cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.cd5s5/2
title: microsatellite genotypes for all sample sets with &gt;5 individuals

description: Microsatellite genotypes for 7 loci for 49 individuals of leafy seadragons (Phycodurus eques) in genepop format. Sample sets with &lt;5 individuals and individuals of unknown geographic origin were excluded.
DOI: 10.5061/dryad.cd5s5/3
title: Geographic distance matrix

description: Pairwise geographic distance in km between sample sets. Distance was measured along the coastline but straight-line connections were allowed across Spencer Gulf and Gulf St Vincent.
DOI: 10.5061/dryad.cd5s5/4
title: Geographic distance matrix South Australia

description: Pairwise geographic distance in km between sample sets, for South Australian sites only. Distance was measured along the coastline but straight-line connections were allowed across Spencer Gulf and Gulf St Vincent.
DOI: 10.5061/dryad.cd5s5/5
title: Sequences mitochondrial control region

description: Sequences of the mitochondrial control region for 56 leafy seadragons (Phycodurus eques) in fasta format.
DOI: 10.5061/dryad.cd5s5/6
title: Sequences mitochondrial NADH subunit 4 (ND4)

description: Sequences of the mitochondrial NADH subunit 4 (ND4) for 56 leafy seadragons (Phycodurus eques) in fasta format.
DOI: 10.5061/dryad.dk51c/1
title: raw behavioural and eye tracking data
DOI: 10.5061/dryad.dk563/2
title: scripts used in R for linear models

description: Data were created in R
DOI: 10.5061/dryad.dk563/3
title: Data frame with distances among pairs of populations

description: tab delimited table containing all the pairwise distances among populations, including geographical distance and obtained from particle dispersal model as well as calculated index of directionality
DOI: 10.5061/dryad.dk563/4
title: particle dispersal simulation video

description: example of direct dispersal simulation from the sampling sites over one simulation period (jul-sept)
DOI: 10.5061/dryad.dk563/5
title: autocorrelation kinship resutls

description: Autocorrelation file with distance and kinship coefficient among samples.
DOI: 10.5061/dryad.dk563/6
title: markers score input for genpop

description: Edited microsatellite analysis result used as input in genpop, GenALEx and GENETIX.
DOI: 10.5061/dryad.gc850/1
title: Attalea_bruchidae_defaunation

description: Data providing evidence of the cascading effects of defaunation on the coexistence of the two specialized insect seed predators of the Neotropical palm Attalea butyracea.
DOI: 10.5061/dryad.gp5j0/1
title: boscai_spain_contigs

description: Contigs generated by Trinity assembler from all the reads belonging to boscai from Spain
DOI: 10.5061/dryad.gp5j0/2
title: boscai_portugal_contigs

description: Contigs generated by Trinity assembler from all the reads belonging to boscai from Portugal.
DOI: 10.5061/dryad.k9087/1
title: Bump et al. 2016 DATA - Nutrient release from moose bioturbation in aquatic ecosystems - Oikos

description: Excel file of raw nutrient data for Bump et al. 2016 Nutrient release from moose bioturbation in aquatic ecosystems. Oikos.
DOI: 10.5061/dryad.kd3qm/1
title: Data_Segall_et_al_2016

description: PC scores of all the species included in the analysis. These scores were used for all statistical analyses performed.
DOI: 10.5061/dryad.kv57r/1
title: ASZ1.nex alignment

description: Nexus file containing the trimmed alignment of amino acid sequences from salamanders and other vertebrates used to generate the phylogeny in the manuscript.
DOI: 10.5061/dryad.kv57r/2
title: Ddx4.nex alignment
DOI: 10.5061/dryad.m35k6/113
title: ModelSel_VATH_2013_Dynamic

description: AIC model selection table and associated coefficients for varied thrush 2013 for dynamic models (colonization and extinction). Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/114
title: ModelSel_WETA_2012_Dynamic

description: AIC model selection table and associated coefficients for western tanager 2012 for dynamic models (colonization and extinction). Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/115
title: ModelSel_WETA_2013_Dynamic

description: AIC model selection table and associated coefficients for western tanager 2013 for dynamic models (colonization and extinction). Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/116
title: ModelSel_WIWA_2012_Dynamic

description: AIC model selection table and associated coefficients for Wilson’s warbler 2012 for dynamic models (colonization and extinction). Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/117
title: ModelSel_WIWA_2013_Dynamic

description: AIC model selection table and associated coefficients for Wilson’s warbler 2013 for dynamic models (colonization and extinction). Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy. Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.n358r/1
title: All data

description: Data collected in the field. Id, identity of individuals; body size in kg except for elephants, height in cm; reproductive status of females where "no" is no offspring and "yes" is offspring produced; twin, if an individual is a twin "yes" or not "no"; mother primiparity is whether or not the individual was born from primiparous mother "yes" or not "no".
DOI: 10.5061/dryad.nq2j7/1
title: Chillo et al_Data

description: Sampling sites locations, Index values for every sampling site, R scripts for SEM analyses and TDvsFD trajectory analyses
DOI: 10.5061/dryad.p811t/1
title: Baltic Sea phytoplankton monitoring data from 1981-2008

description: Phytoplankton species composition and metadata of 7941 monitoring samples, and functional trait table of phytoplankton. For more details, see the ReadMe file.
DOI: 10.5061/dryad.sg280/1
title: Unique_Exon_Read_Counts

description: RNA-seq read count data for killifish individuals with northern or southern mitochondrial genotypes that were acclimated to either 15 or 5 degrees Celsius.
DOI: 10.5061/dryad.sg280/2
title: Gene_IDs_Names_Lengths

description: Reduced gene model information for the Fundulus heteroclitus genome containing gene IDs, gene names and gene lengths. Information was obtained from the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).
DOI: 10.5061/dryad.sg280/3
title: GO_IDs

description: Orthologous GO annotations for the gene models in the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).
DOI: 10.5061/dryad.v8rq0/1
title: List of deleterious SNPs
DOI: 10.5061/dryad.09q2b/1
title: Subjects1_2

description: Raw pressure data from subjects 1 and 2 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.09q2b/2
title: Subjects3_4

description: Raw pressure data from subjects 3 and 4 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.09q2b/3
title: Subjects5_6

description: Raw pressure data from subjects 5 and 6 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.09q2b/4
title: Subjects7_8

description: Raw pressure data from subjects 7 and 8 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.223p4/16
title: 2011_Germination

description: Data on whether seeds from crosses made within and between dune and non-dune ecotypes (in the field in 2011) and seeds from open pollinated plants germinated
DOI: 10.5061/dryad.223p4/17
title: 2008_Populations

description: Latitude and longitude information for each population used in this study
DOI: 10.5061/dryad.223p4/18
title: GSD_Barriers_Rcode

description: The R code used to produce each statistical analysis and figure presented in this manuscript. The code is presented in the same order that the analyses are presented in the manuscript.
DOI: 10.5061/dryad.22s3p/1
title: JEB-2016-00542 - Dryad Data File

description: An R script file (.R extension) containing survival time data for various Pristionchus nematodes.  Data are provided as R objects and as CSV data tables.  Comments are included to define the data columns within each object.
DOI: 10.5061/dryad.311mm/1
title: Illumina_Read_Files
DOI: 10.5061/dryad.3b15s/1
title: Stand structure and live/dead biomass in 24 year old lodgepole pine forests

description: Includes: stand structure, derived topographic and environmental variables, live and dead forest fuels, 83 plots collected across the 1988 wildfire footprint within Yellowstone National Park.  Full metadata available in the readme file.
DOI: 10.5061/dryad.4ch10/1
title: Retinal Data and Stimuli

description: This dataset contains the visual stimuli that were used for the retina recordings and also the spike trains and thereceptive fields of the recorded retinal ganglion cells.
DOI: 10.5061/dryad.728hn/1
title: Assemblies of mitochondrial genomes of Chelonoidis alburyorum, C. carbonarius, C. chilensis, C.  denticulatus, C. vicina, Geochelone sulcata.

description: Text files created with Tablet 1.15.09.1.
DOI: 10.5061/dryad.7ff11/5
title: core 5

description: Core 5 LOI, XRF
DOI: 10.5061/dryad.7ff11/6
title: core 6

description: Core 6 LOI, XRF
DOI: 10.5061/dryad.7ff11/7
title: Surface samples

description: Surface sample XRF
DOI: 10.5061/dryad.7q4r8/1
title: Dataset1: Population level analysis

description: Dataset used (1) to determine if females who used social incentives were more likely to direct aggression at males who had recently defected, but groom males who had recently cooperated, and (2) if target males were more likely to participate after receiving social incentives than before.
DOI: 10.5061/dryad.7q4r8/2
title: Dataset2: Individual level analyses

description: Dataset used to test (1) if individual males were more likely to participate after receiving social incentives than before, and (2) if individuals who received social incentives participated above their personal base-line level (i.e. the proportion of aggressive episodes participated in during intergroup fights where they were not the male to receive social incentives).
DOI: 10.5061/dryad.7q4r8/3
title: Dataset3: spatio-temporal variability in the occurrence of social incentives

description: Dataset used in the GLMM testing the spatio-temporal variability in the occurrence of social incentives (punishment and/or rewards). The summer season (when high quality fruits were available) was indexed by the NDVI, the birth season was indexed by the number of small infants (&lt;3 months old) in the group, and the mating season was a dichotomous variable. The spatial distribution of food in the different areas (mapping units) of each home range was determined by mapping the distribution of important tree species and monitoring their fruit abundance on a monthly basis.
DOI: 10.5061/dryad.8br5c/10
title: raxml

description: We used RAxML v8.1.1 (Stamatakis 2014) to created a maximum-likelihood phylogeny for our concatenated data. Input and output files provided.
DOI: 10.5061/dryad.8br5c/11
title: beast2

description: The folder BFD* contains .xml input files and output logs for Bayes Factor Delimitation with genomic data (Leache et al. 2014) implemented in SNAPP/BEAST 2.3.1 (Bryant et al. 2012, Bouckaert et al. 2014). The concatenated folder includes input and output for a concatenated analysis of RAD data in BEAST 2.1.2. The SNAPP folder contains species tree input and output for SNAPP 1.1.5 implemented in BEAST 2.1.2.
DOI: 10.5061/dryad.8br5c/4
title: starBEAST

description: Included are input xml files and a summary of results for Bayes Factor Delimitation (BFD, Grummer et al. 2014) and *BEAST (Heled and Drummond 2010) analysis of species trees in BEAST v1.8.1 (Drummond et al. 2012).
DOI: 10.5061/dryad.8br5c/5
title: raw_HiSeq_data1

description: These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
DOI: 10.5061/dryad.8br5c/6
title: raw_HiSeq_data2

description: These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
DOI: 10.5061/dryad.8br5c/7
title: raw_HiSeq_data3

description: These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
DOI: 10.5061/dryad.8br5c/8
title: raw_HiSeq_data4

description: These data were collected using ddRADseq (Peterson et al. 2012) and sequenced on a single lane of an Illumina HiSeq 2500, UC Riverside. They are already demultiplexed by Illumina index and adapter index. See Appendix A for specimen information.
DOI: 10.5061/dryad.8br5c/9
title: pyRAD

description: We used pyRAD v2.1.2 (Eaton 2014) with muscle3.8.31 and usearch7.0.1090 to filter and process raw data files. Two example parameter files are provided. Please see “raw_HiSeq_data” to download the .fastq files.
DOI: 10.5061/dryad.8gg57/10
title: Modularity_SA

description: Source R code to conduct analyses. Includes functions for modularity assessment, significance test using Poisson GLM, and modularity decomposition.
DOI: 10.5061/dryad.8gg57/4
title: A_juveniles

description: Transition matrix with observed juvenile dispersal
DOI: 10.5061/dryad.8gg57/5
title: A_males

description: Transition matrix with observed adult male dispersal
DOI: 10.5061/dryad.8gg57/6
title: A_seasonal

description: Transition matrix with observed seasonal movements (breeding season to October (non-breeding season))
DOI: 10.5061/dryad.8gg57/7
title: A_within

description: Transition matrix with observed within breeding season adult movements
DOI: 10.5061/dryad.8gg57/8
title: Master Locations List

description: List of wetland sites with centroid locations
DOI: 10.5061/dryad.8gg57/9
title: Modularity assessment with significance test

description: R code to perform (1) modularity assessment, (2) significance test using Poisson GLM, (3) modularity decompistion, and (4) modularity assessment using spatial null model (Qspa)
DOI: 10.5061/dryad.9mk20/1
title: Divergence dates from 100 trees

description: Divergence dates in Ma from 100 trees randomly selected from Bayesian posteriors.
DOI: 10.5061/dryad.9mk20/2
title: Sample from Bayesian posterior

description: Sample of 500 trees from the Bayesian posterior of dated phylogenies from: Rojas, D., O. M. Warsi, and L. M. Dávalos. 2016. Bats (Chiroptera: Noctilionoidea) challenge a recent origin of extant neotropical diversity. Syst Biol 65:432–448.
DOI: 10.5061/dryad.9mk20/3
title: Sample from Bayesian posterior

description: Sample of 100 trees form Bayesian posterior from analyses of combined morphological and molecular data by Tavares*, V. D. C., L. M. Dávalos*, O. M. Warsi, F. Balseiro, C. A. Mancina, and J. Rothleder. In Prep. Out of the Antilles: Fossil phylogenies support reverse colonization to South America.
DOI: 10.5061/dryad.b58dv/1
title: microsatellite and chloroplast sequence data for 8 tree species from the Guiana shield

description: Data represent two subsets of individuals sequenced at two chloroplast loci and genotyped for a variable number of microsatellite loci (depending on species). FIle names correspond to species name codes as follows: Carapa surinamensis (Cs), Dicorynia guianensis (Dg), Jacaranda copaia (Jc),  Simarouba amara (Sa), Symphonia globulifera (Sg), Symphonia sp1 (Ssp1), Virola michelii (Vm), eastern Vouacapoua americana (Va(E)) and western Vouacapoua Americana (Va(W)). FIle format: input file for DIYABC 2.0.
DOI: 10.5061/dryad.c96md/1
title: Strain Catalogue and Reproductive Data per Generation

description: Strain catalogue with full genotypes, data for all genealogies (offspring per generation and RCO measures), and data for control conditions and heat map analysis.
DOI: 10.5061/dryad.c96md/2
title: Design for Genetic Crosses Unique to Experiment

description: Method of multi-generational crosses for construction of selected mutant strains. Page 1 features daf-7; AMPK method, and Page 2 features daf-7; daf-16 method.
DOI: 10.5061/dryad.gd14g/1
title: Genome alignment for 3,442 isolates of S. pyogenes

description: Fasta formatted genome alignment of 3,442 isolates of Streptococcus pyogenes considered in the study.
DOI: 10.5061/dryad.gd14g/2
title: Genome alignment for 3,156 isolates of S. pneumoniae

description: Fasta formatted genome alignment of the Maela Streptococcus pneumoniae isolates considered in the study.
DOI: 10.5061/dryad.gd14g/3
title: TableS5

description: Coupling estimates for the 5078 locus M1 data set
DOI: 10.5061/dryad.gp5j0/3
title: boscai_spain_annotation

description: Annotations generated by Sma3s software for contigs belonging to boscai from Spain
DOI: 10.5061/dryad.gp5j0/4
title: boscai_portugal_annotation

description: Annotations generated by Sma3s software for contigs belonging to boscai from Portugal
DOI: 10.5061/dryad.gp5j0/5
title: SNPs_fixed

description: SNPs fixed in boscai from Portugal and Spain
DOI: 10.5061/dryad.gp5j0/6
title: SNPs_exclusive_in_boscai_portugal

description: Exclusive SNPs in boscai from Portugal
DOI: 10.5061/dryad.gp5j0/7
title: SNPs_exclusive_in_boscai_spain

description: Exclusive SNPs in boscai from Spain
DOI: 10.5061/dryad.gp5j0/8
title: SNPs_shared_between_boscai_portugal_and_boscai_spain

description: SNPs shared between boscai from Portugal and boscai from Spain
DOI: 10.5061/dryad.hp730/1
title: SuppInfo
DOI: 10.5061/dryad.kv57r/10
title: Prmt5.nex alignment
DOI: 10.5061/dryad.kv57r/11
title: Tdrd1.nex alignment
DOI: 10.5061/dryad.kv57r/3
title: FKBP6.nex alignment
DOI: 10.5061/dryad.kv57r/4
title: Hen1.nex alignment
DOI: 10.5061/dryad.kv57r/5
title: KIF17.nex alignment
DOI: 10.5061/dryad.kv57r/6
title: Mov10l1.nex alignment
DOI: 10.5061/dryad.kv57r/7
title: Piwil1.nex alignment
DOI: 10.5061/dryad.kv57r/8
title: Piwil2.nex alignment
DOI: 10.5061/dryad.kv57r/9
title: Pld6.nex alignment
DOI: 10.5061/dryad.nf4bm/1
title: Roeder_et_al_Biotropica_Kilimanjaro_arthropod_abundances_data_and_meta-data

description: Raw data of arthropod abundances per trap for pitfall traps. Taxonomical resolution: order to family (depending on taxon).
DOI: 10.5061/dryad.sg280/4
title: KEGG_IDs

description: Orthologous KEGG annotations for the gene models in the F. heteroclitus genome assembly (http://marmot.bio.indiana.edu:7151/EvidentialGene/killifish/).
DOI: 10.5061/dryad.sg280/5
title: RNA-seq and enrichment analyses R script

description: R code used for analysis of RNA-seq read count data and GO/KEGG enrichment analyses. All data used in these analyses are found in the additional files associated with this Dryad submission.
DOI: 10.5061/dryad.t9m6c/1
title: Empirical Data set for all recorded variables

description: Empirical data set for school sizes, proportion of the school injured, capture success rate, approach frames, injuries on individual fish, number of attacks and captures, and whether scales were removed during attacks or not.  Data are labelled accordingly.
DOI: 10.5061/dryad.v1jv1/1
title: Supplemental data explanation
DOI: 10.5061/dryad.v1jv1/2
title: Supplemental_Data_File_1_BYU_20808

description: Ceratodus kirklandi n. sp., BYU 20808 (holotype), right pterygopalatine plate. Specimen from BYU locality 1667, Grand County, Utah; Yellow Cat Member, Cedar Mountain Formation, Lower Cretaceous (Valanginian).
DOI: 10.5061/dryad.v1jv1/3
title: Supplemental_Data_File_2_BYU_20809

description: Ceratodus kirklandi n. sp., BYU 20809, left prearticular plate. Specimen from BYU locality 1667, Grand County, Utah; Yellow Cat Member, Cedar Mountain Formation, Lower Cretaceous (Valanginian).
DOI: 10.5061/dryad.v1jv1/4
title: Supplemental_Data_File_3_NCSM_30253

description: Ceratodus molossus n. sp., NCSM 30253 (holotype), right pterygopalatine plate; locality near Emery, Emery County, Utah, Mussentuchit Member, Cedar Mountain Formation, Upper Cretaceous (Cenomanian).
DOI: 10.5061/dryad.09q2b/5
title: Subjects9_10

description: Raw pressure data from subjects 9 and 10 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.09q2b/6
title: Subjects11_12

description: Raw pressure data from subjects 11 and 12 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.09q2b/7
title: Subjects13_14

description: Raw pressure data from subjects 13 and 14 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.09q2b/8
title: Subjects15_16

description: Raw pressure data from subjects 15 and 16 collected from 5 different speeds for 5 minutes per speed.
DOI: 10.5061/dryad.292dd/1
title: README

description: README file describes the file type and contents of all files in this data repository.
DOI: 10.5061/dryad.292dd/2
title: PteroGW-pruned

description: The pruned most-parsimonious tree of the pterocephaliid trilobites from Hopkins (2011) is provided as a NEXUS file
DOI: 10.5061/dryad.292dd/3
title: PCscores-pterocephaliid

description: The principal component scores from a PCA of the geometric morphometric landmark data for those pterocephaliid taxa is provided as a tab-delimitted .txt table