cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t951d/1
title: Greenish Warbler consensus genome v1.0

description: Contains a consensus greenish warbler genome assembly, based on a consensus of genome assemblies of three greenish warbler (Phylloscopus trochiloides) individuals (viridanus TL2; trochiloides LN10; and plumbeitarsus BK2). The file contains sequences for 31 chromosomes and chromosome fragments, based on mapping of greenish warbler contigs to the zebra finch genome assembly (version 3.2.4; Warren et al. 2010). The file is in standard Fasta format. It needs to be un-compressed first by running the command:  gunzip Phylloscopus_trochiloides.Greenish_warbler.3sample.consensus.wrapped.toplevel.fa.gz    The three whole-genome shotgun assemblies have been deposited at DDBJ/ENA/GenBankunder the accessions LXPA00000000 (viridanus), LXOZ00000000 (trochiloides), and LXOY00000000 (plumbeitarsus).
DOI: 10.5061/dryad.t951d/2
title: Greenish Warbler VCF files: invariant and SNPs

description: This folder contains 31 files in the VCF format. Each contains genotypic information for a single chromosome (or chromosome fragment) for all individuals in the two GBS (genotype by sequencing) plates in the study. The files have names corresponding to "GW_Lane5plusLiz.GWref.genotypes.allSites.chr*.infoSites.vcf"; the * represents the chromosome name. All sites, both variant and invariant, where there was a total of more than 10 sequencing reads among all individuals were included. The chromosomes refer to those in the Zebra Finch assembly (version 3.2.4; Warren et al. 2010). For details of how these VCF files were produced and how they were then used, see the associated paper (Irwin et al., in review, Molecular Ecology) and this file in this same Dryad package: "GW_islands_of_diff_processing_scripts.txt"
DOI: 10.5061/dryad.t951d/3
title: Greenish Warbler genotypes: 45-sample analysis

description: This folder contains genotypic information used in the 45-sample analysis comparing the taxa viridanus, trochiloides, and plumbeitarsus (15 individuals each). For each chromosome, there is a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "GW_islands_of_diff_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package.  The metadata file ("GW_Lane5_plus_Liz.45samples.Fst_groups.txt"; also in this package) will be needed in the R processing.
DOI: 10.5061/dryad.t951d/4
title: Genotypes: outgroup analysis

description: This folder contains genotypic information used in the 9-sample analysis comparing greenish warbler and outgroup taxa (1 individual for each of 9 taxa). For each chromosome, there is a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "GW_islands_of_diff_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package. The metadata file ("GW_Lane5_plus_Liz.nine-taxa.Fst_groups.txt"; also in this package) will be needed in the R processing.
DOI: 10.5061/dryad.1040d/1
title: Full nucleotide sequences alignment

description: Alignments of the 12 H-stranded protein-coding genes (i.e. all the protein-coding genes except NADH-dehydrogenase 6, ND6) for 475 species
DOI: 10.5061/dryad.26j38/1
title: Concatenated alignment and tree

description: Alignment and phylogenetic tree of the concatenated 1,101 exon DNA alignment from 15 louse taxa.  Genes were assembled from raw genomic DNA with aTRAM and exons extracted and stitched together. Third codon position was removed due to base composition bias, and tree build in RAxML.
DOI: 10.5061/dryad.27056/1
title: Dryad

description: Data of trace elements of feathers, sediment and salt from samples collected between July and August 2014, during the ringing operations of three breeding colonies of Greather flamingo,  Phoenicopterus roseus, of the western Mediterranean: Aigues-Mortes (AIG), southern France (N 43° 33’, E 4° 11’); Fuente de Piedra (FDP), southern Spain (37° 06’N, 04° 45’W) and the heavily polluted Odiel marshes (ODI), southern Spain (37º 17′ N, 06º 55′ W).
DOI: 10.5061/dryad.2b7d5/1
title: Online_Figures_Sanchez_Reyes_etal

description: Supplementary figures S1 to S7 referenced in the text.
DOI: 10.5061/dryad.2b7d5/2
title: Tables_Suppl_Sanchez_Reyes_etal

description: Supplementary tables S1-S4, mentioned in the text.
DOI: 10.5061/dryad.2g3s4/2
title: Simulated data: with SNPs (no indels)
DOI: 10.5061/dryad.2g3s4/3
title: Simulated data: with SNPs and indels
DOI: 10.5061/dryad.2g3s4/4
title: Scripts used for the analysis
DOI: 10.5061/dryad.3c435/1
title: Raw Data
DOI: 10.5061/dryad.5s500/1
title: Boyle&Ryan2016_Appendix 1_PhylogeneticMatrix

description: Phylogenetic matrix of 73 brachythoracid taxa with 121 characters used in Boyle & Ryan 2016.
DOI: 10.5061/dryad.5s500/2
title: Boyle&Ryan2016_Appendix 2_CharacterChanges

description: Changes to phylogenetic character codings in Boyle & Ryan 2016 relative to those reported in Zhu et al. 2013 or Rucklin et al. 2015.
DOI: 10.5061/dryad.6ph26/1
title: Playbacks

description: Playback experiments conducted in the field. Experiment 1 - Focal individuals presented with control close calls and recruitment calls. Experiment 2 - Focal individuals presented with recruitment calls by weaker and stronger affiliates.
DOI: 10.5061/dryad.70917/1
title: Supplementary Figure 1

description: Illustration of the morphological characters used in this analysis. The first number denotes the character followed by the state illustrated, see Supporting Table 1,2 for details. All characters and states except Character 12 (Growth pattern) are figured. Taxa represented are: A) Charniodiscus arboreus; B) Avalofractus abalculus; C) Swartpuntia germsi; D) Charnia masoni; E) Pectinifrons abyssalis; F) Culmofrons plumosa; G)Ernietta plateauensis; H) Rangea schneiderhoehni; I) Beothukis mistakensis; J) Fractofusus misrai specimen that is overfolded showing both the dorsal and ventral planes and K) Charniodiscus arboreus specimen overfloded showing differences in coronal plane.  The reconstruction of Rangea is modified from Vickers-Rich et al. (2013, Fig. 9).
DOI: 10.5061/dryad.70917/2
title: Supplementary Table 1

description: Character list
DOI: 10.5061/dryad.70917/3
title: Supplementary Table 2

description: Character matrix
DOI: 10.5061/dryad.7j2t2/1
title: Trajectories of groups navigating obstacles, and associated files

description: This zip file contains a file explaining the types of data (1.readMe), a metadata file with information about each trial (2.metaData), and three folders for each of the other types of data: 3. pngs of group trajectories, 4. text files containing the x and y coordinates of the group through time, and 5. text files indicating the locations of the obstacles in each trial. These folders each contain a file associated with every trial.
DOI: 10.5061/dryad.8538d/1
title: Dataset

description: Please refer to ReadMe file.
DOI: 10.5061/dryad.88t58/1
title: Census data of ostracod in Daidokutsu Cave and outside of the cave

description: Sheet "Core06": Census data of ostracod species in Core 06; Sheet "Core 19": Census data of ostracod species in Core 19; Sheet "IR1": Census data of ostracod species in surface sediment IR1
DOI: 10.5061/dryad.b1039/1
title: R Code

description: R code to determine the optimal sampling strategy for unfamiliar prey belonging potentially to three different profitability classes. Simulations conducted to draw the graphs in the AmNat article.
DOI: 10.5061/dryad.cb7ns/1
title: CSV files

description: Compressed zip file of all the CSV files containing the data for all figures for the paper.
DOI: 10.5061/dryad.cd546/78
title: Chloroplast alignment, 70 taxa
DOI: 10.5061/dryad.cd546/79
title: Chloroplast tree, unpartitioned
DOI: 10.5061/dryad.cd546/80
title: Chloroplast tree, partitioned
DOI: 10.5061/dryad.cd546/81
title: Chloroplast alignment of Sanger loci
DOI: 10.5061/dryad.cd546/82
title: Chloroplast tree of Sanger loci
DOI: 10.5061/dryad.cd546/83
title: Mitochondrial alignment, 66 taxa
DOI: 10.5061/dryad.cd546/84
title: Mitochondrial tree, unpartitioned
DOI: 10.5061/dryad.cd546/85
title: Mitochondrial tree, partitioned
DOI: 10.5061/dryad.cm08m/1
title: HDplot R code

description: Code to run HDplot in R with generic format as input.  Example input file is HDplot_R_genericInput
DOI: 10.5061/dryad.cm08m/2
title: HDplot_R_genericInput

description: Example input file for HDplot R package.  Each row is a locus entry, there are five columns of data associated with each locus.  Column locus_ID contains the locus name.  Sequence reads for each allele are given in columns depth_a and depth_b.  Sequence reads for each allele are summed over heterozygous individuals for each locus.  The num_hets column indicates the number of heterozygous individuals for each locus while the num_samples column contains the total number of individuals in the data set.
DOI: 10.5061/dryad.cm08m/3
title: HDplot_python

description: Python code to run HDplot.  This can take input directly from the Stacks program in the form of the .vcf output from Stacks.  The file HDplot_python_exampleInput.vcf is included as an example of the required format.  The file vcf_to_depth.py is necessary to run HDplot_python and must be included in the same directory.
DOI: 10.5061/dryad.cm08m/4
title: vcf_to_depth

description: Python package called by HDplot_python.py that extracts sequence read counts from the .vcf format input.
DOI: 10.5061/dryad.cm08m/5
title: HDplot_python_exampleInput

description: Example .vcf format input for the HDplot_python.py program.
DOI: 10.5061/dryad.cn6v1/1
title: MOLECOL_KRAEMER
DOI: 10.5061/dryad.d04s0/1
title: Experiment 1 – Quantifying anabolism from glucose in cold-hardy versus -susceptible fly lines

description: Cold hardy and susceptible flies were fed a dilute U13C-6-glucose tracer, left to metabolize for 4h, then homogenized and enrichments in glucose and amino acids were analyzed using GC-MS as described in Williams et al. (in review). Data are Atom Percent Excess (APE).
DOI: 10.5061/dryad.d04s0/2
title: Experiments 2 and 3 - Oxidation rates of glucose and leucine tracers

description: Oxidation rates of glucose and leucine tracers before, during and after cold exposure for cold-hardy and -susceptible flies.
DOI: 10.5061/dryad.d04s0/3
title: Experiments 2 and 3 - Tracer enrichments in body pools

description: 13C enrichments in lipid, carbohydrate and protein pools resulting from glucose and leucine tracer ingestion, before during and after cold exposure for cold-hardy and cold-susceptible flies.
DOI: 10.5061/dryad.g977f/1
title: duque_stevens

description: This zip file includes data files, an R script, and a README file to analyze pinyon jay food sharing data.
DOI: 10.5061/dryad.j8r08/1
title: Data from: Climate, invasive species and land-use drive population dynamics of a cold-water specialist

description: The attached spreadsheet includes the raw redd counts for 92 bull trout populations (sheet 1) and the raw environmental data for the streams in those populations inhabit (sheet 2).  These data are sufficient to replicate all analyses in the associated manuscript.
DOI: 10.5061/dryad.k88h6/1
title: SRS PlantSR

description: Plant species richness data collected at the Savannah River Site near Aiken, SC, USA.  Data were collected in 8 experimental blocks; with five patches in each block.  Data were collected annually from 2001-2014. Details of experimental design found in Damschen, E. I., N. M. Haddad, J. L. Orrock, J. J. Tewksbury, and D. J. Levey. 2006. Corridors increase plant species richness at large scales. Science 313:1284-1286.
DOI: 10.5061/dryad.k88h6/2
title: Arthropod Species Richness

description: Data collected from eight experimental blocks, where the habitat was moss.  Each block included two treatments, an 0.25m2 control (continuous moss) and an 0.25m2 area that had experimental fragments that were 20cm2 or 200cm2 in area.  Details found in Gonzalez, A. 2000. Community relaxation in fragmented landscapes: the relation between species richness, area and age. Ecology Letters 3:441-448.
DOI: 10.5061/dryad.km3qd/1
title: PONE-D-16-04036R2

description: Resting and maximal metabolic rates, and metabolic scope of LPS, SRBC, PBS-challenged mosquitofish
DOI: 10.5061/dryad.m2j85/1
title: LateralAllometryRemovedF3impFormat

description: Lateral landmarks with allometry removed
DOI: 10.5061/dryad.m2j85/2
title: ventralallometrycorrectedLMs

description: Ventral landmarks with allometry removed
DOI: 10.5061/dryad.m2j85/3
title: All_F3_phenotypes

description: All traits from F3 hybrid cichlids, including the genetic map.
DOI: 10.5061/dryad.n21f4/10
title: Nexus file including 818 cytochrome-b sequences of Sicyopterus stimpsoni

description: Nexus file including 818 cytochrome-b sequences (612bp) of Sicyopterus stimpsoni from Hawaii analyzed in Alda et al.
DOI: 10.5061/dryad.n21f4/2
title: Nexus file including 2229 cytochrome-b sequences (512bp) of Awaous stamineus

description: Nexus file including 2229 cytochrome-b sequences (512bp) of Awaous stamineus from Hawaii analyzed in Alda et al.
DOI: 10.5061/dryad.n21f4/3
title: Sample and sequence data information for Eleotris sandwicensis

description: Excel file including sample data information for the 497 cytochrome-b sequences (943bp) of Eleotris sandwicensis from Hawaii analyzed in Alda et al. Sample ID, Year of collection, Watershed, Islands, Hawaiian Division of Aquatic Resources (DAR) Code, Sequence name.
DOI: 10.5061/dryad.n21f4/4
title: Nexus file including 497 cytochrome-b sequences (943bp) of Eleotris sandwicensis

description: Nexus file including 497 cytochrome-b sequences (943bp) of Eleotris sandwicensis from Hawaii analyzed in Alda et al.
DOI: 10.5061/dryad.n21f4/5
title: Sample and sequence data information for Sicyopterus stimpsoni

description: Excel file including sample data information for the 110 cytochrome-b sequences (430bp) of Sicyopterus stimpsoni from Hawaii analyzed in Alda et al. Sample ID, Year of collection, Watershed, Islands, Hawaiian Division of Aquatic Resources (DAR) Code, Sequence name.
DOI: 10.5061/dryad.n21f4/6
title: Nexus file including 110 cytochrome-b sequences of Sicyopterus stimpsoni from Hawaii analyzed

description: Nexus file including 110 cytochrome-b sequences (430bp) of Sicyopterus stimpsoni from Hawaii analyzed in Alda et al.
DOI: 10.5061/dryad.n21f4/7
title: Sample and sequence data information for Neritina granosa

description: Excel file including sample data information for the 606 cytochrome-c oxidase I (578bp) of Neritina granosa from Hawaii analyzed in Alda et al. Sample ID, Year of collection, Watershed, Islands, Hawaiian Division of Aquatic Resources (DAR) Code, Sequence name.
DOI: 10.5061/dryad.n21f4/8
title: Nexus file including 606 cytochrome-c oxidase I of Neritina granosa

description: Nexus file including 606 cytochrome-c oxidase I (578bp) of Neritina granosa from Hawaii analyzed in Alda et al.
DOI: 10.5061/dryad.nc95n/1
title: Butterfly species abundance matrix

description: Species abundance matrix and associated environmental variables.
DOI: 10.5061/dryad.qp0qv/1
title: DevelopmentalHippCA1Data

description: Raw EMG (.rw), LFP (.csc), and pre-processed spike data for the article submitted to PLoSONE. For more details, please contact to Jangjin Kim (kim.jangjin@gmail.com)
DOI: 10.5061/dryad.qv807/1
title: Mitchell_Oikos_Data

description: Excel file containing environmental data used in analysis, and variability measures used in analysis.
DOI: 10.5061/dryad.rf452/1
title: Brassica rapa herbivory phenotype and MSAP profiles

description: Phenotypic data (morphological traits and floral volatiles) and MSAP profiles of Brassica rapa R-o-18 plants under herbivore (Pieris brassicae) and methyl jasmonate treatment.
DOI: 10.5061/dryad.rf452/2
title: Brassica rapa 5-azacytidine phenotype and assay

description: Phenotypic data (morphological traits and floral volatiles) and results of a two-choice assay with the pollinator Bombus terrestris of Brassica rapa rapid-cycling plants under 5-azacytidine treatment.
DOI: 10.5061/dryad.rk568/1
title: Huang et al. Data
DOI: 10.5061/dryad.t951d/10
title: SNPs only across the whole-genome

description: This folder contains genotypic information for variant sites across the whole genome, among all greenish warbler individuals in the study. This information was used to produce Figure S1. The folder contains a file containing the genotypes (ending in "012NA"), a file containing the list of individuals (ending in "012.indv"), and a file containing the list of positions on the chromosome (ending in "012.pos"). For details of how these files were produced see the file "GW_islands_of_diff_processing_scripts.txt", also provided in this Dryad package. These files are ready to be used for subsequent analysis and presentation in the R scripts supplied in this package. The metadata file ("GW_Lane5_plus_Liz.GW_only.adults_only.Fst_groups.txt"; also in this package) will be needed in the R processing.
DOI: 10.5061/dryad.t951d/11
title: metadata for Figure S1 (whole-genome PCA)

description: This file contains metadata for greenish warbler individuals used in the whole-genome PCA analysis (Figure S1). The R script in this package uses this information to color points in the PCA.
DOI: 10.5061/dryad.t951d/5
title: metadata for the 45-sample analysis

description: This file is required for conducting the 45-sample analysis using the R script provided in this package. The file provides the names of each individual, the location code, the "group" (used for coloring points in various plots) and "Fst_group" (used for defining groups in the Fst analysis), and the "plot_order" (not used in the present paper).
DOI: 10.5061/dryad.t951d/6
title: metadata for the outgroup analysis

description: This file is required for conducting the 9-sample analysis using the R script provided in this package. The file provides the names of each individual, the location code, the "group" (used for coloring points in various plots) and "Fst_group" (used for defining groups in the Fst analysis), and the "plot_order" (not used in the present paper).
DOI: 10.5061/dryad.t951d/7
title: main R analysis script

description: This file contains the main R scripts used to conduct the analysis and produce the figures. It uses as input the "012NA" files (and associated files) produced as described in the "GW_islands_of_diff_processing_scripts.txt" file. Note that two metadata files (also contained in this Dryad package) are also needed. Also crucial is a file of R functions ("genomics_R_functions.R") written especially for this analysis, but designed to work more generally; these functions are called by this script file.
DOI: 10.5061/dryad.t951d/8
title: custom R functions file

description: This R file contains functions written by Darren Irwin for the analysis of Greenish Warbler GBS variation, but are designed to work more broadly for any dataset in similar input format. To reproduce the analysis in the paper, the main R script file ("GW_GBS_R_analysis_script_for_Dryad.R") should be run; it calls functions in the present file.
DOI: 10.5061/dryad.t951d/9
title: SiteStats and WindowStats R files

description: This folder contains files containing locus-based statistics ("SiteStats") and window-based statistics (WindowStats) for each chromosome. These files can be produced by the R script (in this package), and they can also be used by that script (whether the script saves and/or loads SiteStats and WindowStats files can be adjusted in that script using the setting for "calculate_or_load_stats" and the related settings below that). Producing these files can take days of processing time; I have included them here so you can produce most of the figures in the paper, by running the R script below the heading "GENOME-WIDE plots". That script will call the appropriate files (as long as you have designated a path/folder structure that matches the R script). Files are included for both the "45-sample" analysis and the "nine_taxa.one_per_taxon" analysis.
DOI: 10.5061/dryad.1040d/2
title: Phylogenetic tree

description: Phylogenetic tree of 475 species following the topology of Prum et al. (2015)
DOI: 10.5061/dryad.1040d/3
title: Chronogram Calibration sets 2

description: Chronogram estimated using the calibration sets 2 (see table 1 of Nabholz et al. 2016)
DOI: 10.5061/dryad.1040d/4
title: Chronogram Calibration sets 4

description: Chronogram estimated using the calibration sets 4 (see table 1 of Nabholz et al. 2016)
DOI: 10.5061/dryad.1040d/5
title: R script to convert branch length in divergence dates

description: A R script to compute the mass-corrected substitution rate and compute the divergence dates. This program convert branch length in divergence dates by computing the mass-corrected molecular rates as described in Nabholz et al. 2016. Header of the script contains useful informations.
DOI: 10.5061/dryad.1040d/6
title: Harrier_Oatley_2015

description: This dataset is used as the first working example in Nabholz et al. 2016
DOI: 10.5061/dryad.1040d/7
title: Xiphorhynchus_Rocha_2015

description: This dataset is used as the second working example in Nabholz et al. 2016
DOI: 10.5061/dryad.18j1h.2
title: Data from: Variation of anal fin egg-spots along an environmental gradient in a haplochromine cichlid fish
DOI: 10.5061/dryad.19r0c/1
title: Interactive Contest Duration Simulator

description: Interactive contest duration simulator based on our model. The file contains two sheets, one with the linear scaling relationship and another with the power scaling relationship
DOI: 10.5061/dryad.19r0c/2
title: R-version of the predictive model

description: Similar to the interactive file, but in R-code
DOI: 10.5061/dryad.19r0c/3
title: RHP variance test

description: R-code of the RHP variance test
DOI: 10.5061/dryad.1n542/1
title: NMR data

description: zipped archive of representative NMR spectra
DOI: 10.5061/dryad.1n542/2
title: fluorescence images and data

description: zipped archive of fluorescence data at different time points and excel files listing data, fitting and calculations of point spread functions
DOI: 10.5061/dryad.237hs/1
title: Brans_etal_PhilTransB_EcoEvoUrbanLandscapes_data

description: Data1: Body size data on all species present in the communities sampled along the urbanization gradient. Data2: Relative abundances of all species present in the communities sampled along the urbanization gradient. Data3: GBG values for all ponds, indicating the percentage built-up area and thus the degree of urbanization. Data4: Experimental genotypic size at maturity data of Daphnia magna reared at two different temperatures (20°C and 24°C). Data5: Adult field body size data of Daphnia magna to extend estimations in the GTV analyses.
DOI: 10.5061/dryad.26j38/2
title: Individual Gene Trees and Alignments

description: All 1,101 gene trees and alignments for the 15 taxon dataset. Each gene was aligned using PASTA and UPP for fragmentary sequences. Each gene tree was built using ASTRAL.
DOI: 10.5061/dryad.26j38/3
title: SupplementaryTable

description: DNA extraction, and quality clean up for each dataset. Illumina reads. Alignments of each gene and the tree analysis.
DOI: 10.5061/dryad.26j38/4
title: Supplementary Figure

description: Box plot of the standard deviations away from mean foreach codon position for each of the GTR rate parameters. The majorities of the extreme outliers fell above 10 standard deviations from the mean and were removed from the analysis.