cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2ds7p/3
title: CC_volume_data

description: Stereological analyses were performed using StereoInvestigator to determine the volume loss of the corpus callosum at adulthood after injury at either p21 or p35.
DOI: 10.5061/dryad.2ds7p/4
title: Res-Intr_test_data

description: Social investigation of a novel (male or female) stimulus mouse was quantified as duration spent investigating different regions (e.g. anogenital), during the resident-intruder task.
DOI: 10.5061/dryad.2ds7p/5
title: Scent_mark_test_data

description: Grid squares containing scent marks were quantified during the scent marking test towards a novel female mouse, of sham or TBI (traumatic brain injury) mice at adulthood after injury at p21 or p35.
DOI: 10.5061/dryad.2ds7p/6
title: USV_data

description: Ultrasonic vocalizations (USVs) were recorded during encounters of the test mouse (sham or brain-injured) with (1) a novel male, (2) a novel female, or (3) soiled bedding from a novel female. Several parameters including total number of calls, high frequency calls (&gt; 75 kHz) and # calls in bursts were quantified.
DOI: 10.5061/dryad.2n545/10
title: M1748
DOI: 10.5061/dryad.2n545/12
title: M3475
DOI: 10.5061/dryad.2n545/13
title: cats-dogs
DOI: 10.5061/dryad.2pj70/2
title: Bourret_env_and_pca_factors

description: Environmental data used in the principal component analysis and 10 pca factors values obtained and used in the redundancy analysis.
DOI: 10.5061/dryad.367d0/1
title: R Functions

description: R functions for summarising and analysing spectral data.
DOI: 10.5061/dryad.367d0/2
title: Spectrum files

description: Spectra folder contains all spectral datum files collected from spiders.
DOI: 10.5061/dryad.3db81/2
title: Seed_Set
DOI: 10.5061/dryad.3h7s9/1
title: Strain Data

description: Columns F-T indicate the presence or absence of each functional gene. Columns U-AB provide the coordinates of each strain on the axes of the correspondence analysis performed in the computer program TANAGRA on the strains functional genotypes.
DOI: 10.5061/dryad.3rp1p/2
title: Rego_species_summary2

description: Sizes of the largest specimens for each species in each stage, compiled from the specimen-level data.  Also included are the observed stratigraphic ranges for each species.
DOI: 10.5061/dryad.41mj8/1
title: input Structure Podarcis filfolensis

description: input file from structure software with 11 STRs analysed in Podarcis filfolensis
DOI: 10.5061/dryad.41mj8/2
title: P. filfolensis_sequences

description: Relation between GenBank accession numbers and specimens.
DOI: 10.5061/dryad.6347b/3
title: regionNICHE

description: #File 3 - temperature dataset on thermal niches of each region (Celsius degrees)# Data collected from May - June 2010.# Data first variance and mean calibrated to the thermal environment inside 4 cow-pats probed with thermometers for two weeks in Zurich during June 2010.# Data then mean calibrated to 20-30 year dataset, for the period May-September, from each of the regions (based on population averages). Datasets available online at:http://www.weatherbase.com
DOI: 10.5061/dryad.6544v/2
title: Yale Clinical Trial Data Sharing Survey Data Dictionary

description: Data dictionary.
DOI: 10.5061/dryad.67p55/1
title: dated.phylogeny

description: Dated version of the phylogeny from Porter et al. (2010). This is a simple newick file. (Porter, M. L., Y. Zhang, S. Desai, R. L. Caldwell, and T. W. Cronin. 2010. Evolution of anatomical and physiological specialization in the compound eyes of stomatopod crustaceans. Journal of Experimental Biology 213:3473-3486.)
DOI: 10.5061/dryad.7137r/15
title: bird1394_pair5_son2_all_songs
DOI: 10.5061/dryad.7137r/16
title: bird640_pair6_tutor_all_songs
DOI: 10.5061/dryad.7137r/17
title: bird1402_pair6_son1_all_songs
DOI: 10.5061/dryad.7nd70/1
title: Lunzer Curated Biochemistry

description: Model-fit Km and performance (P = kcat/Km) against NAD and NADP, together with preference (PNAD/PNADP) for each allele.
DOI: 10.5061/dryad.85qv1/2
title: Gevaert_SupMat_FigureS1

description: This figure shows the results of a STRUCTURE analysis (Pritchard et al. 2000) with K = 5 genetic clusters for 10 native populations and 2 transplant populations of Helianthus porteri. Bars for each individual indicate the average result across fifteen independent iterations. Each individual is represented along the x-axis, with populations presented in order of geographical location, CMR being farthest west and HR being farthest east, along the y-axis. PL and NC populations refer to the 2 transplant populations, where PL is adjacent to HR and NC is isolated from all populations in North Carolina.
DOI: 10.5061/dryad.8fc60/3
title: my functions

description: Customized functions used in the main R code analyses and simulations.
DOI: 10.5061/dryad.8h6nf/1
title: Hind limb morphometric data

description: Table in Excel format with morphometric data averaged per species for each hind limb bone analysed. Centroid size, log-transformed centroid size and Procrustes coordinates are shown for pelvis (1st and 2nd sheets), femur (3rd and 4th sheets) and tibia (5th and 6th sheets). 1st, 3rd and 5th sheets show values for all the species; 2nd, 4th and 6th sheets include only extant species.
DOI: 10.5061/dryad.9v852/6
title: Input data file to BEAST based on 5699 bp of mtDNA
DOI: 10.5061/dryad.b8h1n/2
title: NEXUS alignment Calligrapha HARS data
DOI: 10.5061/dryad.b8h1n/3
title: NEXUS alignment Calligrapha Wg data
DOI: 10.5061/dryad.b8h1n/4
title: NEXUS alignment Calligrapha mtDNA data
DOI: 10.5061/dryad.bh4kt/1
title: The maternal, newborn and child health (MNCH) household survey data

description: The data include household information, antenatal care, delivery and neonatal care, breastfeeding and nutrition, immunization, etc.
DOI: 10.5061/dryad.c0164/4
title: male reinf learn loop program

description: Program for the section of the paper titled "Male learning model: Learning increases bias towards conspecifics and against heterospecifics I: Male learning from female identity"
DOI: 10.5061/dryad.c2124/4
title: Mapping and variant calling data on SSC11:53500000-55500000
DOI: 10.5061/dryad.c75nn/5
title: Multivariate_results_MEC-12-0462

description: Multivariate analyses results
DOI: 10.5061/dryad.cs947/1
title: Alignment of Artemisia tridentata consensus sequences

description: Concatenated consensus sequence of 25 amplicons from 49 populations including diploid and tetraploid populations. Readme file describes the populations.
DOI: 10.5061/dryad.fj594/2
title: snp_table_deserticola

description: List of SNPs for H.deserticola. Column 1 refers to the reference sequence. Column 2 to the position were the SNP is located. Column 3 and after are the genotypes per individual
DOI: 10.5061/dryad.fj594/5
title: coverage_per_gene_individuals

description: Coverage (Number of reads aligned) per individuals and per gene.
DOI: 10.5061/dryad.g5jj6/2
title: paradoxus_fastq

description: fastq files split by barcode for S. paradoxus isolates
DOI: 10.5061/dryad.hh74n/1
title: CoMEstimationInstructions

description: Instructions for using the code and data here
DOI: 10.5061/dryad.j5c2j/1
title: Aligned and unaligned sequences use for phylogenetics analyses

description: The gene folder contains three type of files :1) The *.fst files are unaligned nucleotides sequences2) The *.mafft.fst are aligned amino-acid sequences3) The *_base.fst are aligned nucleotides sequencescorvusBrachyrhynchos, parusCaeruleus, manacusVitellinus, ficedulaHypoleuca sequences were obtained from brain transcriptome sequencing (see Nabholz B, Jarvis ED, Ellegren H. 2010. Obtaining mtDNA genomes from next-generation transcriptome sequencing: a case study on the basal Passerida (Aves: Passeriformes) phylogeny. Mol. Phylogenet. Evol. 57:466–470)
DOI: 10.5061/dryad.jv0gh/2
title: subjectData_2of2

description: Data from subjects 7-12
DOI: 10.5061/dryad.jv2hd/1
title: Msat_data

description: The file "Msat_data.txt" contains data for 21 microsatellite loci that map to mouse chromosomes 3 and 8. Locus names follow Dietrich et al (1996): DXmitY; Where X refers to the chromosome, and Y refers to the specific locus. Loci are arranged by column, locus names are in the first row. The study involved 179 samples (house mice), which are arranged by row. Samples are divided by geographic region of origin and then by specific population/race.
DOI: 10.5061/dryad.n57ph/1
title: Microsatellite data and D-loop sequences of 535 samples
DOI: 10.5061/dryad.p7639/2
title: RCODE-adegenet-spca

description: This file contains code used to run the sPCA analysis in R using the package adegenet. Annotations to the code are given in lines beginning with #.
DOI: 10.5061/dryad.pc7pg/1
title: Track data deposition

description: Latitude & Longitude position fixes recorded at 1Hz for each treatment group
DOI: 10.5061/dryad.q827h/1
title: Quantitative information for Flaveria leaf transcriptome reads mapped in a cross species approach onto the reference transcriptome from Arabidopsis thaliana.

description: The transcriptomes of mature leaves from nine Flaveria species with different type photosynthesis (C3, C4 and C3-C4 intermediate) were sequenced by Illumina sequencing leading to 30 to 58 million reads per species and experiment. Four independent experiments were performed and the reads were mapped in a cross species approach onto the minimal set of Arabidopsis thaliana coding sequences in the protein space using the BLAST-like alignment tool BLAT. In the table the normalized read counts in rpkm (reads per million and kilo base) for all Arabidopsis cds are give alongside the TAIR and MapMan annotations of the respective Arabidopsis genes.
DOI: 10.5061/dryad.s5b62/1
title: R analysis

description: This folder contains the R script file used in the analyses, including all referenced data as individual csv files.
DOI: 10.5061/dryad.s904k/1
title: Dang et al HRM Aligned rps16 sequences

description: Aligned rps16 sequences for 20 haplotypes of Arenaria ciliata and A. norvegica (C01-c18, and N01-N02 resepctively). Alignment presented in fasta format and saved as .txt.
DOI: 10.5061/dryad.td28r/1
title: Sampling Locations

description: This Excel sheet provides the coordinates (latitude and longitude) for all sampling locations, as well as the number of individuals that were successfully genotyped (microsatellitess) and sequenced (mtDNA cytb) at each site.
DOI: 10.5061/dryad.td28r/2
title: Haplotype Frequencies

description: This spreadsheet contains mtDNA haplotype frequencies across all ten sampling locations.
DOI: 10.5061/dryad.td28r/3
title: Microsatellite Genotypes

description: This spreadsheet contains all individual genotypes for the 14 microsatellite loci used in the study. Individuals are grouped by sampling location.
DOI: 10.5061/dryad.td28r/4
title: Aligned mtDNA sequences

description: This fasta file includes all aligned sequences for the mtDNA cytb haplotypes.
DOI: 10.5061/dryad.v561f/1
title: Fossil Record of Xyelydidae and  Summary of nygmata positions for extant Symphyta

description: Table 1 Fossil Record of Xyelydidae;  Table 2 Summary of nygmata positions for extant Symphyta
DOI: 10.5061/dryad.0g0fs/1
title: Lohse_2012_data.tar

description: The python scripts polarize.py and polarizeSumStat condense a file of multiple alignmnets (fasta format) into either a list of binary alignmnets (O=ancestral, 1=derived state) or a list summary statitsics (for details see Mathematica notebook Lohse_et_al 2012_Analysis). Both are simple text files which use Mathematica's list notation. The archive Lohse_2012_data.tar contains both the python scripts and the data files for each of the four parasitoid species. These are used as input for the likelihood analysis (see in Mathematica notebook Lohse_et_al 2012_Analysis).
DOI: 10.5061/dryad.1b68v/1
title: multi-locus genotyping at 17 markers of Batrachochytrium strain EV001

description: Multi-locus genotype data from strain EV001 of Batrachochytrium dendrobatidis isolated from Ubaque, Cundinamarca, Colombia. Genetic data were generated by direct Sanger sequencing using the 17 markers reported in: James TY, Litvintseva AP, Vilgalys R, Morgan JAT, Taylor JW, Fisher MC, et al. (2009). Rapid global expansion of the fungal disease chytridiomycosis into declining and healthy amphibian populations. PLoS Pathogens 5:e1000458. doi: 10.1371/journal.ppat.1000458
DOI: 10.5061/dryad.25131/9
title: plotting_anag_results_08-23-12

description: R file for plotting Figure 7 of the main text, which is the analysis comparing rates of sampling and differentiation.
DOI: 10.5061/dryad.277g0/7
title: EcJME_R2-part2

description: This is part 2 of the reverse raw reads from Illumina sequencing. Please download all three parts and recombine them using the following command in Terminal or Command Prompt: cat xaa2 xab2 xac2 &gt; EcJME_R2.fastqsanger
DOI: 10.5061/dryad.3066j/1
title: Adaptation in the weak mutation regime

description: Results of simulations in a weak mutation regine (U&lt;
DOI: 10.5061/dryad.3t9k2/4
title: treefile (100 trees from BEAST)

description: For bGMYC analysis
DOI: 10.5061/dryad.4194c/1
title: Ojala et al. (2013) - raw data

description: See README.txt for instructions in interpreting the data.
DOI: 10.5061/dryad.44pm4pq6/1
title: ALL

description: Includes all genotypes obtained from the focal Bellbekken river as well as the adjacent Julussa river, SE Norway. In the file are included a column with the individual ID (trout), the season (fall/autumn), the year (2002-2006), the river (Bellbekken/Julussa), the age and correspondligly the year an individual is born, the station (2-25) for the Bellbekken fish, as well as all 15 microsatellite loci the individuals were genotyped for. Julussa fish were not aged. The file also includes the recaptures from Bellbekken.
DOI: 10.5061/dryad.49m52/2
title: Badgley Finarelli.Suppl Text Figures

description: In this file, we describe a subsampling procedure and present two figures (Figs S1, S2) that depict the results of the subsampling method. Data analyzed are summarized in the supplementary tables in a separate file.
DOI: 10.5061/dryad.52j07/1
title: Microsatellite_data_SPAGEDI

description: Microsatellite data set (n=938) follows the SPAGEDI input file format. It contains codes for localities, latitude-longitude coordinates as well as projected coordinates using a Gnomonic projection.
DOI: 10.5061/dryad.6h3f7/1
title: Data Coding Info

description: Codes for other data files
DOI: 10.5061/dryad.73180/1
title: CHC profiles

description: CHC profiles of nymphs and adults used in the experiment
DOI: 10.5061/dryad.7m6kg/41
title: Fig. 7a: ROM 59668 — Nectocaris pteryx mouthparts from the Burgess Shale

description: ROM 59668, denticles associated with relief
DOI: 10.5061/dryad.7m6kg/45
title: Fig. 7c: ROM 60100 — Nectocaris pteryx mouthparts from the Burgess Shale

description: Low-angle light, emphasizing relief
DOI: 10.5061/dryad.7m6kg/49
title: Fig. 9b: ROM 59664 – Nectocaris pteryx from the Burgess Shale

description: Gill laminae distend from zig-zagging lateral axis
DOI: 10.5061/dryad.82h0m/2
title: squam_shl_names

description: Maximum-likelihood phylogeny containing 4162 species, with names changed to reflect the December, 2012 update of the Reptile Database (see Table S1).
DOI: 10.5061/dryad.8kc1v/1
title: Current Species Models

description: These are Maxent outputs of each species for present day climate conditions. These outputs are used to determine distribution presence/absence for phylogeographic endemism calculations in Biodiverse.
DOI: 10.5061/dryad.8kc1v/2
title: Stability Models

description: These are the processed stability estimates of the Atlantic Forest used in Figure 2, and Supplemental Figure S2. They are again grouped by forest region (entire forest, northern forest, southern forest) and into 0-21kybp and 0-120kybp analyses, and additionally by dispersal level (0m/year, 5m/year & 10m/year).
DOI: 10.5061/dryad.8kc1v/3
title: Climate Data

description: Climate and paleoclimatic data (Bioclim - see www.worldclim.org) for the Atlantic Forest. Folders are organized by climate age - e.g. 0 is present, 21 is 21 kybp, and 120 is 120kyp.
DOI: 10.5061/dryad.8kc1v/4
title: Raw Stability Models

description: These are Maxent outputs of the Atlantic Forest over many timeslices used to determine forest stability. The outputs are grouped by forest region (entire forest, northern forest, southern forest) and into 0-21kybp and 0-120kybp analyses.
DOI: 10.5061/dryad.8sb02/1
title: analytical files

description: Wolfram Mathematica Notebook files
DOI: 10.5061/dryad.cj48b/1
title: Burton et al Juvenile mass data
DOI: 10.5061/dryad.cj48b/2
title: Burton et al Juvenile SMR data
DOI: 10.5061/dryad.cj48b/3
title: Burton et al Juvenile social status data
DOI: 10.5061/dryad.f727j/1
title: Raw presence/absence scores of MSAP bands

description: This file contains the raw scores of 129 MSAP bands scored across 234 red grouse individuals. Use this file as input for the R package "msap" to do basic methylation analyses.
DOI: 10.5061/dryad.f727j/2
title: Transformed MSAP scores and morphological data

description: This file contains 303 epiloci that were generated by transforming 129 MSAP bands into binary loci. The file also provides morphological data in order to do regression analyses.
DOI: 10.5061/dryad.f727j/3
title: Nomenclature for MSAP bands and corresponding epiloci

description: Contains identifiers for each MSAP band and each corresponding epilocus alongside represented methylation state (unmethylated, hemimethylated, fully methylated)
DOI: 10.5061/dryad.f727j/6
title: Pairwise geographic distances

description: Contains a matrix with pairwise geographic distances among the 21 study populations.
DOI: 10.5061/dryad.f727j/7
title: Complete R analysis script

description: Contains R code for analysing the input files using "msap" and custom logistic regressions.
DOI: 10.5061/dryad.f727j/8
title: Readme

description: Details file contents
DOI: 10.5061/dryad.fj472/1
title: MonteithAndrewsSmisethJEB2012

description: Data file for relationship between egg size and offspring growth and survival from a laboratory experiment on Nicrophorus vespiloides. The data are based on a parental removal design in which the effect of egg size is compared in the absence or presence of post-hatching parental care.
DOI: 10.5061/dryad.g9s2k/1
title: Prunus_lusitanica_Table S4

description: Sampled individuals, populations and vouchers
DOI: 10.5061/dryad.g9s2k/2
title: Prunus_lusitanica_nSSR

description: Microsatellite data for P. lusitanica individuals. Data follows FDASH software format. Columns are separated by TABs. Alleles are separated by "," whereas "?" indicates missing data. Due to the polyploid constitution of these taxa, multiple alleles per individual and locus were scored, but fixed heterozygosity of a few allele variants can be observed at several loci.
DOI: 10.5061/dryad.gf3qp/4
title: AFLP Matrix

description: AFLP data matrix (excluding not repeatable, monomorphic and single fragments) with individuals in rows and markers in columns. Regions are given in the second column.
DOI: 10.5061/dryad.h0228/4
title: DarwinTunes-medley-at-400-generations

description: A medley of audio loops selected manually from a particular point in the evolution of experimental population 1 (EP1).
DOI: 10.5061/dryad.hh74n/2
title: CoM Estimation Code Instructions

description: Word '97 document version of code usage instructions
DOI: 10.5061/dryad.hh74n/3
title: Mass Segment objs

description: .obj graphics files (data)- 3D body segment dimensions of archosaurs
DOI: 10.5061/dryad.hh74n/4
title: CoM Calcuation Code

description: Matlab code for analyzing data
DOI: 10.5061/dryad.hh74n/5
title: Mesquite Data

description: Mesquite (Nexus) data files for phylogenetic analysis of evolutionary patterns in body dimensions. http://mesquiteproject.org/mesquite/mesquite.html for information on usage and free software download.
DOI: 10.5061/dryad.j5240/4
title: Rag1 fasta alignment

description: Alignments of Rag1 gene. Sequences are identified as haplotype (see article text for more details) and GenBank number.
DOI: 10.5061/dryad.j57c0/5
title: 4_ITS_haplotypes

description: ITS alignment collapsed to haplotypes
DOI: 10.5061/dryad.m1b66/1
title: AFLP data

description: Presence/absence matrix (1/0) of AFLP markers. The first column provides the sample ID (population ID + individual sample number) and the first row provides the marker ID (selective primer combination + fragment size).
DOI: 10.5061/dryad.m1b66/2
title: MSAP data

description: MSAP data at different levels of data processing: The spreadsheet “Raw_msap_calc” contains the input file for msap_calc.R, spreadsheet “MSAP Raw Data” contains the multistate data of combined HpaII and MspI profiles at the epilocus level, and spreadsheet “MSAP Subepiloci Data” contains the final binary data at the subepilocus level. For “Raw_msap_calc” the first three columns provide the population ID, the sample ID (population ID + individual sample number) and used methylation sensitive restriction enzymes (H=HpaII, M=MspI). The first row provides the marker ID (selective primer combination + fragment size). For “MSAP Raw Data” and “MSAP Subepiloci Data” the first column provides the sample ID and the first row provides the marker ID. In addition, for “MSAP Subepiloci” the three subepiloci types (n, m, h) are indicated in the second row.
DOI: 10.5061/dryad.m1b66/3
title: plant sampling & hemispherical photography

description: Grid based distribution maps (1 x 1m) and results of hemispherical photography based light measurements for the six surveyed populations of Viola elatior. Populated grid cells, grid cells for plant sampling and grid cells for hemispherical photographs are indicated by different colors, respectively.
DOI: 10.5061/dryad.mk471/6
title: Breast_ERHigh_GSEA_Results

description: Results from GSEA Analysis in ER+ high proliferation subtype of breast cancer
DOI: 10.5061/dryad.p7639/3
title: RCODE-spdep-spatial-regression

description: This file contains code used to run the spatial regression analysis in R using the package spdep. Annotations to the code are given in lines beginning with #.
DOI: 10.5061/dryad.p8791/1
title: Voles testes length data

description: Excel file containing 5 spreadsheets of vole testes length, body mass and capture date data.
DOI: 10.5061/dryad.p8791/2
title: Voles testes mass data

description: Subset of data containing testes length and testes mass, body mass and capture date.
DOI: 10.5061/dryad.p8791/3
title: Voles density data

description: Summer and autumn density data for 5 species of data from 1970 onwards.
DOI: 10.5061/dryad.q36nr/1
title: Mugil_cephalus_RRL_454

description: Roche GS-FLEX SFF files of sequence data generated from sequencing EcoRI/MseI reduced complexity libraries prepared from sea mullet (Mugil cephalus) genomic DNA. Samples were collected from the east coast of Australia.
DOI: 10.5061/dryad.q8758/1
title: Body size_Wing_Tibia

description: Spreadsheet of wing and tibia sizes of D. mauritiana (TAM16), D. simulans (yvf) and D. melanogaster (M36).
DOI: 10.5061/dryad.qn1cj/1
title: Yannic_data_DRYAD_RSPB-2014-0502

description: Introductory information: Caribou (Rangifer tarandus) capture and genotype data.  Please contact either Glenn Yannic (glenn-dot-yannic-at-gmail-dot-com) or Steeve D. Côté (Steeve-dot-Cote-at-bio-dot-ulaval-dot-ca) with any questions of location and genotype data. Identification – lab ID (ID number used in lab), capture ID (ID number used in field), sex (male or female). Capture Location - latitude (Y) and longitude (X) coordinates (datum = WGS84) of capture. Loci - names of microsatellite loci analyzed - 16 in total, two alleles provided per loci in adjacent columns, missing data given 000.
DOI: 10.5061/dryad.r0789/1
title: Davies et al 2013