRAL.tre'.
DOI: 10.5061/dryad.s11f216/8
title: Bayesian phylogeny inferred under best-fit model

description: Contains the consensus tree with posterior probabilities in Newick format. Obtained using ExaBayes v. 1.5 using matrix 'echinoids70_noarba.fa'.
DOI: 10.17632/b2x74y8djh.1
title: Data for: Spatial and temporal variations of precipitation concentration and their relationships with large-scale atmospheric circulations across Northeast China
DOI: 10.17632/mtgvrd5t68.1
title: Data for: "Unmotivated Bias" and Partisan Hostility: Empirical Evidence

description: Data and code for the paper
DOI: 10.5061/dryad.1c9g5mm.2/12.2
title: min30.phy

description: Concatenated phylip alignment for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/13.2
title: min4.nex

description: Concatenated nexus alignment for the dataset containing minimum 4 samples per locus. See "params_Darter_m4_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/14.2
title: min10.nex

description: Concatenated nexus alignment for the dataset containing minimum 10 samples per locus. See "params_Darter_m10_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/15.2
title: min20.nex

description: Concatenated nexus alignment for the dataset containing minimum 20 samples per locus. See "params_Darter_m20_RAxML" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/16.2
title: min30.nex

description: Concatenated nexus alignment for the dataset containing minimum 30 samples per locus. See "params_Darter_m30_RAxML.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.2/17.2
title: params_Darter_m4_RAxML

description: Pyrad parameter file for minimum 4 samples per locus assembly.
DOI: 10.5061/dryad.1c9g5mm.2/18.2
title: params_Darter_m10_RAxML

description: Pyrad parameter file for minimum 10 samples per locus assembly.
DOI: 10.5061/dryad.1c9g5mm.2/19.2
title: params_Darter_m20_RAxML

description: Pyrad parameter file for minimum 20 samples per locus assembly.
DOI: 10.5061/dryad.1c9g5mm.2/20.2
title: params_Darter_m30_RAxML

description: Pyrad parameter file for minimum 30 samples per locus assembly.
DOI: 10.5061/dryad.20vd145/1
title: 01_Dryad_DJ12_groups

description: This file contains five variables of 503 groups (rows).

date contains information of the sampling period;
calf is the presence or absence of calves in the group;
behavior contains information of the behavioural state (D = travelling; DP = travelling and foraging; DS = travelling and socializing; P = foraging; S = socializing);
coop contains information about the cooperative foraging behaviour, where S refer to groups engaged in cooperative foraging and N to groups that were foraging independently from fishermen.
IDs contains the identity of all individuals observed in the groups.
DOI: 10.5061/dryad.20vd145/3
title: 03_Dryad_DJ12_id_cov

description: This file contains nine covariables of 52 photo-identified individuals.

Id contains the identity of all 52 photo-identified individuals;
Freq_Int contains the relative frequency of participation (fp), ranging from 0 to 100%;
SEX contains the sex of each individual, where M refer to male individuals, F to femeales and I for those individuals that we were unable to determine the sex;
age contains the age class for each individual, classified as adult or senior (individuals observed in the area for more than 30 years);
HR is the home range area in km², estimated via fixed kernel methods with a 95% probability contour for each individual
DOI: 10.5061/dryad.20vd145/4
title: 04_Dryad_DJ12_relatedness_Q

description: This file contains the pairwise genetic relatedness (Queller and Goodnight index) among 13 individuals.
DOI: 10.5061/dryad.20vd145/5
title: 02_Dryad_DJ12_homerange

description: This file contains a 35x35 matrix with home range overlap values, ranging from 0 (no overlap) to 1 (completely overlapped).
DOI: 10.5061/dryad.30326v6/1
title: Indo-Pacific mtDNA database 2019_01_08

description: This is the full database that we used in the paper. Sequence data are contained in the "sequence" field, and are aligned within each species. The bioregion that each sample fell into under the various regionalizations are in columns named for that regionalization. Most other columns are self explanatory, or are defined as part of DarwinCore: https://dwc.tdwg.org/terms/. All of these data and metadata are also available in GeOMe -https://geome-db.org
DOI: 10.5061/dryad.30326v6/2
title: IPDB_UPPER-OverWater_LOWER-Euclidean

description: These are the overwater and Euclidean distances that were calculated for dbRDA analysis. Methods can be found in the readme file.
DOI: 10.5061/dryad.56bk548/1
title: Data_Camenzind 2019

description: These data include all hyphal length counts presented in this manuscript, as well as PLFA data and "AM-like" hyphal length. Furthermore, cation, nitrogen and phosphorus content measured before and after the experiment in nutrient loaded mesh bags are reported.
DOI: 10.5061/dryad.6d13255/1
title: 1. environmental data

description: Hourly soil temperature (degrees C) and soil moisture (m^3 water/m^3 soil) recorded for the duration of our experiment (November 2011 to July 2013). Data were obtained using Onset HOBO data loggers, and one sensor for each environmental variable was placed at each of 12 spatial blocks. Columns D-O represent soil temperature for each individual block, while columns P to AA represent soil moisture for each individual block.
DOI: 10.5061/dryad.6d13255/2
title: 2. germination data

description: Germination date for 5297 individual seedlings observed in our study. Seeds were dispersed in 5 seasonal cohorts over the course of 1 full year (“Dispersal”). Block refers to each of 12 spatial blocks, and row and column represent the spatial position within each block. The majority of the data in this file come from germination pots (“Pot_type”); however, if no seeds germinated in the germination replicate within the block, we included germination data from the life-history pot for that particular genotype and treatment combination. Thus, some “life-history” pots are included in the dataset. Genotype refers to one of eight genotypes included in the study. Mat refers to the temperature (degrees C) experienced by maternal plants before seeds were dispersed. Germ Date represents the date the seedling was first observed in the field. Number of seedlings per pot is calculated for each pot ID, and thus is not unique to each seedling. The experimental design included a dispersal of 15 seeds per pot; however, because seeds are extremely small, in some pots greater than 15 seeds were dispersed.
DOI: 10.5061/dryad.6d13255/3
title: 3. life history and fitness data

description: Life history and fitness data for 418 focal individuals observed in our study. Seeds were dispersed in 5 seasonal cohorts over the course of 1 full year (“Dispersal”). Block refers to each of 12 spatial blocks, and row and column represent the spatial position within each block. Data come exclusively from life-history pots. Genotype refers to one of eight genotypes included in the study. Mat refers to the temperature (degrees C) experienced by maternal plants before seeds were dispersed. Dispersal date represents the calendar date when seeds were placed in the field, while germination date, bolt date, flower date, 90% seed maturation, and dead date represent the first date during which these developmental stages were observed. Days to germ represents the number of days from dispersal until germination, while days to bolt, flower, mature, and death (lifespan) represent the number of days between germination and the first observation of each developmental stage. Survival to flowering is binary; 0 = individual died before reproduction; 1= individual survived to flowering. Flowering time represents the number of days from germination until appearance of the first flower. Flowering interval represents the number of days from appearance of the first flower until 90% seed maturation. Fecundity represents total number of siliques produced. Number of unique treatment combinations (n=413) is slightly lower than total number of focal individuals (n=418), as five treatment combinations included two replicate pots within a single block.
DOI: 10.5061/dryad.7651036/1
title: Supplemental Data HOPE Trail_ Dryad

description: Supplemental Tables for the HOPE Trail Manuscript
DOI: 10.5061/dryad.7k1j1j3/1
title: Responses of ecosystem functions, environmental factors, species richness, and functional traits to N addition
DOI: 10.5061/dryad.8md5419/1
title: Bee habitats

description: A big data frame collected by Sam Droeges' team, containing information about individual bee species, the coordinates where they were found and the habitat extracted from the USGS land use raster layer
DOI: 10.5061/dryad.96n24g7/1
title: relatedness

description: Relatedness values of parents, along with reproductive data
DOI: 10.5061/dryad.bn0655b/2
title: R_scriptsTielemanetal_auk_2019

description: R-scripts for analyses in Tieleman et al., Auk, 2019
DOI: 10.5061/dryad.cm1h0p6/1
title: Fast-start swimming data
DOI: 10.5061/dryad.cm1h0p6/2
title: Oxygen consumption rate data
DOI: 10.5061/dryad.cm1h0p6/3
title: Prolonged swimming endurance data
DOI: 10.5061/dryad.fc56203/1
title: Mueller_et_al_J_Appl_Ecol_data

description: all raw data for manuscript Mueller et al. 2019 in J Appl Ecol
DOI: 10.5061/dryad.hg225q3/1
title: Publish Figures

description: Publish Figures
DOI: 10.5061/dryad.hg225q3/2
title: original figures

description: original figures
DOI: 10.5061/dryad.k4pf189/1
title: Data from Abayarathna et al.

description: Excel file with five spreadsheets that contain the raw data that was used in the statistical analyses. The spreadsheet column headings are self-explanatory so a readme file has not been attached.
DOI: 10.5061/dryad.k540b54/1
title: Uruguay trawl

description: Uruguay trawl effort. Description provided in the first tab of the data file.
DOI: 10.5061/dryad.k540b54/2
title: Namibia trawl

description: Namibia trawl effort. Description provided in first tab of the data file.
DOI: 10.5061/dryad.kp524f5/1
title: Data of great tit maternal yolk THs in Bennekom, The Netherlands

description: The data contains maternal yolk thyroid hormone levels measured from great tits in Bennekom, The Netherlands in 2013-2016, along with other variables used to analyze the between- and within-individual variation in thyroid hormones levels for this study.
DOI: 10.5061/dryad.m42t6tm/5
title: Fig. S5 trace elements

description: Trace elements of selected specimens (Mn, Fe, Sr).
DOI: 10.5061/dryad.np0s26r/1
title: chronograms

description: Set of output chronogram files for each set of model parameters.
DOI: 10.5061/dryad.np0s26r/2
title: datedists

description: Set of date dist files for each set of model parameters.
DOI: 10.5061/dryad.np0s26r/3
title: Chitinase Alignment TenChar

description: Fasta file with 10 character names
DOI: 10.5061/dryad.np0s26r/5
title: Chitinase Alignment

description: FASTA
DOI: 10.5061/dryad.pd3061s/1
title: Sex conflict intensity and signa DRYAD

description: Data showing the effect of sex-ratio bias on spermatophore thickness, signa width and height and CSP size. Relative male and female weight are included as covariates
DOI: 10.5061/dryad.r974n41/1
title: Host.Plant.Usage.analysis_MS

description: R script for data analysis.
DOI: 10.5061/dryad.r974n41/2
title: split.develop

description: Split development csv data file for figure 3, 4 and supplemental table 1 and 3.
DOI: 10.5061/dryad.r974n41/3
title: split.survival

description: Split survival csv data file for figure 3, 4 and supplemental table 1 and 3.
DOI: 10.5061/dryad.r974n41/4
title: pp.survival

description: Preference-performance survival csv data file for figure 7 and supplemental table 2.
DOI: 10.5061/dryad.r974n41/5
title: pp.development.seasonalityANDgroup

description: Preference-performance development csv data file for figure 7 and supplemental table 2.
DOI: 10.5061/dryad.r974n41/6
title: Host.Plant.Usage.plots_MS

description: R scripts for plots in the manuscript.
DOI: 10.5061/dryad.rm8bk77.2/1.2
title: Table S1

description: List of cranial specimens examined first-hand in the study
DOI: 10.5061/dryad.rm8bk77.2/2.2
title: NMVP229196-tiffs-6-199

description: MicroCT tiff series, holotypic maxilla (NMV P229196) of Galleonosaurus dorisae (part 1); Zeiss Xradia XRM Versa520 X-Ray Microtomography: voxel size 45.61 µm; power 10 W; voltage 140 kV
DOI: 10.5061/dryad.rm8bk77.2/3.2
title: NMV P229196-tiffs-202-499

description: MicroCT tiff series, holotypic maxilla (NMV P229196) of Galleonosaurus dorisae (Part 2); Zeiss Xradia XRM Versa520 X-Ray Microtomography: voxel size 45.61 µm; power 10 W; voltage 140 kV
DOI: 10.5061/dryad.rm8bk77.2/4.2
title: NMVP229196-tiffs-503-899

description: MicroCT tiff series, holotypic maxilla (NMV P229196) of Galleonosaurus dorisae (part 3); Zeiss Xradia XRM Versa520 X-Ray Microtomography: voxel size 45.61 µm; power 10 W; voltage 140 kV
DOI: 10.5061/dryad.rm8bk77.2/5.2
title: NMVP229196-tiffs-901-1199

description: MicroCT tiff series, holotypic maxilla (NMV P229196) of Galleonosaurus dorisae (part 4); Zeiss Xradia XRM Versa520 X-Ray Microtomography: voxel size 45.61 µm; power 10 W; voltage 140 kV
DOI: 10.5061/dryad.rm8bk77.2/6.2
title: NMV P229196-tiffs-1203-1499

description: MicroCT tiff series, holotypic maxilla (NMV P229196) of Galleonosaurus dorisae (part 5); Zeiss Xradia XRM Versa520 X-Ray Microtomography: voxel size 45.61 µm; power 10 W; voltage 140 kV
DOI: 10.5061/dryad.rm8bk77.2/7.2
title: NMVP229196-tiffs-1505-1689

description: MicroCT tiff series, holotypic maxilla (NMV P229196) of Galleonosaurus dorisae (part 6); Zeiss Xradia XRM Versa520 X-Ray Microtomography: voxel size 45.61 µm; power 10 W; voltage 140 kV
DOI: 10.5061/dryad.rm8bk77.2/8.2
title: Text S1

description: Additional remarks and information on the phylogenetic data and analyses used in the study
DOI: 10.5061/dryad.rm8bk77.2/9.2
title: Text S2

description: Phylogenetic character list
DOI: 10.5061/dryad.rs39059.1
title: Data from: Fishing pressure impacts the abundance gradient of European lobsters across the borders of a newly established marine protected area
DOI: 10.5061/dryad.rs39059.1/3.1
title: Fishing spots 2009
DOI: 10.5061/dryad.rs39059.1/4.1
title: Fishing spots 2014
DOI: 10.5061/dryad.rs39059.2/2.2
title: TVEDESTRAND hummer 2010-2016

description: Raw data file- Nillos Kleiven et al.
DOI: 10.5061/dryad.rs39059.2/3.2
title: Fishing spots 2009
DOI: 10.5061/dryad.rs39059.2/4.2
title: Fishing spots 2014
DOI: 10.5061/dryad.rs39059.2/5.2
title: Fishing spots 2015
DOI: 10.5061/dryad.rs39059.2/6.2
title: Fishing spots 2016
DOI: 10.5061/dryad.s11f216/16
title: Phylogenies inferred after pruning by TreeShrink

description: The .rar file contains the topologies obtained using matrix 'echinoids70_noarba_treeshrink.fa' with IQ-TREE v1.6.6 (model PMSF), ExaBayes v. 1.5 (automatic model selection) and ASTRAL-II.
DOI: 10.5061/dryad.s11f216/17
title: Species trees inferred from randomly subsampled gene trees

description: 100 species trees obtained using ASTRAL-II, each one inferred from 345 randomly subsampled gene trees from file 'all_gene_trees.tre'.
DOI: 10.5061/dryad.s11f216/18
title: R code and necessary data files

description: R code to replicate all analyses, as well as data files needed for some of the calculations.
DOI: 10.5061/dryad.sk2pd88/1
title: VCF: SNP Set 1 (92 individuals)

description: VCF file for SNP Set 1 described in the paper. Although reads were mapped to the Hmel2 scaffolds, the coordinate system has been converted to chromosomes according to the Hmel2.5 scaffolding. Genotypes of females on chromosome 21 are given as haploid.
DOI: 10.5061/dryad.sk2pd88/10
title: Proportion CDS

description: Proportion of CDS per 100 kb window based on the Hmel2 genome annotation. Coordinates are converted to chromosomes based on the Hmel2.5 scaffolding.
DOI: 10.5061/dryad.sk2pd88/2
title: VCF: SNP Set 2 (92 individuals)

description: VCF file for SNP Set 2 described in the paper. Although reads were mapped to the Hmel2 scaffolds, the coordinate system has been converted to chromosomes according to the Hmel2.5 scaffolding. Genotypes of females on chromosome 21 are given as haploid.
DOI: 10.5061/dryad.sk2pd88/3
title: Whole genome distance matrix for 92 Heliconius individuals

description: Pairwise absolute genetic distances among the 92 individuals computed using SNP Set 1, further filtered to retain only SNPs separated by at least 1 kb. This file was used as input for SplitsTree to generate the network in Figure 1B.
DOI: 10.5061/dryad.sk2pd88/4
title: PCA results (90 Heliconius individuals)

description: Eigenstrat SmartPCA results for 90 individuals (outgroups excluded), presented in Figure 1B.
DOI: 10.5061/dryad.sk2pd88/5
title: Topology weightings from Twisst (42 files)

description: Twisst data underlying figures 2 & 3 and supplementary figures S1-S4. 42 files are provided, two for each chromosome. Files ending in ".weights.tsv.gz" give the topology weightings for the fifteen possible topologies (see Figure 2). Each line represents a different 50 SNP window. Files ending in ".data.tsv" give the chromosome and coordinates of each window.
DOI: 10.5061/dryad.sk2pd88/6
title: Population recombination rates from LDhelmet (84 files)

description: Maximum likelihood estimates of the population recombination rate for each 100 kb window. 84 files are provided: one for each chromosome for four separate populations of Heliconius cydno, timareta, melpomene (west) and melpomene (east)
DOI: 10.5061/dryad.sk2pd88/7
title: Admixture proportion data (fd) (14 files)

description: Estimated admixture proportions (fd) along with related estimates, used to generate figures 3 and 4 and supplementary figures S7, S8 and S11-S13. 14 files are provided, covering different population sets as described in supplementary figure S6. File names indicate the populations used in the order P1, P2, P3 and Outgroup (always "num"). Files of two different window sizes are provided: 100 kb windows, sliding in increments of 20 kb, with a minimum of 1000 genotyped sites per window required ("w100m1s20"); and 20 kb windows, sliding in increments of 5 kb, with a minimum of 300 genotyped sites per window required ("w20m300s5"). Two files are also provided giving estimates for whole-chromosomes.
DOI: 10.5061/dryad.sk2pd88/8
title: Simulation results (3 files)

description: Simulated topology weighting results presented in S2 Fig. are provided in the files "sim_weights_means_S2_Fig.tsv" (mean values) and "sim_weights_fixed_S2_Fig.tsv" (fixed values). The three lines in each file represent the three scenarios shown in S2 Fig. Simulated values for divergence and admixture statistics presented in S5 Fig. are provided in the file "div_admix_stats_polarized.50k_100_inst.mean.tsv". The "Scenario" column refers to the three scenarios shown on the left in S5 Fig.
DOI: 10.17632/5m75jrt2fd.3
title: Data for: QUANTITIATIVE ESTIMATES OF ORBITAL AND MILLENNIAL SCALE CLIMATIC VARIABILITY IN CENTRAL MEXICO DURING THE LAST 35,000 YEARS.

description: Diatom-based transfer functions for the Chalco B core, lake Chalco, Basin of Mexico. Data include the age model of the Chalco B core and the estimated anomalies (three point running means) for Total Dissolved Solids (TDS), Mean Annual Precipitation (MAP) and Mean Annual Temperatrue (MAT).
DOI: 10.17632/7ym3nrnskd.3
title: Data for: n-Hexadecane and pyrene biodegradation and metabolization by Rhodococcus sp. T1 isolated from oil contaminated soil

description: Research data
DOI: 10.17632/7ym3nrnskd.4
title: Data for: n-Hexadecane and pyrene biodegradation and metabolization by Rhodococcus sp. T1 isolated from oil contaminated soil

description: Research data
DOI: 10.17632/7ym3nrnskd.5
title: Data for: n-Hexadecane and pyrene biodegradation and metabolization by Rhodococcus sp. T1 isolated from oil contaminated soil

description: Research data
DOI: 10.17632/s6bhf644zw.1
title: Data for: Diagnostic Utility of Gut α-Synuclein in Parkinson’s Disease: A Systematic Review and Meta-Analysis

description: Fig1:Flow chart for the systematic literature search. Fig2. Forest plot demonstrating the association between gut α-synuclein and PD(CI, conﬁdence interval; PD, Parkinson’s disease; OR, odds ratio). Fig3. Forest plot in subgroup analysis demonstrating the association between gut α-synuclein and PD(a: subgroup analyzes by IHC sites; b: subgroup analyzes by antibody species). Fig4. SROC curve(a: sites:colon and stomach; b:antibody: α-synuclein and phosphorylated α-synuclein).
DOI: 10.17632/xkj48kymn3.1
title: Data for: Performance improvements of AlGaN-based deep-ultraviolet light-emitting diodes with specifically designed irregular sawtooth hole and electron blocking layers

description: It contains all the origin diagrams in the article.（Output power for the four structures（5outp) and Internal quantum efficiency(5iqe);Energy band diagrams of: (a) structure A; (b) structure B; (c) structure C at 180 mA,(elc) Electron current density and (hcd) Hole current density at 180 mA;(elec) Electron concentration and (holec) hole concentration; (rd) Radiative recombination rates and (sp) spontaneous emission rates)
DOI: 10.5061/dryad.1c9g5mm.2/21.2
title: Figure A1

description: Figure A1. Species trees inferred by tetrad, with bootstrap support values = 100% unless indicated. Nodes with less than 50% boostrap support have been collapsed. White nodes represent topological conflicts between the tetrad min4 tree and min30 tree. Gray nodes represent topological conflicts between either of the tetrad trees and the RAxML tree (Fig. 1). Black nodes represent topological conflicts between the tetrad min4 tree and m30 tree plus conflict between either of the tetrad trees and the concatenated RAxML tree.
DOI: 10.5061/dryad.1c9g5mm.2/22.2
title: Figure A2

description: Figure A2. ASTRAL species tree. Nodes have local posterior probability = 1.0 unless otherwise noted. Branch lengths are in coalescent units. ASTRAL cannot estimate terminal branch lenghs, so all terminal branches arbitrarily = 1.0 coalescent units. Black nodes represent topological conflicts between the ASTRAL species tree and the concatenated RAxML tree.
DOI: 10.5061/dryad.1c9g5mm.2/23.2
title: Figure A3

description: Figure A3. Primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% CI in parentheses. Dotted lines indicate conflicting topologies with concordance factor 95% CIs that overlap with the concordance factor 95% CI of a bipartition in the primary concordance tree.
DOI: 10.5061/dryad.1c9g5mm.2/24.2
title: Figure A4

description: Figure A4. Primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% CI in parentheses.