cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.84gf5/2
title: Torres Dowdall et al. 11-0833 Water colum data

description: Data use in the analysis of water column use. Data correspond to proportion of guppies (Poecilia reticulata) using the surface of the water column. Drainage refer to the drainage from were wild fish used to generate second generation of lab-reared experimental fish were collected. Predation refers to the community from which the wild caught fish were collected. "low" represent low predation risk, simple fish communities. "High" refer to downstream complex communities where predation risk is higher. Family refers to the family lines used in the experiment. "trt" refers to the two treatments used in our experiment. "P" means that fish were reared in the presence of predator cues, "NP" means that they were raised in the absence of such cues. Only significant interactions between terms were kept in the final model.
DOI: 10.5061/dryad.84gf5/3
title: Torres Dowdall et al. 11-0833 Procrustes coordinates data for Yarra fish

description: Data used in the analysis of head morphology from the Yarra Drainage. This text file contains the Procrustes Coordinates that were used for all multivariate analyses of morphology in the manuscript. The Procrustes Coordinates were produced by performing a Generalized Procrustes Analysis (GPA) on the original Cartesian Coordinates to remove size, orientation, and position effects from the data with the TPSRelw software packackage. Additionally, sliding semi-landmarks were aligned during the GPA with the TPSRelw software. Columns are as follow: “Id” refers to the individual assigned identification. Family refers to the family lines used in the experiment. “Predation” refers to the community from which the wild caught fish were collected; "low" represent low predation risk, simple fish communities; "High" refer to downstream complex communities where predation risk is higher. "Treatment" refers to the two treatments used in our experiment. "Cue" means that fish were reared in the presence of predator cues, "No Cue" means that they were raised in the absence of such cues. Drainage refer to the drainage from were wild fish used to generate second generation of lab-reared experimental fish were collected. Population refers to the interaction between Drainage and Predation. Data was analyzed in MANCOVA model combining both drainages, and later in separate CVAs.
DOI: 10.5061/dryad.84gf5/4
title: Torres Dowdall et al. 11-0833 Procrustes coordinates data for Guanapo fish

description: Data used in the analysis of head morphology from the Guanapo Drainage. This text file contains the Procrustes Coordinates that were used for all multivariate analyses of morphology in the manuscript. The Procrustes Coordinates were produced by performing a Generalized Procrustes Analysis (GPA) on the original Cartesian Coordinates to remove size, orientation, and position effects from the data with the TPSRelw software package. Additionally, sliding semi-landmarks were aligned during the GPA with the TPSRelw software. Columns are as follow: “Id” refers to the individual assigned identification. Family refers to the family lines used in the experiment. “Predation” refers to the community from which the wild caught fish were collected; "low" represent low predation risk, simple fish communities; "High" refer to downstream complex communities where predation risk is higher. "Treatment" refers to the two treatments used in our experiment. "Cue" means that fish were reared in the presence of predator cues, "No Cue" means that they were raised in the absence of such cues. Drainage refer to the drainage from were wild fish used to generate second generation of lab-reared experimental fish were collected. Population refers to the interaction between Drainage and Predation. Data was analyzed in MANCOVA model combining both drainages, and later in separate CVAs.
DOI: 10.5061/dryad.87b01fq0/1
title: Chiari_amnios248genes_nt.nex

description: Nucleotides (codons) concatenation of 248 genes for 16 vertebrate taxa.
DOI: 10.5061/dryad.87b01fq0/2
title: Chiari_amnios248genes_aa.nex

description: Amino acids concatenation of 248 genes for 16 vertebrate taxa.
DOI: 10.5061/dryad.8kk12/1
title: Proteome_t0

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 0 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.8kk12/3
title: Proteome_t4

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 4 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.99n02/1
title: Species descriptions of Ectyphus and Parectyphus in SDD format

description: Natural language species descriptions of Ectyphus and Parectyphus as exported from Lucid Builder 3.5 in SDD format.
DOI: 10.5061/dryad.9b8tt/1
title: Neumeyer et al European Polistes data used for morphometry

description: A tab delimited text file including all body measurements in micrometers used for morphometric analyses. In addition, images showing the exact character definitions.
DOI: 10.5061/dryad.b4d75m52/2
title: Sequences after initial processing in QIIME (seqs.fna, library 2)

description: Raw sequence data from the Roche 454 GS FLX sequencer, region 2 (split_library_output_2). These data are the output of the command: split_libraries.py -m 454_Map.txt -f 2.TCA.454Reads.fna -q 2.TCA.454Reads.qual -o split_library_output_2/ -l 100 -L 700 -H 9 -M 2 -b 10 -n 55100
DOI: 10.5061/dryad.c3b75/3
title: Tait and Havenhand Synthetic AHL data

description: Synthetic AHL data.txt: This data records the number of Balanus improvisus cyprids exploring agarose films containing 5 µM C6-HSL, C8-HSL, OC10-HSL and C12-HSL after 2 days incubation. Data is the percent number of cyprids actively exploring (crawling) on the biofilms. Also recorded is the numbers of cyprids settled within vessels containing the same synthetic AHLs dissolved in seawater to the following concentrations: 0.5, 5 and 50 µM. Data is the percent number of cyprids settled within the vessels. This data was recorded by Karen Tait, Plymouth Marine Laboratory (ktait@pml.ac.uk) at the Department of Biological and Environmental Sciences, Tjarno, Sweden in June 2009. Column headings: Synthetic AHL in agarose film; Vessel number (numbered 1 – 18); C6; C8; OC10; C12; no AHL. Synthetic AHL in seawater; AHL concentration (0, 0.5, 5 or 50 µM); Vessel number (numbered 1 – 21 for each treatment); C6; C8; OC10; C12.
DOI: 10.5061/dryad.c5m7m/1
title: C_dilutus_genotypes

description: Genotypes of 654 green mirid individuals sampled across Australia between 2006 and 2008. These samples were screened using 9 fluorescently labelled microsatellite loci separated by capiliary electrophoresis. Details of the location and host plant of each sample are available in the manuscript.
DOI: 10.5061/dryad.c74nv/1
title: Species descriptions of Leptomydas, Mydaselpis, Syllegomydas, and Vespiodes in SDD format

description: Natural language species descriptions of Leptomydas, Mydaselpis, Syllegomydas, and Vespiodes as exported from Lucid Builder 3.5 in SDD format.
DOI: 10.5061/dryad.d0md6/10
title: transposable elements_repeatmodeler_kmer70-v2-min200-scaffolds.fa

description: ################################### RepeatModeler #################################### version: 1.0.7## command:BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.faRepeatModeler -database goldenEagle_v2_tmpRepeatMasker -nolow -no_is -norna -dir .  -lib  Ach-v2.consensi.fa.classified  kmer70-v2-min200-scaffolds.fa## output files:Ach-v2.consensi.fa.classifiedrepeatmodeler_kmer70-v2-min200-scaffolds.fa.maskedrepeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl
DOI: 10.5061/dryad.d0md6/11
title: transposable elements_Ach-v2.consensi.fa

description: ################################### RepeatModeler #################################### version: 1.0.7## command:BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.faRepeatModeler -database goldenEagle_v2_tmpRepeatMasker -nolow -no_is -norna -dir .  -lib  Ach-v2.consensi.fa.classified  kmer70-v2-min200-scaffolds.fa## output files:Ach-v2.consensi.fa.classifiedrepeatmodeler_kmer70-v2-min200-scaffolds.fa.maskedrepeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl
DOI: 10.5061/dryad.d0md6/12
title: transposable elements_kmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200

description: ####################################### trf ########################################## version:  4.04## command: trf kmer70-v2-min200-scaffolds.fa 2 7 7 80 10 50 200 -f  -h## output files:kmer70-v2-min200-scaffolds.fa.2.7.7.80.10.50.200.dat
DOI: 10.5061/dryad.d0md6/5
title: transposable elements_RepeatProteinMask output_ge_v2_all

description: ################################# RepeatProteinMask ################################## version: 4.0.2## command: RepeatProteinMask -noLowSimple -pvalue 1e-4 -engine abblast kmer70-v2-min200-scaffolds.fa## output files:ge_v2_all.annot
DOI: 10.5061/dryad.d0md6/6
title: transposable elements_repeatmasker_kmer70-v2-min200-scaffolds.fa

description: ################################## RepeatMasker ###################################### RepeatMasker version 4.0.2## RepeatMaskerLibrary-20130422 version## command:RepeatMasker -nolow -no_is -norna -dir .  \-lib RepeatMaskerLib.embl.lib \kmer70-v2-min200-scaffolds.fa## output files:repeatmasker_kmer70-v2-min200-scaffolds.fa.maskedrepeatmasker_kmer70-v2-min200-scaffolds.fa.tbl
DOI: 10.5061/dryad.d0md6/7
title: transposable elements_repeatmasker_kmer70-v2-min200-scaffolds.fa

description: ################################## RepeatMasker ###################################### RepeatMasker version 4.0.2## RepeatMaskerLibrary-20130422 version## command:RepeatMasker -nolow -no_is -norna -dir .  \-lib RepeatMaskerLib.embl.lib \kmer70-v2-min200-scaffolds.fa## output files:repeatmasker_kmer70-v2-min200-scaffolds.fa.maskedrepeatmasker_kmer70-v2-min200-scaffolds.fa.tbl
DOI: 10.5061/dryad.d0md6/8
title: annotated genes_gff

description: 16,571 genes were annotated in the golden eagle genome, this is the .gff file associated with the annotations (see readme.pdf for additional information).
DOI: 10.5061/dryad.d0md6/9
title: transposable elements_repeatmodeler_kmer70-v2-min200-scaffolds.fa.tar

description: ################################### RepeatModeler #################################### version: 1.0.7## command:BuildDatabase -name goldenEagle_v2_tmp -engine ncbi kmer70-v2-min200-scaffolds.faRepeatModeler -database goldenEagle_v2_tmpRepeatMasker -nolow -no_is -norna -dir .  -lib  Ach-v2.consensi.fa.classified  kmer70-v2-min200-scaffolds.fa## output files:Ach-v2.consensi.fa.classifiedrepeatmodeler_kmer70-v2-min200-scaffolds.fa.maskedrepeatmodeler_kmer70-v2-min200-scaffolds.fa.tbl
DOI: 10.5061/dryad.d6p27/1
title: Microsatellite and MHC genetic data

description: First sheet: Neutral microsatellite data for 10 loci in 203 raccoon samples analyzed from four regions (Ontario, New York, Alabama and Florida). Second sheet: MHC alleles identified in 203 raccoon samples including information of animals positive or negative to rabies virus, years of exposure per region, and alleles identified as resistance or susceptible to rabies and within their corresponding lineage 1 (L1) or lineage 3 (L3). Third sheet: number of alleles associated to lineage 1 and 3 per individual and region
DOI: 10.5061/dryad.fc57r/2
title: Figure 02 Antennae

description: Figure 2. Antenna of Adialytus species A Adialytus ambiguus B Adialytus cf. ambiguus C Adialytus arvicola D Adialytus salicaphis E Adialytus thelaxis F Adialytus veronicaecola.
DOI: 10.5061/dryad.h3r16/1
title: supplemental data
DOI: 10.5061/dryad.k7d00/10
title: sperm length data

description: Sperm lengths in different inbreeding levels. Column abbreviations:  trt = treatment: ob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25),male = male id, line = the line male originated from, (within treatment), Thorax = male thorax lentgh, Slentgh = sperm lentgh (mm)
DOI: 10.5061/dryad.k7d00/11
title: sperm velocity

description: Sperm velocity in different male inbreeding levels. Column abbreviations: id = male id, trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25), Track = individual sperm followed for ten frames, velocity = sperm velocity, spermcount = number of sperm in seminal receptacle, Fthorax = female thorax lentgh, Mthorax = male thorax lentgh, correctedvelocity = velocity in microm/s, locvel = log-transformed correctedvelocity
DOI: 10.5061/dryad.k7d00/12
title: egg-to-adut viability

description: Egg-to-adult viability on days 1, 3 and 5 in the single-mating-productivity experiment. Column abbreviations:  trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25), Maleth = male thorax lentgh, Femaleth = female thorax lentgh, viab = viability, fday = day as a factor
DOI: 10.5061/dryad.k7d00/4
title: mating latency (male attractiveness)

description: Mating latencies with virgins in the single-mating-productivity experiment. Column abbreviations: trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25), Femaleth = female thorax lentgh, Maleth = male thorax lentgh, Matlat = mating latency (min), copdur = copulation duration
DOI: 10.5061/dryad.k7d00/9
title: sperm counts 6 days after 2nd copulation

description: Sperm counts from the 6 day ASM treatment. Column abbreviations: ID = female id, trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25), Fthorax = female thorax lentgh, M2thorax = 2nd male thorax lentgh, bursagr = 1st male sperm in bursa, bursared = 2nd male sperm in bursa, prSRgr = 1st male sperm in proximal SR (seminal receptacle), prSRred = 2nd male sperm in proximal SR, distSRgr = 1st male sperm in distal SR, distSRgr = 2nd male sperm in distal SR, SPT1gr = 1st male sperm in spermatheca (SPT) 1, SPT1red = 2nd male sperm in spermatheca 1, SPT2gr = 1st male sperm in spermatheca 2, SPT2red = 2nd male sperm in spermatheca 2, duct1gr = 1st male sperm in spermathecal duct 1, duct1red = 2nd male sperm in spermathecal duct 1, duct2gr = 1st male sperm in spermathecal duct 2, duct2red = 2nd male sperm in spermathecal duct 2, SRtotred = 2nd male sperm in SR, TOTred = total number of 2nd male sperm, SPTtotred = total number of 2nd male sperm in SPT, STOREDred =total number of 2nd male sperm in SR and SPT, remday = remating day, copdur = copulation duration, totgr = total number of first male sperm, logGR = log transformed 1st male sperm, S2 = proportion of second male sperm in SR, asS2= acrsin sqrt transformed S2 value, S2spt = proportion of second male sperm in SPT
DOI: 10.5061/dryad.kc6m8/5
title: CO endogenous leaf damage
DOI: 10.5061/dryad.q31f8/2
title: Arlq_cytb_populations

description: Arlequin input files with population grouping for cytochrome-b data.
DOI: 10.5061/dryad.r606d128/11
title: Lemmon-etal2012_Phylogenetics_BEST_Amniote
DOI: 10.5061/dryad.rc6m9/1
title: Figure 1: Phylogeny of 126 B. anthracis strains based on whole-genome SNP analysis

description: Phylogeny of 126 B. anthracis strains based on whole-genome SNP analysis. A. Minimum spanning tree based on 3987 chromosomal SNPs (obtained with BioNumerics 6.6 from Applied Maths). The 3 canSNP groups present in France are color-coded: B.Br CNEVA in light blue, A.Br 011/009 in purple and A.Br 001/002 in green. The African lineage A.Br 005/006 is indicated in red. Positions of the B. anthracis Sterne (in green), Ames ancestor (in yellow) and A1055 (in black) strains are also marked. Each circle represents a unique SNP genotype. The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the position and name of the new identified French canSNPs. The star marks the approximate branching point of the B. anthracis lineage within the B. cereus group. Based on a parsimony approach, the tree size is 4018, i.e. it contains approximately 0.77% of homoplasia. B. Linear phylogenetic tree rooted with the B. cereus AH820 strain as outgroup. This figure illustrates the relationship between French and globally diverse B. anthracis strains.
DOI: 10.5061/dryad.rc6m9/2
title: Figure 2: Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage

description: Minimum spanning tree of 67 French B. anthracis strains belonging to the B.Br.CNEVA canSNP lineage (obtained with BioNumerics 6.6 from Applied Maths).  Data are based on 345 chromosomal SNPs (A), 14 pXO1 SNPs (B) and 15 pXO2 SNPs (C). The geographic clustering of the French strains is color-coded:  Alps in green (34 strains), Pyrenees in purple (9 strains), Massif Central in red (18 strains) and Saône et Loire department in yellow (6 strains). The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the position and name of four French canSNPs described in this study. Based on a parsimony approach, the tree size is 352, i.e. it contains approximately 1.98% of homoplasia. Concerning the plasmids, the tree sizes are 14 and 15 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia.
DOI: 10.5061/dryad.rc6m9/3
title: Figure 3: Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup

description: Minimum spanning tree of 31 French B. anthracis strains belonging to the A.Br.011/009 canSNP subgroup (obtained with BioNumerics 6.6 from Applied Maths).  Data are based on 560 chromosomal SNPs (A), 20 pXO1 SNPs (B) and 18 pXO2 SNPs (C). The six resolved branches are color-coded. The diameter of each circle varies according to the number of isolates having the same genotype. The length of each branch is proportional (logarithmic scale) to the number of SNPs identified between strains. Indicated in red are the positions and names for two canSNPs described in this study. NE: North-East, SW: South-West, SE: South-East. Based on a parsimony approach, the tree size is 561, i.e. it contains approximately 0.18% of homoplasia. Concerning the plasmids, the tree sizes are 20 and 18 for pXO1 and pXO2, respectively, i.e. it contains no homoplasia.
DOI: 10.5061/dryad.sp0ts0hc/1
title: Swift_etal_2012_AgeComp_Grip_DataSPSS

description: SPSS Data file with variable labels and details of participants, experimental condition, demographics, self-report arthritis and measures of grip strength and persistence
DOI: 10.5061/dryad.t6m37/1
title: disc_packing_08175.tar
DOI: 10.5061/dryad.t6m37/2
title: disc_packing_08183.tar
DOI: 10.5061/dryad.t6m37/3
title: disc_packing_08209.tar
DOI: 10.5061/dryad.t6m37/4
title: disc_packing_08229.tar
DOI: 10.5061/dryad.tk718/1
title: serotinyData

description: Field data collected in Yellowstone National Park, USA
DOI: 10.5061/dryad.v7cj8/1
title: Photometric data ouabain sensitivity of Na+/K+-ATPase

description: Descriptions are included in the data file.
DOI: 10.5061/dryad.vh36n/10
title: Fig3C

description: Microsoft excel file containing raw data for Fig 3C.
DOI: 10.5061/dryad.vh36n/11
title: FigS2

description: Microsoft excel file containing raw data for Fig S2.
DOI: 10.5061/dryad.vh36n/4
title: Fig3B_AICAR

description: Microsoft excel file containing raw data for Fig3B AICAR.
DOI: 10.5061/dryad.vh36n/5
title: Fig3B_Methionine

description: Microsoft excel file containing raw data for Fig3B Methionine.
DOI: 10.5061/dryad.vh36n/6
title: Fig3B_Homocysteine

description: Microsoft excel file containing raw data for Fig3B Homocysteine.
DOI: 10.5061/dryad.vh36n/7
title: Fig3B_Glycine

description: Microsoft excel file containing raw data for Fig3B  Glycine.
DOI: 10.5061/dryad.vh36n/8
title: Fig3B_Serine

description: Microsoft excel file containing raw data for Fig3B Serine.
DOI: 10.5061/dryad.vh36n/9
title: Fig3B_dUMP

description: Fig3B_dUMP.xls: Microsoft excel file containing raw data for Fig3B dUMP.
DOI: 10.5061/dryad.vj4f7/2
title: Khanshour et al_SupMat_Figure S2

description: Hardy-Weinberg equilibrium status in 14 populations and 15 loci. For the total markers together in each population, the Fisher’s method was used after Bonferroni correction to determine the significant deviation of a population from H-W equation. Population abbreviations could be seen in Table 1
DOI: 10.5061/dryad.16737/4
title: Acuclavella_EF1a_Richart&Hedin_Outgroup_IngroupIntron

description: Alignment of 37 sequences: 7 Dyspnoi outgroup and 30 Acuclavella ingroup.  Alignment contains introns for ingroup sequences only.
DOI: 10.5061/dryad.510sb/2
title: Cooper&Nunn_PhylogeneticModels

description: This contains the data needed to identify well- and poorly-sampled primate species in relation to their geographic range. And also the data needed to fit models of sampling events against primate characteristics.
DOI: 10.5061/dryad.510sb/3
title: Cooper&Nunn_GeographicalModels

description: This contains the data needed to identify well- and poorly-sampled countries in relation to their primate species richness. And also the data needed to fit models of sampling events against country characteristics.
DOI: 10.5061/dryad.510sb/4
title: Cooper&Nunn_CountryParasiteSAC

description: This contains the data needed to plot parasite species accumulation curves for each country
DOI: 10.5061/dryad.5c20k/1
title: Data format Kaarlejarvi Transplant

description: DATA COLLECTION: This data were collected in beginning of August 2011 in Kilpisjärvi, NW Finland (69.055⁰N, 20.887⁰E). Data comes from full-factorial warming-fertilization-herbivore exclusion experiment, where transplants of three forbs were grown for two growing seasons. For detailed methods see Kaarlejärvi et al. 2013, Funct Ecol. The file contains total biomass estimates of the three transplant species, reproductive biomass for two of the species and estimates of total vascular plant biomass on the study plots using point-intercept method. DATA FORMAT: Year: sampling year, PlotID: Individual identification code for each of 56 study plots (7 replicates of each of 8 treatment combinations), Exclosure: “grazed” indicates plots without exclosure, “ungrazed” refers to plots with exclosures against mammalian herbivores, Fertilization: Self-explanatory, whether a plot was fertilized or not using NPK-fertilizer, Warming: Self-explanatory, whether a plot was warmed or not using Open Top Chamber, bmEpiang: Biomass of transplanted Epilobium angustifolium after two growing seasons (expressed in grams), bmSildio: Biomass of transplanted Silene dioica after the second growing season (expressed in grams), bmSolvir: Biomass of transplanted Solidago virgaurea  after the second growing season (expressed in grams), bmSildioF: Reproductive biomass of transplanted Silene dioica after the second growing season (expressed in grams), bmSolvirF: Reproductive biomass of transplanted Solidago virgaurea  after the second growing season (expressed in grams), VascularTotalHits: Total number of vascular plant hits per 108 pins systematically spread over 25 x 50 cm2 area in the middle of each study plot.
DOI: 10.5061/dryad.5fr85/3
title: Herb_Para_Int_20farms_0506

description: Data on insect herbivore and parasitoid interactions on 20 farms.
DOI: 10.5061/dryad.65r9c/1
title: development stages

description: Survival of eggs, larvae and pupae after cold shocks and chill coma recovery times of adults