cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.25131/2
title: ntaxa_constant_07-01-12

description: R script for the 'size-constant' simulations described in the paper.
DOI: 10.5061/dryad.2sc4n/10
title: Jockuschetal_SupplementalFigures_S1-S7

description: pdf file of gene trees for 6 genes (Supplemental Figures S1-S6) and species trees (Supplemental Figure S7) for analyses examining leverage of mitochondrial DNA
DOI: 10.5061/dryad.2sc4n/12
title: Jockuschetal_Supplemental TableS1

description: sample inclusion for replicated subsamples
DOI: 10.5061/dryad.2sc4n/24
title: Jockuschetal_89Individual_6Gene_StrictClock_StarBEAST

description: xml file for 89-individuals, 6 genes that produced tree Figure 2a.
DOI: 10.5061/dryad.2sc4n/25
title: Jockuschetal_SpeciesTrees_Fig2

description: Tree file, in nexus format, of trees shown in Figure 2.  (File contains multiple tree and taxa blocks.)
DOI: 10.5061/dryad.2sc4n/26
title: MPEST_BootstrapScripts

description: This zipped file unpacks into a folder with R and shell scripts for running MP-EST bootstrap analyses
DOI: 10.5061/dryad.2sc4n/27
title: Jockuschetal_GeneAlignments_nexusFiles

description: This zip file contains 6 nexus files, one for each gene
DOI: 10.5061/dryad.2sc4n/28
title: Jockuschetal_SuppFigS1-S6Trees_nexusFormat

description: This zip files includes nexus-formatted gene trees shown in Supplemental Figures S1-S6.
DOI: 10.5061/dryad.2sc4n/29
title: Jockuschetal_BatrachosepsSpeciesTrees_Primers_SuppTable2

description: Primers used for amplification and sequencing of nuclear genes
DOI: 10.5061/dryad.600nd/1
title: Dendrogram showing genomic fingerprints of V. cholerae O1 strains isolated in Nepal in 2012.

description: The fingerprint pattern in the gel was analyzed using a computer software package, Bionumeric (Applied Maths, Belgium). After background subtraction and gel normalization, the fingerprint patterns were typed according to banding similarity and dissimilarity as recommended by the manufacturer. , using the Dice similarity coefficient and unweighted-pair group method employing average linkage (UPGMA) clustering, by using pulsed-field gel electrophoresis (PFGE) images of NotI- restriction digested genomic DNA  of the tested Nepalese V. cholerae strains; PFGE images of contemporary V. cholerae O1 El Tor strains from Haiti and Bangladesh, including El Tor reference strain N16961 were also included. The scale bar at the top (left) indicates similarity coefficient. The banding patterns and the similarity coefficient revealed 100% similarity for all the tested Nepalese, Haitian, and Bangladeshi V. cholerae strains included in the dendrogram, suggesting high level of clonal relatedness.
DOI: 10.5061/dryad.650gr/1
title: Bateman gradient data on 4 species
DOI: 10.5061/dryad.6d8g5/4
title: SPAGeDi_Reef20genospace

description: Input file for the program, Spatial Pattern Analysis of Genetic Diversity (SPAGeDi; Hardy and Vekemans 2002) giving spatial and multi-locus genetic data for Pocilopora damicornis samples taken from Reef 20, one of the "neighboring reefs" in our study. From left to right, columns represent Sample ID Number, x coordinate, y coordinate, and genotypes at each of 6 microsatellite loci.
DOI: 10.5061/dryad.6f267/1
title: High-resolution image stack of the Platynereis larval primary optic neuropil

description: High-resolution (1.13 nm/pixel) image stack (tiff series) of the Platynereis larval primary optic neuropil. Contains 4 layers of 22,304 x 5680 pixels.
DOI: 10.5061/dryad.6f267/10
title: Phototaxis ImageJ Macro

description: ImageJ macro used to score phototaxis videos.
DOI: 10.5061/dryad.6f267/2
title: acetylated tubulin staining registered to the unbiased nuclear reference

description: Tiff stack of average acetylated tubulin staining registered to the unbiased nuclear reference of 3-day-old Platynereis larvae. The antibody labels cilia and the axonal scaffold (white).
DOI: 10.5061/dryad.6f267/3
title: Average full-body gene expression patterns of r-opsin1, hdc and VAChT

description: RGB tiff stack of average registered full-body gene expression patterns of eye marker gene r-opsin1 (red) and neurotransmitter marker genes hdc (green) and VAChT (blue), created by RNA whole mount in situ hybridization in 3-day-old Platynereis larvae. Note that signal present in spinning glands, parapodia and chaetae of larvae is background.
DOI: 10.5061/dryad.6f267/4
title: Average full-body gene expression patterns of VGluT, TrpH and ChAT

description: RGB tiff stack of average registered full-body gene expression patterns of neurotransmitter marker genes VGluT (red), TrpH (green) and ChAT (blue), created by RNA whole mount in situ hybridization in 3-day-old Platynereis larvae. Note that signal present in spinning glands, parapodia and chaetae of larvae is background.
DOI: 10.5061/dryad.6f267/5
title: Average full-body gene expression patterns of gad, TyrH and dbh

description: RGB tiff stack of average registered full-body gene expression patterns of neurotransmitter marker genes gad (red), TyrH (green) and dbh (blue), created by RNA whole mount in situ hybridization in 3-day-old Platynereis larvae. Note that signal present in spinning glands and chaetae of larvae is background, however, signal in the parapodia in the TyrH (green) channel represents real gene expression.
DOI: 10.5061/dryad.6f267/6
title: Double in situ hybridization for r-opsin1 and hdc

description: RGB tiff stack of raw data from high-resolution apical scan of double RNA whole mount in situ hybridization with r-opsin1 (red) and hdc (green) in 3-day-old Platynereis larvae. Larva is counterstained with acetylated tubulin antibody (blue) to show cilia and axonal scaffold.
DOI: 10.5061/dryad.6f267/8
title: Node ranking in the Platynereis eye circuitry

description: Node ranking in the Platynereis eye circuitry based on various centrality measures.
DOI: 10.5061/dryad.6f267/9
title: 3-day-old nuclear-stain whole-body reference template

description: Nuclear-stain whole-body reference template for 3-day-old (72 hours post fertilization) Platynereis larvae (tiff image stack). The whole-body nuclear-stain reference template was generated by the iterative registration of 40 individual scans.
DOI: 10.5061/dryad.7j1q0/1
title: Lenz_ParasiteData

description: Individual parasite data for community comparison among habitats and host species.
DOI: 10.5061/dryad.878p7/1
title: X. birchmanni (SP and CU pops) Multiple Mating

description: This file includes (1) basic info describing the gravid females included in our analysis, such as female size and brood size,  (2) the results of our microsatellite parentage analysis and SNP analysis and (3) calculated variables such as the Index of Monopolization and the number of fathers subsampled in ten offspring.   Further inquiries about the data can be addressed to Kim Paczolt by email at kpaczolt-at-umd-dot-edu.
DOI: 10.5061/dryad.8v0v6/1
title: Supplemental Datasets C3 vs C4 Cleomaceae transcriptome atlases

description: Transcriptome atlases from two Cleomaceae species and down-stream analyses. Reads generated on the HISEQ2000 Illumina platform, and mapped with BLAT V35.
DOI: 10.5061/dryad.90hc5/1
title: Primer details for grass/rice comparative mapping

description: The file gives details of all the primers used to physically map SNPs on the Lolium/Festuca introgression maps. These primers were generated from rice coding sequences. The file therefore also gives the accession number and locus identifier of the rice coding sequence used to generate the primers.
DOI: 10.5061/dryad.bt848/1
title: Phenotype_CraniofacialShape

description: The file contains the skull and mandible shape and size data. Centroid size (CS) and principal components (PC) were standardized to have mean=0 and standard deviation =1. Data was obtained after analyzing raw landmark coordinates in MorphoJ.
DOI: 10.5061/dryad.bt848/2
title: KinshipMatrix

description: Centered kinship matrix generated in GEMMA using all LD-pruned SNPs
DOI: 10.5061/dryad.bt848/3
title: SNPdata.bed

description: Bed file generated in PLINK using the LD-pruned SNPs.
DOI: 10.5061/dryad.bt848/4
title: SNPdata.bim

description: Bim file generated in PLINK using all LD-pruned SNPs
DOI: 10.5061/dryad.bt848/5
title: SNPdata.fam

description: Fam file generated in PLINK using all the LD-pruned SNPs
DOI: 10.5061/dryad.bt848/6
title: OriginalSNPdata.map

description: .map file with the original set of SNPs previous to LD-pruning
DOI: 10.5061/dryad.bt848/7
title: OriginalSNPdata.ped

description: .ped file with the original set of SNPs previous to LD-pruning
DOI: 10.5061/dryad.f5q4s/1
title: Raw data

description: Raw data for the study in RData format.
DOI: 10.5061/dryad.ff749/61
title: Result of SH test on matrix “&gt;3.4_excluded” with unlinked branch lengths.
DOI: 10.5061/dryad.ff749/62
title: Result of SH test on matrix “&gt;3.3_excluded” with linked branch lengths.

description: Tab delimited text file.
DOI: 10.5061/dryad.ff749/63
title: Result of SH test on matrix “&gt;3.3_excluded” with unlinked branch lengths.
DOI: 10.5061/dryad.ff749/64
title: Result of SH test on matrix “&gt;3.0_excluded” with linked branch lengths.

description: tab delimited text file.
DOI: 10.5061/dryad.ff749/65
title: Result of SH test on matrix “&gt;3.0_excluded” with unlinked branch lengths.
DOI: 10.5061/dryad.ff749/66
title: AIR analysis output, based on 7 trees

description: AIR analysis output, average rates for each site in matrix “Allsites_noAno” for 7 trees with p&gt;0.05 from SH test of “Allsites_noAno” with linked branch lengths. Tab delimited text file.
DOI: 10.5061/dryad.ff749/67
title: AIR analysis output, based on 12 trees

description: AIR analysis output, average rates for each site in matrix “Allsites_noAno” for 12 trees with p&gt;0.05 from SH test of “Allsites_noAno” with unlinked branch lengths. Tab delimited text file.
DOI: 10.5061/dryad.ff749/68
title: Sites removed by GBLOCKS and AIR sorted by genomic feature

description: Genomic features associated with sites excluded from the alignment of 12 full plastomes by GBLOCKS to produce matrix Allsites_noAno and by AIR to produce matrix &gt;3.0_excluded, data for Figure 4. Tab delimited text file.
DOI: 10.5061/dryad.ff749/69
title: Morphological character matrix: pollen aggregation.
DOI: 10.5061/dryad.j015n/11
title: fish-partitioned-phylip-file-for-raxml-partitions.txt.gz

description: Partitions for use with RAXML.
DOI: 10.5061/dryad.m184s/1
title: Juniper woodland long-term spatial dynamics

description: For each study subplot we report: i) ID; ii) associated PLOT; iii) time lag; iv) distance from the nearest woodland patch; v) spatial coordinates (X,Y); vi) initial density; and vii) density variation.
DOI: 10.5061/dryad.m4v48/1
title: Principal Components values

description: The universal facial attractiveness (UFA) hypothesis proposes that some facial features are universally preferred because they are reliable signals of mate quality. The primary evidence for this hypothesis comes from cross-cultural studies of perceived attractiveness. However, these studies do not directly address patterns of morphological variation at the population level. An unanswered question is therefore: Are universally preferred facial phenotypes geographically invariant, as the UFA hypothesis implies? The purpose of our study is to evaluate this often overlooked aspect of the UFA hypothesis by examining patterns of geographic variation in chin shape. We collected symphyseal outlines from 180 recent human mandibles (90 male, 90 female) representing nine geographic regions. Elliptical Fourier functions analysis was used to quantify chin shape, and principle components analysis was used to compute shape descriptors. In contrast to the expectations of the UFA hypothesis, we found significant geographic differences in male and female chin shape. These findings are consistent with region-specific sexual selection and/or random genetic drift, but not universal sexual selection. We recommend that future studies of facial attractiveness take into consideration patterns of morphological variation within and between diverse human populations.
DOI: 10.5061/dryad.s1p14/1
title: Enpoints results from in vivo 1 and 2

description: The file contains all the measured endpoints of the two in vivo experiments (Worksheet 1 and 2) described in the manuscript, including: plasma ions concentrations and gene expression levels of NKA and CA2 in samples of gills and intestine. The spreadsheet also reports fish sex, copper exposure concetrations and salinity. The datasets are presented in a format that can be easily used for PCA analysis.
DOI: 10.5061/dryad.s631d/1
title: Supplementary Tables

description: Supplementary Table 1. Primers used for PCR amplification and sequencing.Supplementary Table 2. General properties of the DNA matrix. Invar = number of invariant sites. Var = number of variable sites. PI = number of parsimony informative sites. A, T, C, G = proportion of respective base.
DOI: 10.5061/dryad.sj3vp/4
title: Phenotypes_Genotypes

description: This file contains the individuals we have collected from the South Sierra mountains as well as the Genotypes and Phenotypes. The Genotypes are in the format needed for Structure Software
DOI: 10.5061/dryad.tf81g.1
title: Data from: Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity and turn-over rates are disconnected
DOI: 10.5061/dryad.tf81g.2
title: Data from: Fossils and a large molecular phylogeny show that the evolution of species richness, generic diversity and turnover rates are disconnected
DOI: 10.5061/dryad.tf81g.2/2.1
title: Fagales_MCC_lognormal

description: Fagales MCC tree using lognormal priors
DOI: 10.5061/dryad.tf81g.2/3
title: Fagales_fossil

description: Fagales fossils used in the analysis
DOI: 10.7925/drs1.ucdlib_31757
title: 49 Grafton Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_31763
title: 51-51A Grafton Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_31769
title: 55 Grafton Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 2 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_31775
title: 57 Grafton Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 3 levels above ground.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_31778
title: 58 Grafton Street, Dublin 2, Ireland

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork structure, 4 levels above ground, constructed 1870.
description: Dublin City Council, Record of Protected Structures (2010), no. 3250
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_31790
title: 65-68 Grafton Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork & stone structure, 5 levels above ground, constructed 1948.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.7925/drs1.ucdlib_31796
title: 65-68 Grafton Street, Dublin

description: Consists of an orthorectified image of the structure in Adobe PhotoShop (PSD) format. The orthorectified image has been derived from one or more photographic images that are included as layers in the original Adobe PhotoShop (PSD) file. The composite and all other image layers have been extracted and saved in TIFF image files, and JPEG files in various resolutions have been derived from the flattened image layer to facilitate inspection.
description: Brickwork & cladding structure, 4 levels above ground, constructed 1948.
description: Funded by an award from the Irish Research Council for Science, Engineering and Technology (IRCSET), Embark Initiative Postgraduate Scholarship, grant identifier RS/2011/435.
DOI: 10.5061/dryad.15570/3
title: Munoz_etal_2013_msat_dataset

description: Microsatellite data used for demographic analyses. Loci and scores are given for each individual from each population.
DOI: 10.5061/dryad.3r8n2/1
title: Grooming and ectoparasite load in wild baboons.

description: This data set underlies results presented in Akinyi et al. 2013, Animal Behaviour, (Role of grooming in reducing tick load in wild baboons (Papio cynocephalus)). The study was conducted on adult members of a wild baboon population in Amboseli, southern Kenya. The data set includes demographic data on individual age, sex and group membership, as well as behavioural data on grooming and dominance rank. The dataset also includes tick counts and packed cell volume (PCV) analysis from baboons darted during darting and immobilization projects in 2007–2008. Subject numbers represent each individual data was collected for. Sex describes whether the individual was female (F) or male (M). Year darted indicates the year in which each individual was darted. Age describes each individual’s age (to the nearest year) at darting. Social group at darting categorises the group each individual belonged to at the time of darting and group size indicates the total number of individuals in the group during the six months that grooming data was retrieved. Grooming counts 6 months prior to darting contains the counts of grooming received by each study animal in the 6 months prior to their darting date. Mean PCV at darting is calculated from the average of two to three replicate PCV measurements were obtained per animal during darting. Adult and larvae tick counts are the number of ticks collected and counted from each individual. These data were extracted from the long-term relational database for the Amboseli Baboon Research Project, BABASE.
DOI: 10.5061/dryad.3r8n2/2
title: Summary of parasites in a wild baboon population

description: This data set is a summary of the parasites collected for the study reported in Akinyi et al. 2013, Animal Behaviour, (Role of grooming in reducing tick load in wild baboons (Papio cynocephalus)). The table indicates the types of parasites encountered and their relative abundance in the darted individuals. The ectoparasites data are presented by the species of ticks collected and the number collected in each animal. The blood parasite data indicate the haemoparasites screened for by PCR and whether the individuals screened were positive or negative.
DOI: 10.5061/dryad.6475n/1
title: Female misltetoe volume and total mistletoe volume per tree

description: A dbase 3 file with total mistletoe volume and total volume of female mistletoe per tree
DOI: 10.5061/dryad.6f267/11
title: Phototaxis videos of control and mecamylamine-treated larvae

description: Videos of phototaxis experiments. 3-day-old control larvae and larvae treated with 50 μm mecamylamine were imaged with 15 frames per second in a split phototaxis assay cuvette. The length of the cuvette is 15 mm. Directional white stimulus light was provided from the left. Each video is 600 frames. The videos are in Zeiss zvi format. The files were compressed with tar -jcvf archive_name.tar.bz2 directory_with_files/*, use tar –jxvf to uncompress them.
DOI: 10.5061/dryad.6f267/7
title: Blender file containing the complete virtual anatomical atlas of the Platynereis eye circuitry

description: Simplified 3D models of all neurons, synapses, muscles and ciliated cells are included. The file can be viewed with the Blender software http://www.blender.org/.
DOI: 10.5061/dryad.7gm28/1
title: Mass loss data set
DOI: 10.5061/dryad.7m621/1
title: Map, genotypic data, and phenotypic data for M. lewisii x M. cardinalis F2 population

description: This is a QTL cartographer .mcd input file containing the LC linkage map, as well as the raw genotypic data (used for generating the LC map in Joinmap) and the phenotypic trait data used for QTL mapping. It should be readable as text. Genotypic data code: A = M. cardinalis homozygote, H = heterozygote, B = M. lewisii homozygote.
DOI: 10.5061/dryad.7p42b/1
title: Hatch Rates
DOI: 10.5061/dryad.7p42b/2
title: Spermatophore size
DOI: 10.5061/dryad.863c0/1
title: didymocarpoideae_data

description: Trait data of 56 species of the Didymocarpoideae subfamily
DOI: 10.5061/dryad.863c0/2
title: didymocarpoideae_tree

description: Phylogenetic tree for 56 Didymocarpoideae species
DOI: 10.5061/dryad.863c0/3
title: primulina_data

description: Trait data of 100 species of the Primulina genus
DOI: 10.5061/dryad.863c0/4
title: primulina_tree

description: Phylogenetic tree for 100 Primulina species
DOI: 10.5061/dryad.863c0/5
title: R script

description: R script for measuring pylogenetic signal in the Primulina genus
DOI: 10.5061/dryad.863c0/6
title: R script

description: R script for measuring pylogenetic signal in the Didymocarpoideae subfamily
DOI: 10.5061/dryad.863c0/7
title: R script

description: R script for PGLS regressions for the Didymocarpoideae subfamily