cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m5pr3/9
title: Part 3(6) of the data package for Heron Reef.
DOI: 10.5061/dryad.0732g/1
title: Flower color datasets

description: The zip folder includes four datasets: Antirrhineae, Iochrominae, Loeselieae, and Quamoclit.  Each clade has a file with flower color scoring (.csv), a BEAST input file (.xml), and the subsampled trees (..BEAST100.nex) that were used for analyses. The .R scripts are for running the full model MCMC with diversitree. See manuscript for model description.
DOI: 10.5061/dryad.16n10/1
title: RSOS Submission Code and Data

description: Data files used in analysis of Pedruski et al. "Predicting the outcome of competition when fitness inequality is variable", and script files (code) necessary to produce these data files and associated figures.
DOI: 10.5061/dryad.1j25j/1
title: Phenotypic data: number of available broods

description: This file contains the phenotypic data for the univariate quantitative genetic analyses of the number of available broods (Nbroods).
DOI: 10.5061/dryad.1j25j/2
title: Phenotypic data: Psire and number of available offspring

description: Phenotypic data for the univariate quantitative genetic analyses of the probability that an offspring within an available brood (or litter) will be sired as an EPO by a focal male (Psire) and the number of available offspring.
DOI: 10.5061/dryad.1j25j/3
title: Pedigree for Psire, Nbroods, and number of offspring

description: This file contains the non-zero elements of the inverted A (relationship) matrix data for the animal model analyses of Psire, Nbroods, and number of offspring.
DOI: 10.5061/dryad.26d32/1
title: Araujo & Austin_Journal of Ecology_ Pine afforestation and decomposition

description: This file contains data for litter mass remaining, litter quality and soil characteristics used for figures, tables and statistical analysis in the publication 'A shady business: pine afforestation alters the primary controls on litter decomposition along a precipitation gradient in Patagonia, Argentina' by Patricia I Araujo and Amy T. Austin
DOI: 10.5061/dryad.36td2/1
title: Fitness_evolved

description: Competitive fitness measurements for 46 evolved populations of Escherichia coli. Three replicate fitness assays were performed for each population. Founding genotypes are also indicated, as are numbers of high confidence substitutions (hc_fixed), polymorphisms (hc_poly), and total number of mutations (hc_total, the sum of hc_fixed and hc_poly).
DOI: 10.5061/dryad.36td2/2
title: MIC

description: Measurements of ciprofloxacin resistance for all strains and populations used in this study. Resistance is measured as the minimal inhibitory concentration (MIC), the concentration of antibiotic required to inhibit growth by 90% in an overnight culture. MIC is given both in absolute terms (ng/mL cup) and in terms of fold-increase over the susceptible ancestor MG1655.
DOI: 10.5061/dryad.36td2/3
title: Data_by_progenitor

description: Data on progenitor strains and summaries for evolved populations by progenitor. See readme file for details.
DOI: 10.5061/dryad.36td2/4
title: Mutation data

description: Table S1 from paper. All mutations found in whole genome sequencing of evolved populations.
DOI: 10.5061/dryad.45595/1
title: MoralityData

description: MortalityData.xlsx is associated with Figure 1 and Table 1.
DOI: 10.5061/dryad.45595/2
title: BdLoadData

description: BdLoadData.xlsx is associated with Figure 2 and Table 2.
DOI: 10.5061/dryad.4r910/1
title: Supplementary Material for “Integrating Sequence Evolution into Probabilistic Orthology Analysis”

description: This document contains the supplementary information including synthetic data parameters, figures, and tables for the paper “Integrating Sequence Evolution into Probabilistic Orthology Analysis”
DOI: 10.5061/dryad.5090r/1
title: Fox et al_Reviewer and editor gender influence the peer review process
DOI: 10.5061/dryad.591q3/25
title: AT2G03667
DOI: 10.5061/dryad.591q3/26
title: AT2G04620
DOI: 10.5061/dryad.591q3/27
title: AT2G04740
DOI: 10.5061/dryad.591q3/28
title: AT2G05120
DOI: 10.5061/dryad.591q3/29
title: AT2G05320
DOI: 10.5061/dryad.591q3/30
title: AT2G17265
DOI: 10.5061/dryad.591q3/31
title: AT2G20330
DOI: 10.5061/dryad.591q3/32
title: AT2G20790
DOI: 10.5061/dryad.591q3/33
title: AT2G31890
DOI: 10.5061/dryad.5j4kh/10
title: S1_Ref_2

description: A CT scan made by scanner 1 containing no metal implants.
DOI: 10.5061/dryad.5j4kh/11
title: S1_Ref_3

description: A CT scan made by scanner 1 containing no metal implants.
DOI: 10.5061/dryad.5j4kh/12
title: S2_MA_1_MDT

description: A CT scan made by scanner 2 containing metal implants and reconstructed using the MDT.
DOI: 10.5061/dryad.5j4kh/13
title: S2_MA_1_sMAR

description: A CT scan made by scanner 2 containing metal implants and reconstructed using sMAR.
DOI: 10.5061/dryad.5j4kh/5
title: S1_MA_2_OMAR

description: A CT scan made by scanner 1 containing metal implants and reconstructed using OMAR.
DOI: 10.5061/dryad.5j4kh/6
title: S1_MA_3_MDT

description: A CT scan made by scanner 1 containing metal implants and reconstructed using the MDT.
DOI: 10.5061/dryad.5j4kh/7
title: S1_MA_3

description: A CT scan made by scanner 1 containing metal implants and reconstructed using the standard algorithm.
DOI: 10.5061/dryad.5j4kh/8
title: S1_Misc

description: Miscellaneous data from scanner 1 (e.g. topogram, dose report)
DOI: 10.5061/dryad.5j4kh/9
title: S1_Ref_1

description: A CT scan made by scanner 1 containing no metal implants.
DOI: 10.5061/dryad.f0ph9/1
title: environmental data for the 163 plots

description: This file lists seven environmental variables for 163 plots used in the paper.
DOI: 10.5061/dryad.f0ph9/2
title: 580 species in the 163 plots

description: This file lists the 580 species in the 163 plots used in this paper.
DOI: 10.5061/dryad.f0tt2/1
title: Semi quantitative data

description: Raw semi-quantitative data and descriptive statistics
DOI: 10.5061/dryad.j05b3/1
title: PHASED.FASTA.FILES

description: Fasta files include the mitochondrial control region and 19 phased nuclear loci for 15 Hawaiian duck, 21 Laysan duck, and 25 mallard individuals (see Supporting information Table S1 & S2 for marker information).
DOI: 10.5061/dryad.j05b3/2
title: IMa2.Input.FILES

description: IMa2 input files consisting of 19 nuclear markers filtered for the largest non-recombinant fragment in the program IMgc for 15 Hawaiian duck, 21 Laysan duck, and 25 mallard individuals. The two files differ in starting phylogenetic relationships with mtDNA-like topology (Hawaiian duck sister to mallard) and nuDNA-like topology (Hawaiian duck sister to Laysan duck).
DOI: 10.5061/dryad.j05b3/3
title: STRUCTURE.Input.FILES

description: Input files for STRUCTURE runs. Three files include analyses between 15 Hawaiian duck, 21 Laysan duck, and 25 mallard samples with data sets where (a) recombination was ignored, (b) loci were filtered for recombination, and (c) 17 diagnostic SNPs ascertained by comparing Laysan ducks and mallards (Table S2). Similar to the latter file, a fourth file (Structure.Multi-species.SNP.Input.FILE.stru) includes 16 diagnostic SNPs assayed across 8 taxonomicunits of the mallard complex.
DOI: 10.5061/dryad.j05b3/4
title: SplitsTree.Input.FILE

description: Fasta file of 19 nuclear loci concatenated for a total  of 6,682 aligned nucleotides for 15 Hawaiian duck, 21 Laysan duck, and 25 mallard samples.
DOI: 10.5061/dryad.ks546/1
title: BWTE_data
DOI: 10.5061/dryad.p2pn8/1
title: BEAST xml file for taxon set with molecular data

description: This .xml file includes the alignments and specifications used in the analysis of the molecular data matrix. Additionally, this file includes the code that helped to resolve the convergence problems (low ESS values) stemming from a sparse molecular data matrix.
DOI: 10.5061/dryad.p2pn8/2
title: Stein et al. 2015 - BEAST xml file for simulation of the calibrated tree prior on the MCC tree from analysis of the taxon set with molecular data

description: This .xml file includes the specifications used to simulate the calibrate tree prior on the fully constrain maximum clade credibility trees generated from three replicate analyses of the molecular data matrix using:Stein et al. 2015 - BEAST xml file for taxon set with molecular data.xml
DOI: 10.5061/dryad.1g5kb.1
title: Data from: Allometry of animal-microbe interactions and global census of animal-associated microbes
DOI: 10.5061/dryad.1g5kb.2
title: Data from: Allometry of animal-microbe interactions and global census of animal-associated microbes
DOI: 10.5061/dryad.1g5kb.2/2.2
title: Kieft and Simmons diversity data

description: Diversity data calculated from MG-RAST data
DOI: 10.5061/dryad.1g5kb.2/3.2
title: Ley diversity data-1

description: Species richness data from Ley et al., 2008 Supplemental information
DOI: 10.5061/dryad.1j25j/4
title: Pedigree for analysis of Pat.success

description: This file contains the non-zero elements of the inverted A (relationship) matrix data for the animal model analysis of Pat.success.
DOI: 10.5061/dryad.1j25j/5
title: Phenotypic data: Ppat.success

description: This file contains the phenotypic data for the univariate quantitative genetic analyses of the probability that an offspring within an available brood (or litter) will be sired as an additional EPO by a focal male given that he sired one EPO in that brood (Ppat.success).
DOI: 10.5061/dryad.4tp56/1
title: Data all

description: All data from processus manipulation experiments 1-3
DOI: 10.5061/dryad.4tp56/2
title: CT scan files

description: Raw slice images from CT scans, and VAXML files and 3D pdfs of 3D reconstructions.
DOI: 10.5061/dryad.591q3/34
title: AT2G31890A
DOI: 10.5061/dryad.591q3/35
title: AT2G44660A
DOI: 10.5061/dryad.591q3/36
title: AT2G44760
DOI: 10.5061/dryad.591q3/37
title: AT2G46100
DOI: 10.5061/dryad.591q3/38
title: AT3G01380F
DOI: 10.5061/dryad.591q3/39
title: AT3G04650F
DOI: 10.5061/dryad.591q3/40
title: AT3G04650R
DOI: 10.5061/dryad.5j4kh/14
title: S2_MA_1

description: A CT scan made by scanner 2 containing metal implants and reconstructed using the standard algorithm.
DOI: 10.5061/dryad.5j4kh/15
title: S2_MA_2_MDT

description: A CT scan made by scanner 2 containing metal implants and reconstructed using the MDT.
DOI: 10.5061/dryad.5j4kh/16
title: S2_MA_2_sMAR

description: A CT scan made by scanner 2 containing metal implants and reconstructed using sMAR.
DOI: 10.5061/dryad.5j4kh/17
title: S2_MA_2

description: A CT scan made by scanner 2 containing metal implants and reconstructed using the standard algorithm.
DOI: 10.5061/dryad.5j4kh/18
title: S2_MA_3_MDT

description: A CT scan made by scanner 2 containing metal implants and reconstructed using the MDT.
DOI: 10.5061/dryad.5j4kh/19
title: S2_MA_3_sMAR

description: A CT scan made by scanner 2 containing metal implants and reconstructed using sMAR.
DOI: 10.5061/dryad.5j4kh/20
title: S2_MA_3

description: A CT scan made by scanner 2 containing metal implants and reconstructed using the standard algorithm.
DOI: 10.5061/dryad.5n60v/1
title: Data for tab1

description: 4 columns (cortisol, study_area, sex, trend), 178 rows, see describtion in tab 1
DOI: 10.5061/dryad.5n60v/2
title: Data for tab2

description: 4 columns (Cortisol, Individual, Sex, diff), 44 rows, see description of tab 2
DOI: 10.5061/dryad.5n60v/3
title: Data for tab3

description: 3 columns (Cortisol, male, time), 40 rows, for description see tab 3
DOI: 10.5061/dryad.5n60v/4
title: Data for tab4

description: 3 columns (Cortisol, Individual, Sex), 35 rows, for description see tab 4
DOI: 10.5061/dryad.d0826/1
title: community data matrix

description: Samples are in rows, species in columns, matrix values contain wet weight biomass. Note the many zeros of a typical community matrix.
DOI: 10.5061/dryad.d0826/2
title: functional traits of phytoplankton species

description: species in rows, traits in columns: nfix - nitrogen fixing ability;         silica - silica cell wall;  motility - possession of flagella;    buoyancy - buoyancy regulation with gas vesicles;    heterotrophy - ability of heterotrophic nutritional model; autotrophy - ability of autotrophic nutritional mode;fyco - possession of phycobilins;  chlb - possession of chlorophyll b; chlc - possession of chlorophyll c;  radius - cell size (radius) in μm;   chain - ability to form chains or colonies
DOI: 10.5061/dryad.d0826/3
title: samples table

description: Samples in rows. Row-names are arbitrary sample codes, which match the row-names of the community matrix. Columns are: "lat" - latitude;  "lon" - longitude;  "obstime" - sampling date;   "basin" - Baltic Sea basin;  "dist" - distance from the shoreline (km);      "Temp" - sample temperature (°C);      "Salin" - salinity;     "RUEP" - Phosphorus use efficiency;      "RUEN" - Nitrogen use efficiency;  "ww" - total phytoplankton wet weight (μg/L);  "ww.fixers" - wet weight of nitrogen fixers (μg/L); "ww.apha" - wet weight of Aphanizomenon;  "ww.nodu" - wet weight of Nodularia
DOI: 10.5061/dryad.d0826/4
title: phylogeny file

description: phylogeny file in Newick format. See http://en.wikipedia.org/wiki/Newick_format for format details. Can be read with read.tree function of the ape library in R software.
DOI: 10.5061/dryad.hr05m/1
title: gompertz_model_parameters

description: Parameters used in the Gompertz population models for each species. See supporting information S2 for further details of the model.
DOI: 10.5061/dryad.hr05m/2
title: POMDP_input_files.tar

description: Symbolic Perseus POMDP input files for each species. See readme file for additional information.
DOI: 10.5061/dryad.hr05m/3
title: sea_level_rise_by_model

description: Estimated extent of sea level rise for each region and scenario with and without compensatory loss. For further details, see Iwamura, T (2012)  Spatial conservation prioritisation under global threats: University of Queensland.
DOI: 10.5061/dryad.hr05m/4
title: network_capacities

description: Node capacity (number of birds) for each species network model.
DOI: 10.5061/dryad.k3f17/1
title: Pyrosequencing competition data

description: Calibrated pyrosequencing data from Competition 1. The frequency of each competitor species in either paired competition with S. cerevisiae or in pooled monocultures. The adjusted frequency is based on calibration curves and eliminates negative values.
DOI: 10.5061/dryad.k3f17/2
title: Sequencing competition data

description: Calibrated sequencing data from Competition 2. The frequency of each competitor species in competition with different reference strains, along with concatenated barcode and indexes used for sample ID. The fitness difference and experimental metadata is also included.
DOI: 10.5061/dryad.k3f17/3
title: High-sugar environment

description: Data from assays (gren01 and nut01) to determine the intrinsic growth rate of each yeast species in high-sugar environments including grape juice. The OD600 (cell density) is given for time-points between zero and 48 hrs.
DOI: 10.5061/dryad.k3f17/5
title: Supernatant inhibitors

description: Data from assay to determine whether Saccharomyces cerevisiae produces unknown compounds that inhibit the growth of other yeast species. OD600 (cell density) is given for for time-points between zero and 48 hrs in supernatant cultures. A small number of samples (24/432) registered growth in un-innoculated controls before 36 hours, and these samples were omitted from our analysis. Following the removal of those samples, Lachancea kluyveri lacked sufficient control samples for analysis and was not included in the analysis.
DOI: 10.5061/dryad.n0h37/1
title: Solomon-Lane et al_behavior, reproduction, hormones
DOI: 10.5061/dryad.p2pn8/3
title: Stein et al 2015 - BEAST xml file for taxon-complete analyses

description: This xml file includes the alignments, specifications and additional taxonomic constraints used in the taxon-complete analyses. Additionally, this file includes the code that helped to resolve the convergence problems (low ESS values) stemming from a sparse molecular data matrix. The approach was developedby Dr. Joseph W. Brown and involves the following:1. Create a new compoundParameter to update mean clock rates as a set    see lines:   19329 - 193392. Comment out the upDownOperators for each mean clock rate     see lines:  20378 - 204833. Create a new upDownOperator for the new compound parameter     see lines:  20495 - 20504Searching for “compoundParameterSetUp” (omitting the “”) within the .xml file will locate each of the edits associated with setting up the new compoundParameter for mean clock rates.
DOI: 10.5061/dryad.p2pn8/4
title: Stein et al. 2015 Fig. 1 in nexus file format

description: Phylogenetic hypothesis resulting from analysis of the molecular data matrix in the nexus file format.
DOI: 10.5061/dryad.p2pn8/5
title: Stein et al. 2015 Fig. 1 in newick file format

description: Phylogenetic hypothesis resulting from analysis of the molecular data matrix in the newick file format.
DOI: 10.5061/dryad.q35s1/1
title: Moa-HCl-1

description: Moa HCl extraction run #1 on Orbitrap XL
DOI: 10.5061/dryad.rm907/12
title: README

description: README file
DOI: 10.5061/dryad.rm907/2
title: supplementary_table_1

description: Supplementary Materials Table 1. List of publications used in constructing the synthetic supermatrix. Focal group, number of taxa, and number of fin, limb, and girdle characters, states and phenotype annotations. Studies focused explicitly on the fin to limb transition are denoted by an asterisk.
DOI: 10.5061/dryad.rm907/3
title: supplementary_table_2

description: Supplementary Materials Table 2. Taxa (136) present in the variable-only synthetic supermatrix based on inferred data alone.
DOI: 10.5061/dryad.rm907/4
title: supplementary_table_3

description: Supplementary Materials Table 3. Conflicting characters. Characters with conflicting states in the variable-only supermatrix, listed by taxon. Conflict type (between direct assertions, direct vs. inferred, and inferred vs. inferred) indicated in right-most column.
DOI: 10.5061/dryad.17331/1
title: Harvey_MacDougall_AmNat_2015

description: The zip file contains two excel sheets, one for plant, and one for arthropod data. Each excel sheet is a community data matrix where each row represents a sampling plot, and each column a plant or arthropod taxa. Additional information on treatments, and geographical location is provided in the different corresponding columns. For more details on the sampling design in itself, please see the Methods section of the main paper. Please note that this data can be used directly with the R code provided in the Appendix E of the paper to reproduce the results.
DOI: 10.5061/dryad.2c2d2/1
title: Functional properties of plant community from five land use types in Bolivia

description: Community weighted mean, coefficient of variation, and kurtosis  of 12 plant functional traits
DOI: 10.5061/dryad.2c2d2/2
title: Metadata of Carreno-Rocabado et al2015

description: Data description
DOI: 10.5061/dryad.4p9j3/1
title: Raw 454 reads of transcriptomes

description: edinburgh.sff - Oulanka reads produced in Genepool in Edinburgh. liverpool.sff & RocheLiverpool.sff - Vancouver reads produced by the CGR in Liverpool, the former contained less reads than quoted so the library was run again to produce the latter file. All files were used for the assembly.
DOI: 10.5061/dryad.4p9j3/2
title: Scripts used to identify and filter the best SNPs.
DOI: 10.5061/dryad.4p9j3/3
title: QTL analysis data

description: Genotyping data separated by chromosome, pedigree data and phenotypic (song and CHC) data. 'v' in the filenames stands for Vancouver, 'k' stands for Kuusamo, Oulanka.
DOI: 10.5061/dryad.4p9j3/4
title: assembled Transcriptome

description: Fasta file with first blast hit of the assembled transcriptome, and blast2GO project with the same information.
DOI: 10.5061/dryad.591q3/41
title: AT3G14910
DOI: 10.5061/dryad.591q3/42
title: AT3G21540F
DOI: 10.5061/dryad.591q3/43
title: AT3G22660
DOI: 10.5061/dryad.591q3/44
title: AT3G54460
DOI: 10.5061/dryad.591q3/45
title: AT4G00560F
DOI: 10.5061/dryad.591q3/46
title: AT4G14605
DOI: 10.5061/dryad.591q3/47
title: AT4G19900
DOI: 10.5061/dryad.591q3/49
title: AT5G04910
DOI: 10.5061/dryad.5j4kh/21
title: S2_Ref_3

description: A CT scan made by scanner 2 containing no metal implants.
DOI: 10.5061/dryad.5j4kh/22
title: S2_Misc

description: Miscellaneous data from scanner 2 (e.g. topogram, dose report)
DOI: 10.5061/dryad.5j4kh/23
title: S2_Ref_1

description: A CT scan made by scanner 2 containing no metal implants.
DOI: 10.5061/dryad.5j4kh/24
title: S2_Ref_2

description: A CT scan made by scanner 2 containing no metal implants.
DOI: 10.5061/dryad.5j4kh/25
title: S3_MA_1_DE120keV

description: A CT scan made by scanner 3 containing metal implants using a dual energy acquisition and reconstructed at 120 keV.
DOI: 10.5061/dryad.5j4kh/26
title: S3_MA_1_DE150keV

description: A CT scan made by scanner 3 containing metal implants using a dual energy acquisition and reconstructed at 150 keV.
DOI: 10.5061/dryad.5j4kh/27
title: S3_MA_1_MARIS0

description: A CT scan made by scanner 3 containing metal implants and reconstructed using MARIS0.
DOI: 10.5061/dryad.5j4kh/28
title: S3_MA_1_MARIS1

description: A CT scan made by scanner 3 containing metal implants and reconstructed using MARIS1.
DOI: 10.5061/dryad.5j4kh/29
title: S3_MA_1_MARIS2

description: A CT scan made by scanner 3 containing metal implants and reconstructed using MARIS2.
DOI: 10.5061/dryad.7k434/1
title: Cervus infile for seeds collected in 1998 at the selectively logged plot

description: Genotypes of 10 microsatellite markers. Lines 2 to 39 were genotypes of adult trees (more than 20 cm dbh) in the selectively logged plot (5.5 ha). Genotypes of seeds collected from four mother trees were started from Line 40.
DOI: 10.5061/dryad.7k434/2
title: Cervus infile for seeds collected in 2005 at the selectively logged plot

description: Genotypes of 10 microsatellite markers. Lines 2 to 39 were genotypes of adult trees (more than 20 cm dbh) in the selectively logged plot (5.5 ha). Genotypes of seeds collected from four mother trees were started from Line 40.
DOI: 10.5061/dryad.7k434/3
title: Cervus infile for seeds collected in 1998 at the undisturbed plot

description: Genotypes of 10 microsatellite markers. Lines 2 to 145 were genotypes of adult trees (more than 20 cm dbh) in the undisturbed plot (6.0 ha). Genotypes of seeds collected from four mother trees were started from Line 145.
DOI: 10.5061/dryad.7v81b/1
title: LongoetalRSOS.tar

description: This archive contains four files: (1) mapping file, (2) OTU table, (3) split libraries using the forward sequence read, and (4) tree file.
DOI: 10.5061/dryad.8cg8h/1
title: Tago_Burks_alignment_file

description: 16S rRNA gene sequences of the Burkholderia spp. were aligned using MEGA 6.
DOI: 10.5061/dryad.8cg8h/2
title: Tago_Burks_MLtree_file

description: Maximum Likelihood tree of the Burkholderia spp. based on 16S rRNA gene sequences using MEGA 6.
DOI: 10.5061/dryad.8cg8h/3
title: Tago_Colony_counting_data
DOI: 10.5061/dryad.bk175/1
title: Selection on floral traits

description: Collected at two common garden field sites in Poverty Gulch, Gunnsion County, CO. Corollalength and corollawidth are in mm. NPR24 is in uL/24 hr. RminusG is proportion of petal reflectance in red compared to in green. Seeds is total seeds produced by the plant, and flowers is total flowers.
DOI: 10.5061/dryad.bt7v0/1
title: Behavioural data (Fig 1B)

description: CSV sheet containing the data used in the behavioural analysis shown in figure 1B of the manuscript. Each row represents one subject. The column headings are as follows:  Column 1 - Accuracy on 'target left, cued' trials Column 2 - Accuracy on 'target right, cued' trials Column 3 - Accuracy on 'target left, uncued' trials Column 4 - Accuracy on 'target right, uncued' trials Column 5 - Reaction Time on 'target left, cued' trials Column 6 - Reaction Time on 'target right, cued' trials Column 7 - Reaction Time on 'target left, uncued' trials Column 8 - Reaction Time on 'target right, uncued' trials