cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0g6hq/3
title: Hardy Weinberg equilibrium

description: Hardy Weinberg equilibrium: Locus summary by population including estimates of the genotyping success rate (GSR), the P-value from a chi-square test of the deviation from Hardy-Weinberg Equilibrium (HWE, * reported is the raw uncorrected p-value, the Bonferroni threshold p-value for 19,703 comparisons at α=0.05 level is 0.05/19703 = 0.00000254), the observed heterozygosity (Ho), the expected heterozygosity based on HWE (He), and the minor allele (Q) frequency (MAF).  Populations are numbered according to Table 1, and the colored font corresponds to the lineage of the population (blue, North Coastal Lineage; red, South Coastal Lineage; green, Interior Columbia River Stream-Type Lineage).
DOI: 10.5061/dryad.0g6hq/5
title: GENEPOP-Rangewide_NeutralSNPs

description: Input file for GENEPOP
DOI: 10.5061/dryad.0g6hq/6
title: LOSITAN-Rangewide

description: Input file for Lositan for all populations, 19,703 SNPs
DOI: 10.5061/dryad.0g6hq/7
title: Ots_RADcatalog_21504SNPs

description: Pre-filtered RAD catalog of 21,504 SNPs
DOI: 10.5061/dryad.0g6hq/8
title: Mantel-Hecht-Moran FST full matrices

description: Input files for Mantel test between Hecht Fst values and Moran et al. (2013) Fst values.  Each set of Fst values are included in full matrix format in separate tabs of the Excel file.  See Table S2 for corresponding triangular matrices and results of Mantel tests.
DOI: 10.5061/dryad.0g6hq/9
title: PCA-adegenet_neutralSNPs

description: Input file for PCA in adgenet for all populations; 5,007 putatively adaptive SNPs
DOI: 10.5061/dryad.31227.1
title: Data from: Age-dependent speciation can explain the shape of empirical phylogenies
DOI: 10.5061/dryad.31227.2
title: Data from: Age-dependent speciation can explain the shape of empirical phylogenies
DOI: 10.5061/dryad.31227.2/1.2
title: Data-set empirical trees

description: The input file” treebase_input.rda” has the trees cached from TreeBase by the R-package treebase (Sanderson, M.J., Donoghue, M.J., et al. 1994). The file was later treated for specific statistics and compared with simulated trees, as described in out methodology. For that the “processing_treebase.R” R-script was used, being the file “treebaselist_output.RData” the final output. We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.
DOI: 10.5061/dryad.31227.2/2.2
title: Empirical trees parameter estimation based on simulated trees

description: “SBFUSED_input.RData” is the main input data that was generated from simulations using the central high-performance computer cluster of ETH Zurich (Brutus) and the R-package TreeSimGM (Hagen, O., Stadler, T. 2013). Inputs from “treebase_output.RData” (that can be found at “data-set_empirical_trees.zip”) are also used, once we use here empirical trees for the fitting. For more details please consult the respective R-package tutorials. All other files are the sub products of the “procedure_rscript.R” script. More details can be found at  the methodology section. Figure 3 originates mainly from “SBep_output.RData”, “SBleast.square_output.RData” and “plot_script.R”.We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.
DOI: 10.5061/dryad.31227.2/3.2
title: Reliable estimates of shape on simulated phylogenies

description: Data and scripts used to test our procedure for parameter estimation over the three sets of simulated phylogenies (SI_Fig 6, 7, and 8). We would like to stress that this is not a complete catalogue of all R-scripts used in our study, especially regarding plotting and investigation of model behavior, once much was simulated with a cluster computer involving multiple outputs, code files and csv parameter tables that changed over time. If you plan to run similar experiments, we strongly encourage the reading of our TreeSimGM R-package help material.
DOI: 10.5061/dryad.31227.2/4.2
title: Supplementary Figures 1-10
DOI: 10.5061/dryad.31227.2/5.2
title: Supplementary Analytic Results
DOI: 10.5061/dryad.3n2j5/11
title: 2 years data for reproductive success analysis (poisson independent young response)
DOI: 10.5061/dryad.3n2j5/12
title: 4 years data for reproductive success analysis (poisson independent young response)
DOI: 10.5061/dryad.4vd70/1
title: Botrytis_isolates_ploidy1

description: Sequence polymorphism information for : Whole genome resequencing of Botrytis cinerea isolates identifieshigh levels of standing diversity
DOI: 10.5061/dryad.74ms0/22
title: mussel1000plus2_001

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/23
title: mussel1000plus2_002

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/24
title: mussel1000plus2_003

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/25
title: mussel1000plus2_004

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.855m4/5
title: yuhina_relatedness_for_dryad_051815

description: This is relatedness matrix in yuhina breeding group.
DOI: 10.5061/dryad.855m4/6
title: yuhina_extra_pair_offspring_for_dryad_051815

description: Data of extra paired offsprings id and their assigned biological parents.
DOI: 10.5061/dryad.9sk18/1
title: 2ndClutch_Male_2014

description: This table contains data on the number of annual clutch (1 or 2 annual) produced by males during 1990-2014 in a population of barn owls in western Switzerland. For each clutch you will find the different breeding parameters (laying date, clutch size, number of fledglings, breeding site) and information on the individuals and their partner (age, ringing status,…).
DOI: 10.5061/dryad.9sk18/2
title: 2ndClutch_Female_2014

description: This table contains data on the number of annual clutch (1 or 2 annual) produced by females during 1990-2014 in a population of barn owls in western Switzerland. For each clutch you will find the different breeding parameters (laying date, clutch size, number of fledglings, breeding site) and information on the individuals and their partner (age, ringing status,…).
DOI: 10.5061/dryad.9sk18/3
title: Nestling_Condition_2ndClutch_Females

description: This table contains information on the condition of nestlings (mass, wing, age) in relation to annual breeding parameters (1 or 2 annual clutch, laying date, clutch size, number of fledglings, …) of females. These data were collected between 1990 and 2014 in western Switzerland.
DOI: 10.5061/dryad.bd4gs/2
title: AAA_Metadata

description: All experiment scripts, written in Matlab/Cogent 2000.
DOI: 10.5061/dryad.bv3gm/2
title: variant_calling.txt

description: Description of the GATK pipeline used for generating .vcf file for 24 D. magna individuals.
DOI: 10.5061/dryad.bv3gm/3
title: smartpca_run.txt

description: Descriptions of the creation and commands to use SmartPCA to generate PCA eigenvectors and eigenvalues.
DOI: 10.5061/dryad.bv3gm/4
title: Procrustes_test.txt

description: R commands to run Procrustes rotation and significance test.
DOI: 10.5061/dryad.bv3gm/5
title: relatedness_analysis.txt

description: Scripts for using VCFtools and R to assess relationship between pair-wise relatedness and distance.
DOI: 10.5061/dryad.bv3gm/6
title: Geographic_distance_matrix.txt

description: Pair-wise genetic distance between sampled clones, in kilometers.
DOI: 10.5061/dryad.bv3gm/8
title: Pairwise_relatedness_full_MNremoved.txt

description: Estimates of pairwise relatedness derived from a reduced dataset of clones, with the Mongolian clone removed, using VCFtools.
DOI: 10.5061/dryad.cm02v/1
title: ND2 Fragments Alignment

description: fragments of ND2 sequences of ingested scales
DOI: 10.5061/dryad.cr788/1
title: File_1 : Molecular Alignment in nexus/MrBayes format

description: The full molecular alignment in nexus format, with all MrBayes commands appended.  Plain text executable file.
DOI: 10.5061/dryad.cr788/2
title: File_2: Size data for elapids (Excel)

description: Average and maximum body lengths for elapids, with literature sources, in Excel format.
DOI: 10.5061/dryad.cr788/3
title: File_3: BAMM datafiles (zipped)

description: All datafiles for BAMM analyses of diversification rates and body size, in zipped format.  Each analysis has a Tree file, control file, and data file (species diversity and sampling, or body size).
DOI: 10.5061/dryad.cr788/4
title: File_4: BayesTraits files (zipped)

description: Data files  for analysis of relationship between rates of speciation and rates of body size evolution, for BayesTraits, in zipped format.   Tree file and datafile with speciation and size data for all tips.
DOI: 10.5061/dryad.cr788/5
title: Tables S1-2 and Figs S1-S6 (pdf)

description: Pdf file of Supplementary Tables S1-2 and Supplementary Figures S1-S6.
DOI: 10.5061/dryad.h2082/1
title: Raw sequence reads

description: Raw Illumina sequence reads for 34 individuals, demultiplexed by individual barcode tags.  Within each individual, PCR products from 23 nuclear loci and 4 mitochondrial loci were pooled and sequenced.  Individual numbers, barcodes, and Field Numbers/localities corresponding to Table S1 are included in the ReadMe file.
DOI: 10.5061/dryad.h2082/2
title: Sequence Alignments

description: Alignments for 4 mitochondrial fragments and 23 nuclear loci.
DOI: 10.5061/dryad.h2082/3
title: RAxML_mtDNA

description: RAxML infiles and results for analysis of 4 mtDNA fragments.
DOI: 10.5061/dryad.h2082/4
title: BEAST_mtDNA

description: BEAST xml file and results from analysis of 4 mtDNA fragments.
DOI: 10.5061/dryad.h2082/5
title: *BEAST_nDNA

description: Starbeast xml file and results from two separate runs analyzing 23 nDNA loci.
DOI: 10.5061/dryad.j5r51/23
title: Simulated laminar recordings 625 microns from network center

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Virtual electrode is located 625 microns away from network center. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.j5r51/24
title: Simulated laminar recordings 875 microns from network center

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Virtual electrode is located 875 microns away from network center. Each row is a different depth. Input intensity is 1.5 sp/ms
DOI: 10.5061/dryad.j5r51/25
title: Simulated laminar recordings 1000 microns from network center

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Virtual electrode is located 1000 microns away from network center. Each row is a different depth. Input intensity is 1.5 sp/ms.
DOI: 10.5061/dryad.j5r51/26
title: Simulated laminar recordings for input intensity 0.5 sp/ms when synaptic model is conductance-based

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with conductance-based synapses described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/27
title: Simulated laminar recordings for input intensity 1.0 sp/ms when synaptic model is conductance based

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with conductance-based synapses described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/28
title: Simulated laminar recordings for input intensity 1.5 sp/ms when synaptic model is conductance based

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with conductance-based synapses described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/29
title: Simulated laminar recordings for input intensity 2.0 sp/ms when synaptic model is conductance based

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with conductance-based synapses described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/30
title: Simulated laminar recordings for input intensity 2.5 sp/ms when synaptic model is conductance based

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network with conductance-based synapses described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title
DOI: 10.5061/dryad.kb0pq/1
title: Algal species abundances

description: Species abundance data were collected in rocky intertidal habitat on a moderately exposed shore at Rush, Co. Dublin, Ireland between August 2012 and August 2013.Column headers are as follows:(A) Common headers: "Date" = Sampling date (yyyy-mm-dd); "Cage" = Cage present (C1 = caged, using 35 x 35 cm fence enclosed with lid; C0 = uncaged); "Variability" = Consumer (Littorina littorea) variability treatment (Const = constant, i.e. maintained at 30 individuals per cage; Var_1 = 'variable1', i.e. alternating between 15 and 45 individuals/cage every 2 months; Var_2 = 'variable2', i.e. alternating between 45 and 15 individuals/cage every 2 months; Amb = ambient, i.e. unmanipulated in uncaged plots); "Sediment" = Sedimentation treatment (S0 = ambient, i.e. no additional sediment added; S1 = elevated, i.e. 400 g sediment added to plot every month); "Plot_no" = Unique plot identifier.(B) 'Macroalgae' datasheet: "Lit_lit_m-2" = Adult (&gt;5 mm) Littorina littorea density (per sq. m) within 35 x 35 cm caged and 25 x 25 cm uncaged plots; Macroalgal species percentage cover values, estimated using 25 x 25 cm quadrat with 64 intersections: "Lith_spp" = 'Lithothamnia spp.'; "Bry_sp1" = Bryopsis sp.; "Cer_shu" = Ceramium shuttleworthianum; "Cha_lin" = Chaetomorpha linum; "Cho_cri" = Chondrus crispus; "Cla_rup" = Cladophora rupestris; "Cor_off" = Corallina officinalis; "Dic_dic" = Dictyota dichotoma; "Dum_con" = Dumontia contorta; "Fuc_ves" = Fucus vesiculosus; "Gel_pus" = Gelidium pusillum; "Gra_sp1" = Gracilaria sp.; "Him_elo" = Himanthalia elongata; "Lea_dif" = Leathesia difformis; "Mas_ste" = Mastocarpus stellatus; "Osm_spp" = Osmundea spp.; "Pol_sp1" = Polysiphonia sp.; "Por_umb" = Porphyra umbilicalis; "Ral_ver" = Ralfsia verrucosa; "Ulo_sp1" = Ulothrix sp.; "Ulv_int" = Ulva intestinalis; "Ulv_lac" = Ulva lactuca.(C) 'Microalgae' datasheet: "Sample_no" = Replicate sample (representing one of three readings taken per settlement tile fixed within each plot); "Total_conc_ug.cm-2" = Total microalgal concentration, micrograms per sq. cm, measured using Benthotorch benthic fluorometer (bbe Moldaenke GmbH, Germany).
DOI: 10.5061/dryad.m1c1g/1
title: step variables spreadsheet

description: Spreadsheet containing the scalar values measured for each step, including the leg contact conditions, peak forces, horizontal and total force impulse and net change in body center of mass energy. See the paper for full details on how the variables were calculated.
DOI: 10.5061/dryad.m1c1g/2
title: Normalization parameters

description: The values of normalization parameters used in the analysis, for each individual, to allow back-calculation to SI units if necessary.
DOI: 10.5061/dryad.nd848/3
title: Population Variation
DOI: 10.5061/dryad.nh448/1
title: Copy of Brook Trout Genotypes - December 17 2015

description: excel file containing multilocus genotypes for 11 microsatellite loci in 1783 brook trout individuals from 14 locations in 12 streams
DOI: 10.5061/dryad.nh597/1
title: Annual home range and foraging predictors

description: Excel file containing data on group ID, hydrological year, average group size, cumulative rainfall, rainfall evenness, average maximum temperature, percent time foraging, and annual home range size.  These data were used to determine the predictors of the proportion of time foraging and the predictors of annual home range size.  See manuscript for more information.
DOI: 10.5061/dryad.q660q/1
title: Grevy's zebra and wild asses affiliation groups

description: Affiliation groups over time for grevy's zebra and wild asses. Data in contains three columns: day, group no., individual id. Day is the day (an encoding of a date) on which the groups of animals have been sighted. Group no. is the unique group id for each sighted group. All animals with the same group no. have been seen together. All group numbers are unique and do not repeat across days. Animal id is the unique identifier of an individual animal. The letter after the id indicates demographic status: Grevy's [s- stallion, b - bachelor, n - non-lactating, l - lactating], wild asses [T - territorial male, N - non-lactating, L - lactating].
DOI: 10.5061/dryad.s60k4/1
title: Nest size vs. clutch size
DOI: 10.5061/dryad.s60k4/2
title: Nest size vs. brood size
DOI: 10.5061/dryad.s60k4/3
title: Nest size vs. offspring return rate

description: ReturnNO = nest volume of nests with no fledglings returned to study site  ReturnYES = nest volume of nests with one or more fledglings returned to study site
DOI: 10.5061/dryad.s60k4/4
title: Experimental nest size enlargement vs. nestling body weight

description: date 1 = 1st May;treatment: C = control, ZV = enlarged
DOI: 10.5061/dryad.s60k4/5
title: Feeding effort vs. experimental nest size enlargement

description: date 1 = 1st May;treatment: C = control, ZV = enlarged
DOI: 10.5061/dryad.s60k4/6
title: Feeding effort vs. nest size

description: date 1 = 1st May
DOI: 10.5061/dryad.s60k4/7
title: Nest size vs. nestling body weight

description: date 1 = 1st May
DOI: 10.5061/dryad.t1b23/1
title: Data from: Conjugation is necessary for a bacterial plasmid to survive under protozoan predation

description: Data presented in the MS
DOI: 10.5061/dryad.t47g3/1
title: hip-samples

description: The zipped file contains 587 .tsv files, one each for each of the 587 subjects included in the study. Each .tsv file (named with the unique identifier for that subject, for example HIPNNNN.tsv) contains a row for each unique nucleotide sequence identified in the analysis. Column titles are defined in the attached ReadMe.
DOI: 10.5061/dryad.13t18/1
title: Table S1

description: Voucher specimens from which tissues were obtained for molecular data. Standard abbreviations are as follows: Louisiana State University Museum of Natural Science, LSU; Yale Peabody Museum, YPM; California Academy of Sciences, CAS; University of Kansas, KU; Museum of Vertebrate Zoology, University of California Berkeley, MVZ; San Diego State University, SDSU; University of Michigan Museum of Zoology, UMMZ. Non-standard abbreviations include the following: APR (Achille P. Raselimanana field series); ATOL (Assembling the Tree of Life voucher series); BPN (Brice P. Noonan field series); JAC (Jonathan A. Campbell field series); JAM (Jimmy A. McGuire field series); JJK (Jason J. Kolbe field series); JPV (John Pablo Valladares field series); LJA (Luciano J. Avila field series); SDZoo (Oliver Ryder, San Diego Zoo); POE (Steve Poe field series); RAN (Ronald A. Nussbaum field series); REE (Richard E. Etheridge field series); RLB (Robert L. Bezy field series); SBH (S. Blair Hedges field series); SDZoo (San Diego Zoo Series); TJS (Thomas J. Sanger field series); TWR (Tod W. Reeder field series), WL (William Lamar), YPM (Yale Peabody Museum). For each newly sequenced sample, a Sequence Read Archive (http://www.ncbi.nlm.nih.gov/sra) and GenBank numbers are provided.
DOI: 10.5061/dryad.13t18/2
title: Table S2

description: Oligonuclotides used for construction of 43 uniquely barcoded adaptors. Index sequences (i.e., barcodes) are bolded.
DOI: 10.5061/dryad.1f6m9/1
title: Soil Quality Index Data

description: Soil Parameters used to prepare soil quality index
DOI: 10.5061/dryad.1f6m9/2
title: Species diversity in the Eastern Ghats

description: List of species recorded in different hills in the Eastern Ghats of TamilNadu
DOI: 10.5061/dryad.4q230/1
title: LH-PCR, Ecoplate, CO2 and Dung mass loss data
DOI: 10.5061/dryad.5m8f6/1
title: Price et al. JAPPL-2015-count-data

description: salamander counts, site covariates and sampling covariates
DOI: 10.5061/dryad.7md3q/1
title: Genetic data for 30 populations of great tits across Europe

description: This file contains the combined dataset collected on great tits (Parus major) from 30 sites in Europe. Provided are individual data for microsatellites (GenData) and environmental data  by site (EnvData)