cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.s612m/2
title: ms_Strategic_Coop_analyses_output_main_doc_POSTREVIEW

description: A printout of the analyses conducted in SPSS for the results in the main document. Analyses were conducted via the GUI, but the log records the equivalent syntax.
DOI: 10.5061/dryad.s612m/3
title: ms_Strategic_Coop_analyses_output_ESM_POSTREVIEW

description: The printout from the analyses conducted in SPSS for the ESM.
DOI: 10.5061/dryad.tt743/1
title: Young inversion with multiple linked QTLs under selection in a hybrid zone
DOI: 10.5061/dryad.v01m0/1
title: Europe_Asia_establishments_Dryad

description: Historical numbers of European and Asian Scolytinae established in USA by decade
DOI: 10.5061/dryad.0p264/1
title: Microsatellite dataset of 1765 Annona cherimola DNA samples

description: A total of 1765  A. cherimola DNA samples collected in the highlands of Guatemala, Honduras, Costa Rica, Ecuador, Peru and Bolivia geopositioned in decimal degrees were analyzed with 9 selected microsatellite loci. Those microsatellites were previously shown to be highly informative in A. cherimola (Escribano et al. 2008; van Zonneveld et al. 2012): LMCH1, LMCH4, LMCH16, LMCH48, LMCH69, LMCH87, LMCH122, LMCH139 and LMCH144.
DOI: 10.5061/dryad.0s9j3/1
title: background_by_month_year

description: This is the background climate file.  This is where all the black lines and dots from figure 3 come from.
DOI: 10.5061/dryad.1gr29/1
title: Na-GST-1 immunigenicity data
DOI: 10.5061/dryad.1k79k/1
title: Data

description: This file contains the raw data for all analyses involved in the study. Variable names should be self-identifying, and all analyses from the study should be reproducible. Please contact Bowen J Fung (bowenjfung@gmail.com) if you require clarification or more information.
DOI: 10.5061/dryad.20hd2/1
title: Eimeria_AA_ alignment_ for_DRYAD

description: 28 species FASTA file of amino acid alignment (1,100 aa alignment) of mitochondrial DNA coding regions (Cytochrome b, COI, COIII) of poultry infecting Eimeria species and close relatives. Contains complete cytochrome b coding sequence (360 amino acids); a partial COI coding sequence (486 amino acids); and partial COIII coding sequence (254 amino acids), and using Choleoeimeria sp. as outgroup.
DOI: 10.5061/dryad.20hd2/2
title: Nucleotide alignment for DRYAD

description: Nucleotide_alignment_for_DRYAD.fsa  
54 species FASTA file of complete mitochondrial DNA sequence alignment (6,628 bp alignment) of Eimeria species and their relatives.
DOI: 10.5061/dryad.20hd2/3
title: Nucleotide alignment E zuernii root DRYAD

description: Nucleotide_alignment_E_zuernii_root_DRYAD.fsa 
42 species FASTA file of complete mitochondrial DNA sequence alignment (6,488 bp alignment) focused on the chicken infecting Eimeria species and strains, and their nearest relatives using Eimeria zuernii as outgroup.
DOI: 10.5061/dryad.34m6j/1
title: Data for Children’s Visuospatial Memory Predicts Gains in Mathematics Achievement Through Early Adolescence’ by Yaoran Li and David C. Geary. PLoS ONE

description: Raw data.Date file names:

Race = W (white), B (Black), A (Asian), M (mixed), U (unknown)
05-13 = year of data collection, 2005 to 2013
WS = winter semester
FS = fall semester
WR = Word Reading
NO = Numerical Operations
RAN_a = Rapid automatized naming of letters
RAN_1 = Rapid automatized naming of numbers
SWAN = Strength and Weaknesses of ADHD–symptoms and normal-behavior
PL_TS = phonological loop total score
VSSP_TS = visuospatial sketch pad total score
CE_TS = central executive total score
DOI: 10.5061/dryad.34qd7/1
title: Protein alignments

description: Alignments of organellar proteins
DOI: 10.5061/dryad.34qd7/2
title: Phylogenomic dataset

description: Single gene alignments used for phylogenomic analysis
DOI: 10.5061/dryad.34qd7/3
title: Data Sources

description: Fasta files with assembled transcriptomes of Carpediemonas-like organisms
DOI: 10.5061/dryad.3vr00/1
title: Crossing Data used to Calculate Isolation Values

description: This file contains data obtained from controlled hybridizations (crosses) in the greenhouse, among different Jaltomata 
species and their F1 hybrids. These data were used to calculate measures of reproductive isolation for the following stages:
fruit set, fruit size, seed set, viable seed set, F1 fruit set, F1 fruit size, and F1 seed set.
DOI: 10.5061/dryad.3vr00/2
title: Measured Floral Color Attributes used to Calculate Floral Distances Metrics

description: This file contains measures of color attributes for petal and nectar color. For each color trait, images were standardized 
for lighting, and then different color attributes were measured in ImageJ. These data were used to calculate floral distance metrics.
DOI: 10.5061/dryad.3vr00/3
title: Measured Floral Morph Traits used to Calculated Floral Distance Metrics

description: This file contains measures of floral organs and nectar volume, which were collected on fresh mature flowers. These data were used to calculate floral distance metrics.
DOI: 10.5061/dryad.3vr00/4
title: Pollen Growth Data used to Calculate Pollen-Pistil Isolation

description: This file contains data obtained from pollen growth assays, which were used to determine extent of pollen-pistil isolation. It includes species pairs, individuals used, pollination and style collection dates, and pollen tube length information.
DOI: 10.5061/dryad.3vr00/5
title: Pollen Viability Data used to Calculate F1 Hybrid Pollen Isolation

description: This file contains pollen count data, which were used to determine F1 pollen fertility isolation. Pollen counts were obtained using aniline-blue stain.
DOI: 10.5061/dryad.3vr00/6
title: Loci used to Estimate Genetic Distance among Species

description: This is a compressed file containing alignments for the 60 loci used to estimate genetic distance among Jaltomata species.
DOI: 10.5061/dryad.3vr00/7
title: Short Description File

description: This is a readme file containing descriptions of the included data files.
DOI: 10.5061/dryad.43hd6/1
title: Genotypes sporophytes

description: Genotypes of sporophytes individuals identified (based on diagnostic microsatellite, ITS1 and species-specific cytoplasmic marker) as E. siliculosus (Esil, n = 338) and E. crouaniorum (Ecro, n = 151). This identification was used previous to the admixture analyses. The number of samples in each population, name of the strain, ITS1 length (850 = Esil, &gt;1000 = Ecro) and positive amplification in the cytoplasmic marker (Esil = positive amplification Esil, Ecro = positive amplification Ecro) are shown. In diagnostic loci, the non-amplification in one of the parental species corresponds to a phylogenetic signal but should be distinguished from a null allele. To solve this problem, these missing data points were replaced by an artificial allele of an arbitrary size of (800bp). In contrast, missing data or null alleles were noted as 0.
DOI: 10.5061/dryad.43hd6/2
title: Genotype gametophyte

description: Genotypes of gametophytes individuals identified (based on diagnostic microsatellite, ITS1 and species-specific cytoplasmic marker) as E. siliculosus (Esil, n = 158) and E. crouaniorum (Ecro, n = 176). This identification was used previous to the admixture analyses. The number of samples in each population, name of the strain, ITS1 length (850 = Esil, &gt;1000 = Ecro) and positive amplification in the cytoplasmic marker (Esil = positive amplification Esil, Ecro = positive amplification Ecro) are shown. In diagnostic loci, the non-amplification in one of the parental species corresponds to a phylogenetic signal but should be distinguished from a null allele. To solve this problem, these missing data points were replaced by an artificial allele of an arbitrary size of (800bp). In contrast, missing data or null alleles were noted as 0.
DOI: 10.5061/dryad.48j0m/1
title: Southeast Alaska sea lion philopatry
DOI: 10.5061/dryad.48j0m/2
title: Forrester Island Complex sea lion philopatry
DOI: 10.5061/dryad.5mh53/1
title: plos1chef

description: Survey data from chefs
DOI: 10.5061/dryad.5mh53/2
title: plos1public

description: Survey data from public
DOI: 10.5061/dryad.5mh53/3
title: plos1

description: Stata do file (text file) to replicate results in Tables 3, 4, 5, 6.
DOI: 10.5061/dryad.68r7s/1
title: JEBvirulencedata
DOI: 10.5061/dryad.6mp5q/1
title: Pond Metacommunity Plankton Dispersal Data

description: These data describe the plankton metacommunity in ponds at Lux Arbor Reserve (Barry County, Michigan, USA) from May-September 2011 and associated dispersal and experimental mesocosm data. Data are separated into phytoplankton/protozoa and metazoan zooplankton. Five types of plankton sample data are included: (P) local pond surveys, (A) dispersal trap abundances, (B) unassembled mesocosms with filtered water from the adjacent focal pond, (C) assembled mesocosms with unfiltered water from the adjacent focal pond, and (D) unassembled mesocosms with well water. Data for B, C, and D are only available for metazoan zooplankton.
DOI: 10.5061/dryad.7ck13/1
title: GopoMhcIex3S-nexus

description: Gopher tortoise MHC class I exon 3 sequences in nexus format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.
DOI: 10.5061/dryad.7h398/1
title: Appendix 1. Specimens examined from the Meade Basin.

description: List of fossils squirrel specimens from the Meade Basin examined for this study. Material is organized alphabetically by genus and species, then within species by age (oldest to youngest), alphabetically by locality, and element preserved.
DOI: 10.5061/dryad.89459/1
title: FE-2016-01148-R1-Data of leaf anatomical traits

description: leaf anatomical traits
DOI: 10.5061/dryad.b87h6/1
title: TrapNest_Data_Dainese_etal_2017_JAPPL

description: The file contains all data used in the analyses of this paper.
DOI: 10.5061/dryad.cn74h/4
title: read_subsets_3

description: Files with the subsets of reads used in the study

Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).

cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
DOI: 10.5061/dryad.cn74h/5
title: read_subsets_4

description: Files with the subsets of reads used in the study

Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).

cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
DOI: 10.5061/dryad.cn74h/6
title: read_subsets_5

description: Files with the subsets of reads used in the study

Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).

cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
DOI: 10.5061/dryad.cn74h/7
title: read_subsets_6

description: Files with the subsets of reads used in the study

Each subset is composed of three files. R1 indicates the first read, R2 indicates second read, SE indicates a single read (not paired, due to quality filtering).

cp indicates chloroplast reads
mt indicates mitochondrial reads
nr indicates nuclear ribosomal reads
DOI: 10.5061/dryad.f9320/1
title: barcoding_sequences

description: DNA-barcoding sequences obtained from the surface of the seeds sampled.
A column specifies the length of the resulting sequences.
DOI: 10.5061/dryad.f9320/2
title: coordinates_UTM30S_genotyped_trees

description: UTM30S coordinates of the genotyped wild olive trees in forest and matrix.
DOI: 10.5061/dryad.f9320/3
title: fully_identified_dispersal_events

description: Dataset of the fully characterised seed dispersal events, belonging to seeds for which we identified both the frugivore species responsible of dispersal and the source tree.
This dataset also includes the dispersal distance (m) and the canopy cover (%) within a 25-m buffer along each dispersal event.
DOI: 10.5061/dryad.f9320/4
title: genotypes_seeds_trees

description: Dataset with the microsatellite genotypes in 11 loci analyzed in dispersed seeds (endocarps), wild olive trees (leaves), and crop olive trees (leaves).
DOI: 10.5061/dryad.f9320/5
title: seed_rain_density

description: Data on seed density measured during the fruiting seasons 2013–2014 and 2014–2015 in seed traps, in the base of electricity pylons and along transects.
This dataset contains information of the distance from the forest edge of each sampling site (0: forest; 1: 0–50 m; 2: 50–100 m; 3: 100–150 m; 4: 150–200 m; 5: &gt; 200 m).
This dataset does not include those seed traps placed beneath fruiting wild olive trees within the forest (n = 5) in order to account for actual dispersal events, that is, involving horizontal movement away from the canopies of source trees.
DOI: 10.5061/dryad.f9320/6
title: seeds_sampled

description: Data on the seeds sampled for barcoding and microsatellite analyses.
Codes for columns of disperser and source-tree identification are: 1: yes; 0: no; NA: not applicable.
This dataset contains information of the distance from the forest edge of each sampling site (0: forest; 1: 0–50 m; 2: 50–100 m; 3: 100–150 m; 4: 150–200 m; 5: &gt; 200 m).
DOI: 10.5061/dryad.f9320/7
title: README_Gonzalez-Varo_etal_2017_MolecularEcology

description: Information on the content of each data file.
DOI: 10.5061/dryad.g6g2r/1
title: Dryad_Submission

description: These files include alignments for each gene, xml files used in BEAST and *BEAST analyses, resulting consensus tree files, and the data file used in the Structure analysis.
DOI: 10.5061/dryad.h6s54/1
title: ITS2 and psbA sequences

description: This folder contains the fasta files used to create the figures in our manuscript titled: Host specificity of Symbiodinium variants revealed by an ITS2 metahaplotype approach.
Full description of the processing of reads is provided in detail in the Supplementary Information of the manuscript.
Each file contains the sequences for a single individual and a single marker (see sample.key).
Individuals were subsampled to 4500 and 2000 sequences for the ITS2 and psbAncr markers respectively.

If you have any questions or queries, please feel free to contact Ed Smith, edsmith@nyu.edu
DOI: 10.5061/dryad.k4p46/1
title: Data UK porpoises DRYAD

description: Data UK porpoises including:  stranding locations and dates, sex, age and body length of the animals (when known), and microsatellite genotyping. Note that EV104 was not considered because of null allele issues.
DOI: 10.5061/dryad.p397k/1
title: Code S1. Analysis code for program R

description: Code S1. Analysis code for program R that we used to: 1) generate models of fisher (Pekania pennanti) detection and patch use in Pennsylvania, USA from July 2007 to October 2008 within an occupancy modelling framework; and 2) compare these models using Akaike’s information criterion.
DOI: 10.5061/dryad.p397k/2
title: Data S2. Capture history and coordinates of survey cells

description: Data S2. Capture history and coordinates of survey cells used to examine fisher (Pekania pennanti) detection and patch use in Pennsylvania, USA from July 2007 to October 2008 within an occupancy modelling framework.
DOI: 10.5061/dryad.p46n0/2
title: Aidley_Bayliss_Archive_Map

description: Map of archive. This archive contains the scripts and data files contained within an mBio paper with first author Jack Aidley and last author Chris Bayliss. The scripts are for modelling the effect of non-selective bottlenecks on phase variable genes of Campylobacter jejuni. The data files contains the outputs of the scripts and related experimental data.
DOI: 10.5061/dryad.p46n0/4
title: ExperimentalData

description: This folder contains the experimental data on bottlenecks and phase variation.
DOI: 10.5061/dryad.pd7vt/1
title: Endlein_etal_2016_data

description: Data for figures 2-4.
DOI: 10.5061/dryad.q51ph/1
title: primate phylogenies

description: Phylogenies originally from Springer et al. 2012. Pruned to 340 species based on recent taxonomic revisions. Branches scaled to Ma.
DOI: 10.5061/dryad.q51ph/2
title: BAMM files

description: Control files and sampling ratios for running BAMM analyses on the provided primate phylogenies.
DOI: 10.5061/dryad.q51ph/3
title: Phylogenetic Imbalance Function

description: R script for determining patterns of phylogenetic imbalance through time across a phylogeny.
DOI: 10.5061/dryad.r1m19/1
title: bmjopen-2017-015936

description: the predictors for receiving ultrasonography surveillance three times or more during the 2 years preceding a liver cancer diagnosis
DOI: 10.5061/dryad.s0t00/1
title: Data from the acclimated experiment
DOI: 10.5061/dryad.s0t00/2
title: Data from the non-acclimated experiment
DOI: 10.5061/dryad.tk751/1
title: Vegetation Type Raster

description: Raster of vegetation/landcover type for study area.  Spatial reference coordinate system: NAD_1983_UTM_Zone_10N.  Datum: NAD1983.
DOI: 10.5061/dryad.tk751/2
title: Alleles Table

description: Table of alleles (length in bp) at each microsatellite locus (15 loci).
DOI: 10.5061/dryad.tk751/3
title: Genotype Table

description: Table of genotypes (lengths in bp) for microsatellite loci (15 loci).
DOI: 10.5061/dryad.02j5s/1
title: B.bicudatus genepop file
DOI: 10.5061/dryad.02j5s/2
title: B. tricaudatus genepop file
DOI: 10.5061/dryad.02j5s/3
title: CO_Final_Circuit_Data_S1

description: Landscape resistance data
DOI: 10.5061/dryad.0s9j3/2
title: mvdl

description: This is the file that contains the locations and dates of all the M. verticillata specimen records used to construct the seasonal and conventional SDMs.  This is the source of the red lines and dots in Figure 3.
DOI: 10.5061/dryad.0s9j3/3
title: aet

description: This is the raster file for actual evapotranspiration used to construct the conventional SDM in Figure 2.
DOI: 10.5061/dryad.0s9j3/4
title: soil_thick

description: This is the raster file of soil thickness used to construct the conventional SDM in figure 2.
DOI: 10.5061/dryad.0s9j3/5
title: tmean

description: This is the raster file of mean (mean monthly temperature) used in the conventional SDM in figure 2.
DOI: 10.5061/dryad.0s9j3/6
title: tdiff

description: This is the raster file of tdiff (difference between monthly low and high temperature) used to construct the conventional SDM in figure 2.
DOI: 10.5061/dryad.0s9j3/7
title: ppt

description: the raster of annual precipitation.  This file is discussed but was excluded from the conventional SDM.
DOI: 10.5061/dryad.0s9j3/8
title: cwd

description: the raster of climatic water deficit.  This file was not included in the conventional SDM but is discussed in the text.
DOI: 10.5061/dryad.327t0/1
title: Wason_etal_2017_JApplEcol_data

description: Datasets on Whiteface Mountain microclimate, tree growth (from permanent plots and tree cores), and plot level basal area and density for dominant tree species.
DOI: 10.5061/dryad.406fd/1
title: broodsizemanipulation
DOI: 10.5061/dryad.406fd/2
title: nb_sums
DOI: 10.5061/dryad.406fd/3
title: parent sums
DOI: 10.5061/dryad.411hr/1
title: Temperature and Oxygen Consumption Data

description: A .csv file with the data for experiments 1 and 2.
DOI: 10.5061/dryad.51883/1
title: Data
DOI: 10.5061/dryad.54df2/1
title: Alignments

description: Alignments of chloroplast sequences used in manuscript 'Monophyletic origin and evolution of the largest crucifer genomes'.
DOI: 10.5061/dryad.6r6t2/1
title: learning.data

description: Describes experiments testing larval learning behavior in fruit flies.
DOI: 10.5061/dryad.6r6t2/2
title: pupation.data

description: Describes experiments testing pupation plasticity in fruit flies.
DOI: 10.5061/dryad.74f2r/1
title: Maximum clade credibility tree of FBDl

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 21 fossils, resulting from the beast2 analysis using the FBDl.xml input-file.
DOI: 10.5061/dryad.74f2r/2
title: Subsample of trees from FBDl analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 21 fossils (see FBDl.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r/3
title: Input file for FBDl analysis

description: This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 21 fossils (FBDl). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r/4
title: Maximum clade credibility tree of FBDs

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 14 fossils, resulting from the beast2 analysis using the FBDs.xml input-file
DOI: 10.5061/dryad.74f2r/5
title: Subsample of trees from FBDs analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 14 fossils (see FBDs.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.7c4g3/1
title: Improving HybrID: Champion Genomes and Fitness Values

description: An archive containing champion genomes and fitness values for algorithms tested in the paper Improving HybrID: How to best combine indirect and direct encoding in evolutionary algorithms, as well as the configuration files used to produce the populations.
DOI: 10.5061/dryad.7ck13/2
title: GopoMhcIIBex2S-nexus

description: Gopher tortoise MHC class II B exon 2 sequences in nexus format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.
DOI: 10.5061/dryad.7ck13/3
title: GopoMhcIex3S-arlequin

description: Gopher tortoise MHC class I exon 3 alleles in Arlequin format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.
DOI: 10.5061/dryad.7ck13/4
title: GopoMhcIIBex2S-arlequin

description: Gopher tortoise MHC class II B exon 2 alleles in Arlequin format, detailing which individuals are in which populations for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.
DOI: 10.5061/dryad.7ck13/5
title: microsats_GopoMhcIex3S-pops

description: Gopher tortoise alleles for 10 microsatellite loci in Arlequin format, detailing which individuals are in which populations those populations being the same as for the MHC class I exon 3 alleles for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.
DOI: 10.5061/dryad.7ck13/6
title: microsats_GopoMhcIIBex2S-pops

description: Gopher tortoise alleles for 10 microsatellite loci in Arlequin format, detailing which individuals are in which populations those populations being the same as for the MHC class II B exon 2 alleles for the publication: Elbers, J.P., R.W. Clostio, and S.S. Taylor (2017) Neutral genetic processes influence MHC evolution in threatened gopher tortoises (Gopherus polyphemus). Journal of Heredity.