cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.h30t5/3
title: tera.gut.trees.450

description: 450 trees (after 10% burn-in) from the BEAST analysis.
DOI: 10.5061/dryad.h30t5/4
title: tera.gut.star.beast.174

description: XML file used in the *BEAST species tree analysis.
DOI: 10.5061/dryad.h30t5/5
title: tera.gut.star.beast.174.species.trees2

description: Resulting tree from the *BEAST species tree analysis.
DOI: 10.5061/dryad.jm453/21
title: frog_DEC_M0_unconstrained_v1

description: R Data object containing results from DEC analysis of frog subtree in BioGeoBEARS (Appendix S3). Load this for ancestral-state estimates (see R code above).
DOI: 10.5061/dryad.jm453/22
title: frog_DECJ_M0_unconstrained_v1

description: R Data object from DECj model of frog subtree. Load for ancestral-state estimates.
DOI: 10.5061/dryad.jm453/23
title: amph_ecoregions_reduced

description: Ecoregion data for 3309-taxon whole-tree analysis of amphibians in BioGeoBEARS (Appendix S4).
DOI: 10.5061/dryad.jm453/24
title: amph_ecoregions_reduced

description: R code for whole-tree analysis of amphibians (Appendix S4) in BioGeoBEARS.
DOI: 10.5061/dryad.jm453/25
title: amph_shl_dates_trim

description: 3309-taxon amphibian tree for whole-tree analysis using BioGeoBEARS. This tree is "amph_shl_dates.tre" trimmed of the outgroup Homo_sapiens.
DOI: 10.5061/dryad.jm453/26
title: amph_DEC_M0_unconstrained_v1

description: R Data object from DEC analysis of amphibians (Appendix S4).
DOI: 10.5061/dryad.jm453/27
title: amph_DECJ_M0_unconstrained_v1

description: R Data object for DECj analysis of amphibians as a whole (Appendix S4). Load for ancestral-state estimates.
DOI: 10.5061/dryad.jm453/28
title: New_Names

description: The taxonomic database used here is from the 2009 update of AmphibiaWeb (http://www.amphibiaweb.org/). The genus-level taxonomy of amphibians is in constant flux recently, and many genera have changed in the last few years. This document translates the taxon labels in the 3309-taxon matrix into the name appearing in a 2014 update of AmphibiaWeb. Notably, the genera _Rana_ and _Bufo_ were broken up by Frost et al. (2006) and others, and the monophyly of these groups is actually supported in the current tree using their names. Some other genera are still not monophyletic, even using recently updated names. However, for those wishing to use the trees presented here for comparative analyses, this chart shows the most recent "correct" names that should be used, and for which data may have been gathered.
DOI: 10.5061/dryad.jm453/29
title: README

description: Guide to the supplemental materials.
DOI: 10.5061/dryad.m9t12/9
title: Silverman_et_al_2011_Annual_Survey_Report_for_2010

description: Reference S8. Silverman E, Koneff M, Fleming K, and Wortham J. 2011. 2010 Atlantic coast wintering sea duck survey. Laurel, Maryland: U.S. Fish and Wildlife Service.
DOI: 10.5061/dryad.ms8k7/1
title: Supplementary Data for Perry et al. PNAS (all files)
DOI: 10.5061/dryad.mv332/1
title: Population level dataset

description: The excel file contains for each population: the name (Patch_ID), informations on the location (commune, village and geographic coordinates), the fraction of leaves bearing chamsothecia averaged over the analyzed plants (prop_chasmos), the powdery mildew abundance in July 2012 (PM_AA_july12), the total number of samples analyzed, the number of samples positive for Ampelomyces.
DOI: 10.5061/dryad.mv332/2
title: Sample level dataset

description: The excel file contains for each sample: the name (Sample_ID), the population of origin (Patch), the plant name (Plant_Code), the fraction of leaves bearing chasmothecia (estimated at the plant level, Prop_chasmo_Plant), the presence/absence of multiple strains of powdery mildew within the sample (Mult_PM_strains) and the presence/absence of Ampelomyces based on the molecular detection test (Aq_PA)
DOI: 10.5061/dryad.mv332/3
title: Quadrat level dataset

description: For each quadrat, the excel sheet contains: the quadrat name (Quadrat_ID), population (Patch), the prevalence of Ampelomyces within the quadrat in autumn 2011 (Aq_prev), the proportion of plants found to be infected by the powdery mildew in july 2012 (Prop_PM_infect_plants_2012) and the proportion of leaves bearing chasmothecia in autumn 2011 (Prop_chasmos_2011)
DOI: 10.5061/dryad.n56t9/2
title: Codes for Species Identification Efficiencies

description: A custom Perl package called PESDET (version 0.1) for calculating species identification success rates, using the BLAST and BLAST+P distance (BLAST+PD) methods
DOI: 10.5061/dryad.n56t9/3
title: Dataset I

description: Dataset I used for the analyses of DNA barcoding gaps, species identification efficiency, sequence length and GC content
DOI: 10.5061/dryad.n56t9/4
title: Dataset II

description: Dataset II used for the analysis of primer universality
DOI: 10.5061/dryad.n7080/2
title: Wing centroid size and Nf1 SNP genotyping results (Figure2_data)

description: Wing centroid size and Nf1 SNP genotyping (by high resolution melt analysis) were obtained from D. melanogaster samples originated from Innisfail and Coffs Harbour, Australia, for genotype-phenotype association analyses.
DOI: 10.5061/dryad.q03g2/2
title: Combined Resistance Matrix

description: Cumulative resistance matrix from the combined model (maximum value from slope^1.5 and (1/RSPF^0.33 resistance surfaces)
DOI: 10.5061/dryad.q96d7/8
title: fossils as nodes actual values

description: This R script conducts MCMC analyses using informative node priors centered on the nodes' true values. The script was written to run multiple analyses simultaneously on a cluster. See fossils as tips description for more information.
DOI: 10.5061/dryad.qd734/4
title: Quémeneur et al. SOM 4

description: Paleobiological inference models in an Excel workbok. There are two models, one binary and one ternary, each on its sheet. Insert the data about size and microanatomy, and the inferred lifestyle appears.
DOI: 10.5061/dryad.rr65n/20
title: Genotype calls for Heliconius, 4 erato and 2 melpomene populations (vcf format)

description: Vcf files were generated by aligning to a reference using BWA.  Genotypes were called using GATK.  File prefix is _.  Files are standard vcf format.
DOI: 10.5061/dryad.s1092/10
title: Velocity.mel

description: Sperm velocity and sperm numbers in the SR for D. melanogaster. Variables: Fem – identity assigned to individual female; Movie – name of movie file from which data were collected; Treat – treatment (A = virgin mating, B = remating, C = no remate); Region – region of the female reproductive tract, bursa or SR; Male – first- or second-male sperm; Velmps – instantaneous linear velocity in microns per second, averaged for each sperm and for all sperm recorded in a movie; N – number of sperm tracked per movie; SR1 – number of first-male sperm in the SR; SR2 – number of second-male sperm in the SR
DOI: 10.5061/dryad.s1092/11
title: P2.sim

description: Paternity and sperm count data for D. simulans. Variables: Treat – time after mating for which paternity and sperm numbers in the female reproductive tract were quantified; FirstM – transgenic line of first male by sperm label, GFP or RFP. Second male is automatically the reciprocal label; Remate – day after first mating (day 0) on which female remated; Cop1 – duration in minutes of the first copulation; Cop2 – duration in minutes of the second copulation; PriorProg – number of progeny produced by female before remating; P2.24 – proportion of progeny sired by the second male (P2) for the first 24 hrs after mating; P2.48 – P2 for the first 48 hrs after mating; P2.72 - P2 for the first 72 hrs after mating ; P2 – P2 over entire time period; Bursa1 – number of first-male sperm in the bursa; Bursa2 – number of second-male sperm in the bursa; Prox1 – number of first-male sperm in the proximal half of the SR; Prox2 – number of second-male sperm in the proximal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist1 – number of first-male sperm in the distal half of the SR; Dist2 – number of second-male sperm in the distal half of the SR; Caps1 – number of first-male sperm in the two spermathecal caps combined; Caps2 – number of second-male sperm in the two spermathecal caps combined; Ducts1 – number of first-male sperm in the two spermathecal ducts combined; Ducts2 – number of second-male sperm in the two spermathecal ducts combined; SR1 – number of first-male sperm in the entire SR; SR2 – number of second-male sperm in the entire SR; Sp1 – number of first-male sperm in both spermathecae combined; Sp2 – number of second-male sperm in both spermathecae combined
DOI: 10.5061/dryad.s1092/14
title: Sperm.Length

description: Sperm lengths in mm for D. simulans and D. mauritiana. Variables: Species – sim or maur; Thorax – thorax length as a measure of body size, in an aritrary unit, to be entered as a covariate in analyses. Thorax length should be correlated with SR length but not sperm length.; Sperm1-5 – length in mm for each of 5 sperm measured per male. Average sperm lengths for each male are calculated from the four longest measurements.
DOI: 10.5061/dryad.s1092/9
title: Velocity.maur

description: Sperm velocity and sperm numbers in the SR for D. mauritiana. Variables: Fem – identity assigned to individual female; Movie – name of movie file from which data were collected; Treat – treatment; A = virgin mating, B = remating, C = no remate; Region – region of the female reproductive tract, bursa or SR; Male – first- or second-male sperm; Velmps – instantaneous linear velocity in microns per second, averaged for each sperm and for all sperm recorded in a movie; N – number of sperm tracked per movie; SR1 – number of first-male sperm in the SR; SR2 – number of second-male sperm in the SR
DOI: 10.5061/dryad.s571g/1
title: Populations_with_simulated_null_alleles

description: As described in our paper, we used two datasets: control and noisy. Each dataset contained 120 populations. In each population there were 100 individuals with 20 loci. Populations were originally simulated using SPAms program as described by Dąbrowski et al. 2014 (Mol Ecol Res, Volume 14, Issue 2, pages 361-373). In each population we simulated randomly two null alleles using NullAlleleGenerator (NAG) tool. Here we provide 240 populations with simulated 'true' null alleles in the noisy and control dataset. There are genotypes of individuals from each population and summary file where you will find in which loci the null alleles were simulated. For more information about simulating null alleles please download our tool NAG where you will find manual with detailed explanation http://www.lcb.uu.se/papers/dabrowski/NullAlleleGenerator.zip
DOI: 10.5061/dryad.1q88j/10
title: Biomass_Total_Residual

description: Plot-level estimates of total above-ground biomass over the study period (1979 to 2008) for all residual species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are Mg/ha.
DOI: 10.5061/dryad.1q88j/11
title: Cover_Herb_Colonist

description: Plot-level values of total (summed) cover over the study period (1979 to 2008) of colonizing herbaceous species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are % (values can exceed 100%).
DOI: 10.5061/dryad.1q88j/3
title: Biomass_Herb_Residual

description: Plot-level estimates of total above-ground biomass over the study period (1979 to 2008) for residual herbaceous species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are Mg/ha.
DOI: 10.5061/dryad.1q88j/5
title: Biomass_Shrub_Colonist

description: Plot-level estimates of total above-ground biomass over the study period (1979 to 2008) for colonizing shrub species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are Mg/ha.
DOI: 10.5061/dryad.1q88j/6
title: Biomass_Shrub_Residual

description: Plot-level estimates of total above-ground biomass over the study period (1979 to 2008) for residual shrub species (see Appendix A for species classification). Column headings are: Plot number (first digit is watershed number, 1 or 3); the remainining columns are sampling dates (1979, 1980, 1983, 1987, 1990, 1994, 1997, 2002, and 2008. Units are Mg/ha.
DOI: 10.5061/dryad.2189s/1
title: Hellbender Data
DOI: 10.5061/dryad.277g0/9
title: eyegenehits

description: Annotated predicted peptides of all E. carcharodonta sequences used in our phylogenetic analyses.
DOI: 10.5061/dryad.2k55t/3
title: Fever

description: Please see README file for description of all data files.
DOI: 10.5061/dryad.3pc64/1
title: Supplementary Material 1

description: Nexus file with the characters-taxa matrix used for the phylogenetic analysis.
DOI: 10.5061/dryad.4605c/4
title: Morphometric_Lab-reared 3 and 7 month fish

description: TPS file for geometric and morphometric analysis on mouth asymmetry of laboratory-reared 3 and 7 month old juvenile Perissodus microlepis fish
DOI: 10.5061/dryad.4gk00/1
title: Newcomer et al. 2012 (Ecological Monographs) Organic C and Denitrification in Streams

description: The file “Newcomer et al. 2012 (Ecological Monographs) Organic C and Denitrification in Streams.xlsx” provides original data from the manuscript. The worksheets are named to correspond with the figures in the manuscript. “Figure 4” has field measurements of nitrate and DOC loads (g ha-1 day-1) and runoff (mm day-1). We measured discharge at Spring Branch and discharge was downloaded from USGS gaging stations at the other sites. “Figure 5” was created using discharge (cfs) downloaded from USGS gaging stations and dividing it by watershed area to get runoff (mm day-1). “Figure 6” has field measurements of mean C:N molar ratios for leaves, periphyton, grass, sediment, and stream particulate organic matter (POM). “Figure 7” has field measurements of 15N and 13C stable isotope signatures for leaves, periphyton, grass, sediment, and stream POM. “Figure 8” has laboratory measurements of denitrification potentials associated with glucose versus nitrate amendments. “Figure 9” has laboratory measurements of denitrification potentials associated with the use of leaves, periphyton, and grass as a carbon source.
DOI: 10.5061/dryad.5p0c3/3
title: processed_data.tar.gz

description: This file contains all the analysis files except raw Illumina data (available as a separate file) and raw Oxford Nanopore read in FAST5 format. As FAST5 files require Oxford Nanopore's proprietary software to analyze and are large (~30G compressed), they are probably not useful to most readers, but are available from the authors upon request.
DOI: 10.5061/dryad.5p0c3/4
title: Illumina forward reads for the Protobothrops flavoviridis transcriptome

description: From: Aird, S.D. et al., 2013. Quantitative high-throughput profiling of snake venom gland transcriptomes and proteomes (Ovophis okinavensis and Protobothrops flavoviridis). BMC Genomics, 14(1), p.790.
DOI: 10.5061/dryad.5p0c3/5
title: Illumina reverse reads for the Protobothrops flavoviridis transcriptome

description: From: Aird, S.D. et al., 2013. Quantitative high-throughput profiling of snake venom gland transcriptomes and proteomes (Ovophis okinavensis and Protobothrops flavoviridis). BMC Genomics, 14(1), p.790.
DOI: 10.5061/dryad.77077/1
title: current_veg

description: asc file that describes suitability of each deme based on ecological niche modeling of current climate condition using MaxEnt. Original suitability score (0-1) was classified into 20 bins (0-20) with equal intervals, which inform differences in carrying capacities of each deme.
DOI: 10.5061/dryad.774s8/1
title: Simulation Gravity Model

description: Simulated genotypes for low and high density populations.
DOI: 10.5061/dryad.774s8/2
title: Cornus Gravity Model

description: Raw data analyzed in the gravity model for flowering dogwood, Cornus florida.
DOI: 10.5061/dryad.77bt2/2
title: Supermatrix alignment

description: Supermatrix alignment of 7 genes as used for phylogenetic and divergence time analysis. Please see readme file for details of gene partitions.
DOI: 10.5061/dryad.8674d/1
title: TE annotation of Arabidopsis thaliana accession Bur-0

description: TE annotation for Arabidopsis thaliana accession Bur-0. Coordinates are extracted from Bur-0 genome assembly (http://1001genomes.org/projects/MPIWang2012/). File format: TE id | Chromosome | start position | stop position.
DOI: 10.5061/dryad.8f6nq/1
title: Plate growth fitness data
DOI: 10.5061/dryad.8kk12/10
title: Proteome_t18

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 18 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.8kk12/4
title: Proteome_t6

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 6 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.8kk12/5
title: Proteome_t8

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 8 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.8kk12/6
title: Proteome_t10

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 10 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.8kk12/7
title: Proteome_t12

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 12 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.8kk12/8
title: Proteome_t14

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 14 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.8kk12/9
title: Proteome_t16

description: Protein-level quantitative proteomics data (protXML format) of the diel proteome of Prochlorococcus MED4 for timepoint 16 hours. Includes peptide-spectrum matches generated by X!Tandem, OMSSA and Myrimatch (and combined with iProphet), and 15N-labeling-based quantifications performed with ASAPratio.
DOI: 10.5061/dryad.9js92/8
title: IL-tophat-run

description: Commands used to map the reads to the reference genome, Larvae sample
DOI: 10.5061/dryad.9k6k0/1
title: CalculatingORPscoresAndComplexityCorrelationEffect

description: This file reads in the data--the order in which tasks were evolved and the order they are expressed--and calculates both the ontogeny recapitulates phylogeny (ORP) scores and the Complexity Correlation Effect (via Tukey’s Jackknife Method described in Sokal and Rohlf, 1995).
DOI: 10.5061/dryad.9k6k0/2
title: Data-OrderTasksEvolvedAndAreExpressed

description: See the readme file.
DOI: 10.5061/dryad.b35td/2
title: SNP and microsatellite data

description: RAD, transcriptomic, and microsatellite data used in the manuscript, as well as inputs/outputs of analyses. This archive contains the complete RAD .vcf file. For the complete transcriptomic .vcf file, see doi:10.5061/dryad.606j6, which is described in doi:10.1111/1755-0998.12190.
DOI: 10.5061/dryad.f058c/21
title: Pop18

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 18. Individuals that belong to population-pool 18 are listed in Table 1.
DOI: 10.5061/dryad.f058c/23
title: Pop20

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 20. Individuals that belong to population-pool 20 are listed in Table 1.
DOI: 10.5061/dryad.g5jj6/1
title: cerevisiae_fastq

description: fastq files split by barcode for S. cerevisiae isolates
DOI: 10.5061/dryad.g5jj6/5
title: para_assembly_d500

description: S. paradoxus assembly
DOI: 10.5061/dryad.gd031k26/3
title: Supplemental Dataset 4
DOI: 10.5061/dryad.gd031k26/4
title: Supplemental Dataset 5
DOI: 10.5061/dryad.gd031k26/5
title: Supplemental Dataset 6
DOI: 10.5061/dryad.gd031k26/6
title: Supplemental Dataset 7
DOI: 10.5061/dryad.j6kd3/1
title: TMS

description: The data file contains MEPs, silent periods and meanEMGs - from individual volunteers. The rows correspond to the same volunteer for all measures. The data is in MATLAB format.
DOI: 10.5061/dryad.jm453/30
title: Pyron_Appendix_S1

description: Appendix S1: caecilian subtree (DEC/DECj).
DOI: 10.5061/dryad.jm453/31
title: Pyron_Appendix_S2

description: Appendix S2: salamander subtree (DEC/DECj).
DOI: 10.5061/dryad.jm453/32
title: Pyron_Appendix_S3

description: Appendix S3: frog subtree (DEC/DECj).
DOI: 10.5061/dryad.jm453/33
title: Pyron_Appendix_S4

description: Appendix S4: whole-tree analysis of amphibians (DEC/DECj).
DOI: 10.5061/dryad.jm453/34
title: Pyron_Appendix_S5

description: Appendix S5: whole-tree analysis of amphibians (Mk1: MESQUITE).
DOI: 10.5061/dryad.jn14d/2
title: Griffiths2013Genotypes2011ChignikLake

description: Single-nucleotide polymorphism (SNP) genotypes for juvenile sockeye salmon (Oncorhynchus nerka) collected in 2011 in Chignik Lake, AK.
DOI: 10.5061/dryad.k9f7t/1
title: Goulart et al. (2013) - behavioral data

description: Color discrimination data of ten capuchin monkeys (Sapajus spp), two Female, eight Male. Discrimination thresholds obtained for each monkey in 20 test vectors around three different background coordinates (CIE 1976 u' v' chromaticity diagram). Thresholds are presented in terms of distance from background point (u' v' units x10^-4) and of u' v' coordinates.
DOI: 10.5061/dryad.k9f7t/2
title: Goulart et al. (2013) - genetic data

description: Amino acid sequences from exons 3 and 5 of the X-linked opsin genes of ten capuchin monkeys (Sapajus spp), two Female, eight Male. Sequencing of exons 3 and 5 allowed the deduction of the amino acid combinations at positions 180, 277, and 285 of the resulting opsins, from which the range of potential absorption maxima of the corresponding photopigments was inferred.
DOI: 10.5061/dryad.k9g50/7
title: IBDWS infile for IBD regression

description: Matrixes of geographic distance (in meters; above diagonal) and genetic distance (below diagonal) for Isolation by Distance Web Service analysis. Genetic distances calculated as Fst/(1-Fst) in Genepop v4.2.
DOI: 10.5061/dryad.k9g50/8
title: IBDWS infile for IBR regression

description: Matrixes of resistance distance (above diagonal) and genetic distance (below diagonal) for Isolation by Distance Web Service analysis. Genetic distances calculated as Fst/(1-Fst) in Genepop v4.2.
DOI: 10.5061/dryad.kp98j/1
title: LL_suppTable1

description: Microsatellite profiles of 10 loci for 241 Leptographium longiclavatum isolates (isolates in grey are clones). First column is the name of the isolates, and the second represents the location.
DOI: 10.5061/dryad.kt09v/1
title: Experiment 1

description: latency to safe zone access (in seconds) in experiment 1.