cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rs4k0/1
title: reference transcriptome

description: fasta file containing reference transcriptome (16312 contigs) described in the method section.
DOI: 10.5061/dryad.rs4k0/2
title: snp_table

description: Table containing genotypes for all 433,257 SNPs. First column contains contig name were the SNP is found, second column the reference allele, third column the position of the SNP within the contig, last three columns Fst values for the three comparisons (annuus-debilis, annuus-petiolaris, debilis-petiolaris). Species identification of individuals can be found in table 4. File was compressed (.zip).
DOI: 10.5061/dryad.t5v58/1
title: genomes

description: Data set of nuclear genes used for dating analyses
DOI: 10.5061/dryad.t5v58/10
title: FigureS3

description: Supplementary Figure 3: Comparison of prior and posterior distribution of nodes for the plastid phylogeny under calibration #2. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.
DOI: 10.5061/dryad.t5v58/11
title: FigureS4

description: Supplementary Figure 4: Comparison of prior and posterior distribution of nodes for the nuclear phylogeny under calibration #1. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.
DOI: 10.5061/dryad.t5v58/3
title: genomes_beast_2

description: This file contains the consensus tree inferred on nuclear markers by BEAST with the topology fixed. External calibration plus phytoliths were used. Each time unit corresponds to 20 million years.
DOI: 10.5061/dryad.t5v58/4
title: plastid28

description: Data set of plastid markers for 28 species used for dating analyses.
DOI: 10.5061/dryad.t5v58/5
title: plastid245

description: Data set of plastid markers for 245 species used for dating analyses.
DOI: 10.5061/dryad.t5v58/6
title: plastid245_beast_1

description: This file contains the consensus tree inferred on plastid markers by BEAST with the topology fixed. External calibration only was used. Each time unit corresponds to 20 million years.
DOI: 10.5061/dryad.t5v58/7
title: plastid245_beast_2

description: This file contains the consensus tree inferred on plastid markers by BEAST with the topology fixed. External calibration plus phytoliths were used. Each time unit corresponds to 20 million years.
DOI: 10.5061/dryad.t5v58/8
title: FigureS1

description: Supplementary Figure 1: Comparison of concatenated and partitioned analyses. Ages are plotted in million years ago for a) plastid markers and b) nuclear markers. Analyses were performed with BEAST and the dataset was partitioned by codon position. Black lines indicate 1:1 relationships.
DOI: 10.5061/dryad.t5v58/9
title: FigureS2

description: Supplementary Figure 2: Comparison of prior and posterior distribution of nodes for the plastid phylogeny under calibration #1. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.
DOI: 10.5061/dryad.v21k1/1
title: Egg and acanthor dimensions of Echinorhynchus salmonis

description: Measurements of 135 eggs (3 from each of 45 acanthocephalans) in micrometres.
DOI: 10.5061/dryad.v21k1/2
title: Morphometric and meristic data from female Echinorhynchus salmonis

description: Morphometric and meristic data for 122 specimens of female Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.
DOI: 10.5061/dryad.v21k1/3
title: Morphometric and meristic data from male Echinorhynchus salmonis

description: Morphometric and meristic data from 17 specimens of Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.
DOI: 10.5061/dryad.v21k1/4
title: Hook measurements from female Echinorhynchus_salmonis

description: Hook measurements from 36 female specimens of Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.
DOI: 10.5061/dryad.v21k1/5
title: Hook measurements from male Echinorhynchus salmonis

description: Hook measurements from six specimens of male Echinorhynchus salmonis from the Bothnian Bay, Baltic Sea. All measurements in micrometres.
DOI: 10.5061/dryad.v7b3n/1
title: Fish dissections data
DOI: 10.5061/dryad.v7b3n/2
title: Paternity data
DOI: 10.5061/dryad.vt8t7/1
title: heterozygosity-fitness data for Silene vulgaris

description: These data provide sampling meta-data, genetic summary statistics (multi-locus heterozygosity and STRUCTURE Q-scores), and common garden fitness data for 163 families of Silene vulgaris collected from across Europe (native) and North America (introduced)
DOI: 10.5061/dryad.vt8t7/2
title: Microsatellite genotypes from 15 loci for Silene vulgaris

description: These data are diploid microsatellite genotypes, in units of allele size (bp), for 15 co-dominant loci. Data are formatted as an input file for STRUCTURE, with missing values are coded as '-9'.
DOI: 10.5061/dryad.vt8t7/3
title: Genotype data for DIYABC analysis of demographic history for Silene vulgaris

description: These data provide sampling meta-data, microsatellite genotypes, and input file formatting for the DIYABC approximate Bayesian computation analysis.Two sheets are provided: sheet "data, K=2" provides the genotype data and accompanying metadata used to produce the input file for DIYABC; sheet "forDIYABC" provides the formatted input file for the DIYABC analysis
DOI: 10.5061/dryad.vv82q/1
title: IonXpress_001_Macrozamia riedlei
DOI: 10.5061/dryad.vv82q/2
title: IonXpress_015_Podocarpus drouynianus
DOI: 10.5061/dryad.vv82q/3
title: IonXpress_016_Ricinocarpos
DOI: 10.5061/dryad.2r107/1
title: Fig Core Collection Metadata

description: Detailed 9 simple sequence repeats used in this work, developed by Giraldo et al. 2005. SSR matrix of all accessions. Fig tree Germplasm Bank dendrogram. Summary of all genetic parameters obtained with 4 approaches.
DOI: 10.5061/dryad.30320/2
title: ThompsonHurdCrespi-MRTData

description: MRT data
DOI: 10.5061/dryad.4067d/1
title: Cladistic data matrix

description: Cladistic data matrix
DOI: 10.5061/dryad.40f6d/1
title: Cladistic data matrix

description: Cladistic data matrix
DOI: 10.5061/dryad.4dp71437/10
title: dataFig2b_3

description: Influence of the migration rate eta on the equilibrium percentage of sexual females in the 20 patches for varying mortality strength 1/n (simulated electronically), eta=0.03
DOI: 10.5061/dryad.4dp71437/11
title: dataFig2b_10

description: Influence of the migration rate eta on the equilibrium percentage of sexual females in the 20 patches for varying mortality strength 1/n (simulated electronically), eta=0.1
DOI: 10.5061/dryad.4dp71437/5
title: dataFig1e

description: Average equilibrium percentage of sexual females in dependence of minimum adult body mass Ba (simulated electronically), here no migration is allowed, i.e., migration rate eta=0
DOI: 10.5061/dryad.4dp71437/6
title: dataFig2a_1

description: Influence of the migration rate eta on the equilibrium percentage of sexual females in the 20 patches for varying resource diversity L (simulated electronically), eta=0.01
DOI: 10.5061/dryad.4dp71437/7
title: dataFig2a_3

description: Influence of the migration rate eta on the equilibrium percentage of sexual females in the 20 patches for varying resource diversity L (simulated electronically), eta=0.03
DOI: 10.5061/dryad.4dp71437/8
title: dataFig2a_10

description: Influence of the migration rate eta on the equilibrium percentage of sexual females in the 20 patches for varying resource diversity L (simulated electronically), eta=0.1
DOI: 10.5061/dryad.4dp71437/9
title: dataFig2b_1

description: Influence of the migration rate eta on the equilibrium percentage of sexual females in the 20 patches for varying mortality strength 1/n (simulated electronically), eta=0.01
DOI: 10.5061/dryad.4m0v8474/1
title: Data-Supporting-Figure4-and-FigureS14

description: Number of Illumina HiSeq 2000 reads returned for TruSeq indexes versus indexes designed using EDITTAG and incorporated to TruSeq-style sequencing adapters.
DOI: 10.5061/dryad.4m0v8474/2
title: Data-Supporting-FigureS11

description: Number of 454 FLX Titanium reads returned for PCR primers incorporating 10 nt edit distance sequence tags and amplifying RbcLa in land plants.
DOI: 10.5061/dryad.4m0v8474/3
title: Data-Supporting-FigureS12

description: Number of Illumina GAIIx reads returned for Epicentre Nextera indexes versus indexes designed using EDITTAG and incorporated to Epicentre Nextera-style sequencing adapters.
DOI: 10.5061/dryad.4m0v8474/4
title: Data-Supporting-FigureS13

description: Number of Illumina GAIIx reads returned for TruSeq-style adapters incorporating indexes designed using EDITTAG and ligated onto pooled DNA templates (Tab 1) versus the  number of Illumina HiSeq 2000 reads returned for TruSeq-style adapters incorporating indexes designed using EDITTAG and ligated onto DNA individually.  The variance in read number is the important difference to note.
DOI: 10.5061/dryad.56mv5/1
title: Encounter histories adult spoonbills 1994-2010

description: This datafile (plain textfile to be imported in program E-Surge) contains the encounter histories of 2095 adult (&gt;3cy) Eurasian spoonbills, born between 1988 and 2007 and resighted between summer 1994 and summer 2010. Two resighting periods per year are defined (summer = March-September, winter = December-January for France and Iberia and October-February for Mauritania & Senegal). Events are coded as: (0) not resighted, (1) resighted in summer in The Netherlands, (2) resighted in winter in France, (3) resighted in winter in Iberia, (4) resighted in winter in Mauritania & Senegal. Columns refer to encounter history (H:), sample size (S:) and 'standardized' year of birth (COV:yb), calculated as ([year of birth]-2000)/10.
DOI: 10.5061/dryad.5s2h3/1
title: Raw Respondent Survey Data

description: Complete dataset for 2556 physician respondents.
DOI: 10.5061/dryad.5s2h3/2
title: Data dictionary
DOI: 10.5061/dryad.5s2h3/4
title: Survey Instrument
DOI: 10.5061/dryad.5v42p/1
title: Egg phenotypes

description: These data were collected from a laboratory experiment. Abbreviations used for column headings are described below. MotherID - a distinct code for the female that laid the clutch described; Mothersize - pronotum width; labtime - the number of days the particular female spent in the lab before her clutch was collected;  FatherID - a distinct code for the male mated to the female that laid the clutch described; Eggsaturation - (r) calculated as the shortest (Euclidian) distance from the achromatic origin, where saturation increases the further a point is from the origin; Eggbrightness - overall reflectance across the spectrum, and calculated independently of colour by applying the formula: (LW+MW+SW+UV)/4; Egghue1 - (LW+MW) / (SW+UV); Egghue2 - (LW+UV) / (SW+MW); Eggcoc - concentration of coccinelline in the eggs; Eggprecoc - concentration of precoccinelline in the eggs; Eggcarotenoids - concentration of carotetenoids in the eggs
DOI: 10.5061/dryad.5v42p/2
title: Offspring phenotypes

description: These data were collected from a laboratory experiment. Abbreviations used for column headings are described below. OffspringID - a distinct code for the individual offspring with the phenotype described; MotherID - a distinct code for the mother of the offspring described;  FatherID - a distinct code for the male mated to the mother of the offspring described; Eggsaturation - (r) calculated as the shortest (Euclidian) distance from the achromatic origin, where saturation increases the further a point is from the origin; Eggbrightness - overall reflectance across the spectrum, and calculated independently of colour by applying the formula: (LW+MW+SW+UV)/4; Egghue1 - (LW+MW) / (SW+UV); Egghue2 - (LW+UV) / (SW+MW); Eggcoc - concentration of coccinelline in the eggs; Eggprecoc - concentration of precoccinelline in the eggs; Eggcarotenoids - concentration of carotetenoids in the eggs; hatchsuccess - hatched larvae / total eggs; Sex - male or female; Offspringgrowthrate - calculated as the regression coefficient of an exponential curve fitted to the x(age in days at the start of each instar stage) and y(body mass) for each larva; Offspringmass - weighed to the nearest 0.1µg upon eclosion; Offspringdevtime - total number of days between hatching and eclosion as adults; Offspringsat - (r) calculated as the shortest (Euclidian) distance from the achromatic origin, where saturation increases the further a point is from the origin; OffspringBrightness - overall reflectance across the spectrum, and calculated independently of colour by applying the formula: (LW+MW+SW+UV)/4; Offspringhue1 - (LW+MW) / (SW+UV); Offspringhue2 - (LW+UV) / (SW+MW); Offspringcoc - concentration of coccinelline in the individual; Offspringprecoc - concentration of precoccinelline in the individual
DOI: 10.5061/dryad.5v42p/3
title: Survival

description: These data were collected from a laboratory experiment. Abbreviations used for column headings are described below. LarvaeID - a distinct code for the individual described; MotherID - a distinct code for the female that laid the clutch described; FatherID - a distinct code for the male mated to the female that laid the clutch described; Eggcarotenoids - concentration of carotetenoids in the eggs; Survival - whether the individual survived to adulthood.
DOI: 10.5061/dryad.64p8t/1
title: Individual Genotypes

description: This file contains genotypes (i.e allele sizes) of all the stains used in the publication HDY-12-OR0095R. The file include two sheets for the two different data sets (see Fig 1 of the manuscript). NA indicates a missing data.
DOI: 10.5061/dryad.6mp50/1
title: Thelomma_data_packet

description: This data packet comprises a zipped folder that contains the alignments used in the following analyses for this study. 1) ML analysis of Physciaceae with results presented in Appendix 1. 2) MP, ML, and BI analyses of a smaller dataset examining the placement of the taxon in question.
DOI: 10.5061/dryad.71k17/1
title: Gazella skull measurements, raw data (A morphometric and genetic framework for Gazella)

description: This file includes the linear measurements of Gazella skulls from several museum specimens. Measurements were taken with callipers (except L F+P2 and HL2, these were measured with a tape measure) and are given in mm. Figure 2 in the original publication depicts the measurements taken.
DOI: 10.5061/dryad.860jq72n/1
title: msat_data_dryad

description: Microsatellite data and locality information for normal and waveform Sphagnum cribrosum samples. 188 samples at 14 loci.
DOI: 10.5061/dryad.8tg11/1
title: Urinary incontinence dataset
DOI: 10.5061/dryad.9v7bn/1
title: SSRs matrix
DOI: 10.5061/dryad.cp00b/1
title: all data

description: Above and belowground biomass of rumex plants collected from rabbit exclusion plots at Silwood Park England and grown in a common garden (greenhouse) with one tab for all plant data and another for plot means (for regressions). A tab for plant oxalate concentration data measured using phtoteospectometry. Another tab for plant tannin concentration. Finally, another tab for biomass of oenothera (our competitor).
DOI: 10.5061/dryad.d85ng/1
title: Data and analysis files for Domestication and the Mitochondrial Genome, Moray et al., GBE

description: Please see README file for details.
DOI: 10.5061/dryad.df854/1
title: Seifan et al - Field survey information

description: Species recorded in the field survey under different environmental conditions. DRY/WET – plots with low/high flooding probabilities respectively; M+/ M– – plots with/without mole activity respectively. For each species listed, its abundance (number of individuals found in the survey plots) per environmental condition is given.
DOI: 10.5061/dryad.f3050/1
title: Dong_et_al_2004_datamatrix

description: Cladistic data matrix
DOI: 10.5061/dryad.f37km/1
title: Questionnaires

description: Filetype: Microsoft Word 2010Contents: Questionnaires (in Dutch)
DOI: 10.5061/dryad.fc615/1
title: Cladistic data matrix

description: Cladistic data matrix
DOI: 10.5061/dryad.fn78r/1
title: Cladistic data matrix

description: Cladistic data matrix
DOI: 10.5061/dryad.fv35j/1
title: Dimensions of catfish spines

description: Relationship of spine and girdle dimensions to fish dimensions.
DOI: 10.5061/dryad.fv35j/2
title: Wt vs GW

description: Girdle weight vs fish weight
DOI: 10.5061/dryad.fv35j/3
title: Wt vs SpW

description: Spine weight against fish weight
DOI: 10.5061/dryad.fv35j/4
title: TL vs SpL

description: Spine length against total length
DOI: 10.5061/dryad.gv5ss/1
title: SAT-EU SurveySummary_Survey Monkey_10172013_EUROPE_Dryad_UploadVersion 2

description: Original source of information is an excel download from Survey Monkey, which was used to collect the survey data.
DOI: 10.5061/dryad.hd300/16
title: RatDems-ML-RELATE-PL2-V2

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 2 in Pau da Lima (valley 2) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/17
title: RatDems-ML-RELATE-PL6-V4

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 6 in Pau da Lima (valley 4) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/18
title: RatDems-ML-RELATE-PL8-V2

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 8 in Pau da Lima (valley 2) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/19
title: RatDems-ML-RELATE-PL9-V3

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 9 in Pau da Lima (valley 3) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/20
title: RatDems-ML-RELATE-SA3-V5

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 3 in Sete de Abril (valley 5) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/21
title: RatDems-House5-ML-RELATE

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in House 5 in Pau da Lima are included in this file to test for pairwise relatedness within the household. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hv75h/10
title: Infinuim_Chip_annotations

description: Annonations for Infinium contigs using BlastX against human proteome.  Used in GO Enrichment analyses.
DOI: 10.5061/dryad.hv75h/11
title: Infinium_Parva_Goodei_Fst

description: Fst calculations between 33 L. goodei and 39 L. parva genotyped on the Infinium Chip.  Calculations done in hierfstat in R.
DOI: 10.5061/dryad.hv75h/3
title: Annotated_gene_universe_Lucania

description: List of annotations for all Lucania reference contigs using blastX and human proteome.  Gene universe used in GO enrichment analyses.
DOI: 10.5061/dryad.hv75h/4
title: Goodei_Parva_Outliers

description: List of annotations for outliers between species (L. goodei vs. L. parva) using blastX and human proteome.  Target gene file used in GO enrichment analyses.
DOI: 10.5061/dryad.hv75h/5
title: Goodei_outliers

description: List of annotations for outliers within L. goodei (Upper Bridge vs. Everglades) using blastX and human proteome.  Target gene file used in GO enrichment analyses.
DOI: 10.5061/dryad.hv75h/6
title: SWSW_outliers

description: List of annotations for outliers within L. parva between geographically distant saltwater populations (Indian River and Bolivar Peninsula) using blastX and human proteome.  Target gene file used in GO enrichment analyses.  These outliers were removed from all freshwater-saltwater drainage analyses.
DOI: 10.5061/dryad.hv75h/7
title: Parva_outliers1Drain_SWrem

description: List of annotations for outliers between freshwater-saltwater drainages in L. parva using blastX and human proteome.  Outliers in at least one drainage (and not present in saltwater-saltwater outliers). Target gene file used in GO enrichment analyses.
DOI: 10.5061/dryad.hv75h/8
title: Parva_outliers2-3Drainages

description: List of annotations for outliers between freshwater-saltwater drainages in L. parva using blastX and human proteome.  Outliers present in two to three drainages shown (and not present in saltwater-saltwater outliers). Target gene file used in GO enrichment analyses.
DOI: 10.5061/dryad.hv75h/9
title: Infinium Chip Souce Sequences

description: Source sequences for Illumina Infinium Bead Chip custom designed for Lucania.  4,545 SNPs from 454 contigs (assembled using Newbler).  Contains 1,679 candidate SNPs segregating between species, 1,497 SNPs segregating between Everglades and Upper Bridge L. goodei, 1,369 SNPs segregating between Florida Atlantic saltwater and Texas Gulf freshwater L. parva).
DOI: 10.5061/dryad.k83b8/1
title: gene_counts

description: Gene level read counts for the eight libraries reported in the manuscript.
DOI: 10.5061/dryad.mm296/1
title: Dehling&Sinsch2013Ptychadena_morphometricsDRYAD
DOI: 10.5061/dryad.n09f3/1
title: Cladistic data matrix

description: Cladistic data matrix
DOI: 10.5061/dryad.nh43g/1
title: Betini et al. weight

description: Fresh weight of females
DOI: 10.5061/dryad.nh43g/2
title: Betini et al. time series

description: Time series
DOI: 10.5061/dryad.rs4k0/3
title: raw read count per gene

description: Number of reads aligned, per contig, per individuals. Column one contains contig name, column two length of the contig.
DOI: 10.5061/dryad.s022h/1
title: Soil enzyme (phosphatase, b-glucosidase and urease) data from encroached/unencroached Stipa tenacissima steppes from Spain
DOI: 10.5061/dryad.s3031/1
title: Kelp growth and erosion. A Canadian Healthy Oceans Network Ecosystem Function Project, EF-11

description: Data on individual kelp growth, erosion, and biomass from all sites and all sampling periods in the data set. Also included are data on the % of kelp blade area covered by Membranipora membranacea and % of the distal 1/3 of the kelp blade grazed by Lacuna vincta.
DOI: 10.5061/dryad.s3031/2
title: Kelp Biomass and Density. A Canadian Healthy Oceans Network Ecosystem Function Project, EF-11

description: Kelp biomass and density measured in quadrats at each site during each sampling period.
DOI: 10.5061/dryad.t5v58/12
title: FigureS5

description: Supplementary Figure 5: Comparison of prior and posterior distribution of nodes for the nuclear phylogeny under calibration #2. For each calibration point, the calibration density is indicated by the black line, the marginal prior distribution by the blue bars and the posterior distribution by the red bars.