cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.3p1tj06/1
title: Carex guyana SNP dataset, Andean wetland plant community dataset, and environmental data for species genetic diversity correlation study

description: This data folder includes the five filtered SNP datasets for the plant species, Carex guyana, a common sedge in high elevation Andes wetlands (final_partitioned_SNPdatasets). Details regading the partitioned neutral and adaptive datasets can be found in the accompanying Ecology and Evolution 2018 paper. The folder also contains the plant community datasets (DatosPlantsCommunity_modified) used to contrast plant species and Carex guyana genetic diversity in the species genetic diversity correlation study, as well as the environmental data (EnvData).
DOI: 10.5061/dryad.4m485m0/5
title: Development of PBT

description: Review of candidate action list and selection of actions comprising practice-based tool with reasoning for decisions.
DOI: 10.5061/dryad.4qk32tp/1
title: Nodule trait and plant biomass data of two invasive legumes in Pittsburgh, Pennsylvania

description: Includes details on species, accession, and location of plants used in the common garden experiment. Also includes data on nodule traits (nodule number, nodule biomass) and plant biomass (dry shoot and root biomass).
DOI: 10.5061/dryad.64048p0/2
title: Martin et al. 2018 Supplementary Data from Heaviside's dolphins (Cephalorhynchus heavisidii) relax acoustic crypsis to increase communication range

description: This .wav file includes an example of each pulsed signal type described for Heaviside's dolphins in Martin et al. 2018. The signal types are in the order: 1) broadband click train, 2) burst-pulse, 3) buzz and 4) NBHF click train.
DOI: 10.5061/dryad.64048p0/4
title: Martin et al. 2018 Supplementary Methods from Heaviside's dolphins (Cephalorhynchus heavisidii) relax acoustic crypsis to increase communication range

description: Supplementary Methods contain details about the statistical analyses used to classify the pulsed signal types of Heaviside's dolphins. Also, methods include the steps and figures used to model the active space of a NBHF click compared to a click extracted from a lower-frequency burst-pulse signal.
DOI: 10.5061/dryad.64048p0/5
title: Martin et al. 2018 Appendix S1 from Heaviside’s dolphins (Cephalorhynchus heavisidii) relax acoustic crypsis to increase communication range

description: Appendix S1 contains acoustic parameter measurements from pulsed signals measured from Heaviside's dolphins
DOI: 10.5061/dryad.6839bg5/3
title: Halodule wrightii Structure formatted file

description: This file contains the Structure-formatted dataset to accompany the 2017 ms A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii.
DOI: 10.5061/dryad.6839bg5/4
title: Halodule wrightii Migrate-formatted data files

description: This file contains Migrate-n formatted datasets to accompany the 2017 ms A map-based approach to assessing genetic diversity, structure, and connectivity in the seagrass Halodule wrightii.
DOI: 10.5061/dryad.6jk8h77/1
title: Tropical South America Diatom Database

description: This database consists in two different datasets:
1) Diatom dataset: include the individual diatom datasets (presence/absence data) of the study regions
2) Environment dataset: include limnological and geo-climatic variables of the study lakes
DOI: 10.5061/dryad.6rb12hk.1/1.1
title: Dataset used in the study
DOI: 10.5061/dryad.6rb12hk.2
title: Data from: Predation risk determines pigmentation phenotype in nuthatches by melanin-related gene expression effects
DOI: 10.5061/dryad.6rb12hk.2/1.2
title: Dataset used in the study
DOI: 10.5061/dryad.751pv76/1
title: SwiSCI community survey 2012

description: Participants of the community survey of the Swiss Spinal Cord Injury Cohort study (SwiSCI) who completed the 'Health Behavior and Psychological Personal Factors Module'
DOI: 10.5061/dryad.7cr0q/3
title: O. sativa japonica gene and its orthologous sequences aligned

description: Oryza sativa japonica gene model and its orthologous sequences from O. sativa indica, O. sativa aus, O. rufipogon, O. nivara, O. barthii, and O. punctata in FASTA format. Each O. sativa japonica gene has a directory and within the directory there are 3 files: *.4D.fa, four-fold degenerate sites; *.CDS-3.fa, 3rd position sites of coding DNA sequence; *.CDS.fa, entire coding DNA sequence. Names of species were shortened and corresponds to: BAR, O. barthii; NIV, O. nivara; PUN, O. punctata; RUF, O. rufipogon; SAA_DJ123, Oryza sativa aus cv. DJ123; SAA_KASALATH, Oryza sativa aus cv. Kasalath; SAI, Oryza sativa indica cv. 93-11; SAI_IR64, Oryza sativa indica cv. IR64; SAJ, Oryza sativa japonica
DOI: 10.5061/dryad.7cr0q/4
title: Multi-genome alignment in MAF format

description: Genome alignments for domesticated and wild rice genomes in MAF format. Oryza sativa japonica genome was used as reference and genomes of O. rufipogon, O. sativa indica cv. 93-11, O. sativa indica cv. IR64, O. sativa aus cv. DJ123, O. sativa aus cv. Kasalath, O. nivara, O. glaberrima, O. barthii, O. glumaepatula, O. longistaminata, O. meridionalis, O. punctata, and O. brachyantha were aligned using LASTZ and MULTIZ.
DOI: 10.5061/dryad.7cr0q/5
title: Oryza sativa japonica genome coordinates with significant phastcons score

description: Oryza sativa japonica genome coordinates that had phastcons score greater then 0.8 in BED format. Significant regions that were 10bps apart were merged into one and flanking 100bps were also considered.
DOI: 10.5061/dryad.7cr0q/6
title: Repeatmodeler identified repeat sequences

description: Repetitive DNA sequences identified by Repeatmodeler from the genomes of O. sativa japonica, O. sativa indica cv. 9311, O. rufipogon, O. nivara, O. glaberrima, O. barthii, O. glumaepatula, O. longistaminata, O. meridionalis, O. punctata, and O. brachyantha
DOI: 10.5061/dryad.7t8550v/1
title: Stoichiometric phenotype of stickleback

description: Data from stickleback (adults or juveniles) raised in two environments (lab and mesocosms) from different populations (Constance, Geneva, Constance x Geneva hybrid). Standard Length, Wet weight, Fulton K, %N, %P and N:P are shown as well as lateral plate number for adults.
DOI: 10.5061/dryad.84q03k0/1
title: Species specific log odds ratio (yi) and its variation (vi) per publication in response to urbanisation.

description: Species specific log odds ratio (yi) and its variation (vi) per publication. This data was used to calculate species-specific estimated effect size of urbanisation. Log-odds ratios are derived from lists and numbers of species sampled and provided by the original author's publication. Further details concerning authors, publications, and which habitat types in urban versus non-urban areas where used to calculate the log odds ratio are provided in Table SI1 of this publication.
DOI: 10.5061/dryad.b0p66dn/1
title: 01-RDA_candidate_snps

description: script to perform RDA for detecting candidate SNPs
DOI: 10.5061/dryad.cp45ht6/1
title: Cambronero_etal_Environmental metadata

description: Paleolimnological and historical data are shown for the sedimentary archive of Lake Ring. For each radiometrically dated year, Daphnia magna ephippia count, Cladocera assemblage, carbamate insecticides, Loss on Ignition (LOI), transparency measured as Secchi disk depth, total Nitrates (TN) and total Phosphates (TP) are shown. Na = missing data. Data for transparency, TN and TP are available between 1971 and 1999
DOI: 10.5061/dryad.cp45ht6/2
title: Cambronero_etal_pesticides

description: List of insecticides sold in Denmark according to the Danish county authority between 1955 and 2010 (www.middeldatabasen.dk). The total amount of each insecticide is show in tons. Yellow lines highlight carbamate insecticides, of which the commercial brand Carbaryl was used in this study.
DOI: 10.5061/dryad.cp45ht6/3
title: Cambronero_etal_life history traits

description: IndividualID, populationID, experimental exposure and life history traits (mortality, size at maturity, age at maturity and fecundity) measured after controlling for maternal effect in the three common garden experiments are shown. CGE1: temperature; CGE2: temperature and food levels; CGE3: temperature and insecticide Carbaryl concentrations. Temperatures used are: 18C and 24C; food levels are 0.2 mg Carbon/L and 2.4 mg Carbon/L; Carbaryl concentrations are 4 μg/L and 10 μg/L. Experimental exposures are as follows: T18 – Temperature 18C; T24 - Temperature 24C; TFH18 - Temperature 18C and high food levels; TFL18 - Temperature 18C and low food levels; TFH24 - Temperature 24C and high food levels; TFL24 - Temperature 24C and low food levels; TIH18 - Temperature 18C and high insecticide levels; TIL18 - Temperature 18C and low insecticide levels; TIH24 - Temperature 24C and high insecticide levels; TIL24 - Temperature 24C and low insecticide levels.
DOI: 10.5061/dryad.d4q57s5/1
title: Full SNP panel (756 SNPs)

description: 756 SNPs that were identified for Sagmariasus verreauxi in a genpop file format.
DOI: 10.5061/dryad.d4q57s5/2
title: Neutral SNP Panel

description: 645 neutral SNPs identified for Sagmariasus verreauxi in a structure file format.
DOI: 10.5061/dryad.d4q57s5/3
title: Outlier SNP Panel

description: 15 outlier SNPs identified for Sagmariasus verreauxi in a structure file format.
DOI: 10.5061/dryad.d4q57s5/4
title: Migrate-N input file

description: Input file containing 50 loci for Migrate-n analysis between NSW and NZ.
DOI: 10.5061/dryad.f0s23r8/60
title: Donor20: Bw4 Stability

description: Data corresponding to HLA-Bw4 stability for Donor 20.
DOI: 10.5061/dryad.f0s23r8/61
title: Donor62: Bw4 Stability

description: Data corresponding to HLA-Bw4 stability for Donor 62.
DOI: 10.5061/dryad.f0s23r8/62
title: Donor80: Bw4 Stability

description: This data corresponds to the HLA-Bw4 stability data (flow cytommetry files) for Donor 80.
DOI: 10.5061/dryad.f0s23r8/63
title: Donor64_Part2/2: Bw4 Stability

description: This data corresponds to the HLA-Bw4 stability data (flow cytommetry files) for Donor 64 (Part 2/2).
DOI: 10.5061/dryad.f0s23r8/64
title: Donor64_Part1/2 Bw4 Stability

description: This corresponds to the HLA-Bw4 stability flow cyvtometry fcs files for Donor 64.
DOI: 10.5061/dryad.f0s23r8/65
title: Donor156: Bw4 Stability

description: This corresponds to the HLA-Bw4 stability flow cyvtometry fcs files for Donor 156.
DOI: 10.5061/dryad.f0s23r8/66
title: Donor91: Bw4 Stability

description: This corresponds to the HLA-Bw4 stability flow cyvtometry fcs files for Donor 91.
DOI: 10.5061/dryad.f0s23r8/67
title: Donor111: Bw4 Stability

description: This corresponds to the HLA-Bw4 stability flow cyvtometry fcs files for Donor 111.
DOI: 10.5061/dryad.f0s23r8/68
title: Donor121: Bw4 Stability

description: This corresponds to the HLA-Bw4 stability flow cyvtometry fcs files for Donor 121.
DOI: 10.5061/dryad.j5t58j4/1
title: Raw diversity dataset (.dat format)

description: Raw diversity dataset in .dat format for use in PAST, contains additional color-coding and formatting.
DOI: 10.5061/dryad.j5t58j4/3
title: Raw diversity dataset (.csv format)

description: Raw diversity dataset in .csv format for use in Microsoft Excel.
DOI: 10.5061/dryad.n3m2qh2/1
title: data1: multivariate mixed models data

description: This table contains the data used for producing Table 1 (bivariate mixed model: diet and provisioning rate) and Table S2 (multivariate mixed model: prey types)
DOI: 10.5061/dryad.n3m2qh2/2
title: data2: data of univariate mixed models of diet and provisioning rate

description: data set used to produce Table 2 (univariate mixed models of diet and provisioning rate) and Table S3A and S3B (Covariation between foraging behavior and the main preys found in the diet)
DOI: 10.5061/dryad.n3m2qh2/3
title: data3: fitness data and parent's provisioning behaviour

description: Data set used to produce Table 3 (Best general linear models explaining variation in components of annual fitness)
DOI: 10.5061/dryad.rj4cg1t/1
title: Supplement Table 1-core data

description: Absolute abundances of molluscs in two cores at Piran 1 and Piran 2, including two surface living assemblages collected by Van Veen grabs at the same sites in 2014 (1 mm mesh size). Complete valves or fragments with umbo preserved were selected from the &gt;1 mm sieve fraction of each increment, identified to species level, and counted. For each species, the higher number of single valves (either right or left) was added to the number of double-valved specimens to get the final count in each increment.
DOI: 10.5061/dryad.rj4cg1t/2
title: Supplement Table 2-Gouldia age data

description: Amino acid racemization data and calibrated estimates of postmortem age of Gouldia minima collected from the shell bed at Piran 1 and Piran 2.
DOI: 10.5061/dryad.rj4cg1t/3
title: Supplement Table 3-Corbula age data

description: Amino acid racemization data and calibrated estimates of postmortem age of Corbula gibba and Piran 2.
DOI: 10.5061/dryad.rj4cg1t/4
title: Supplement Table 4-LA data

description: Absolute abundances of molluscs in living assemblages collected by Van Veen grabs at 11 stations in 2011.
DOI: 10.5061/dryad.rj4cg1t/5
title: Gouldia age unmixing final

description: R language source code for analyses of age data and age unmixing
DOI: 10.5061/dryad.t76fk80.1
title: Data from: Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences
DOI: 10.5061/dryad.t76fk80.1/11.1
title: si_files_SA.tar

description: SLiM simulations
DOI: 10.5061/dryad.t76fk80.1/14.1
title: 1000G.extraData_distanceHotspotPhastcons

description: Annotations of distance to hotspots and distance to conserved elements (phastcons) in centimorgans for 1000G data.
DOI: 10.5061/dryad.t76fk80.1/15.1
title: 1000G_genot-table

description: Contains as a compressed file the genotype table with annotation for 1000G data. Please see the README file for further description and information on how to make the figures. Author: Fanny Pouyet
DOI: 10.5061/dryad.t76fk80.1/16.1
title: 1000G_Nb_DerAll_byPop

description: Files from which the SFS are computed. Author:  Fanny Pouyet
DOI: 10.5061/dryad.t76fk80.1/17.1
title: figures_data_SFS_Rscripts

description: Files to make figures of SFS and scripts to compute the SFS too. The SFS are done from files in "1000G_Nb_derAll.zip". For further details, see README file
DOI: 10.5061/dryad.t76fk80.1/18.1
title: Main README

description: This dryad page provides the data and the source code for the figures in " Background selection and biased gene conversion affect more than 95% of the human genome and bias demographic inferences " by Pouyet F,* Aeschbacher S*, Thiery A and Excoffier L. 
* first co-authors 

It contains as compressed files: 
-- 1 -- Genotype tables and annotations from 1000G and SGDP data 1000G_genot-table.zip SGDP_genotypetable-annotation.zip with README files that describe the data and how to use them.   
-- 2 -- the R scripts to perform the figures of INDA figures_INDA_Rscripts.zip  
-- 3 -- the confidence intervals of the estimates as well as the source code to estimate them confidenceIntervals.zip  
-- 4 -- the scripts (R and python) to make the SFS figures as well as estimate confidence intervals and compute the SFS figures_data_SFS_Rscripts.zip  
-- 5 -- the setting parameters for FastSimCoal demographic inferences Supplementary file - settings files for demographi ...  
-- 6 -- the scripts for SLiM simulations and analyses (bash and R code) + a table with parameters used in the SLiM simulations (.csv) + the scripts and raw data that I used to make the figures (.txt and .R) si_files_SA.tar.gz 

Extra READMEs describe the files and how to launch them to compute the statistics or to make the figures.
DOI: 10.5061/dryad.t76fk80.1/8.1
title: confidence Intervals

description: Files with 95% CI
DOI: 10.5061/dryad.t76fk80.2/2.2
title: regions.YRIrecomb1p5.nophastConsElements46wayPrimates100bp

description: Same as "regions.YRIrecomb1p5.bed" + the removal of regions close to conserved elements (see Fig1S9 and Fig2S4 for the impact of conserved elements on DAFi and on the SFS). For this file, the removed regions are less than 100bp from conserved elements.
DOI: 10.5061/dryad.vn36290/1
title: Claireau_et_al_bat_crossings

description: Number of bat crossings per site, per pair and per date within the context of the habitat (A, agricultural land; F, forest; H, hedgerow; O, bat overpass and S, stream).
DOI: 10.17632/ts244wjfnd.1
title: Data for: Are agricultural researchers working on the right crops to ensure food and nutrition security under future climates?

description: R script developed for analysis.
DOI: 10.17632/zs3ztb7dc5.1
title: Data for: Fossil herbivores and crocodiles as paleoclimatic indicators of environmental shifts from Bed I and Bed II times of the Olduvai Gorge, Tanzania

description: This data set contains carbon and oxygen isotope values of fossil teeth of crocodiles and herbivores from the Olduvai Gorge of Tanzania, from 2.1 to 1.5 Ma and present. Materials were collected from the National Natural History Museum in Arusha, Tanzania (NNHM) and from field labs at the Olduvai Gorge collected previously by Mary Leakey.
DOI: 10.5061/dryad.10351qn/10
title: TEM - badp1 - Part 2/8

description: Transmission electron micrographs from guinea pig ventricles treated with badp1 and badp1-scr. Part 2/8
DOI: 10.5061/dryad.10351qn/11
title: TEM - badp1 - Part 3/8

description: Transmission electron micrographs from guinea pig ventricles treated with badp1 and badp1-scr. Part 3/8
DOI: 10.5061/dryad.10351qn/12
title: TEM - badp1 - Part 4/8

description: Transmission electron micrographs from guinea pig ventricles treated with badp1 and badp1-scr. Part 4/8
DOI: 10.5061/dryad.10351qn/13
title: TEM - badp1 - Part 5/8

description: Transmission electron micrographs from guinea pig ventricles treated with badp1 and badp1-scr. Part 5/8
DOI: 10.5061/dryad.10351qn/14
title: TEM - badp1 - Part 6/8

description: Transmission electron micrographs from guinea pig ventricles treated with badp1 and badp1-scr. Part 6/8
DOI: 10.5061/dryad.10351qn/15
title: TEM - badp1 - Part 7/8

description: Transmission electron micrographs from guinea pig ventricles treated with badp1 and badp1-scr. Part 7/8
DOI: 10.5061/dryad.10351qn/8
title: ECGs

description: Volume conducted ECGs from isolated guinea pig ventricles.
DOI: 10.5061/dryad.10351qn/9
title: TEM - badp1 - Part 1/8

description: Transmission electron micrographs from guinea pig ventricles treated with badp1 and badp1-scr. Part 1/8
DOI: 10.5061/dryad.1bd3931/1
title: Image files

description: .nd2 Nikon image files and .oib Olympus FV 10000-image files
DOI: 10.5061/dryad.1f2c124/1
title: Greenhouse experiment community biomass data
DOI: 10.5061/dryad.1f2c124/2
title: Greenhouse experiment neighborhood data

description: Individual biomass, trait, and neighborhood composition for Trifolium greenhouse experiment
DOI: 10.5061/dryad.1hr1n52/1
title: naturalized pine occurrences and associated climatic data

description: A comma-delimited data file that contains naturalized occurrences for 25 pine species, globally. Each occurrence is a row, with species indicated, georeferenced coordinates, country, and associated climate data. Each occurrence corresponds with an herbarium specimen; for herbarium data, contact the authors. Climatic data column names correspond with BioClim variables downloaded from CliMond and other sources. See main article text for further details and variables used in main analyses. Native range occurrences are available from the Conifer Database (for use, contact Aljos Farjon; a.farjon@kew.org).
DOI: 10.5061/dryad.1hr1n52/2
title: global climate data

description: A comma-delimited file that contains climate data used to create the global climate space background. Data is in point format, where x and y locations correspond to the center of a 10 arc-minute grid cell. Column names correspond with climatic variables downloaded from CliMond and other sources. See main article text for further details and the specific variables used in main analyses.
DOI: 10.5061/dryad.2bs408m/1
title: parental care and variation in body size in N. vespilloides families

description: The dataset consists of 7 columns: Column 1 is a unique identifier for the family.  Column 2 is the mass of the breeding carcass in grams.  Column 3 is the parental care treatment (Full = full care, No = no care).  Column 4 is the number of larvae at dispersal (i.e. brood size).  Column 5 is the mean ponotum width (in mm) of adults from each family.  Column 6 is the standard deviation of pronotum width.  Column 7 is the coefficient of variation of pronotum width.
DOI: 10.5061/dryad.315km76/1
title: data

description: Input and output files for all analyses - ADMIXTURE, DAPC, BEAST, SNAPP, EEMS, dadi. Also included are STACKS output files and ENMs
DOI: 10.5061/dryad.3g2n7dc/1
title: Supplemental Figure 1
DOI: 10.5061/dryad.3st56j0/1
title: CroninEtAl_R_Script_and_Data

description: .zip file contains R script for all calculations in the manuscript and the data files needed to run it. .csv files include counts for each site, global; regional, and local maximum ages; and ages and measurements for all individuals collected that were at least one year old.
DOI: 10.5061/dryad.588g0cf/1
title: Computer code and output

description: Textfile containing computer code and output
DOI: 10.5061/dryad.6rb12hk.1
title: Data from: Predation risk determines pigmentation phenotype in nuthatches by melanin-related gene expression effects
DOI: 10.5061/dryad.859nv4m/1
title: DNA sequence alignment

description: DNA sequence alignment used in the phylogenetic analysis.
DOI: 10.5061/dryad.859nv4m/2
title: BEAST_controlfile

description: The control file used in the BEAST analysis.
DOI: 10.5061/dryad.859nv4m/3
title: BEAST mcc tree

description: The maximum clade credibility tree inferred with the BEAST analysis and used in the analyses.
DOI: 10.5061/dryad.859nv4m/4
title: ML_tree

description: The maximum likelihood tree inferred in RaxML, used as a starting tree in the BEAST analysis.
DOI: 10.5061/dryad.859nv4m/5
title: Geographic incidence matrix

description: The species by area geographic incidence matrix used for the analyses.
DOI: 10.5061/dryad.97p31jr/1
title: De Silva-Manville et al 2018 Supplementary Tables

description: Supplementary tables describing functional effects of M. oppositifolius leaf extract components on KCNQ1 channels, alone and with regulatory proteins. Effects of the leaf extract components on mutant KCNQ1 and KCNQ2/3 channels are also described.
DOI: 10.5061/dryad.9bs6rq3/1
title: Whittingham et al. Migration & MHC_JEB2018
DOI: 10.5061/dryad.9vv1vb6/1
title: Behaviour Data

description: All data used to generate the results for the behavioural component of the study
DOI: 10.5061/dryad.9vv1vb6/2
title: Learning Data

description: All data used to generate the results for the learning component of the study
DOI: 10.5061/dryad.b0p66dn/2
title: 02-compute_polygenic_scores

description: script to compute polygenic scores across candidate SNPs
DOI: 10.5061/dryad.b0p66dn/3
title: 3699snps_freqs

description: allele frequencies for RDA
DOI: 10.5061/dryad.b0p66dn/4
title: candidates.frq

description: candidate frequencies for polygenic scores
DOI: 10.5061/dryad.b0p66dn/5
title: meanbottomtemp_atsites

description: bottom temperature at sites for polygenic scores
DOI: 10.5061/dryad.dr1qs08/1
title: Dryad Table 1-cand genes within lineages

description: Candidate genes within each phylogenetic lineage of Chinook salmon.
DOI: 10.5061/dryad.dr1qs08/2
title: Dryad Table 2-cand genes between lineages

description: Candidate genes between lineages of Chinook salmon.
DOI: 10.5061/dryad.dr1qs08/3
title: Dryad Table 3-GO enrichment results

description: GO enrichment results for candidate genes.
DOI: 10.5061/dryad.dr1qs08/4
title: Annotation of genome assembly

description: annotation file for CHI06 genome assembly (gzip compressed)
DOI: 10.5061/dryad.f0s23r8/69
title: Donor126: Bw4 Stability

description: This corresponds to the HLA-Bw4 stability flow cyvtometry fcs files for Donor 126.