cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.067qg/1
title: HarrisonLarsson_AmongCharacterRates

description: This archive contains supporting materials for Harrison and Larsson (201X) Among-Character Rate Variation Distributions in Phylogenetic Analysis of Discrete Morphological Characters.SuppTable1.xlsx: Supplementary Table 1. List of data sets and TreeBase Accession NumbersSuppTable2.xlsx: Supplementary Table 2. Results of the main Bayesian analysis for ACRV model selectionSupplementaryReferences.docx: Full references for the studies included in Supp. Table 1.MainAnalysis_MBControlFiles: MB Control files for the main analysis described in the text.NumberofRateCategoriesAnalysis_MBControlFiles: MB control files for the discrete rate category analysis.In the preceding two folders, all control files are indexed by Tree Base Accession number and by among-character rate variation model (and prior type).RScripts: folder containing R scripts (further explanation inside the .R files) 1. CombineLogExtractMCMC.R: script to process the output of MrBayes stepping-stone analysis to extract the initial MCMC portion (i.e. from the posterior) and summarize the posterior of these samples using MrBayes. 2. mb_to_beast_trees.sh: short BASH shell script to convert MrBayes formatted trees to BEAST-readable tree (used by #1, above). 3. PAUPOutputProcessor.R: R script to call PAUP* 4b10 (using Wine on Linux) and calculate per character change counts automatically given a data block (in special R format, please see the script file for details) and tree 4. PAUPLogProcessor.R: Simpler version of #3 to extract change counts from PAUP* log text file (but not call PAUP* directly). 5. S2128.rDa: the S2128 (TreeBaseID) data set in the correct R format for #3 6. S2128_Example.tree: a tree corresponding to the S2128 data set to test #3
DOI: 10.5061/dryad.7m5p4/1
title: 13C allocation and individual descriptives

description: Excel file of 13C measurements (adjusted and transformed), individual organ weights, LPS dose and temperature
DOI: 10.5061/dryad.94r9s/1
title: Samples to File Mapping

description: Mapping information between Sample IDs, modulation condition to FCS and Gating image files.
DOI: 10.5061/dryad.94r9s/2
title: README
DOI: 10.5061/dryad.94r9s/3
title: Flow Cytometry Data (FCS FIles) and Gating Image Files

description: For each sample data is include for three wells: unmodulated (UM) condition at 15 min timepoint, unmodulated condition at 24 hour timepoint and AraC+Daunorubicin treated condition at 24 hour timepoint. For each well the zipped archive file consists of one FCS files and one gating image file.
DOI: 10.5061/dryad.9pg3r/1
title: Maximum Clade Credibility Tree of Poales
DOI: 10.5061/dryad.9pg3r/2
title: Maximum Clade Credibility Tree of Fagales
DOI: 10.5061/dryad.9pg3r/3
title: Maximum Clade Credibility Tree of Ericaceae
DOI: 10.5061/dryad.s25d3/1
title: Larval Density and Mean Size
DOI: 10.5061/dryad.54cd3/1
title: Local land use intensity index

description: Local land use intensity for each study plot, published by Blüthgen, N., Dormann, C.F., Prati, D., Klaus, V.H., Kleinebecker, T., Holzel, N., Alt, F., Boch, S., Gockel, S., Hemp, A., Muller, J., Nieschulze, J., Renner, S.C., Schoning, I., Schumacher, U., Socher, S.A., Wells, K., Birkhofer, K., Buscot, F., Oelmann, Y., Rothenwohrer, C., Scherber, C., Tscharntke, T., Weiner, C. N., Fischer, M., Kalko, E. K. V., Linsenmair, K.E., Schulze, E.D. & Weisser, W.W. (2012) A quantitative index of land-use intensity in grasslands: Integrating mowing, grazing and fertilization. Basic and Applied Ecology, 13, 207–220.
DOI: 10.5061/dryad.54cd3/2
title: Butterfly abundance data

description: Butterfly abundance data; see Börschig, C., Klein, A.M., von Wehrden, H. & Krauss, J. (2013) Traits of butterfly communities change from specialist to generalist characteristics with increasing land-use intensity. Basic and Applied Ecology, 14, 547–554 for more details.
DOI: 10.5061/dryad.54cd3/3
title: Traits for butterfly species

description: Traits for butterfly species (larval-feeding breath, male forewing length and migratory tendency) were compiled from: Higgins, L.G. & Riley, N.D. (1970) A field guide to the butterflies of Britain & Europe, 1st edn. Collins, London; Koch, M. (1991) Schmetterlinge, 3rd edn. Neuman Verlag Radebeul, Germany; Settele, J., Feldmann, R. & Reinhardt, R. (1999) Die Tagfalter Deutschlands, 1st edn. Eugen Stuttgart: Ulmer Verlag, Germany; Settele, J., Steiner, R., Reinhardt, R., Feldmann, R. & Herrmann, G. (2009) Schmetterlinge. Die Tagfalter Deutschlands. 2nd edn. Stuttgart: Ulmer Verlag, Germany.
DOI: 10.5061/dryad.54cd3/4
title: Coordinates of study sites
DOI: 10.5061/dryad.54cd3/5
title: Landscape metrics

description: The Shannon diversity index of land cover types (SHDI) and the mean of the perimeter to area ratio of patches within the landscape (PAR). For more details see: Steckel, J., Westphal, C., Peters, M.K., Bellach, M., Rothenwoehrer, C., Erasmi, S., Scherber, C., Tscharntke, T. & Steffan-Dwenter, S. (2014) Landscape composition and configuration differently affect trap-nesting bees, wasps and their antagonists. Biological Conservation, 172, 56–64.
DOI: 10.5061/dryad.bk200/1
title: data on cockle body composition and density

description: This file contains the field data underlying the analyses of density dependence among cockles (figure 1 and Table 1) as well as for calculating relative body composition (online figure S2). An explanation of the variables is included in the supplementary file "1_body_composition_density_dependence_readme.txt".
DOI: 10.5061/dryad.bk200/2
title: r script for calculating relative body composition

description: This is the R script to calculate relative cockle body compositions using the data from file 1: "1_body_composition_density_dependence.csv".
DOI: 10.5061/dryad.bk200/3
title: spatial data on densities of cockles before and after predation

description: This file contains the data underlying the analyses of spatial density distributions of cockles before and after predation (figure 2), and for calculating autocorrelation functions (figure 3). An explanation of the variables is included in the supplementary file "2_spatial_density_distribution_predation_readme.txt".
DOI: 10.5061/dryad.bk200/4
title: data on length distributions and body composition before and after predation

description: This is the data underlying the analyses of length distributions (figure 4) and cockle body composition (figure 5 and online Table S1) before and after predation by red knots, as well as for calculating selection gradients (Table 2). An explanation of the variables is included in the supplementary file "3_body_composition_predation_readme.txt".
DOI: 10.5061/dryad.2p00v/1
title: Data_biomass, carbon and enery in sprouts with averagege sprout parameters of 10 largest sprouts

description: Data for whole resprouting woody plants. They include sprout biomass weight, carbon content, average sprout parameters for 1-10 largest sprouts - basal diameter (BD), diameter at breast height (DBH) and height (H).
DOI: 10.5061/dryad.2p00v/2
title: Data for individual sprouts_size and weight

description: Data on individual sprouts of 5 common temperate woody species. They include sprout weight and sprout parameters - length, basal diameter and diameter at breast height (DBH) - for 3 sprouts per plant: large (A), medium (B) and small (C)  (within resprouting woody plant identified by ID).
DOI: 10.5061/dryad.6c1h2/1
title: IIGE phenotypic covariance

description: Enchenopa treehoppers were reared from nymph to adult on replicated clone lines of their host plant Viburnum lentago. We then recorded male signals and constructed female mate preference functions from female responses to playback stimuli that varied in frequency. Male signal frequency was calculated from the signal waveform. Female peak preference was determined from each female's preference function. The columns denote the clone line and replicate that each treehopper developed on, an individual identifcation number, and the signal frequency or peak preference for each male or female, respectively, in hertz.
DOI: 10.5061/dryad.7s7s7/1
title: Structure Main Data File

description: This text file contains SNP data at 3644 loci for 78 samples of Hyperolius molleri and H. thomensis from São Tomé and Príncipe. The dataset includes only the first SNP from loci that are present in at least 75% of individuals in each of the three lineages (H. molleri Príncipe, H. molleri São Tomé, H. thomensis São Tomé). The first row of the file is the locus name, which corresponds to the locus ID in the catalog of loci generated by STACKS. Missing data indicated by “0".
DOI: 10.5061/dryad.7s7s7/2
title: SNAPP Input File

description: This xml file contains SNP data at 467 loci for 5 samples of Hyperolius molleri from São Tomé,  5 samples of H.  molleri from Príncipe, 5 H. thomensis from São Tomé, and  6 samples of the out group H. cinnamomeoventris from Gabon. The dataset includes biallelic SNPs present in at least two individuals in each of the four lineages. Homozygous positions indicated by 0 or 2, heterozygous positions indicated by 1, missing data indicated by “-“.
DOI: 10.5061/dryad.8h8fh/1
title: Fukumoto_et_al_2015_raw_data

description: The file contains following data: 1) raw data of real-time PCR for endemic species, 2) raw data of real-time PCR for exotic species, and 3) raw
DOI: 10.5061/dryad.bk200/5
title: general documentation

description: Read me first.
DOI: 10.5061/dryad.mb804/1
title: Codeset Info

description: Nanostring perturbation data
DOI: 10.5061/dryad.2q940/1
title: TOJdata_Nisikawa_etal

description: response data of each participant.
DOI: 10.5061/dryad.39h5m/10
title: Dataset 1

description: GROWTH CURVES (Figure 1, S1-3, S11A-B; Also used in figure 3, 4, 7C). Contains .csv files of raw OD600 readings from plate reader.
DOI: 10.5061/dryad.39h5m/11
title: Dataset 2

description: DIAUXIC GROWTH TIMECOURSE ON BC187 AND YJM978 (Figure 2, 5A-B, S4B-D, S5, S7C, S11C; Also used in figure 5C, S7B). Contains .fcs files of raw flow cytometry data and .csv files of sugar concentrations.
DOI: 10.5061/dryad.39h5m/12
title: Dataset 4

description: MEDIUM SHIFT AND STEADY-STATE EXPRESSION (Figure 4, S6; Also used in figure S9A, S12). Contains .fcs files of raw flow cytometry data.
DOI: 10.5061/dryad.39h5m/13
title: Dataset 3

description: DIAUXIC GROWTH TIMECOURSE ON MULTIPLE STRAINS (Figure 3, S7A-B,D-F,I, S9A). Contains .fcs files of raw flow cytometry data.
DOI: 10.5061/dryad.39h5m/14
title: Dataset 5

description: STEADY-STATE FITNESS OF BC187 AND YJM978 (Figure 5C, S12). Contains .fcs files of raw flow cytometry data.
DOI: 10.5061/dryad.39h5m/15
title: Dataset 6

description: SYNTHETIC INDUCTION (Figure 6). Contains .fcs files of raw flow cytometry data.
DOI: 10.5061/dryad.7s7s7/3
title: NewHybrids Input File

description: This text file contains SNP data for 61 samples of Hyperolius molleri and H. thomensis from São Tomé. The complete set of 3644 SNPs used in the STRUCTURE analysis was pruned to only include SNPs with a minor allele frequency &gt; 0.2 (386 SNPs). The fifth row of the file is the locus name, which corresponds to the locus ID in the catalog of loci generated by STACKS. Samples with assignment probabilities &gt; 0.99 to either the H. molleri or H. thomensis deme in the STRUCTURE analysis are designated as “parental” genotypes with either the z0 or z1 flags. Missing data indicated by “00".
DOI: 10.5061/dryad.39h5m/16
title: Dataset 7

description: STEADY-STATE FITNESS OF MULTIPLE STRAINS (Figure 7, S14). Contains .fcs files of raw flow cytometry data.
DOI: 10.5061/dryad.39h5m/17
title: Datasets 8-10

description: Dataset 8. ABSOLUTE COUNTING CONTROL (Figure S4A). Contains .fcs files of raw flow cytometry data. Dataset 9. LONG TIMECOURSE INDUCTION (Figure S8, S9B). Contains .fcs files of raw flow cytometry data. Dataset 10. PRE-CONDITION EFFECT ON INDUCTION KINETICS (Figure S10). Contains .fcs files of raw flow cytometry data.
DOI: 10.5061/dryad.39h5m/18
title: Dataset 11

description: TIMELAPSE MICROSCOPY (Figure S13). Contains .tiff files of raw microscopy data.
DOI: 10.5061/dryad.39h5m/19
title: MATLAB analysis code

description: MATLAB scripts for reproducing the analysis and generating all the figures in the paper. Scripts are organized into subfolders according to which dataset they are meant to analyze. See README.txt for entire repository for details and usage instructions.
DOI: 10.5061/dryad.n15m7/1
title: Plumage and body size traits for lark buntings from 1999-2003. Chaine and Lyon; Functional Ecology 2015

description: Data includes 3 tables: 1) ID and traits for all males caught from 1999-2003. This includes raw data for body size, patch color, and patch area. It also includes the principal component scores extracted from raw data which were used in the published analyses. Comments in the data header line provide additional information. 2) Data used to estimate repeatability of spectrometry data. 3) Measures of birds from the UC Berkeley Museum for repeatability of plumage.
DOI: 10.5061/dryad.p0v93/1
title: Morphometric measurements

description: Morphometric measurements taken from museum round skins with a digital calipers. Specimen locality information can be found in Supplementary Appendix 2 of the manuscript.
DOI: 10.5061/dryad.sc286.3
title: Data from: Functional traits in parallel evolutionary radiations and trait-environment associations in the Cape Floristic region of South Africa
DOI: 10.5061/dryad.sc286.3/8.3
title: README

description: README file for all files.
DOI: 10.5061/dryad.2386p/1
title: Models 1,3,4, paired analysis, supplement models, figures - nestling survival and recruitment

description: Nestling survival and recruitment in relation to morphometrics and demographic data. Data to produce models 1,3,4, and the paired analysis in the main text, models in the supplementary information, and figures in the main text and supplementary information. For a description of the column names, advice on using the data, and units, see the README file.
DOI: 10.5061/dryad.2386p/2
title: Model 2 - recruitment

description: Nestling recruitment in relation to morphometrics and demographic data. Slightly more individuals in this file than the data set for models 1,2,3 etc because the condition of knowing mass on day 2 is relaxed. Data to produce model 2 in the main text. For a description of the column names, advice on using the data, and units, see the second half of the README file.
DOI: 10.5061/dryad.3cp3t/1
title: Diniz-Filho_etal_MER_2015

description: The following data and achieves are available from DRYAD for Diniz-Filho et al. - Mol. Ecol. Res.1) Sampling localities, codes, latitudes and longitudes, Heterozygosity for 25 populations of D. alata in Brazilian Cerrado (Baru25pops.xlsx);2) Genotypes for 8 microsatellite loci for 642 individuals of D. alata from 25 populations (baru_FSTAT_8loci.dat);3) R-script for the analyses shown in this paper, including generating heterozygosity by resampling and the random selection of ENMs for ensemble correlations (ENM_selection.R);4) Vector of heterozygosity used in the analyses (he.txt);5) Environmental suitabilities of ENMs in the 25 populations of D. alata (ENM.txt);6) Occurrence records for D. alata in Brazilian Cerrado (D_alata_occurrence_records.txt);7) Occurrence records in a Neotropical grid with resolution of 0.5o (D_alata_neotropic_grid.txt), used in BIOENSEMBLES;8) One of the environmental data (CCSM climatic model for current time) in the Neotropical grid used in the modeling process with BIOENSEMBLES (be_biovar_CCSM_0k_neotropic.txt  - other similar data sets are available at www.ecoclimate.org).
DOI: 10.5061/dryad.cd0cq/1
title: Foreletal. APPENDIX 1

description: Stratigraphical log, samples positions and distribution of the ostracods species through the productive portion of the Elikah river section, Alborz, Iran. W.: Wuchiapingian stage, Jul.: occurrence of the conodont Hindeodus julfensis, par.: occurrence of the conodont Hindeodus parvus (PTB: red line). Brachiopods bizones: P. ova.: Permophricodothyris ovata Biozone, E. lat.: Enteletes lateroplicatus Biozone (Angiolini et al. 2010).
DOI: 10.5061/dryad.cd0cq/2
title: Foreletal. APPENDIX 2

description: Abundance and occurrences of the cf. and open nomenclature ostracod species from the Permian-Triassic transition of the Elikah river section (Iran).
DOI: 10.5061/dryad.g611t/1
title: Simulation of polyploid scenarios

description: priorgenWGD.py is a python script to generate prior distribution for the nine described models (a detailed help-menu is available typing ./priorgenWGD.py --help), bpfile_test.txt is an example file used by priorgenWGD.py, and text_S1.docx contains the used command-lines.
DOI: 10.5061/dryad.g611t/2
title: Capsella_alignments.tar

description: Used alignements for the empirical application from Capsella. The sequences came from St Onge KR, Foxe JP, Li J et al. (2012, Molecular biology and evolution), Slotte T, Huang H, Lascoux M, Ceplitis A (2008, Molecular biology and evolution) and Foxe JP, Slotte T, Stahl EA et al. (2009, Proceedings of the National Academy of Sciences of the United States of America).
DOI: 10.5061/dryad.p0v93/2
title: Plumage spectra

description: Plumage reflectance spectra from 10 patches. The first column is the wavelength, and each additional column represents the mean of three readings for each patch. Specimen locality information can be found in Supplementary Appendix 2 of the manuscript.
DOI: 10.5061/dryad.p0v93/3
title: Vocal_Frequency_Selections

description: Vocal frequency tables. Each table was produced by drawing selection boxes around songs in Raven Pro v1.4 (Cornell Lab of Ornithology).
DOI: 10.5061/dryad.s1b7q/1
title: data_package_AlbrechtEtAl2015_JournalOfEcology

description: This data package contains data from the publication: Albrecht, Jörg, Bohle, Victoria, Berens, Dana, Jaroszewicz, Bogdan, Selva, Nuria & Farwig, Nina (2015) Variation in neighbourhood context shapes frugivore-mediated facilitation and competition among co-dispersed plant species. Journal of Ecology. Details about the content of the package can be found in the README.txt file and in the data_description.txt file in the zip folder.
DOI: 10.5061/dryad.sc286.3/1.3
title: Protea_CFR_DATA

description: Site and trait data for Protea individuals used in this study.
DOI: 10.5061/dryad.sc286.3/10.3
title: results-2014-03-06-09-01-02

description: Ultrametricized tree used in Pelargonium analysis.
DOI: 10.5061/dryad.sc286.3/2.3
title: Pel_CFR_2011_2012

description: Site and trait data for Pelargonium individuals used in this study.
DOI: 10.5061/dryad.sc286.3/3.3
title: Protea_Pellie_Climate

description: Climate data form Wilson & Silander (2014) for both Protea and Pelargonium sites used in this analysis.
DOI: 10.5061/dryad.sc286.3/4.3
title: traits-environment-with-phylo

description: R code for running JAGS model.
DOI: 10.5061/dryad.sc286.3/5.3
title: traits-environment-with-phylo

description: JAGS model code for running analysis.
DOI: 10.5061/dryad.sc286.3/6.3
title: results-2014-03-08-12-23-06

description: Results from Pelargonium analysis in .txt format.
DOI: 10.5061/dryad.sc286.3/7.3
title: results-2014-03-08-13-25-09

description: Results from Pelargonium analysis in .Rsave format.
DOI: 10.5061/dryad.sc286.3/9.3
title: results-2014-03-06-08-47-40

description: Results from Protea analysis in .txt format.
DOI: 10.5061/dryad.8m2q8/1
title: haootia02

description: Image of the Haootia quadriformis holotype specimen, taken under low lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, Canada, by Duncan McIlroy.
DOI: 10.5061/dryad.8m2q8/2
title: haootia03

description: Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5061/dryad.8m2q8/3
title: haootia04

description: Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5061/dryad.8m2q8/4
title: haootia05

description: Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5061/dryad.8m2q8/5
title: haootia07

description: Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5061/dryad.8m2q8/6
title: haootia09

description: Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5061/dryad.8m2q8/7
title: haootia10

description: Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5061/dryad.sc286.3/11.3
title: valentetree

description: Ultrametricized tree used in Protea analysis, from Valente et al. (2010).
DOI: 10.5061/dryad.sc286.3/12.3
title: FINAL_20112012_ultrametric

description: Ultrametricized tree used in Pelargonium analysis from Ringelberg et al. (unpublished).
DOI: 10.5061/dryad.sc286.3/13.2
title: posterior-comparisons.pdf

description: Contains code, explanation, and results summarized for the posterior comparison.
DOI: 10.5061/dryad.sc286.3/14.2
title: posterior-comparisons.R

description: Contains code for running posterior comparisons in R.
DOI: 10.5061/dryad.sc286.3/15.2
title: posterior-comparisons.Rtex

description: Contains comparisons so that knitr() can run code.
DOI: 10.5061/dryad.sc286.3/17.2
title: posterior-comparisons.tex

description: Posterior comparison results in tex format.
DOI: 10.5061/dryad.8m2q8/8
title: haootia11

description: Image of the Haootia quadriformis holotype specimen, taken under controlled lighting conditions at The Rooms Provincial Museum, St. John's, Newfoundland, by Duncan McIlroy.
DOI: 10.5061/dryad.hq8pd/1
title: Supplementary_File_S1(geografic_location)

description: Geographic location of D. alata populations.
DOI: 10.5061/dryad.hq8pd/2
title: Supplementary_File_S2(ex-situ_data)

description: Excel file containing D. alata ex-situ genotype data (UFG-AS germplasm collection). Individuals are identified in each row. Loci are designated by column with the nine microsatellite listed. (?) refers to missing data.
DOI: 10.5061/dryad.hq8pd/3
title: Supplementary_File_S3(in-situ_data)

description: Excel file containing D. alata in-situ genotype data. Individuals are identified by population in each row. Loci are designated by column with the nine microsatellite listed. (?) refers to missing data.
DOI: 10.5061/dryad.t34m9/1
title: WPP Model Table 1

description: Dataset supporting the results examining the effects of natural variation in food availability on within-pair paternity (Table 1 Model 1).
DOI: 10.5061/dryad.t34m9/2
title: EPP Model Table 1

description: Dataset supporting the results examining the effects of natural variation in food availability on extrapair paternity (Table 1 Model 2).
DOI: 10.5061/dryad.t34m9/3
title: Double brooding Model Table 1

description: Dataset supporting the results examining the effects of natural variation in food availability on double brooding (Table 1 Model 3).
DOI: 10.5061/dryad.t34m9/4
title: Table 2

description: Dataset supporting the results examining the effects of food supplementation on within-pair paternity, extrapair paternity, double brooding and total reproductive success (Table 2 Models 1-4).
DOI: 10.5061/dryad.t34m9/5
title: Poisson Model

description: Dataset supporting the results investigating the relative contribution of within-pair paternity, extrapair paternity and double brooding on total reproductive success (Figure 2).
DOI: 10.5061/dryad.416sp/1
title: Full_Cammoor-Stimpsons_asoc

description: Individual-level data for all birds detected at Cammoor-Stimpsons
DOI: 10.5061/dryad.416sp/2
title: Full_Cammoor-Stimpsons_diffusions

description: Information on the 4 diffusion experiments at Cammoor-Stimpsons