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

description: A dataset containing 315 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "OccurrenceStatus is Present",
 "TaxonKey is Leucaena leucocephala (Lam.) de Wit",
 "Year 1000-2024"
 ]
}

 The dataset includes 315 records from 24 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043235-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.g743jn
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Leptosiphonium guppyi (Hemsl.) Bremek. & Nann.-Bremek."
 ]
}

 The dataset includes 3 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043236-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h4bxkc
title: Occurrence Download

description: A dataset containing 99309 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidium draba L."
 ]
}

 The dataset includes 99309 records from 1190 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0043201-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.nf7697j6/10
title: Ord_TJ-2011-0215R1_phylogenies
DOI: 10.5061/dryad.nf7697j6/9
title: Ord_TJ-2011-0215R1_lizards-distant-orn
DOI: 10.5061/dryad.pt109/1
title: full_data_from_Oostra_et_al_2014

description: See readme.txt
DOI: 10.5061/dryad.r20t0/4
title: Error trimming simulation

description: Sequences of uniform length of 350 bp were drawn at random from Populus trichocarpa chromosomes 1–19 (v3.0, DOE-JGI, http://www.phytozome.net/poplar) at 0.1x coverage using PBSIM v1.0.3, following the observed read length distribution and quality profiles of Triplaris cumingiana CCS reads in this study.
DOI: 10.5061/dryad.03jd7/1
title: Scaptotrigona Genotypes
DOI: 10.5061/dryad.11vj2/1
title: Blank&S-B2010.SSURpoC

description: Mesquite file containing phylogenetic trees and character matrix.
DOI: 10.5061/dryad.11vj2/2
title: Blank&S-B2010.SSULSU

description: Mesquite file containing phylogenetic tree and character matrix.
DOI: 10.5061/dryad.17sr0/1
title: Epicuticular compounds after perfuming

description: This file contains the raw GC data from perfuming experiments. The 'target male' is the type of male that was extracted, and 'males perfumed with' shows the type of males that the target male was housed with for 7 days before extraction.  Also included are control non-perfumed males.  GC data is raw and peaks are labeled 1 through 23.  Each line in the file has the data for one male.
DOI: 10.5061/dryad.17sr0/2
title: CHC character displacement data - females

description: This file contains the raw GC data for females included in the assay for reproductive character displacement.  Each line has the data for one female included in the study.  For each female, the species, population, and whether the population is from the region of sympatry or allopatry is indicated.  See Table 1 of the paper for a description of the population abbreviations.  GC data is raw and peaks are labeled 1 through 21.
DOI: 10.5061/dryad.17sr0/3
title: CHC character displacement data - males

description: This file contains the raw GC data for males included in the assay for reproductive character displacement.  Each line has the data for one male included in the study.  For each male, the species, population, and whether the population is from the region of sympatry or allopatry is indicated.  See Table 1 of the paper for a description of the population abbreviations.  GC data is raw and peaks are labeled 1 through 24.
DOI: 10.5061/dryad.21k5t/1
title: Dryad entry.zip

description: this zip file contains all data required to perfom both the population genetic analysis, outlier tests and seascape genetics on turbot as discribed in the article.
DOI: 10.5061/dryad.2247b/1
title: Cassidy-et-al-data

description: Tab-delimited text file containing individual morphometric data.
DOI: 10.5061/dryad.4108h/3
title: Morphological_counts

description: Number of foraminifera morphospecies counted in the 45 sequenced sediment samples. For each species identifed based on morphological characters (lines), the counts are detailed for each sample (column in spreadsheet "Species") or summed across samples (spreadsheet "final counts").
DOI: 10.5061/dryad.4g832/1
title: Sequence Alignment 9 DNA fragments Mesocarabus
DOI: 10.5061/dryad.4g832/2
title: MITochondrial_combined_dataset_BEAST_imput
DOI: 10.5061/dryad.4g832/3
title: RIBosomal_combined_dataset_BEAST_imput
DOI: 10.5061/dryad.55j7t/3
title: EnosPLS_shapeColor

description: These are the linear combinations of shape variables and of color variables from the two-block partial least squares analysis
DOI: 10.5061/dryad.55j7t/4
title: Enos_pools

description: Genotyping Data for the sample
DOI: 10.5061/dryad.55j7t/5
title: EnosColor

description: Color Data for Individuals for admixture mapping
DOI: 10.5061/dryad.55j7t/6
title: Enos_hybrids_LM

description: ShapeData For admixture mapping
DOI: 10.5061/dryad.56vf1/1
title: dataset

description: List of species (field: "species") with their body size ("max SVL (in mm)") and category (snake-like, padless, continental pad-bearer, NC pad-bearer or NZ pad-bearer) used for the analyses. In "source" appears the reference from which body size was obtained.
DOI: 10.5061/dryad.56vf1/2
title: Genbank_accession_numbers

description: Genbank accession numbers of all the species used in the produce the time calibrated tree of the Australasian diplodactyloid geckos.
DOI: 10.5061/dryad.62285/4
title: Hook measurement data from males

description: Hook measurements from 7 male specimens of the type-material of Echinorhynchus brayi Wayland, Sommerville & Gibson, 1999 (Acanthocephala: Echinorhynchidae). Specimens include holotype.
DOI: 10.5061/dryad.6vk48/1
title: NBR_MICROS

description: Genotype matrix for microsatellite loci in National Bison Range. Individual genotypes are presented as either homozygous (0), heterozygous (1), or missing (NA) at each locus. Loci numbers correspond to those presented in the supplementary tables.
DOI: 10.5061/dryad.71r61/1
title: Blank2009c.NotSoOldArchaea

description: Mesquite file containing phylogenetic tree and character matrix.
DOI: 10.5061/dryad.8c1p6/1
title: figure_2_phase_1_case_a

description: Data showing metadata reuse in Dryad for Case A, during phase 1.
DOI: 10.5061/dryad.8c1p6/2
title: figure_2_phase_1_case_b

description: Data showing metadata reuse in Dryad for Case B, during phase 1.
DOI: 10.5061/dryad.8c1p6/3
title: figure_3_phase_2_case_a

description: Data showing metadata reuse in Dryad for Case A, during phase 2.
DOI: 10.5061/dryad.8c1p6/4
title: figure_3_phase_2_case_b

description: Data showing metadata reuse in Dryad for Case B, during phase 2.
DOI: 10.5061/dryad.92kg0/1
title: Simulation code of the evolution of frugivory without discrimination

description: This is a python script to do the simulations of the evolution of frugivory without frugivore's discrimination. This means that frugivores disperse seeds to any patch (occupied or empty). The approximate time for one simulation is 2 hours in a 50x50 lattice.
DOI: 10.5061/dryad.962mb/1
title: Simulation code: The effect of natural selection on helping in large populations

description: This is c++ code which was used to produce the simulation data presented in Figure 2.
DOI: 10.5061/dryad.962mb/2
title: Simulation code: Conditions for the expected local frequency of helpers to increase.

description: This is c++ code which was used to produce simulation data presented in Figure 3.
DOI: 10.5061/dryad.9m59b/1
title: Morphometric data for limb stages 1 and 2

description: Landmark morphometric data for limb stages 1 and 2
DOI: 10.5061/dryad.9m59b/2
title: Morphometric data for limb stages 3, 4 and 5

description: Landmark morphometric data for limb stages 3, 4, and 5
DOI: 10.5061/dryad.b42r5/1
title: Morphology and preferences of anadromous, benthic and limnetic threespine sticklebacks
DOI: 10.5061/dryad.b7jh4/1
title: Supplemental Materials

description: Supplemental Materials.
DOI: 10.5061/dryad.b9p8v/1
title: GMAP of mRNA to cod reference genome

description: Ensemble mRNA is mapped to cod reference with GMAP
DOI: 10.5061/dryad.b9p8v/2
title: R script calculates Fst from SNP data

description: This script calculates Fst from CLC genomics parsed SNP's
DOI: 10.5061/dryad.bj57t/1
title: Empirical genotypic data of Artibeus lituratus from Paraguay and Argentina

description: This file contains fragment analysis results from genotyping Artibeus lituratus. Genomic DNA was extracted with a QIAGEN DNeasy Blood & Tissue Kit, following manufacturer’s instructions. Five hundred and twenty-six bats were genotyped at 15 microsatellite loci: 3 originally developed for A. jamaicensis (Ortega et al. 2002), and 12 developed specifically for A. lituratus (McCulloch & Stevens 2011). Thermocycler settings, polymerase chain reaction (PCR) conditions, genotyping and scoring information are given in Table S2 and the supplementary methods (Appendix S1) of the associated publication. Genotyped bats came from 19 sites, 14 in eastern Paraguay and 5 in Misiones, Argentina. Data table columns contain, in order, the following information: individual identifiers (original collector number), the site from which bats were collected (refer to Appendix for site abbreviations and additional information), fragment length for each microsatellite locus at each allele (aka "locus1_allele1", "locus2_allele2", "locus2_allele1", ...). Missing data are indicated with "0".
DOI: 10.5061/dryad.bk03m/1
title: Am Nat Data Sheet 4.29.13
DOI: 10.5061/dryad.bp2tg/1
title: JEB Dryad
DOI: 10.5061/dryad.c9q92/1
title: Results of Taraxacum officinale genotyping and Genotype by Environment field experiment

description: Record of T. officinale genotypes identified in sampling of Vancouver populations. Results of T. officinale Genotype by Environment (GxE) field experiment conducted at Totem Field, University of British Columbia, Vancouver, B.C., Canada. GxE results include leaf area of the control treatment at 5 and 8 weeks, root and total biomass of the mow treatment, and number of days to partial and full wilting of the drought treatment.
DOI: 10.5061/dryad.dk712/14
title: filterTrees.py

description: Code used to filter newick-format trees based on their topology.
DOI: 10.5061/dryad.dk712/17
title: set31.Zupdated.autoAndZ.ALLSHARED.PiDiv.w100m10s20.csv

description: Nucleotide diversity for each population and divergence (dxy) between each population pair for 100 kb sliding windows, sliding in increments of 20 kb.
DOI: 10.5061/dryad.g2qp5/10
title: Supplementary File S3_Chaetopteridae within Sedentaria

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/11
title: Supplementary File S4_Magelona and Oweniidae within Sedentaria

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/12
title: Supplementary File S5_Oweniidae and Chaetopteridae within Sedentaria

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/13
title: Supplementary File S6_Magelona within Sedentaria

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/14
title: Supplementary File S7_Oweniidae and Chaetopteridae within Sedentaria

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/15
title: Supplementary File S8_Oweniidae within Sedentaria

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/3
title: Alignment_Dataset_77-1

description: Alignment of the dataset comprising 77 taxa with MARE α=1 applied.
DOI: 10.5061/dryad.g2qp5/6
title: Alignment_Dataset_79-1

description: Alignment of the dataset comprising 79 taxa with MARE α=1 applied.
DOI: 10.5061/dryad.g2qp5/7
title: Alignment_Dataset_79-2

description: Alignment of the dataset comprising 79 taxa with MARE α=2 applied.
DOI: 10.5061/dryad.g2qp5/8
title: Supplementary File S1_Amphinomida within Errantia

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.g2qp5/9
title: Supplementary File S2_Chaetopteridae and Magelona within Sedentaria

description: Plot of psL of each constrained analysis in comparison to the best tree
DOI: 10.5061/dryad.gf3qp/5
title: trnT-trnF Alignment

description: Alignment of trnT-trnF intergenic spacers of Saxifraga oppositifolia including GenBank accession numbers (2nd column).
DOI: 10.5061/dryad.hb84g/1
title: data

description: Two csv files, containing the main experimental data (data-main.csv) and the data from the lytic activity assay (data-lytic.csv).
DOI: 10.5061/dryad.hh12b/10
title: Viburnum Phylogeny reconstructed from the Plastid and ITS data sets

description: Bayesian majority-rule consensus tree of 113 species of Viburnum.  Data generated from the whole plastid sequencing were combined with data from 10 gene regions previously sampled for Viburnum (Clement and Donoghue, 2011; Chatelet et al., 2013).   This tree was generated from the Plastid and ITS data set, and it was used to reconstruct the phylogenies associated with Figure 2.
DOI: 10.5061/dryad.hh12b/7
title: Viburnum Phylogeny reconstructed from Plastid Coding and Non-coding Gene Regions

description: Bayesian majority-rule consensus tree of chloroplast coding and non-coding regions assembled from next-generation sequencing of Viburnum plastids. This tree is associated with the Viburnum Plastid Coding and Noncoding Gene Region data file, and is the tree used in Figure 1.
DOI: 10.5061/dryad.hh12b/8
title: Viburnum Phylogeny reconstructed from 10-gene region Data Set

description: Bayesian majority-rule consensus tree of 113 Viburnum species sampled for nine chloroplast regions and the internal transcribed spacer region (ITS). This phylogeny was reconstructed from the Viburnum 10 gene data set and is in Appendix S4.
DOI: 10.5061/dryad.hh12b/9
title: Viburnum Plastid and ITS Data

description: This nexus file contains 71,935 bp for 113 Viburnum species. It includes the nine chloroplast regions and ITS sampled for the 113 taxa as well as all gene regions assembled from plastid sequencing for 22 Viburnum taxa. The plastid coding, non-coding, and ITS partitions have been identified as character sets at the end of the file. Please refer to other data file submissions associated with this paper to retrieve individual gene regions. These data were used to generate the phylogenies associated with Figure 2.
DOI: 10.5061/dryad.j87v8/1
title: Blank2012.LowRatesofLGT

description: Mesquite file containing phylogenetic tree and character matrix.
DOI: 10.5061/dryad.mf3gd/10
title: real-model2

description: settings and output for migrate-N model 2
DOI: 10.5061/dryad.mf3gd/11
title: real-model3

description: settings and output for migrate-N model 3
DOI: 10.5061/dryad.mf3gd/12
title: real-model4

description: settings and output for migrate-N model 4
DOI: 10.5061/dryad.mf3gd/13
title: real-model5

description: settings and output for migrate-N model 5
DOI: 10.5061/dryad.mf3gd/5
title: matrixLDNL2

description: The matrix with LD pairs for NL population.
DOI: 10.5061/dryad.mf3gd/6
title: matrixLDRUS2

description: The matrix with LD pairs for Russian population.
DOI: 10.5061/dryad.mf3gd/7
title: matrixLDSP2

description: The matrix with LD pairs for Spitsbergen population.
DOI: 10.5061/dryad.mf3gd/8
title: MatrixLDSW2

description: The matrix with LD pairs for Sweden population.
DOI: 10.5061/dryad.mf3gd/9
title: real-model1

description: settings and output for migrate-N model 1
DOI: 10.5061/dryad.p3878/1
title: Table 1, Fig 2 - Model comparison

description: Contains the observed and predicted population means for each selection line. Includes a key identifying the variables.
DOI: 10.5061/dryad.ph40n/1
title: readme: instructions for using code and simulation data here
DOI: 10.5061/dryad.ph40n/2
title: model simulation data and Matlab code for generating paper figures
DOI: 10.5061/dryad.ph40n/3
title: Matlab code for running model simulations
DOI: 10.5061/dryad.ps46g/1
title: Heliotropium_AFLP_Data

description: AFLP data in genpop format
DOI: 10.5061/dryad.ps46g/2
title: Species tree of Heliotropium sect. Cochranea

description: Species tree of Heliotropium sect. Cochranea generated with star-BEAST
DOI: 10.5061/dryad.ps46g/3
title: Additional DNA sequences of Heliotropium sect. Cochranea

description: GenBank accession numbers  KF301622:KF301628. These sequences were added to the dataset of Luebert & Wen (Syst. Bot. 33:390–402, 2008) and used for the species tree analysis in star-BEAST.
DOI: 10.5061/dryad.r1cr4/1
title: Rescue

description: R file to run simulations
DOI: 10.5061/dryad.r1cr4/2
title: Simresults

description: Excel file with the results of the simulations.
DOI: 10.5061/dryad.r1cr4/3
title: DataStuff

description: Mathematica file for plotting the results.
DOI: 10.5061/dryad.rd1bc/4
title: Fig. S4. Outgroup sensitivity analyses
DOI: 10.5061/dryad.rd304/3
title: Tyler_et_al_standard_curves

description: Detail of the standard curves calculated from the Genemapper output. Female.ID: A unique ID number given to each female, here used to identify triads.  Equation:  The equation describing the fit of the curve through the standards for each triad.  R-squared:  The R-squared value for each standard curve.
DOI: 10.5061/dryad.s7t47/1
title: Infants' looking-time data and Figures

description: Infants' mean-percentile fixation duration on each of the face types for figures 1 and 2
DOI: 10.5061/dryad.sn1m7/3
title: DRYAD

description: Examples of Files used to run ABCtoolBox
DOI: 10.5061/dryad.v2v83/1
title: Dryad-files1

description: This file contains the values of kurtosis (Pearson's measure of kurtosis) that were used to describe the functional trait distributions of the secondary forests based on different functional traits. For information on how these values were calculated see methods of the main manuscript.
DOI: 10.5061/dryad.v3144/3
title: ITSPlaty

description: The file contains ITS sequences for the host
DOI: 10.5061/dryad.vm523/1
title: General dataset

description: This dataset contains all information for the analyses in the paper. Each line represents an individual, columns indicate metadata and variables, e.g. assemblage numbers, assemblage age, log-transformed measurements and Procrustes superimposition coordinates.
DOI: 10.5061/dryad.vm523/2
title: R-script for the analyses

description: The analyses by Van Bocxlaer & Hunt were performed in the free software environment R (www.r-project.org). This file contains the R script for all analyses. Please see the paper for specifications related to package versions used. Some analyses may require substantial computer power; solutions may be delayed with minutes up to about an hour depending on computer specifications.
DOI: 10.5061/dryad.vm523/3
title: Randomly resolved phylogenetic trees

description: This file contains the data of 50,000 randomly resolved, time-scaled phylogenetic trees as generated from the code in the provided R-script file. Re-running the code will provide highly similar, but different results. The trees provided in this file are the exact trees that we used for the analyses described in the paper.
DOI: 10.5061/dryad.12ck0.1
title: Data from: Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis)
DOI: 10.5061/dryad.12ck0.2
title: Data from: Neutral and selective processes shape MHC gene diversity and expression in stocked brook charr populations (Salvelinus fontinalis)
DOI: 10.5061/dryad.12ck0.2/1.1
title: 2009 data

description: This dataset contains: gene expression values, physiological parameters, Q_values, Minisatellites length, MHCIIb alleles, parasitological parameters.
DOI: 10.5061/dryad.12ck0.2/2.1
title: 2008-2009_parasites_data

description: This dataset contains parasitological informations for the individuals sampled in 2008 and 2009. The lakes, refere to Amanites (AMA), Belles de jour (BEL), Caribou (Car), Méthot (MET), Main de fer (MAI) and Petit Saint-Bernard (BER).
DOI: 10.5061/dryad.12ck0.2/3.1
title: MHCIIb_genotypes_data

description: This dataset was generated with the genotyping pipeline described in the manuscript. It contains MHCIIb genotypes for all populations. Lakes refere to : Amanites (AMA), Belles-de-Jour (BEL), Methot (MET), Arcand (ARC), Rivard (RIV), Veillette (VEI), Caribou (CAR), Main de fer (MAI), Sorbier (SOR) and Petit saint Bernard (BER).
DOI: 10.5061/dryad.1786p/1
title: Nutrient concentration and density data; A Canadian Healthy Oceans Network Ecosystem Function Project, EF-03

description: Excel file with all nutrient concentrations determined in laboratory from sediment samples as well as bivalve densities from Tier I & II experiments. NA denotes samples that were not collected or missing due to procedural errors in laboratory.  Blank cells are outliers that have been removed from statistical analysis.  Tier III abbreviations are as follows: s = sterilized treatments; sv = sterilized treatments + varnish clams; us = unsterilized treatments; usv = unsterilized treatments + varnish clams.
DOI: 10.5061/dryad.1786p/2
title: Discovery metadata, A Canadian Healthy Oceans Network Ecosystem Function Project, EF-03

description: Excel discovery metadata file
DOI: 10.5061/dryad.1h1f2/1
title: output_read2snps_cov4_10_Q30

description: output data generated by Read2snps tool. This file contain only SNPs sequences with SNPs with a depth sequencing between 4 and 10 for a minimum quality of 30. This file have been used to select and to design primers.
DOI: 10.5061/dryad.1h1f2/2
title: assembling_Ixodes_ricinus_RRL
DOI: 10.5061/dryad.1h1f2/3
title: Bioinformatic_scripts
DOI: 10.5061/dryad.267kc/1
title: HawaiiIsland23PoplnsSSRDataDryad

description: Multilocus (9 loci) nuclear microsatellite genotypes of 407 adult individuals of Metrosideros polymorpha sampled from 23 populations across Hawaii Island.  All five named varieties of M. polymorpha on the island are included: G = var. glaberrima, I = var. incana, M = var. macrophylla, N = var. newellii, and P = var. polymorpha.  The names of the populations are shown, and corresponding GPS coordinates are available in the text of the associated manuscript.  The individual tree IDs are for internal purposes only.
DOI: 10.5061/dryad.2sp72/1
title: Primary data 數字result

description: The ELISA result of autoantibodies of active TB patients
DOI: 10.5061/dryad.2sp72/2
title: Normal population ENA primary result

description: The ELISA result of autoantibodies from control population
DOI: 10.5061/dryad.34621/2
title: López-Fernández et al CichlinaeMCC chronogram

description: This file contains a Newick-formatted version of the MCC chronogram of Neotropical cichlids used in all lineage and phenotypic analyses. African, Indian and Madagascan taxa used for cichlid dating in the BEAST run have been pruned for analysis of Neotropical taxa. This file is directly readable in the relevant R packages used in the paper. This chronogram was pruned to generate trees for the clades Geophagini, Cichlasomatini and Heroini as needed for analysis presented in the paper.