cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6s0h6/1
title: Interaction Matrices and species-level specialization values

description: Interaction matrices of birds and malaria parasites in the two study sites. Also provided are sample sizes (N), the number of associates (degree), species-level specialization (d’), and phylogenetic species-level specialization (wMPD). We placed “TI” in front of each lineage number from Tiputini to distinguish these from “OZ” lineages and an “H” or a “P” in front of each lineage name to distinguish between Haemoproteus and Plasmodium. An “L” is placed after lineage names consisting of more than one haplotype.
DOI: 10.5061/dryad.6s0h6/2
title: GenBank ID numbers

description: GenBank IDs of associate bird species and parasite lineages used in the phylogenetic specificity indices.
DOI: 10.5061/dryad.6s0h6/3
title: Bird RAG-1 alignment

description: Bird RAG-1 alignment file. Outgroup species begin with "out" and are followed by their GenBank ID.
DOI: 10.5061/dryad.6s0h6/4
title: Parasite cytb alignment

description: Parasite cytb alignment file. Outgroup species begin with "O" and are followed by their GenBank ID.
DOI: 10.5061/dryad.7m6kg/8
title: Figs. 2c, 6b & 8b: ROM 60146 — Nectocaris pteryx (head) from the Burgess Shale, direct illumination

description: Specimen with well-preserved soft tissue has smooth, unornamented tentacle margins.  Robustly lined funnel canal is surrounded by fleshy tissue.
DOI: 10.5061/dryad.82hk6/1
title: original data  for all figures

description: The original data for all figures in the manuscript.
DOI: 10.5061/dryad.83164r7v/6
title: Nhum.454
DOI: 10.5061/dryad.83164r7v/7
title: Psub.454
DOI: 10.5061/dryad.8qc20/1
title: Evolved and initial dormancy fractions

description: This file contains data on final evolved dormancy fractions and initial dormancy fractions of ascospores of Neurospora crassa subjected to a range of "bad year" treatments under laboratory conditions.  Column headings: Df=final dormancy fraction; Di=initial dormancy fraction; Delta D=difference in dormancy fraction; % BY=percent "bad year" treatment; GL=genetic lineage; SL=year-type sequence line.
DOI: 10.5061/dryad.c0164/2
title: female reinf learn loop prog familiarity

description: Program for the section of the paper titled "Female learning model: Preference for familiar types"
DOI: 10.5061/dryad.c0164/3
title: female reinf learn loop prog eig

description: Program for the female learning model that calculates the eigenvalues describing the rate of spread of an allele for assortative mating.
DOI: 10.5061/dryad.c459h/1
title: LartillotSB2013suppmat

description: Supplementary information
DOI: 10.5061/dryad.ct70q/1
title: Chemotoxicity phenotypes

description: The file contains fecundity measurements for females dosed with carboplatin, gemcitabine, methotrexate, or mitomycin C using the DSPR panel of recombinant inbred lines and an ABcross design (see http://FlyRILs.org for details about the DSPR and the cross design). There are 3 replicate measures for each cross. See readme file for column names.
DOI: 10.5061/dryad.f058c/20
title: Pop17

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 17. Individuals that belong to population-pool 17 are listed in Table 1.
DOI: 10.5061/dryad.f3b77/1
title: 01_Arthropods_2008

description: The files 01_Arthropods_2008 and 01_Arthropods_2009 include abundance data on adult arthropods per plot and year.SpeciesCode --&gt; Species' identifier, identical across yearsAuthor	--&gt; Author of species' nameOrder --&gt; Taxonomic oderSuborder --&gt; Taxonomic suborderFamily --&gt; Taxonomic familyBody_length_mm --&gt; mean body length [mm] for the species as described in literatureBiomass_mg --&gt; estimated species' biomass [mg] which was calculated from Body_length_mmFeeding --&gt; species' feeding guild (predator or herbivor)AEG01 etc. --&gt; plot-specific ID
DOI: 10.5061/dryad.f3b77/2
title: 01_Arthropods_2009

description: The files 01_Arthropods_2008 and 01_Arthropods_2009 include abundance data on adult arthropods per plot and year.SpeciesCode --&gt; Species' identifier, identical across yearsAuthor	--&gt; Author of species' nameOrder --&gt; Taxonomic oderSuborder --&gt; Taxonomic suborderFamily --&gt; Taxonomic familyBody_length_mm --&gt; mean body length [mm] for the species as described in literatureBiomass_mg --&gt; estimated species' biomass [mg] which was calculated from Body_length_mmFeeding --&gt; species' feeding guild (predator or herbivor)AEG01 etc. --&gt; plot-specific ID
DOI: 10.5061/dryad.f3b77/3
title: 02_Plant_cover_2008

description: The files 02_Plant_cover_2008 and 02_Plant_cover_2009 include cover data of vascular plants per plot and year.SpeciesCode --&gt; Species' identifier, identical across yearsFunctional_type --&gt; Species were assigned as grass, herb or shrub speciesAEG01 etc. --&gt; plot-specific ID
DOI: 10.5061/dryad.f3b77/4
title: 02_Plant_cover_2009

description: The files 02_Plant_cover_2008 and 02_Plant_cover_2009 include cover data of vascular plants per plot and year.SpeciesCode --&gt; Species' identifier, identical across yearsFunctional_type --&gt; Species were assigned as grass, herb or shrub speciesAEG01 etc. --&gt; plot-specific ID
DOI: 10.5061/dryad.f3b77/5
title: 03_Landuse_2006to2008

description: The files 03_Landuse_2006to2008 and 03_Landuse_2007to2009 include land-use information per plot and year.ID --&gt; Row name based on year and PlotIDYear --&gt; Year for which land-use is givenPlotID --&gt; plot specific IDRegion --&gt; One of three regions in Germany in which plot is locatedFertilization --&gt; intensity of fertilization estimated as kg Nitrogen per hectarGrazing --&gt; intensity of grazing estimated as lifestock-units-days per hectarMowing --&gt; number of cutting events per year
DOI: 10.5061/dryad.f3b77/6
title: 03_Landuse_2007to2009

description: The files 03_Landuse_2006to2008 and 03_Landuse_2007to2009 include land-use information per plot and year.ID --&gt; Row name based on year and PlotIDYear --&gt; Year for which land-use is givenPlotID --&gt; plot specific IDRegion --&gt; One of three regions in Germany in which plot is locatedFertilization --&gt; intensity of fertilization estimated as kg Nitrogen per hectarGrazing --&gt; intensity of grazing estimated as lifestock-units-days per hectarMowing --&gt; number of cutting events per year
DOI: 10.5061/dryad.f3b77/7
title: 04_SEMData_2008

description: The files 04_SEMData_2008 and 04_SEMData_2009 include compiled information used for structural equation modeling.PlotID --&gt; plot specific IDRegion --&gt; One of three regions in Germany in which plot is located (SEM was conducted for each region separately)Fertilization --&gt; intensity of fertilization, averaged over three years and standardized per regionGrazing --&gt; intensity of grazing, averaged over three years and standardized per regionMowing --&gt; intensity of mowing, averaged over three years and standardized per regionTime_after_mowing --&gt; Number of days between last mowing event and sampling in the year of samplingPlant_SpeciesRichness --&gt; Number of vascular plant speciesPlant_biomass --&gt; Plant biomass [g dry weight]Herbivore_SpeciesRichness --&gt; Number of herbivorous arthropod speciesPredator_SpeciesRichness --&gt; Number of arthropod predator speciesHerbivore_biomass --&gt; Overall biomass [mg] of herbivore speciesPredator_biomass --&gt; Overaall biomass [mg] of predator speciesLifestock --&gt; Type of lifestock on the plot (only for 2008 data)
DOI: 10.5061/dryad.f3b77/8
title: 04_SEMData_2009

description: The files 04_SEMData_2008 and 04_SEMData_2009 include compiled information used for structural equation modeling.PlotID --&gt; plot specific IDRegion --&gt; One of three regions in Germany in which plot is located (SEM was conducted for each region separately)Fertilization --&gt; intensity of fertilization, averaged over three years and standardized per regionGrazing --&gt; intensity of grazing, averaged over three years and standardized per regionMowing --&gt; intensity of mowing, averaged over three years and standardized per regionTime_after_mowing --&gt; Number of days between last mowing event and sampling in the year of samplingPlant_SpeciesRichness --&gt; Number of vascular plant speciesPlant_biomass --&gt; Plant biomass [g dry weight]Herbivore_SpeciesRichness --&gt; Number of herbivorous arthropod speciesPredator_SpeciesRichness --&gt; Number of arthropod predator speciesHerbivore_biomass --&gt; Overall biomass [mg] of herbivore speciesPredator_biomass --&gt; Overaall biomass [mg] of predator speciesLifestock --&gt; Type of lifestock on the plot (only for 2008 data)
DOI: 10.5061/dryad.f3b77/9
title: ReadMe_Datapackage

description: This file contains a description of the complete datapackage, individual ReadMe files are available for each data file.
DOI: 10.5061/dryad.f50h2/1
title: Matrices.For.Dryad

description: Excel file containing spreadsheet with ahistorical and historical demographic matrices used in deterministic and stochastic invasibility analyses.
DOI: 10.5061/dryad.f5667/1
title: HopkinsLandmarksJEB

description: The text file "HopkinsLandmarksJEB.txt" contains x and y coordinates landmarks for all specimens used in this analysis before paired landmarks were reflected across the sagittal axis. The first column shows the species name. The second column shows the collection number that the specimen came from or the museum repository number for the specimen (all specimens prefaced with “USNM” are held at the National Museum of Natural History, Smithsonian). See Hopkins 2011 (Evolution 65:3252-3273, Tables S1, S2) for locality information for each collection. The remaining columns list the x and y coordinates of each landmark from 1 to 15. See figure in ReadMe file for landmark chart (compare with Figure 1 in which landmarks are numbered after reflection). Missing landmarks are indicated by "NA". The baseline for reflection was defined by landmarks 2 and 4. Some of these data were previously made available on Dryad because they were used in the Evolution paper cited above.
DOI: 10.5061/dryad.ft94b/4
title: MHC_454

description: This compressed file contains two folders with all of the raw 454 files for MHCIIb for this project. Each file name includes on of three libraries (02, 03, or 04) and a MID number 1-153. These numbers correspond to various spreadsheets in the R scripts folder.
DOI: 10.5061/dryad.g6r70/9
title: Boraginaceae_partition

description: File to specify DNA partitions to RAxML. Data were partitioned by genome and codon position.
DOI: 10.5061/dryad.gt875/2
title: Rasic&Keyghobadi_Supl_Tables

description: Supplemental Tables 1-3
DOI: 10.5061/dryad.h658g/1
title: Kirk_microsatellite_genotypes

description: Microsatellite genotyping data for 15 Grapholita molesta individuals from each of 26 populations sampled across the global distribution range.
DOI: 10.5061/dryad.j2r64/12
title: Supplementary Figure 2. Effect of removing the least complete fossils

description: Supplementary Figure 2. Divergence time estimates from total-evidence analyses based on all data (45 fossils; tree and 95% highest posterior density (HPD) interval bars in red) or only the fossils with more than 10% of the 343 morphological characters scored (31 fossils; green bars). While the topology is the same and the median age estimates are similar, the HPD intervals are in general wider when the most poorly preserved fossils are excluded.
DOI: 10.5061/dryad.jk82v/1
title: Curing effect of toxin on infection by nematodes

description: Effect of toxin on infection status of flies. File is text format. Each row is a fly.
DOI: 10.5061/dryad.jk82v/2
title: Survival of adult flies

description: Survival of adult flies from two different populations, exposed or not to toxin.  Each line is an individual fly.
DOI: 10.5061/dryad.jr4dc/4
title: Mutation rate with hydrogen peroxide

description: Mutation rate of P. aeruginosa WT and mutators before treatment and after treatment with hydrogen peroxide washing and non washing the cells calculated with the MSS maximum likelihood method.
DOI: 10.5061/dryad.kc6m8/11
title: Microsatellite data 28 loci from 9 populations
DOI: 10.5061/dryad.kc6m8/12
title: MT&CO Plant Means BC-ratio
DOI: 10.5061/dryad.kc6m8/13
title: NILs 2008 BCMA GS Traits
DOI: 10.5061/dryad.kc6m8/14
title: NILs MT&CO Herbivory
DOI: 10.5061/dryad.kc6m8/15
title: Parker x Ruby GS data
DOI: 10.5061/dryad.kc6m8/16
title: RILs MT&CO FamMeans BCMA nohets
DOI: 10.5061/dryad.kc6m8/17
title: RILs MT&CO indiv plants BCMA nohets
DOI: 10.5061/dryad.kc6m8/18
title: BCMA allele-specific expression
DOI: 10.5061/dryad.m0n61/13
title: *BEAST xml 1

description: 1 of 6 xml files for *BEAST analysis
DOI: 10.5061/dryad.q3d0n/1
title: Quero et al 2013 Ecosystems
DOI: 10.5061/dryad.r1d6g/1
title: Hodgson et al Duffy program and data

description: fastadsim.pl forward simulation computer program and 10k SNP genotype data
DOI: 10.5061/dryad.r5v40/1
title: R script for QTL analysis (A population)

description: This R script allows a user to read in genotype data for the DSPR (Drosophila Synthetic Population Resource, FlyRILs.org) and nicotine resistance phenotype data, and recapitulate the QTL mapping results presented in Marriage et al. for the "A" population of DSPR RILs.
DOI: 10.5061/dryad.r5v40/2
title: R script for QTL analysis (B population)

description: This R script allows a user to read in genotype data for the DSPR (Drosophila Synthetic Population Resource, FlyRILs.org) and nicotine resistance phenotype data, and recapitulate the QTL mapping results presented in Marriage et al. for the "B" population of DSPR RILs.
DOI: 10.5061/dryad.r5v40/3
title: Nicotine Resistance Phenotypes (A population)

description: This file contains nicotine resistance measures for a large number of A lines from the Drosophila Synthetic Population Resource (DSPR, www.FlyRILs.org). Line identifiers are presented in the "patRIL" column, and phenotypes are presented in the "NicotineViability" column. Together with genotype data and analytical R code this file allows users to generate the QTL mapping results presented in Marriage et al. for the A population of DSPR RILs.
DOI: 10.5061/dryad.r5v40/4
title: Nicotine Resistance Phenotypes (B population)

description: This file contains nicotine resistance measures for a large number of B lines from the Drosophila Synthetic Population Resource (DSPR, www.FlyRILs.org). Line identifiers are presented in the "patRIL" column, and phenotypes are presented in the "NicotineViability" column. Together with genotype data and analytical R code this file allows users to generate the QTL mapping results presented in Marriage et al. for the B population of DSPR RILs.
DOI: 10.5061/dryad.r5v40/5
title: DSPR Genotypes (A population)

description: This file contains genotypes for the population A RILs (Recombination Inbred Lines) of the DSPR (Drosophila Synthetic Population Resource). The genotypes were originally published in King et al. (Genome Research 2012, 22:1558-66) and are also available at www.FlyRILs.org (Data Release 2 - HMM Results for pA RILs at regularly spaced 10 kb intervals). The genotypes are derived from a Hidden Markov Model (HMM) at regularly spaced 10KB positions along the Drosophila melanogaster genome. There are no column headers in the file. Columns are: chromosome, genome position, line identifier, 36 columns of founder genotype probabilities, and 8 columns of additive probabilities. The precise names for each of the columns are listed in the analysis R code file for population A. Together with this code, and the nicotine resistance phenotype scores, a user can recapitulate the QTL mapping from Marriage et al.
DOI: 10.5061/dryad.r5v40/6
title: DSPR Genotypes (B population)

description: This file contains genotypes for the population B RILs (Recombination Inbred Lines) of the DSPR (Drosophila Synthetic Population Resource). The genotypes were originally published in King et al. (Genome Research 2012, 22:1558-66) and are also available at www.FlyRILs.org (Data Release 2 - HMM Results for pB RILs at regularly spaced 10 kb intervals). The genotypes are derived from a Hidden Markov Model (HMM) at regularly spaced 10KB positions along the Drosophila melanogaster genome. There are no column headers in the file. Columns are: chromosome, genome position, line identifier, 36 columns of founder genotype probabilities, and 8 columns of additive probabilities. The precise names for each of the columns are listed in the analysis R code file for population B. Together with this code, and the nicotine resistance phenotype scores, a user can recapitulate the QTL mapping from Marriage et al.
DOI: 10.5061/dryad.sc6k5/2
title: Bellamy et al. FIle 2
DOI: 10.5061/dryad.t4n0g/3
title: Viburnum_dentatum_mites

description: The number of non-herbivorous mites collected on experimentally manipulated leaves of Viburnum dentatum. Field experiment conducted at near Ithaca, NY, USA (42 30 1.44N, 76 26 8.52W). Column headings: "TREMNT" = experimental treatment/manipulation applied to plant ("ALL OPEN" = control tar placed near, but not covering, extrafloral nectaries (EFN) and domatia, "BOTHX" = tar blocking/covering both EFN and domatia, "DOMX" = tar blocking/covering domatia and tar control near EFN, "EFNX" tar blocking/covering EFN and tar control near domatia); "Mites" = the number of non-herbivorous mites.
DOI: 10.5061/dryad.0s96k/1
title: Code_Matlab
DOI: 10.5061/dryad.1368p/1
title: Genepop Data File

description: Genepop data file (3 digit format) used for analyses - sample codes are listed in Table 1 of the manuscript.
DOI: 10.5061/dryad.16v7n/1
title: Visitation

description: Per-flowerhead visitation rates to Holocarpha virgata ssp. virgata (Asteraceae) and densities of flower-visiting insects in 2 x 2 m plots spanning the available range of floral densities at a variety of sites and dates within the flowering season
DOI: 10.5061/dryad.1kf76/1
title: Xenopus tail weight experiment
DOI: 10.5061/dryad.1kf76/2
title: Tadpole morphological measurements
DOI: 10.5061/dryad.1kf76/3
title: Natural pond survey
DOI: 10.5061/dryad.1kf76/4
title: Tadpole CORT measurements over time
DOI: 10.5061/dryad.1kf76/5
title: Mesocosm (P and NP) tadpole CORT
DOI: 10.5061/dryad.1kf76/6
title: Tadpole survivorship study
DOI: 10.5061/dryad.271cs/1
title: Leaf size and shape in Ocotea tenera (Lauraceae)

description: measurements of almost 3000 leaves over a 26-year period
DOI: 10.5061/dryad.277g0/2
title: EcJME_protein_ORFs
DOI: 10.5061/dryad.2k462/1
title: Data for Figure 2 (part 1)
DOI: 10.5061/dryad.2ng61/1
title: Bee genotypes

description: Microsatellite genotypes of fighting bees over a three month period in Brisbane
DOI: 10.5061/dryad.367s2.1
title: Data from: Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
DOI: 10.5061/dryad.367s2.2
title: Data from: Estimating quantitative genetic parameters in wild populations: a comparison of pedigree and genomic approaches
DOI: 10.5061/dryad.367s2.2/1.1
title: inversepedigree1
DOI: 10.5061/dryad.367s2.2/2.1
title: inversepedigree2
DOI: 10.5061/dryad.367s2.2/3.1
title: grmdryad.grm.gz
DOI: 10.5061/dryad.367s2.2/4.1
title: grmdryad.grm.id
DOI: 10.5061/dryad.367s2.2/5.1
title: birtweightoldpedigreedryad
DOI: 10.5061/dryad.367s2.2/6.1
title: birtweightnewpedigreedryad
DOI: 10.5061/dryad.3sv4p/1
title: Dryad_Data_for_14-0032.R1

description: Semicircular canal shape and linear data for 14-0032.R1
DOI: 10.5061/dryad.47jh1/1
title: Data on Amazonian bird positions

description: Each spreadsheet contains a different flock.  Positions as grid references are in the first two columns, times in the third.
DOI: 10.5061/dryad.49kt0/1
title: final hhd data for submission

description: Table of all patients included for home visits. Patients were identified by date of birth and hospital number which have been removed for confidentiality. Data extracted from our renal database. Outcome of visits supplied by renal social worker and predialysis nurse from logged home visits. Race as stated by patient. DM refers to diabetic or not, RRT refers to the modality of renal replacement implemented following home visit, DHS relates to whether home met basic government standards, HHSR code lists specific hazards in the home (max 4 per home listed) and temp accom refers to whether the accomodation was of a temporary nature, With regards RRT, APD donates automated peritoneal dialysis, CAPD continual ambulatory peritoneal dialysis, HD haemodialysis and the various initials following HD refer to the different renal units within out catchment.
DOI: 10.5061/dryad.4ms68/1
title: ALL_demographics and baseline_Dryad

description: Demographics and baseline data of all recruited participants
DOI: 10.5061/dryad.52565/1
title: Emberizinae.mtnuc_generic_12_18_09

description: Data set including all sampled genera.
DOI: 10.5061/dryad.5sc31/1
title: Simulated_Data_per_scenario_Genetix

description: Genetic data simulated under 27 different scenarios
DOI: 10.5061/dryad.5sc31/3
title: R_Scripts

description: R scripts used to (i) test msvar MCMC chains convergence (ii) calculate bayes factors for the time of the beginning of demographic changes inferred with msvar (iii) estimate effect sizes and other statistics through posterior parameter distributions for msvar and (iv) to simulate genetic data with ms.
DOI: 10.5061/dryad.6n660/1
title: Trade-offs BMC Evol Biol Matlab scripts + data

description: Matlab scripts to collect data. Data used for analysis.
DOI: 10.5061/dryad.7k2d1/1
title: field_data_tabular

description: These data represent gypsy moth population growth rates, topographic characteristics, and resource density over 22850 1x1 km locations in western Virginia and West Virginia, USA.  They were derived from a combination of sources. Gypsy moth population data were derived from pheromone-baited trap catch data provided by the gypsy moth Slow the Spread Program, Inc.  The basal area of gypsy moth preferred host trees is from: Morin, et al. 2005. Mapping host-species abundance of three major exotic forest pests. USDA Forest Service Research Paper NE-726. Topographic variables were derived from a digital elevation model from the National Elevation Dataset, United States Geologic Survey (2009). Please find additional details in the ReadMe file.
DOI: 10.5061/dryad.7k2d1/2
title: mating_success_model_commented

description: R code for a model of gypsy moth mating success with phenology varying due to changes in elevation and latitude.  Comments to aid in understanding the model are provided in-code.
DOI: 10.5061/dryad.7kd74/2
title: Sampling locations

description: Samples collected are listed as subspecies, sampling localities, geographic coordinates, sample type, and total sample size with corresponding Map references and population labels.1 Numbers corresponding to localities shown in Fig. 1.2 Two types of sample were collected in the present study: b: blood; f: feather.
DOI: 10.5061/dryad.7m6kg/27
title: Figs. 4c & 10c: ROM 60144 – Nectocaris pteryx from the Burgess Shale

description: Complementary preservation of lineations: broad stripes are visible anteriad, fine striations posteriad.  Assuming that this represents a single individual, the anterior portion of this specimen is somewhat oblique to the sediment.  Interference image.
DOI: 10.5061/dryad.7m6kg/28
title: Figs. 4c & 10c: ROM 60144 – Nectocaris pteryx from the Burgess Shale

description: Crossed polars
DOI: 10.5061/dryad.7m6kg/29
title: Figs. 4c & 10c: ROM 60144 – Nectocaris pteryx from the Burgess Shale

description: Direct illumination
DOI: 10.5061/dryad.8339m/1
title: Level-1_Bacharach

description: Structure data file. C. arvensis- and U. dioica-associated populations of H. obsoletus sampled over five consecutive years (2005-2009) at the syntopic site Bacharach, Germany
DOI: 10.5061/dryad.8k015/1
title: resistance data from cross-infection assays

description: Laboratory selection experiment, cross-infection assay data
DOI: 10.5061/dryad.93p4q/5
title: AlyrataNCSpMaQTL