cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.35jt8/3
title: Grouse MHC class II BLB sequences (BLB1 locus)

description: Grouse MHC class II BLB sequences (BLB1 locus). Aligned fasta file.
DOI: 10.5061/dryad.35jt8/4
title: Grouse MHC genotypes by individual (454 pyrosequencing)

description: Grouse MHC class I and class II genotypes by individual, as identified with 454 pyrosequencing. See Grouse MHC class IA sequences.fasta and Grouse MHC class II BLB sequences (all).fasta files for aligned sequences.
DOI: 10.5061/dryad.35jt8/5
title: Grouse MHC genotypes by individual (BLB1 locus sequencing)

description: Grouse MHC class II BLB1 genotypes by individual, as identified with nested PCR locus-specifc approach. See Grouse MHC class II BLB sequences (BLB1 locus).fasta file for aligned sequences.
DOI: 10.5061/dryad.4v131/1
title: data_compilation_Marschner_et_al

description: Compilation of ORTR raw data, histopathological and immunopathological scoring, qRT-PCR data for kidney injury markers and kidney weight data. The data refer to the Figures 1, 3, 4 and 7 of the manuscript.
DOI: 10.5061/dryad.503d9/1
title: Supplementary Materials 1 - Description of characters

description: Characters (Prieto-Márquez, 2010a) used for Sternberg SJB materials in the present study.
DOI: 10.5061/dryad.503d9/2
title: Supplementary Materials 2 - Character state scores

description: Character state scores of Sternberg SJB materials used in this analysis are listed for each respective element.
DOI: 10.5061/dryad.5qb78/1
title: Claw size choice by females

description: data on the OSR treatment, female size and chosen male claw size for all 400 two choice tests. Variables names are explained in the worksheet titled 'information'.
DOI: 10.5061/dryad.60nn7/1
title: Keiser et al 2016 - Data File for Proceedings B

description: All data associated with the manuscript by Keiser et al. published in Proceedings B regarding the transmission of cuticular bacteria between colony-mates in a social spider.
DOI: 10.5061/dryad.73s46/1
title: Raw Data Files

description: Genepop files for simulated and empirical datasets
DOI: 10.5061/dryad.75756/1
title: Henslow's sparrow count data

description: Counts of Henslow's sparrows at Big Oaks National Wildlife Refuge with covariates for years since prescribed fire.
DOI: 10.5061/dryad.7b0v8/1
title: Bruintjes_Data

description: Raw data behavioural and physiological measurements
DOI: 10.5061/dryad.81b74/1
title: Experimental measurements

description: These are the measurement results for the faking of the Bell violation in the Franson interferometer. Filenames starting with A are Alice's measurement results. Filenames starting with B are Bob's measurement results. The three last characters of the filename show the settings of the source and analysis station in multiples of pi/4. The first character is the early setting, the middle is the late setting and the last character is the phase shift in the analysis station. The character N stands for no pulse. The data files are counts, each row is one second of data.  Each column is one detector (plus or minus). The first half of each file is the early timeslot, the second half is the late timeslot. The detectors used in the experiment are commercial products
from Princeton Lightwave. These detectors are InGaAs avalanche photodiodes (APDs) that use Geiger and biased pulse modes at the operating temperature 218 K. The detection wavelength range is 1300 to 1550 nm, giving a maximum detection efficiency of 20 % at 1550 nm. The dark count rate is 5e−5 per nanosecond .
DOI: 10.5061/dryad.8b416/1
title: Sequences used for 10 spruce species in China

description: Source information and GenBank accession numbers all sequences used for 10 spruce species in China.
DOI: 10.5061/dryad.8b416/2
title: Spruce distribution  and climate data

description: Spruce distribution  and climate data  (LAN, latitude; LON, longitude; AL, altitude) and climatic variables for the 10 spruce taxa. MAT, mean annual air temperature; TCM, mean temperature of the coldest month; TWM, mean temperature of the warmest month; GDD5, growing degree days on a 5˚ C basis; GDD0, growing degree days on a 0˚ C basis; MAP, mean annual precipitation; AET, actual evapotranspiration; PET, potential evapotranspiration; α (AET/PET), aridity index.
DOI: 10.5061/dryad.9h7p4/1
title: Grimm_etal_Gehyra_micsats

description: This data file contains the microsatellite loci analysed from genetic samples and individual traits of the gecko Gehyra variegata (alias Gehyra versicolor) population of Kinchega National Park, Australia. These data were used for an application of the R-package NEff.
DOI: 10.5061/dryad.f84d3/1
title: Bennett and Cahill Multi-year competition data with and without fungicide

description: This file contains data on growth and survival for 18 species in a factorial experiment that removed neighbouring plants and applied fungicide in a factorial combination. These treatments and plant measurements were taken from years one and three of the experiment.
DOI: 10.5061/dryad.j82n2/1
title: OTU_table

description: Abundances and taxonomic assignment (98% identity threshold) of bacterial OTUs in the fecal samples of obese subjects undergoing bilio-intestinal bypass surgery. The sample ID indicates the status (pre-surgery, before bilio–intestinal bypass; post-surgery, after bilio–intestinal bypass) followed by patient number.
DOI: 10.5061/dryad.j82n2/2
title: OTU_alignment

description: Consensus sequences representative for each bacterial OTU in the fecal samples of obese subjects undergoing bilio-intestinal bypass surgery.
DOI: 10.5061/dryad.mh57b/1
title: Royal Society Open Science Supplementary info final version
DOI: 10.5061/dryad.nh8c7/1
title: BEAST MCC tree Rhamnaceae Onstein et al

description: For details also see Onstein et al. 2015 Evolution DOI: 10.1111/evo.12605. BEAST MCC tree based on sequence data for species of Rhamnaceae and outgroup taxa collected from GenBank (www.ncbi.nlm.nih.gov) (513 accessions) and generated by ourselves (379 accessions), for six chloroplast markers (matK gene 1593 base pairs (bp), trnL-F genes and intergenic spacer 1232 bp, rbcL gene 1425 bp, psbA gene and psbA-trnH intergenic spacer 775 bp, ndhF gene 2163 bp, rpl16 gene and intron 1344 bp) and one nuclear marker (ITS gene 952 bp).The best fit model for the chloroplast and ITS markers were identified with the Bayesian Information Criterion (BIC) implemented in PartitionFinder v 1.0.1, as follows: GTR + G + I for the linked chloroplast markers, and SYM + G + I for the ITS marker. We used the uncorrelated lognormal relaxed clock and a yule tree prior available in BEAST v.1.7.5. The MCC tree is based on the 10250 subsampled trees.
DOI: 10.5061/dryad.p4s57/10
title: data underlying Fig S8

description: Breadth of expression and maximal expression is compared in three groups of observations: (1) autosomal paralogs of X-linked genes, (2) other autosomal paralogs matched by age, (3) X-linked paralogs. Newly formed paralogs are defined as those mapped by phylogenetic timing to taxa Theria or younger. Pre-existing duplications are defined as those descending from duplication notes mapped by phylogenetic timing to taxa Amniota or older.
DOI: 10.5061/dryad.p4s57/11
title: data underlying Fig7
DOI: 10.5061/dryad.p4s57/12
title: TreeFam data for timing of gene duplications in R environments

description: These files are R environments.Use load() to load them into your R session!You ls() to view contents.You may use attach() syntax to load the namespace or access data members of the environment using the "$"reference operator.There is no warranty for this software
DOI: 10.5061/dryad.p4s57/5
title: raw_Z_Exp_Anc_L

description: Data for Fig 2 "The comparison of change in gene expression (Z) since the human-Chimpanzee common ancestor for five somatic tissues."
DOI: 10.5061/dryad.p4s57/6
title: SUPPLEMENTARY TABLES

description: Data in Table S3 underlies Figure 4. Data in Table S7 partially underlies Fig 1. Data in Tables S4 underlies Fig 3. Data in Tables S10-12 underlies Fig S1.
DOI: 10.5061/dryad.p4s57/7
title: data for Fig1

description: R environment containing data underlying Fig1. The environment contains the following variables sorted identically as the gene list in refSeqs: chromosome (chromosomal location), chromosome_short (location on autosomes,chrX, or chrY?), data_matrix (F5 data matrix in TPM for human tissues)‚ MAX (maximal expression for each RefSeq)‚ max (maximal expression for each tissue)‚ strata_classification (strata classification for genes on chromosome X)‚ refSeqs_2entrezIDs (entrez ids mapped to refseqs)‚ boe (the breadth of expression)
DOI: 10.5061/dryad.p4s57/8
title: GC-contents data for for Fig S6 and S7

description: This R environment contains GC-contents data for either proximal promoters or isochore around the TSS (marked as big). The data is calculated for either masked or unmasked genome seqeuence.
DOI: 10.5061/dryad.p4s57/9
title: data for Fig S3

description: numbers of ENCODE transcription factor binding sites mapped to TSSes of RefSeq genes in symmetrical windows of different sizes (from 250 to 20000 bps) and depending on ENCODE quality cut-off (strict or all).
DOI: 10.5061/dryad.qb4m0/1
title: Individual flight performance and wing shape metrics

description: Fruit fly flight performance and wing shape morphometrics. Trajectory analysis metrics. Principal component scores for left and right wings, where available, for each genotype described in Ray et al.(2016).
DOI: 10.5061/dryad.qj728/1
title: DSC curves of the experimental samples

description: DSC curves for the control samples of pure kaolinite (1), dark portion (DL) (2) and top portion (TL) (3) of the sediment after 6 months, top portion after the adding of CaCl2 (4).
DOI: 10.5061/dryad.rd5rn/1
title: Selection database

description: Database of selection estimates for four types of selection coefficients with associated estimates of population size.
DOI: 10.5061/dryad.rd5rn/2
title: Heritability database

description: Database of narrow-sense heritability estimates with associated estimates of population size.
DOI: 10.5061/dryad.rj87v/2
title: Transcriptome assembly of Amastigomonas sp

description: RNA-seq assembly of Amastigomonas sp. from Genbank SRA accession #SRR2170627. Read quality was assessed with FastQC before and after quality trimming and SMART adaptors removal, which was performed with FastqMcf. Cleaned reads were assembled into contigs with Trinity r20140717 using default parameters.
DOI: 10.5061/dryad.s14s1/1
title: Seedling and species recruitment of sown plant species

description: Seedling and species recruitment data for exotic ("EXO") and native ("NAT") sown species were recorded in the field on 0.5 x 0.5 square meter subplots in seed addition and control subplots (separate column "Control") on 18 experimental sites in two regions (8 Central California ("CA"), 10 Central Germany ("GE")). Data were recorded in 2012 (census 1 and 2) and 2013 (census 3). Subplots were either located in rodent exclosure (Rod), gastropod exclosure (Gas) or control plots (Con). The number of added seeds per species ranged from 50 to 175 (column "Number"), depending on the seed size. The number of sown species ranged from 17 (California) to 20 (Germany). Acronyms for the species can be derived by taking the first 3 letters of the genus and species names (see Table A 4).
DOI: 10.5061/dryad.s630c/10
title: Bayesian tree files - 6-intron+mtDNA partitioned topology

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.s630c/11
title: Bayesian tree files - Rhinolophus capensis clade, mtDNA topology

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.s630c/12
title: Tree files for the Bayesian multi-species coalescent (*BEAST; NEXUS format).

description: Tree files for the Bayesian multi-species coalescent (*BEAST; NEXUS format). This analysis is described in section 2.5 of the paper, Species delimitation & divergence time estimation, and was conducted in BEAST v. 1.8. The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.5. The LogCombiner files contain all trees generated from 5 independent runs with burn-in removed for each analysis (i.e. 180,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 180,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files.
DOI: 10.5061/dryad.s630c/5
title: Bayesian tree files - 6-intron partitioned tree

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.s630c/6
title: Bayesian tree files - 5-intron partitioned topologies

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.s630c/7
title: Bayesian tree files - Combinations-of-two-introns topologies

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.s630c/8
title: Bayesian tree files - Combinations-of-mtDNA+each intron in turn

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.s630c/9
title: Bayesian tree files - Subsets of the mtDNA locus topologies

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.s7ph4/1
title: Data files for American mink SCR study

description: Mink data files (mink encounter histories, x,y coordinates of statespace, trap locations, and rivers)
DOI: 10.5061/dryad.v1r34/1
title: Biomass_Contiguous_forest_areas
DOI: 10.5061/dryad.v1r34/2
title: Biomass_Forest_areas
DOI: 10.5061/dryad.v1r34/3
title: Bird_Contiguous_forest_area
DOI: 10.5061/dryad.v1r34/4
title: Birds_Forest_areas
DOI: 10.5061/dryad.v1r34/5
title: Cover_Contiguous_forest_areas
DOI: 10.5061/dryad.v1r34/6
title: Cover_Forest_areas
DOI: 10.5061/dryad.v1r34/7
title: Density_Contiguous_forest_areas
DOI: 10.5061/dryad.1qt12/1
title: Zinger_et_al_SBB_extracellular_samples

description: This file contains geographic coordinates and other characteristics of each sample
DOI: 10.5061/dryad.1qt12/2
title: Zinger_et_al_SBB_extracellular_rawdata_uniq.tar

description: This tar.gz file contains 3 zipped fasta files of unfiltered sequencing data (i.e. assembled reads assigned to their original sample), corresponding each to Bacteria, Eukaryota and Plants amplicons.
DOI: 10.5061/dryad.1qt12/3
title: Nouragues2013_Plants_GH_uniq

description: This fasta file contains sequence references of the trnL P6 loop from plant specimens occurring in the Nouragues Reserve (French Guiana).
DOI: 10.5061/dryad.1qt12/4
title: Zinger_et_al_SBB_extracellular_filtered.tar

description: This tar.gz file contains 3 txt files (tab delim) of filtered sequencing data (i.e. after sequence clustering and spurious OTUs removal) and associated characteristics, corresponding each to Bacteria, Eukaryota and Plants amplicons. A full description of data curation is provided in the Supplementary Methods of Zinger et al. (2016) Extracellular DNA extraction is a fast, cheap and reliable alternative for multi-taxa surveys based on soil DNA.
DOI: 10.5061/dryad.2js61/1
title: Water availability 2015-12-01

description: Changes in surface water availability for the environment (inflows minus diversions; highlighted in grey) in the Murray-Darling Basin (GL yr-1), calculated from inflow and diversion data in CSIRO (2008) and MDBA (2012). CSIRO (2008) Water Availability in the Murray-Darling Basin. A report to the Australian Government from the CSIRO Murray-Darling Basin Sustainable Yields Project. CSIRO, Canberra. Available at: http://www.csiro.au/science/MDBSY.html MDBA (2012) Hydrologic Modelling to Inform the Proposed Basin Plan: Methods and Results. MDBA Publication No. 17/12. Murray-Darling Basin Authority, Canberra.
DOI: 10.5061/dryad.2js61/2
title: Changes in frequency and volume of floods 2015-12-01

description: . Estimated percentage and ranked changes in the period between floods and flood volumes from current development, 1895-2006 climate to current development, 2030 climate for major floodplains and wetlands in the Murray-Darling Basin. Overall rank change in flood regimes of for wetlands is mapped in Figure 3d. No data was available for the Eastern Mt. Lofty Ranges Catchment. Data on changes in flood return period and volume is from Table 7.2 of each of the CSIRO MDBSY regional reports, http://www.csiro.au/en/Research/LWF/Areas/Water-resources/Assessing-water-resources/Sustainable-yields/MurrayDarlingBasin/Reports
DOI: 10.5061/dryad.2js61/3
title: Ecosystem services 2015-12-01

description: Semi-quantitative changes in bundles of ecosystem services and adaptation services under scenarios of ‘Without development’ ‘Current’, and ‘Climate change’. Potential ecosystem services that may be of value for adaptation were determined based on increase between ‘Current’ and ‘Climate Change’
DOI: 10.5061/dryad.55sh1/1
title: Dataset_Proceed
DOI: 10.5061/dryad.5hs50/1
title: Red fox data_Ghoshal et al, 2016

description: The data consists information on red fox use (tracks per hectare) across ten sampled villages in Trans-Himalaya, village sizes, density of free-ranging dog and diet of red fox.
DOI: 10.5061/dryad.5hs50/2
title: Red fox_PlotLevelData_Ghoshal et al, 2016

description: This data file contains information on number of red fox tracks per plot (5mX5m) across ten villages of different sizes.
DOI: 10.5061/dryad.6008n/1
title: Raw Fecundity Data

description: Data file containing the measures of individual fecundity (egg count) across all treatments in our experiments.  This was used in our analysis shown in Figure 1.
DOI: 10.5061/dryad.6008n/2
title: Mean Fecundity and Mass Data

description: Mean values of our mass and fecundity data across our 26 hemiclone lines.  This was used for our correlation analysis in Figure 2.
DOI: 10.5061/dryad.6008n/3
title: Raw Mass Data

description: Raw data of male hemiclone mass.
DOI: 10.5061/dryad.6008n/4
title: Supplmental R Codes

description: Annotated R codes used for our data analyses.
DOI: 10.5061/dryad.742fp/1
title: a_card.txt
DOI: 10.5061/dryad.742fp/2
title: ana_hatch.R
DOI: 10.5061/dryad.7hb7r.1
title: Data from: Sampling diverse characters improves phylogenies: craniodental and postcranial characters of vertebrates often imply different trees
DOI: 10.5061/dryad.7hb7r.2
title: Data from: Sampling diverse characters improves phylogenies: craniodental and postcranial characters of vertebrates often imply different trees