cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.qp544/2
title: Survival

description: This data file was tailored for the cox regression analysis of survival/mortality over time per treatment combination. The first eight columns represent independent variables: 1. label is the unique number of an individual. 2. Replicate is the number (1, 2 or 3) of the replicate that has been assigned to an individual. 3. Tank is the tank number to which a given individual was assigned. 4. Temperature is the temperature treatment to which a given individual has been randomly assigned (COLD 14ºC or WARM 22ºC). 5. Species is the taxonomic status of a given individual either  LF (Northern leopard frog) or WF (wood frog). 6. Genotypes: we used  one clutch of leopard frog (genotype #1) and two clutches of wood frog (genotypes #2 and #3). 7. Strains: we used three ranavirus strain azaC, SsMeV and the wild type wt-FV3, see our description in the main text. 8. Exposure: either an individual is "exposed" or "control". 9. Day_death represents the number of days an individual survived. 10. Censoring is a variable that specify our knowledge or absence of knowledge about an individual death. The value "1" denotes occurrence and observation of an individual's death during the experiment, and the value "0" denotes that an individual was censored because it survived throughout and may have survived after the end of the experiment but we don't really know.
DOI: 10.5061/dryad.s04v1/2
title: MSAP profiles

description: MSAP profiles for paired leaf and pollen samples from 60 plants of Helleborus foetidus from three locations in the Sierra de Cazorla, southeastern Spain, sampled for the study
DOI: 10.5061/dryad.s04v1/3
title: Seed and seedling data

description: Mean seed mass, seed mass variance, and number of seedlings occurring within a 0.5 m radius, for the 60 individual plants of Helleborus foetidus from three locations in Sierra de Cazorla, southeastern Spain, sampled for the study.
DOI: 10.5061/dryad.s04v1/4
title: Microsatellite profiles

description: Microsatellite profiles for putative maternal parents and associated seedlings in the sample of Helleborus foetidus plants studied
DOI: 10.5061/dryad.s296n/1
title: Tamias alpinus (the Alpine chipmunks) exon capture probe design

description: Targeted exons were derived from 6,249 protein-coding genes with a target size totaling 4Mb, and spanned a wide range of evolutionary rates in the genome (Bi et al. 2012). In addition to the T. alpinus exons, we targeted the ~16 kb T. alpinus complete mitochondrial genome and 350 bp from the consensus Spermophilus (S. fulvus, S. major, and S. pygmaeus) SRY gene to assess empirical error rates and potential sample contamination (Bi et al. 2012). We also selected seven nuclear genes (acrosin, acp5, cmyc, rag-1, anon, zan, and zp2) previously sequenced in Tamias (6,031 bp total), which were used as positive controls in post-capture qPCR assays to determine the initial enrichment quality.
DOI: 10.5061/dryad.s296n/2
title: Tamias alpinus (the Alpine chipmunks) annotated transcripts

description: The Tamias alpinus transcriptome was annotated using the BLASTX algorithm and a database of human, mouse, rat, and thirteen-lined ground squirrel proteins.
DOI: 10.5061/dryad.th092/1
title: Genotypes, SNP information, and sample information for 1,543 cattle from 134 breeds

description: This file contains the genotypes from 43,043 SNP markers scored in 1,543 cattle. Samples were genotyped with the Illumina BovineSNP50 BeadChip. Genotypes were called using GenomeStudio.
DOI: 10.5061/dryad.vc1q1/1
title: Raw data Klepsatel et al 2013 Evolution

description: We examined thermal adaptation in six wild populations of the fruit fly (Drosophila melanogaster) from markedly different natural environments by analyzing thermal performance curves or thermal reaction norms for (1) fecundity (absolute fecundity was defined as the mean cumulative number of eggs laid per female during the first ten days; relative fecundity was defined as a percentage of maximum absolute fecundity (set to 100%)), (2) thorax length (measured in mm), (3) wing area (measured in mm2), (4) wing loading (defined as (thorax length)3/(wing area)), (5) ovariole number (ovariole number was defined as the sum of the number of ovarioles in both ovaries) and (6) ovariole index (i.e., the ratio between ovariole number of and individual and its body size (~cube of thorax length)) under ecologically realistic fluctuating temperature regimes in the laboratory. Here we present the raw data for these traits/measurements; each line represents an individual female fly. For details on experimental design, data collection and statistical analysis see our paper, Klepsatel et al. (2013, title: "Variation in thermal performance and reaction norms among populations of Drosophila melanogaster"; journal: Evolution). For additional, more specific (sub-)datasets based on the raw data presented here, which we have used for particular statistical analyses, or for statistical analyses outputs please contact the corresponding author, Thomas Flatt at thomas.flatt@unil.ch
DOI: 10.5061/dryad.04vh7/1
title: 6-22-08 experiment

description: Data from a dose response experiment using gypsy moths exposed to the gypsy moth baculovirus.  Fraction of virus-induced mortality and speed of kill were recorded for 5 different doses.
DOI: 10.5061/dryad.1p2s5/1
title: Ppinaster_serotiny_phenotypes

description: Sample names, sample location, UTM coordinates and proportion of serotinous cones of 199 trees phenotyped in the east of the Iberian Peninsula, Spain.
DOI: 10.5061/dryad.1p2s5/2
title: Ppinaster_SNPdata_199Ind_251SNPs

description: Sample names, UTM coordinates and SNP genotypes for 251 SNPs and 199 Pinus pinaster trees sampled in the east of the Iberian Peninsula, Spain.
DOI: 10.5061/dryad.1p2s5/3
title: Ppinaster_11SSRs_199Ind

description: Sample name, sample location, UTM coordinates and genotypes of 11 nuclear microsatellites for 199 individuals of Pinus pinaster sampled in the east of the Iberian Peninsula.
DOI: 10.5061/dryad.1qs5c/1
title: Abaeticus12pop

description: Genotype data for four microsatellite loci amplified in Aphanius baeticus. The file corresponds with Genepop's format and includes the populations (N=12) analyzed in the article.
DOI: 10.5061/dryad.2d7j0/2
title: lifespan_data

description: This file contains lifespan data.
DOI: 10.5061/dryad.2f2b3/1
title: Data from: Season and site fidelity determine home range of dispersing and resident juvenile Greenland cod (Gadus ogac) in a Newfoundland fjord. A Canadian Healthy Oceans Network Population Connectivity, PC-03

description: Acoustic telemetry data was collected from October 2010 - October 2011 for 42 individual age 1+ Gadus ogac individuals tagged with Vemco Ltd™ V7-4L coded acoustic tags, programmed to emit a signal at a randomized average delay of every 240 ± 70 s, and a nominal tag life of 415 days. A receiver network comprised of 26 Vemco™ VR2W and VR2 hydrophones allowed for continual detection throughout Newman Sound over a full year. The data presented have been filtered to eliminate spurious detections using both a single detection filter (eliminating lone detections for a single fish over 24 hours) and a conservative speed filter (eliminating detections &gt; 2 body lengths/second apart which could indicate ingestion by a predator). Using known positions of the acoustic receivers, we calculated position estimates in hourly time intervals using a weighted arithmetic mean  to increase precision from a presence/absence dataset to a position-based dataset. Therefore the beginning of each hour time interval is indicated in the "Date" and "Time" field. Positions are indicated in decimal degrees in the "COA_Lat" and "COA_Lon" fields of the CSV files. Also included are the ArcGIS defined "POINT_X" and "POINT_Y" fields using a NAD_1983_UTM_Zone_21N projection. Individual fish IDs are included in the "Tag" field. The "Transplant" field indicates whether the individual was in the control group (site of capture = site of release) or the transplant group (site of capture ≠ site of release). Site of capture is indicated by the "Cove" field (HC = Heffern's Cove; BC= Buckley's Cove).
DOI: 10.5061/dryad.2f2b3/2
title: Season and site fidelity determine home range of dispersing and resident juvenile Greenland cod (Gadus ogac) in a Newfoundland fjord (Year 2). A Canadian Healthy Oceans Network Population Connectivity, PC-03

description: Acoustic telemetry data was collected from November 2011 - November 2012 for 42 individual age 1+ Gadus ogac individuals tagged with Vemco Ltd™ V7-4L coded acoustic tags, programmed to emit a signal at a randomized average delay of every 240 ± 70 s, and a nominal tag life of 415 days. A receiver network comprised of 32 Vemco™ VR2W and VR2 hydrophones allowed for continual detection throughout Newman Sound over a full year. The data presented have been filtered to eliminate spurious detections using both a single detection filter (eliminating lone detections for a single fish over 24 hours) and a conservative speed filter (eliminating detections &gt; 2 body lengths/second apart which could indicate ingestion by a predator). Using known positions of the acoustic receivers, we calculated position estimates in hourly time intervals using a weighted arithmetic mean  to increase precision from a presence/absence dataset to a position-based dataset. Therefore the beginning of each hour time interval is indicated in the "Date" and "Time" field. Positions are indicated in decimal degrees in the "COA_Lat" and "COA_Lon" fields of the CSV files. Also included are the ArcGIS defined "POINT_X" and "POINT_Y" fields using a NAD_1983_UTM_Zone_21N projection. Individual fish IDs are included in the "Tag" field. The "Transplant" field indicates whether the individual was in the control group (site of capture = site of release) or the transplant group (site of capture ≠ site of release). Site of capture is indicated by the "Cove" field (HC = Heffern's Cove; BC= Buckley's Cove).
DOI: 10.5061/dryad.2g257/1
title: Winter_run steelhead hatchery genotypes

description: Genotype data from winter-run hatchery steelhead.
DOI: 10.5061/dryad.2j77t/1
title: Egg Data
DOI: 10.5061/dryad.2j77t/2
title: Morphometric Data
DOI: 10.5061/dryad.2j77t/3
title: Weight Data
DOI: 10.5061/dryad.2j77t/4
title: Survival Data
DOI: 10.5061/dryad.2j77t/5
title: Pedigree Data
DOI: 10.5061/dryad.2j77t/6
title: R Scripts

description: R code for performing all analyses in Hadfield at al. (2013) `Disentangling genetic and prenatal sources of familial resemblance across ontogeny in a wild passerine'
DOI: 10.5061/dryad.2vk30/1
title: Microsatellite genotypes of 750 tree frogs from 30 markers

description: The first column designates sample labels, and the second the population numbers (as in the figures of the paper). Null alleles appears as "0" and missing data as "NA". Genotypes were scored with GeneMapper 4.0 and null alleles detected with Microchecker (see the paper for details)
DOI: 10.5061/dryad.2vk30/2
title: Sequence alignment of cytochrome-b

description: This includes 238 samples of H. arborea and 2 samples of H. orientalis
DOI: 10.5061/dryad.2vk30/3
title: Sequence alignment of the D-loop

description: This includes 238 samples from H. arborea and 2 samples from H. orientalis
DOI: 10.5061/dryad.2vk30/4
title: Sequence alignment of rag-1

description: This includes 108 individuals of H. arborea, with two alleles for each individual (noted 1 and 2) for a total of 216 sequences. Haplotypes were reconstructed with the Phase algorithm of DNAsp. See the paper for details. The alignment also includes published sequences of four other Hylid species.
DOI: 10.5061/dryad.31vn6/1
title: SSR Dataset of Fagus sylvatica from 65 populations in  France and Catalonia

description: SSR Dataset of Fagus sylvatica from 65 populations in France and Catalonia.Populations were sampled in the field and genotyping was performed at the Genome-Transcriptome facility of Bordeaux. Population codes refer to Table S1 in supplementary information. Georeferenced locations of populations are available in Table S1. SSRs used for this study are described in detail in Lefèvre et al (2012), doi: 10.1111/j.1755-0998.2011.03094.x.
DOI: 10.5061/dryad.55d46/5
title: High resolution Fig. 6

description: High resolution Fig. 6
DOI: 10.5061/dryad.55d46/6
title: High resolution Fig. 7

description: High resolution Fig. 7
DOI: 10.5061/dryad.55d46/7
title: High resolution Fig. 8

description: High resolution Fig. 8
DOI: 10.5061/dryad.69329/11
title: C_nidiformis_polygon_file

description: Google Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.
DOI: 10.5061/dryad.69329/12
title: C_pleiocephala_polygon_file

description: Google Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.
DOI: 10.5061/dryad.69329/13
title: C_racemosa_polygon_file

description: Google Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.
DOI: 10.5061/dryad.69329/14
title: C_thespidioides_polygon_file

description: Google Earth modified polygon file. Place in same directory as analysis and species trees file, and make sure they are referenced correctly in the xml file.
DOI: 10.5061/dryad.69329/15
title: Supplementary Figure S1

description: Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
DOI: 10.5061/dryad.69329/16
title: Supplementary Figure S2

description: Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
DOI: 10.5061/dryad.69329/17
title: Supplementary Figure S3

description: Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
DOI: 10.5061/dryad.69329/18
title: Supplementary Figure S4

description: Species polygons in colour with starting locations (circles) and specimens sampled for species tree inference.
DOI: 10.5061/dryad.6mh29/19
title: Cognettia COI run2 p file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/20
title: Cognettia H3 run1 p file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/21
title: Cognettia H3 run2 p file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/22
title: Cognettia ITS run1 p file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/23
title: Cognettia ITS run2 p file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/24
title: Cognettia 16S parts file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/25
title: Cognettia COI parts file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/26
title: Cognettia H3 parts file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/27
title: Cognettia ITS parts file from MrBayes analysis
DOI: 10.5061/dryad.6mh29/28
title: Cognettia 16S run1 t file from MrBayes analysis
DOI: 10.5061/dryad.7gc05/1
title: Metabolic rate and behavioural data for juvenile Ambon damselfish

description: Measures of metabolic rates, before, after and during competitive interactions between juvenile Ambon damselfish. also includes behavioural data from dyadic trials.
DOI: 10.5061/dryad.b2k47/1
title: SNP File in PoPoolation2 format
DOI: 10.5061/dryad.c9m2d/1
title: Artificial Bat Roost Data

description: This file includes data on bat detections, roost temperatures, seed rain, and seedling recruitment. Please see the ReadMe file and the manuscript for more information.
DOI: 10.5061/dryad.cp325/1
title: Data from: Perturbing the cellular levels of steroid receptor coactivator-2 impairs murine endometrial function

description: Ziped folder containing all files. named according to figure number. See README.TXT for details
DOI: 10.5061/dryad.g9735/2
title: Individual-level lab-reared fish morphometric data

description: Morphometric data for examination of genetic basis of population differences using a common-garden experiment.
DOI: 10.5061/dryad.g9735/3
title: Site-level environmental and morphometric data

description: Data for the model selection analysis.
DOI: 10.5061/dryad.gk880/1
title: Mukherjee_Ray_AppendixS1-R2
DOI: 10.5061/dryad.m327n/1
title: PrimateReproductiveSenescenceData_21June2013
DOI: 10.5061/dryad.m81b5/1
title: Nexus_files

description: Compressed zip file containing the alignments of DNA sequences for cyt b and phased alleles of 14 anonymous nuclear loci in nexus format
DOI: 10.5061/dryad.m81b5/2
title: Phase_files

description: Compressed zip file containing the input and output files of PHASE analyses for each of 14 anonymous nuclear loci
DOI: 10.5061/dryad.m81b5/4
title: Beast_files

description: Compressed zip file containing the input files of Extended Bayesian Skyline Plot (EBSP), Standard Random Walk (SRW), and Relaxed Random Walk (RRW) analyses in BEAST. Log files for marginal likelihood estimation (MLE), the maximum credibility tree (MCC), and the KML file for visualization in Google Earth are also included for SRW and RRW analyses.
DOI: 10.5061/dryad.m81b5/5
title: Structure_files

description: Compressed zip file containing the input and output files of STRUCTURE analyses for all loci and for cyt b only.
DOI: 10.5061/dryad.t6b05/1
title: replace95bam_and_ref
DOI: 10.5061/dryad.t6b05/2
title: De novo assembly Chloroplast of Dioscorea rotundata

description: The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Dioscorea elephantipes (EF380353.1)
DOI: 10.5061/dryad.t6b05/3
title: De novo assembly Chloroplast of Digitaria excilis

description: The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Pennisetum glaucum
DOI: 10.5061/dryad.t6b05/4
title: De novo assembly Chloroplast of Cenchrus americanus

description: The software MITObim (v. 1.5, Hahn et al. 2013) was used to reconstruct de novo plastid genomes. We used as initial references: Zea mays
DOI: 10.5061/dryad.t6b05/5
title: RAM63_forward_500k

description: This file contain 500k forward reads Illumina TrueSeq v3 75 PE, from RAM63, an O. sativa ssp indica.These data have been used to validate the assembly method.
DOI: 10.5061/dryad.t6b05/6
title: RAM63_reverse_500k
DOI: 10.5061/dryad.vp51n/1
title: ComBiom

description: Dry mass of major prey species by treatment
DOI: 10.5061/dryad.vp51n/2
title: Community structure: Macrofauna-Density

description: Density of macrofauna species
DOI: 10.5061/dryad.vp51n/3
title: Zooplankton densities

description: Densities of zooplankton species.
DOI: 10.5061/dryad.vp51n/4
title: Size spectra

description: Number of individuals within a given log10 size class. Details are given in the paper.
DOI: 10.5061/dryad.vp51n/5
title: Tadpole mass and counts

description: The data gives the counts and tail damage for three tadpole species. RA= Rana sphenocephala, Hyl=Hyla, and Acris and total biomass and counts summed across all species.
DOI: 10.5061/dryad.vp51n/6
title: Invertebrate counts and dry mass

description: The data describes the dry-mass and counts of all invertebrates (excluding zooplankton) in a given mesocosm. It also lists it separately for invertebrates just found in the vegetation (Veg) subsample and for just small invertebrates (see paper methods for details). For a reference, we also show the total dry biomass estimated from length-weight conversions.
DOI: 10.5061/dryad.vp645/1
title: HMM_and_other_major_analyses

description: This set of scripts recreates most major analyses from our manuscript. This includes PCA analyses, the distribution of nj tress, the distribution of diversity and our hidden Markov Model. This all works with our associated data file.
DOI: 10.5061/dryad.vp645/2
title: Processed_data

description: An R-object containing 'nj.pca.snps' and 'pairwise.focal.mim'.  pairwise.focal.mim is a matrix with genotypes for all samples at all SNPS used in nj and PCA analyses.  'pairwise.focal.mim' a list containing 'comps' and 'bounds.''comps' - itself a list of all pairwise comparisons between focal samples.  For each pairwise comparison between focal samples the number of sites compared & differences between two samples in 1kb windows is contained in a matrix. 'bound' a matrix describing the location of each 1 kb region.
DOI: 10.5061/dryad.0838c/1
title: Magnitude Effect data

description: Preference data from different nectar-feeding animals in choice situations between two different sugar concentrations. Excel Workbook with six Spreadsheets. Sources are cited within the file. For further information, consult the spreadsheet "General Information".
DOI: 10.5061/dryad.31vn6/2
title: Isozyme dataset of Fagus sylvatica from 375 populations across Europe

description: Isozyme dataset originally published in: Comps B, Gömöry D, Letouzey J, Thiébaut B, Petit RJ (2001) Diverging trends between heterozygosity and allelic richness during postglacial colonization in the European beech. Genetics, 157, 389-397.
DOI: 10.5061/dryad.33j1g/1
title: data_for_Dryad

description: The zip file contains an R script to run the statistical analyses and plot the Figure shown in the manuscript. It also contains the data from the original article, presented here in a format appropriate for use with the script. The data from the original article are archived as: Harrison F (2013) Data from: Dynamic social behaviour in a bacterium: Pseudomonas aeruginosa partially compensates for siderophore loss to cheats. Dryad Digital Repository. http://dx.doi.org/10.5061/dryad.t77nc
DOI: 10.5061/dryad.36077/10
title: R. cingulata detail

description: This Excel file provides information about all individuals from Germany, Hungary and USA analyzed in this study i.e. Wolbachia infection of each individual: + infected, - not infected; year of collection; mitochondrial haplotype: HT1-HT8.
DOI: 10.5061/dryad.36077/2
title: cloning wsp

description: Fasta file of the plasmid clones for the locus wsp.
DOI: 10.5061/dryad.36077/3
title: cloning hcpA

description: Fasta file of the plasmid clones for the locus hcpA.
DOI: 10.5061/dryad.36077/4
title: cloning gatB

description: Fasta file of the plasmid clones for the locus gatB.
DOI: 10.5061/dryad.36077/5
title: cloning ftsZ

description: Fasta file of the plasmid clones for the locus ftsZ.
DOI: 10.5061/dryad.36077/6
title: cloning fbpA

description: Fasta file of the plasmid clones for the locus fbpA.
DOI: 10.5061/dryad.36077/7
title: cloning coxA

description: Fasta file of the plasmid clones for the locus coxA.
DOI: 10.5061/dryad.36077/8
title: cloning COII

description: Fasta file of the plasmid clones of the partial COII gene.
DOI: 10.5061/dryad.3ks4v/1
title: FeiAllGenePopFinal

description: Genepop formatted file containing genotypes for eight polymorphic microsatellite loci for nine Galapaganus howdenae howdenae weevils from nine localities in Santa Cruz Island, Galápagos. Individual codes follow locality codes as in Table 1 followed by a letter as a unique identifier for each individual
DOI: 10.5061/dryad.41hc4/1
title: 2013-SystBiol-Adams-SuppMaterial

description: Supplementary material containing additional simulation results
DOI: 10.5061/dryad.59645/1
title: 272 SNP dataset_South America_Yalcindag

description: 272 SNPs from South American populations
DOI: 10.5061/dryad.59645/2
title: adsl_sequences

description: Sequences alignment of adsl gene
DOI: 10.5061/dryad.59645/3
title: serca_sequences

description: Sequences alignment of serca gene
DOI: 10.5061/dryad.59645/4
title: eba140_sequences

description: Sequences alignment of eba-140 gene
DOI: 10.5061/dryad.59645/5
title: eba175_sequences

description: Sequences alignment of eba-175 gene
DOI: 10.5061/dryad.59645/6
title: eba181_sequences

description: Sequences alignment of eba-181 gene
DOI: 10.5061/dryad.59645/7
title: Supp table 1 Yalcindag et al

description: Sampling details for each population
DOI: 10.5061/dryad.5cs38/1
title: Hamilton_etal_DryadData2013

description: Compressed archive of data files and transcriptome assembly used in analysis.