cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.7vg5fd0/3
title: TABLE 5. Table incorporating all other taphonomic classification systems used in this study of the I. duncani specimens from Isisford [13,16,20,26–28,32,101–104,106–114] that were used in conjunction with Table IV in Dodson [19] and trends classified by Beardmore et al. [40].

description: Table incorporating all other taphonomic classification systems used in this study of the I. duncani specimens from Isisford [13,16,20,26–28,32,101–104,106–114] that were used in conjunction with Table IV in Dodson [19] and trends classified by Beardmore et al. [40]. We also chose to include counts of number of individual specimens (NISP) and minimum number of elements (MNE) with and without osteoderms, for ease of comparison in future with other tetrapods lacking dermal skeletons. The maximum number of skeletal elements in I. duncani, both excluding and including osteoderms, are listed next to MNE. Specimens QM F58793 and QM F58794 were found in close proximity, therefore NISP, MNE, and MNI are listed both grouped together (MNI = 2), and separately, to demonstrate the variation in NISP and MNE per individual. Where possible, life stage was determined by identifying closure neurocentral sutures in vertebrae (closure proceeds caudally to cranially throughout ontogeny, with ‘adult’ defined as possessing closed neurocentral sutures in all vertebrae) and size comparison to the holotype that has been identified as an adult (see Salisbury et al. [66]).  By comparing across specimen numbers, we determined whether disarticulated elements showed greater degrees of bone surface modifications. Degrees of articulation and completeness are the sum total of scores for each skeletal unit. The Dodson [19] classification scheme assumes absences are true absences; we selected the most likely class per specimen based on other taphonomic indicators (such as truncation with block, articulation versus completeness, and so on).
DOI: 10.5061/dryad.cp8bh43/1
title: Data from de Avila et al. (2018) - Journal of Applied Ecology

description: Data of aboveground biomass increment from a long-term experiment in the Brazilian Amazon over two recovery periods: post-logging (1983-1989) and post-thinning (1995-2012). In total, 41 permanent sample plots were monitored. The following variables are given: aboveground biomass increment of surviving trees (dAGBsurvivors), aboveground biomass increment of recruit trees (dAGBrecruits), aboveground biomass increment of total community (dAGBgross), disturbance intensity quantified as basal area reduction (BAreduction) and basal area remaining (BAremaining), taxonomic diversity calculated as the rarefied number of species (Srar), functional diversity defined as the multivariate functional trait dispersion (FDis), structural diversity quantified using the Gini coefficient (Gini), and the community-weighted mean (CWM) trait values of five functional traits linked to biomass productivity (specific leaf area - CWM.SLA, leaf nitrogen and phosphorous concentration - CWM.Nleaf and CWM.Pleaf, leaf toughness - CWM.FPs and wood density - CWM.WD).
DOI: 10.5061/dryad.h24r6/1
title: Polio Research_1

description: Primary data of the research stored in SPSS version 20
DOI: 10.5061/dryad.k8b8n/1
title: Gwas_simulations_All_Animals

description: GWAS simulation results obtained for the full data set (1036 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.
DOI: 10.5061/dryad.k8b8n/2
title: Gwas_simulations_centralityG

description: GWAS simulation results obtained for the Network G matrix sample (286 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.
DOI: 10.5061/dryad.k8b8n/3
title: Gwas_simulations_CentralityIBD

description: GWAS simulation results obtained for the full Network IBD sample (210 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.
DOI: 10.5061/dryad.k8b8n/4
title: Gwas_simulations_threshold_Gmatrix

description: GWAS simulation results obtained for the Threshold G matrix (286 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.
DOI: 10.5061/dryad.k8b8n/5
title: Gwas_simulations_thresholdIBD

description: GWAS simulation results obtained for the Threshold IBD sample (203 animals). The file contain the folders with the simulations performed using both heritability value (h2=0.2 and h2=0.5). Inside these folders it is possible to find all the GWAS simulations results (for each replicated), a file with all the results merged and the simulated QTLs.
DOI: 10.5061/dryad.k8b8n/6
title: Tabular_kinship_AllAnimals

description: This file contains the Kinship values between each pair of individuals present in the All animals sample. Theses kinship values were used in each resampling approach applied in the present study.
DOI: 10.5061/dryad.n9r96/1
title: Two Strains: eCFP vs. eYFP inoculated in equal fractions

description: eCFP and eYFP inoculated in equal fractions. Imaged on the 8th day of growth. See the README for more info.
DOI: 10.5061/dryad.n9r96/2
title: Three Strains: eCFP, eYFP, and black inoculated in equal fractions

description: eCFP, eYFP, and black inoculated in equal fractions. Imaged on the 8th day of growth. See the README for more info.
DOI: 10.5061/dryad.n9r96/3
title: Two Strains: black vs. mCherry inoculated in equal fractions

description: black and mCherry inoculated in equal fractions. Imaged on the 8th day of growth. See the README for more info.
DOI: 10.5061/dryad.n9r96/4
title: Three Strains: eCFP, eYFP, and mCherry inoculated in equal fractions

description: eCFP, eYFP, and mCherry inoculated in equal fractions. Imaged on the 8th day of growth. See the README for more info.
DOI: 10.5061/dryad.n9r96/5
title: Four Strains: eCFP, eYFP, black, and mCherry inoculated in equal fractions

description: eCFP, eYFP, black, and mCherry inoculated in equal fractions. Imaged on the 8th day of growth. See the README for more info.
DOI: 10.5061/dryad.n9r96/6
title: Three Strains: 10% eCFP, 10% eYFP, and 80% mCherry

description: eCFP, eYFP, and mCherry inoculated in fractions of 10%, 10%, and 80% respectively. Imaged on the 8th day of growth. See the README for more info.
DOI: 10.5061/dryad.n9r96/7
title: Well-mixed fitness of each strain: FACS measurements

description: See the "Comparing well-mixed fitness to fitness from expansion velocities" section of our paper. The attached excel file contains the abundance of each strain competing against mCherry (BW003) in well-mixed culture vs. time; we obtained this data from a FACS machine. We used this data to determine the selective advantage of every strain relative to mCherry in well-mixed culture.
DOI: 10.5061/dryad.n9r96/8
title: Calculating the Wall Velocity: Single Sectors of each Strain Sweeping through mCherry

description: See the "Measuring the domain wall velocities v_w^{ij}" section of our paper. We inoculated 10% of a more fit strain (eCFP, eYFP, or black) and 90% of mCherry so that single sectors of the more fit strain would sweep through mCherry (i.e. we wanted to avoid the collision of domain walls). We used the data contained in this package to calculate the wall velocity v_w^{iR} of each strain sweeping through mCherry. See the attached README for more info.
DOI: 10.5061/dryad.pc78t/39
title: Figure S9 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/40
title: Figure S10 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/41
title: Figure S11 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/42
title: Figure S12 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/43
title: Figure S13 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/44
title: Figure S14 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/46
title: Figure S15 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/47
title: Figure S16 october 2017

description: supp fig
DOI: 10.5061/dryad.pd959.2
title: Data from: Pluck or luck: does trait variation or chance drive variation in lifetime reproductive success?
DOI: 10.5061/dryad.pd959.2/1.2
title: age2SizePars.R

description: Data file used by IdahoIPMFunctions.R
DOI: 10.5061/dryad.sn00q/1
title: Output of Phylosift (placement and summary files)

description: Phylosift (Darling et al., PeerJ, 2014) was run on sequencing read sets obtained using Illumina technology on metagenomic DNA extracted from salivary samples of 33 human individuals: 12 hunter-gatherers (HG) and 12 traditional farmers (TF) from the Philippines and 9 Western individual controls (WC). Source metagenomic read datasets are available at the ENA (www.ebi.ac.uk/ena): for HGs and TFs (original data), under BioSample accessions ERS1202862-ERS1202885; for WCs (previously published data): under BioSample accessions SRS013942, SRS014468, SRS014692, SRS015055, SRS019120, SRS104275 and SRS147126, and two other non-publicly available read data from BioProject PRJNA231652.
DOI: 10.5061/dryad.td8kt/1
title: XRD-FILE
DOI: 10.5061/dryad.v0s27.2
title: Data from: Automated integration of trees and traits: a case study using paired fin loss across teleost fishes
DOI: 10.5061/dryad.v0s27.2/11.2
title: README file
DOI: 10.5061/dryad.v0s27.2/12.2
title: Supplementary Materials File 1

description: Teleostei species-level tree from Open Tree. Tree description file (Newick) from Open Tree synthesis used as the input into Mesquite.
DOI: 10.5061/dryad.v0s27.2/13.2
title: Supplementary Materials File 2

description: Output files of synthesis tree build from Open Tree. Archive files of the output directory for each step in the synthesis tree build.
DOI: 10.5061/dryad.v0s27.2/14.2
title: Supplementary Materials File 3

description: Merged tree matrix. NEXUS-formatted translation of the final output matrix (Supplementary Materials Matrix 4) merged with the Teleostei species-level tree from Open Tree (Supplementary Materials File 1). This combined matrix and tree file was used for ancestral state reconstruction in Mesquite.
DOI: 10.17632/pzgfz8tgzt.1
title: Data for: Influence of food supply and shore height on the growth of the barnacle Balanus glandula

description: See readme_altasea.txt for description of individual files. These files comprise all of the data for a study of insitu food manipulation for the barnacle Balanus glandula, including water quality, temperature, and barnacle morphometrics
DOI: 10.17632/t2rbsbc2h6.2
title: Data for: Cut-off frequencies of circumferential horizontal shear waves in various functionally graded cylinder shells

description: The program is Maple 14 file. The relation between the cut-off frequencies and the gradient parameter are calculated based on the program.
DOI: 10.5061/dryad.104kg/1
title: Raw metabarcode data Slot 1 (12 libraries)

description: Raw metabarcode data Slot 1 (12 libraries). Inlcudes R1 and R2 files for macrofauna samples from the 3 impacted and 3 control sites, each sampled at two times after pesticide spill. More info on paper.
DOI: 10.5061/dryad.104kg/2
title: Raw_metabarcode_data_Slot_2_(12_libraries)

description: Raw metabarcode data Slot 2 (12 libraries). Inlcudes R1 and R2 files for meiofauna samples from the 3 impacted and 3 control sites, each sampled at two times after pesticide spill. More info on paper.
DOI: 10.5061/dryad.23f0c/1
title: Experiment 1

description: Data files for experiment 1, where the sterile male technique was used to infer patterns of sperm precedence
DOI: 10.5061/dryad.23f0c/2
title: Experiment 2-3 dryad RAB 25_8

description: Data from experiments 2 and 3, where females mated with males of varying relatedness to test whether sperm blocking was less severe when males were brothers vs unrelated
DOI: 10.5061/dryad.6767m/10
title: QuantGenAnalysis

description: Quantitative genetic analysis of BMI evolution
DOI: 10.5061/dryad.6767m/11
title: SelectionAnalysis
DOI: 10.5061/dryad.6767m/2
title: SourceCode

description: Contains most of the source code for Volator. Visit https://github.com/timotheenivalis/Volator to find the components and the executable, which could not be released here because of their licenses.
DOI: 10.5061/dryad.6767m/9
title: InputVolator

description: Input file to set parameter values for Volator
DOI: 10.5061/dryad.7kh2n/2
title: nt123_sitesremoved data matrix - FASTA

description: FASTA file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix with sites removed that are represented in fewer than four taxa. This resulted in a matrix that is 50.7% complete with 605,934 sites.
DOI: 10.5061/dryad.7kh2n/3
title: nt123 data matrix partitioned by codon position - NEXUS

description: NEXUS file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix converted to nexus format with a block partitioning the data by codon position.
DOI: 10.5061/dryad.7kh2n/4
title: nt123 data matrix partitioned by 1st and 2nd positions - NEXUS

description: NEXUS file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix converted to nexus format, with a block added partitioning by codon position but excluding 3rd positions. Only positions 1 and 2 for each codon were included.
DOI: 10.5061/dryad.7kh2n/5
title: nt123 data matrix with sites removed partitioned by codon position - NEXUS

description: NEXUS file with the concatenated individual orthologous group alignments (406 total), with 40 taxa. This is the nt123 data matrix with sites removed converted to a nexus file, with a block added that partitions the data by codon position.
DOI: 10.5061/dryad.7kh2n/6
title: nt123partitioned tree

description: Best tree with bootstrap values from the Garli 2.1 run using the nt123_allsitespartitioned.nex data matrix.
DOI: 10.5061/dryad.7kh2n/7
title: nt123partitioned with sites removed tree

description: Best tree with bootstrap values from the Garli 2.1 run using the nt123_sitesremoved_allsitespartitioned.nex data matrix.
DOI: 10.5061/dryad.7kh2n/8
title: nt123unpartitioned with sites removed tree

description: Best tree with bootstrap values from the Garli 2.1 run using the nt123_sitesremoved.fa data matrix.
DOI: 10.5061/dryad.7kh2n/9
title: nt12partitioned tree

description: Best tree with bootstrap values from the Garli 2.1 run using the nt123_partitionednt12.nex data matrix.
DOI: 10.5061/dryad.900f8/1
title: Appendix_studies_description

description: Data abstraction of all included studies
DOI: 10.5061/dryad.b31h1/1
title: Data for Griffin et al Ecology Letters

description: Human lifespan data from the Finnish population. Data includes lifespan on 1988 individuals from 60 birth cohorts (R1), with environmental data (E1-E8), data on sex, censoring, and socioeconomic status (F1-F3). For further information please see the published article or contact the authors.
DOI: 10.5061/dryad.d1k50/1
title: Dendropsophus ebraccatus call data

description: Call data for Dendropsophus ebraccatus. See Readme file for more details
DOI: 10.5061/dryad.k8b8n/7
title: Tabular_Gmatrix_All_animals

description: This file contains the G matrix (VanRaden, 2009) values between each pair of individuals present in the All animals sample. Theses kinship values were used in each resampling approach applied in the present study.
DOI: 10.5061/dryad.k8b8n/8
title: Supplementary_file1

description: This file contains the R script used to perform the threshold resampling applied in this study.
DOI: 10.5061/dryad.n9r96/10
title: Multiple Strains per Plate: testing if independent radial expansion velocity can predict wall velocity

description: See Appendix S2. Contains data used to argue that even when controlling for colony expansion velocity's plate-to-plate variability, the wall velocity of one strain sweeping through another is vastly overestimated by standard "geometric optics" predictions. The data in this repository was used to generate all Figures and Tables in Appendix S2. See the README for additional information.
DOI: 10.5061/dryad.n9r96/9
title: Independent Radial Expansion Velocities of Each Strain

description: See the "Measuring radial expansion velocities u_i" section of our paper. This dataset contains radius vs. time data of single-strain colonies (one colony per plate) growing on two two separate batches of agar plates. We used this data to determine the average radial expansion velocity of each strain. The third and final batch of plates used to calculate the average radial expansion velocity is in the "Multiple Strains per Plate" repository (it was a control for that experiment, so we included it there). See the README for more information.
DOI: 10.5061/dryad.p46k6/3
title: Antarctic krill swarms in Scotia Sea Summer 2003

description: The dataset contains 2043 krill swarms detected using an EK60 echosounder during transects of the Scotia Sea during Jan and Feb 2003. Each of the swarms was detected using the dB difference method described in Tarling et al. 2009. Corresponding measurements of the vertical velocity within and above and below each swarm were made using an acoustic Doppler current profiler (ADCP). Velocities above and below the swarm were taken from velocities within the swarm to derive a residual. The dataset gives a time and location of each swarm, mean depth of swarm midpoint below surface, swarm properties (depth, length, thickness, packing concentrations) and vertical velocities within, above and below each swarm. There is a further mask which excludes any measurements where there was another swarm present in the ADCP depth/time bin. [Tarling GA, Klevjer T, Fielding S, Watkins JL, Atkinson A, Murphy E, Korb R, Whitehouse M, Leaper R (2009) Variability and predictability of Antarctic krill swarm structure. Deep -Sea Res I 56:1994–2012].
DOI: 10.5061/dryad.pc78t/48
title: Figure S17 october 2017

description: supp fig
DOI: 10.5061/dryad.pc78t/49
title: Movie S1 october 2017

description: supp movie
DOI: 10.5061/dryad.pc78t/50
title: Movie S2 october 2017

description: supp movie
DOI: 10.5061/dryad.pc78t/51
title: Movie S3 october 2017

description: supp movie
DOI: 10.5061/dryad.pc78t/52
title: Movie S4 october 2017

description: supp movie
DOI: 10.5061/dryad.pc78t/53
title: Movie S5 october 2017

description: supp movie
DOI: 10.5061/dryad.pc78t/54
title: Movie S6 october 2017

description: supp movie
DOI: 10.5061/dryad.pc78t/55
title: Movie S7 october 2017

description: supp movie
DOI: 10.5061/dryad.pd959.2/2.2
title: BaselineParameterSets.Rdata

description: Data file used by SizeQualityFunctionsPlot.R and SizeQualityVarPartition.R
DOI: 10.5061/dryad.pd959.2/22.2
title: README
DOI: 10.5061/dryad.pd959.2/3.2
title: growPars.csv

description: Data file used by IdahoIPMFunctions.R
DOI: 10.5061/dryad.pd959.2/4.2
title: IdahoIPMFunctions.R

description: Defines functions needed by IdahoIPMLifeCycleStats.R and IdahoWinnerTraits2Plots.R
DOI: 10.5061/dryad.pd959.2/5.2
title: IdahoIPMLifeCycleStats.R

description: Code to generate Figs. 5 and 6
DOI: 10.5061/dryad.pd959.2/6.2
title: IdahoWinnerTraits2Plots.R

description: Code to generate Figs. 7 and 8
DOI: 10.5061/dryad.pd959.2/7.2
title: KittiwakeMatrices.R

description: Data used by KittiwakeWinnerTraitsFecSurv3.R.  Demographic data are taken from Steiner, U. K., S. Tuljapurkar, and S. H. Orzack. 2010. Dynamic heterogeneity and life history variability in the kittiwake. Journal of Animal Ecology 79:436–444 and Cam, E., W. A. Link, E. G. Cooch, J.-Y. Monnat, and E. Danchin. 2002. Individual covariation in
life-history traits: seeing the trees despite the forest. The American Naturalist 159:96–105.
DOI: 10.5061/dryad.pd959.2/8.2
title: KittiwakeWinnerTraitsFecSurv3.R

description: Code for generating Fig. 4
DOI: 10.5061/dryad.pd959.2/9.2
title: MegamatrixFunctions.R

description: Defines functions needed by KittiwakeWinnerTraitsFecSurv3.R and SizeQualityVarPartition.R
DOI: 10.5061/dryad.pq365/1
title: Primary data from Drott et al. 2017

description: File containing all data used in analyses for Drott et al. 2017.
DOI: 10.5061/dryad.r3765/1
title: CoPhy.pgls

description: Function to perform phylogenetic regression conditioned on two phylogenies.
DOI: 10.5061/dryad.r3765/2
title: FigExample

description: Computer code in R for performing analyses on empirical example of fig and fig wasp trait coevolution
DOI: 10.5061/dryad.r3765/3
title: TraitData

description: Trait data for figs and fig wasps
DOI: 10.5061/dryad.r3765/4
title: SpeciesMatchList

description: List matching fig wasp species to their corresponding host species
DOI: 10.5061/dryad.r3765/5
title: weiblen2000

description: phylogeny of figs
DOI: 10.5061/dryad.r3765/6
title: Weiblen

description: Phylogeny of fig wasps
DOI: 10.5061/dryad.t0553/1
title: Supp_Data_1_mtDNA

description: Spreadsheet list of mitochondrial DNA sequences used in phylogenetic inference, with publication names and web location accessed.
DOI: 10.5061/dryad.t0553/2
title: Supp_Data_2_UCE_backbones

description: List of UCE-derived backbone topologies used in this study, in Newick format.
DOI: 10.5061/dryad.t0553/3
title: Supp_Data_3_bootstrapped_trees

description: List of species-level phylogenetic hypotheses used in this study, in Newick format, with branch lengths.
DOI: 10.5061/dryad.t0553/4
title: Supp_Data_4_cranial_shape

description: Spreadsheet containing new cranial morphometric data published in this study. Tabs contain 1) list of museum specimens used along with housing institutions and provenance; 2) list of codes describing those housing institutions, and; 3) centroid sizes and Procrustes-aligned landmark data for all specimens.
DOI: 10.5061/dryad.t0553/5
title: Supp_Data_5_evol_model_parameters

description: List of macroevolutionary process model parameters inferred in this study for all morphological structures. These parameters were also used as the input for trait simulation.
DOI: 10.5061/dryad.v0s27.2/1.2
title: Supplementary Materials Table 6

description: Ancestral state reconstruction across Anguilliformes Open Tree phylogeny (Supplementary Materials File 4) for pectoral fin gain and loss (Fig. 7).
DOI: 10.5061/dryad.v0s27.2/15.2
title: Supplementary Materials File 4

description: Anguilliformes species-level trees based on subset from Teleostei species-level tree from Open Tree (Supplementary Materials File 1) merged with the final output matrix (Supplementary Materials Matrix 4). File includes 1,000 trees each with randomly resolved polytomies performed using the APE package in R.
DOI: 10.5061/dryad.v0s27.2/16.2
title: Supplementary Materials Matrix 1

description: OntoTrace generated NeXML synthetic morphological supermatrix for pectoral fin and pelvic fin presence and absence, including metadata for supporting states and publication information.
DOI: 10.5061/dryad.v0s27.2/17.2
title: Supplementary Materials Matrix 2

description: The tab-delimited character matrix generated after pre-processing the OntoTrace matrix (Supplementary Materials Matrix 1) by converting from NeXML format.
DOI: 10.5061/dryad.v0s27.2/18.2
title: Supplementary Materials Matrix 3

description: Resulting matrix after the propagation step. The taxon names are based on the VTO, and this matrix is the input for the taxon name reconciliation step.
DOI: 10.5061/dryad.v0s27.2/19.2
title: Supplementary Materials Matrix 4

description: Final output matrix of the pipeline. This tab-delimited file was read into Mesquite v3.10 for mapping onto the Teleostei species-level tree (Supplementary Materials File 1).