cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.rc1jr0v/1
title: Phylip_file

description: This is a variable phylip file created by the populations program in Stacks 1.46. We used a population map that included only samples used in modeling (see Supplemental Table S1). The 4 populations in the phylip file are defined as follows: 1 - WAS; 2 - EGB; 3 - P/W; 4 - WGB. See figures and text for population descriptions.
DOI: 10.5061/dryad.rc1jr0v/2
title: pssp_poly

description: STRUCTURE-formatted file used to investigate variation between diploids and tetraploids using PCA (in adegenet). The file contains 959 individuals and 8945 unlinked loci (i.e., only 1 locus per stack is recorded in this file). The first column contains sampling locality names combined with an ID number (unique per individual). There are 2 rows per individuals -  each records 1 allele. The second column is records a populations identifier - right now all diploids are recorded as "1" and all allotetraploids are recorded as "2". The subsequent columns contain the loci. Missing data is recorded as "-9". See Supplemental Table S1 for more information.
DOI: 10.5061/dryad.rc1jr0v/3
title: pssp_diploid

description: STRUCTURE-formatted file containing 834 P. spicata diploid individuals (wildland collections + commercial germplasm sources). This file was used in PCA (utilizing adegenet in R) and in STRUCTURE and sPCA analyses (not including the commercial germplasm sources). The file 3040 unlinked loci (i.e., only 1 locus per stack is recorded). The first column contains sampling locality names combined with an ID number (unique per individual). There are 2 rows per individuals - each records 1 allele. The second column is records a populations identifier - right now numbers reflect regional population identity, with commercial germplasm sources = "0". The subsequent columns contain the loci. Missing data is recorded as "-9". See Supplemental Table S1 for more information.
DOI: 10.5061/dryad.s7n1b44/1
title: Within-host-spore-counts

description: Raw data of raw spore loads for male and female Daphnia sampled every two days after infection. Included are the genotype of the pathogen (Column Path: C24, C19, C20, C14, C18 or C01), the sex of the infected host (Column Sex: M, F), the sampling age (Column Age: in days post infection), and the spore loads (Column Spores_mil: mature transmission spores in millions per animal). Spore loads at each time point were estimated by destructively sampled up to 20 infected individuals per sex and genotype combination.
DOI: 10.5061/dryad.tg20p4k/1
title: physiological_leaf_function and_ramet_demography_Kawai&Kudo

description: Ramet demographic date over tree years and Physiological function of accumulated leaves
DOI: 10.5061/dryad.vf62744/1
title: Diet_complementation_model_ouputs

description: Excel file containing main model outputs- Changes in plant species relative abundance in the seed availability-seed rain transition (Rsp2), resource provisioning effectiveness (RPE) and seed dispersal effectiveness of focal species (SDE). All datas have a read_me sheet with variables information
DOI: 10.5061/dryad.vg89038/1
title: Gambusia affinis metbolic, excretion, and size data

description: Field metabolic rate, excretion rate, and seine data from 10 field sites.
DOI: 10.5061/dryad.4j2662g/1
title: scripts: converting GBS reads to genotypes

description: This text file contains scripts and notes for the steps used in converting raw Illumina GBS sequencing reads to individual genotypes (at both variant and invariant sites) across the genome. The resulting genotype files (in "012NA" format) were then used as input into R, for the rest of the analysis and production of figures.
DOI: 10.5061/dryad.4j2662g/2
title: custom R functions file

description: This R file ("genomics_R_functions_V2.R" contains functions written by Darren Irwin originally for the analysis of Greenish Warbler GBS variation (in Irwin et al. 2016, Molecular Ecology) and modified more recently for the analysis of 3 North American warbler species groups (in Irwin et al. in review, Molecular Ecology). These functions 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 ("warbler_GBS_analysis_script_for_Dryad.R") should be run; it calls functions in the present file.
DOI: 10.5061/dryad.4j2662g/3
title: warbler_GBS_analysis_script_for_Dryad

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 "warbler_genomics_processing_scripts.txt" file. Note that the metadata files "warbler.Fst_groups_14each.txt" (also contained in this Dryad package) is also needed. Also crucial is a file of R functions ("genomics_R_functions_V2.R") written especially for this analysis, but designed to work more generally; these functions are called by this script file.
DOI: 10.5061/dryad.4j2662g/4
title: warbler.Fst_groups_14each

description: This file is required for conducting the 117-sample analysis (14 individuals per population, except 5 for goldmani) using the R script provided in this package. The file provides the names of each individual, the location code, the "group" (basically the specific or subspecific name) and "Fst_group" (the code used for defining groups in the Fst analysis, and for colouring the figures), and the "plot_order" (not used in the present paper).
DOI: 10.5061/dryad.4j2662g/5
title: warbler genotypes in "012NA" format

description: This folder contains genotypic information used in the 117-sample analysis (14 individuals for each population, plus 5 for goldmani). 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 "warbler_genomics_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 ("warbler.Fst_groups_14each.txt"; also in this package) is also needed in the R processing.
DOI: 10.5061/dryad.4j2662g/6
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). Separate WindowStats files are included for window sizes of 10000 (the main analysis in the paper) and 5000 (referred to briefly in the paper, with one figure in the supplement).
DOI: 10.5061/dryad.4j2662g/7
title: genotypes at SNPs only across the whole genome

description: This folder contains genotypic information for variant sites only (no invariant sites) across the whole genome, among all individuals in the study. 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 "warbler_genomics_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 ("warbler.Fst_groups_14each.txt"; also in this package) will be needed in the R processing.
DOI: 10.5061/dryad.55m2m81/1
title: SFile1_RawFeatureTable

description: This is a table of the raw apLCMS-based peak intensity extraction of HRMS results, including blank (Water) and quality control (NIST, QSTD) samples. Total features detected, 11,188. “NIST” refers to the SRM 1950 reference standard. “QSTD” refers to an in-house prepared mixture of human plasma. All samples were injected in triplicate and the results have been median summarized from the triplicates. The first two columns pertain to the detected m/z value at a specific retention time, given in seconds. The remaining columns pertain to blanks, reference standards and samples. These columns are ordered left-to-right in the order of injection. For the samples, “_A” or “_B” designations pertain to shipment batches that took place between Erasmus and Emory. Three samples were ultimately excluded from analysis: one, 25, because of aberrant global sample composition, and two others, 09_A and 15_A, because aliquots were accidentally shipped and processed two independent times because the samples were blinded. For subsequent analyses, we arbitrarily kept 09_B and 15_B samples from the second batch and discarded their “_A” counterparts, as the “_B” versions were believed to have undergone fewer freeze-thaw cycles than “_A” samples. [This file description may also be found in the Supplementary Information of the corresponding publication.]
DOI: 10.5061/dryad.55m2m81/2
title: SFile2_HRMSResults

description: This is the results file of the untargeted analysis using an in-house R package (https://github.com/kuppal2/xmsPANDA) on raw HRMS data after removing features that did not meet data quality thresholds and dropping poor quality and redundant samples. QC materials were not analyzed in the untargeted test. Columns A-B pertain to observed m/z and retention time. Columns C-E pertain to accurate mass matches to the features (Annotation, Adduct, and ppm mass accuracy error; see Supplementary Methods for details). After accurate mass matching, spectral convolutions (i.e., isotopes and neutral losses) were designated by manual inspection of co-elution, intensity correlation and m/z shift. Retention times were taken into consideration for assignments (e.g., longer retention times generally correspond to hydrophilicity and spectral convolutions of adducts and isotopes should co-elute). Note, the [M+H] ion of lidocaine (235.1804 m/z by 127.6 sec; used as local anesthetic during bronchoscopy) held the maximum intensity value in each sample and was normalized to the same maximal value in each distribution, resulting in its removal during testing. Ppm error was calculated by METLIN except for spectral convolutions, which were calculated manually. Accurate mass annotations are only provided for those results that met significance criteria (p &lt; 0.05, q &lt; 0.25). Columns F-H indicate the raw p-value (“P.value”), q-value (“adjusted.p.value”) and Pearson’s r statistic (“Estimate_var1”), respectively. Remaining columns show log2-transformed and quantile normalized HRMS intensities for each of the study samples. Missing values were imputed as “NA” to avoid skewing the correlation. The sample columns were automatically ordered from low-to-high PRAGMA-%Dis. [This file description may also be found in the Supplementary Information of the corresponding publication.]
DOI: 10.5061/dryad.55m2m81/3
title: SFile3_ClinicalData

description: These data correspond to important clinical variables for the patient samples analyzed in this study. [This file description may also be found in the Supplementary Information of the corresponding publication.]
DOI: 10.5061/dryad.55m2m81/4
title: SFile4_FollowUpStudiesData

description: Results used for follow-up studies with Spearman’s correlations. MetO and methionine (Met) quantifications are based on reference calibration relative to the concentrations determined for SRM 1950 reference material. MPO measurements are based on the ELISA assay. [This file description may also be found in the Supplementary Information of the corresponding publication.]
DOI: 10.5061/dryad.5vv37/1
title: Species Range - Mathematica Code and Example

description: Mathematica code and a working example of the simulations,  Figures with data
DOI: 10.5061/dryad.76p9017/1
title: Wyoming fish and climate change scenario data

description: Presence/ absence data for 1559 sites in Wyoming and associated stream temperature data.Stream temperatures were derived from models generated by the United States Forest Service for the western United States at a 1-km resolution (http://www.fs.fed.us/rm/boise/AWAE/projects/NorWeST.html)
DOI: 10.5061/dryad.797kg/1
title: Read count matrix and treatment information on individuals

description: Read count matrix from RNA-seq experiment of two distinct helper types in the cooperatively breeding cichlid fish Neolamprologus pulcher. 48 individuals in a 2x2 full-factorial design of cleaners and non-cleaners in control and opportunity. 38,2425 genes expressed in the telencephalon 45 min after the onset of the cooperation opportunity.
DOI: 10.5061/dryad.806382j/1
title: Data from: Understanding willingness to use oral pre-exposure prophylaxis for HIV prevention among men who have sex with men in China
DOI: 10.5061/dryad.84g36m4.1
title: Data from: Tracing the effects of eutrophication on molluscan communities in sediment cores: outbreaks of an opportunistic species coincide with reduced bioturbation and high frequency of hypoxia in the Adriatic Sea
DOI: 10.5061/dryad.84g36m4.2
title: Data from: Tracing the effects of eutrophication on molluscan communities in sediment cores: outbreaks of an opportunistic species coincide with reduced bioturbation and high frequency of hypoxia in the Adriatic Sea
DOI: 10.5061/dryad.84g36m4.2/1.2
title: Supplementary Table 1

description: Supplementary Table 1 – 210Pb sediment data (with standard deviations) measures at three stations.
DOI: 10.5061/dryad.84g36m4.2/2.2
title: Supplementary Table 2

description: Supplementary Table 2 – Amino acid racemization and calibrated age data of Corbula gibba from two Po stations (analyzed in this paper), from the Bay of Panzano (Tomasovych et al. 2017, Geology, and analyzed this paper), and from Piran (Mautner et al. 2018, Marine Pollution Bulletin).
DOI: 10.5061/dryad.84g36m4.2/3.2
title: Supplementary code

description: R language source code for age unmixing procedure and for reproduction of some plots and analyses underlying the manuscript.The excel file "Supplementary Table 2" should be saved as tab-delimited txt file. This file is uploaded by the script.
DOI: 10.5061/dryad.84g36m4.2/4.2
title: Supplementary Table 3

description: Supplementary Table 3 – Abundances of mollusks in two replicate cores at Po 3 (cores M13 and M14), at Po4 (cores M20 and M21), and in the Bay of Panzano (cores M28 and M29), and concentrations of elements, TOC, and total nitrogen.
DOI: 10.5061/dryad.b4vg0.2/1.2
title: Adjacency matrix for the trophic layer

description: The file is TAB-delimited and contains 107 lines and 108 columns. The first line is composed by two TAB-keys followed by the numerical IDs of the 106 species. The 106 following lines are composed as follows. The first and second columns display the numerical ID and the name of the species respectively. The species name can include whitespace characters. The remaining columns are the adjancency matrix values, i.e. 1/0 for presence/absence of a link. A link between species i and j means species i is eaten by species j.
DOI: 10.5061/dryad.b4vg0.2/11.2
title: Figure S3 data
DOI: 10.5061/dryad.b4vg0.2/6.2
title: Adjacency matrix for the negative non-trophic layer

description: Adjacency matrix for the negative non-trophic layer. Same format as chilean-TI.txt. A link between species i and j means that species i is the target of a negative interaction and species j is the source.
DOI: 10.5061/dryad.b4vg0.2/7.2
title: Figure 2 data

description: In/out degree for each species in the following order : trophic out, trophic In, positive out, positive in, negative out, negative in.
DOI: 10.5061/dryad.b4vg0.2/9.2
title: Figure 3 data
DOI: 10.5061/dryad.fp4vv8s/1
title: Provost_etal_cardinalis_data

description: This ZIP file contains multiple files of data, including data associated with the playback experiments, generalized linear mixed models, fastsimcoal demography, and STRUCTURE.
DOI: 10.5061/dryad.fp4vv8s/2
title: Provost_etal_cardinalis_scripts

description: This file contains the scripts used to generate and process the data for the playback experiments and STRUCTURE analyses.
DOI: 10.5061/dryad.hq48044/10
title: Raw_data_FIGURE_3_S3
DOI: 10.5061/dryad.hq48044/11
title: Raw_data_FIGURE_3_S4
DOI: 10.5061/dryad.hq48044/12
title: Raw_data_FIGURE_4
DOI: 10.5061/dryad.hq48044/13
title: Raw_data_FIGURE_4_S1
DOI: 10.5061/dryad.hq48044/14
title: Raw_data_FIGURE_4_S2
DOI: 10.5061/dryad.hq48044/15
title: Raw_data_FIGURE_4_S3
DOI: 10.5061/dryad.hq48044/8
title: Raw_data_FIGURE_3_S1
DOI: 10.5061/dryad.hq48044/9
title: Raw_data_FIGURE_3_S2
DOI: 10.5061/dryad.j0t179b/2
title: seedweight

description: This .csv file includes the raw data used for the analysis in this experiment exploring seed performance. Below is 
a description of each of the variables used 

origin: The seed origin or provenance from where the seed was collected. There were 6 different seed origins that were used in this study (N2: Rivière-du-Loup, N1: Montmagny, C2: Sherbrooke, C1: Pennsylvania, S2: Kentucky, and S1: Tennessee). Weight: Mass (in grams) of seed lot (150 seeds).
DOI: 10.5061/dryad.j0t179b/3
title: transplant

description: This .csv file includes the raw data used for the analysis in this experiment that explored the macroscale effect by bioclimatic zone (temperate, mizedwood, and boreal) and seed origin or provenance.
The following information is provided:

stand: The dominant stand type where the seeds were transplanted (boreal, mixed, and temperate). 
site: The transplant site where the seeds were transplanted. 
origin: The seed origin or provenance from where the seed was collected. There were 6 different seed origins used in this study 
(N2: Rivière-du-Loup, N1: Montmagny, C2: Sherbrooke, C1: Pennsylvania, S2: Kentucky, and S1: Tennessee).
first: The number of first year seedlings (count data)
second: The number of second year seedlings (count data)
survival: The proportion of first year seedlings surviving to the second year (second/first=survival).
DOI: 10.5061/dryad.j8c5j18/1
title: SI1-Explanation_of_the_RCC-5_alignment_approach

description: SI1 Explanation of the RCC–5 alignment approach. File format: .pdf
DOI: 10.5061/dryad.j8c5j18/2
title: SI2A-Minyomerus_INT_2018_2015_Class

description: SI2A Input constraints for the Minyomerus [JF2018]/[JF2015] rank-only classification alignment. File format: .txt
DOI: 10.5061/dryad.j8c5j18/3
title: SI2B-Minyomerus_INT_2018_2015_Class

description: SI2B Input visualization for the SI2A input. File format: .pdf
DOI: 10.5061/dryad.j8c5j18/4
title: SI2C-Minyomerus_INT_2018_2015_Class_mir

description: Set of 114 Maximally Informative Relations (MIR) for the SI2A input. File format: .csv
DOI: 10.5061/dryad.j8c5j18/5
title: SI2D-Minyomerus_INT_2018_2015_Class_0_mnpw

description: SI2D Alignment visualization for the SI2A input. File format: .pdf
DOI: 10.5061/dryad.j8c5j18/6
title: SI3A-Minyomerus_INT_2018_2015_Phylo

description: SI3A Input constraints for the Minyomerus [JF2018]/[JF2015] phylogeny alignment – whole-concept resolution with overlap. File format: .txt
DOI: 10.5061/dryad.j8c5j18/7
title: SI3B-Minyomerus_INT_2018_2015_Phylo

description: SI3B Input visualization for the SI3A input. File format: .pdf
DOI: 10.5061/dryad.j8c5j18/8
title: SI3C-Minyomerus_INT_2018_2015_Phylo_mir

description: SI3C Set of 925 Maximally Informative Relations (MIR) for the SI3A input. File format: .csv
DOI: 10.5061/dryad.kf674kb/1
title: genotypes

description: A total of 526,301 SNP markers were produced using PST-I RAD sequencing. They are genotyped in 115 individuals from six redband trout populations.
DOI: 10.5061/dryad.kf674kb/2
title: Genotypes of neutral loci in genepop format

description: This file contains genotypes of 525,866 putative neutral loci for a total of 115 fish from six redband trout populations from southern Idaho
DOI: 10.5061/dryad.kf674kb/3
title: Genotypes of outlier loci in genepop format

description: This file contains genotypes of 435 putative adaptive loci for a total of 115 fish from six redband trout populations from southern Idaho
DOI: 10.5061/dryad.kf674kb/4
title: cardiac phenotypes

description: Phenotype data file for 114 fish from six redband trout populations. Phenotype data of one fish was not collected.
DOI: 10.5061/dryad.pd40m.2
title: Data from: Force encoding in muscle spindles during stretch of passive muscle
DOI: 10.5061/dryad.q9t27n9/5
title: GrantHawthorn.fq.gz

description: Fastq file containing demultiplexed sequences for the control (7 day) samples from the hawthorn selection experiment.
DOI: 10.5061/dryad.q9t27n9/6
title: GrantHawthorn32d.fq.gz

description: Fastq file containing demultiplexed sequences for the long pre-winter treatment (32 day) samples from the hawthorn selection experiment.
DOI: 10.5061/dryad.rc1jr0v/4
title: pssp

description: Variant Call Format (vcf) file created by the populations program in Stacks v1.46. File contains 113,310 loci (in rows) from 834 diploid P. spicata individuals (in columns). Individuals are named with a sampling locality name and unique identifier (i.e., number).
DOI: 10.5061/dryad.s47rq/2
title: FIBROMYALGIA STUDY (DECEMBER 2016)

description: Fibromyalgia study database
DOI: 10.5061/dryad.408d6f0/1
title: mRNA microarray within hippocampus and cortex brain regions of PSEN12 double knockout mice

description: The wild type and PSEN dKO mice were sacrificed at the ages of 7 and 18 months. The complete mouse brain structure was removed and immediately prepared by being frozen on dry ice. The cortex and hippocampus were dissected and stored at -80°C until RNA isolation. Total RNA was isolated using the Trizol reagent. Messenger RNA expression profiling was performed using Affymetrix Mouse Genome 430 2.0 array chip containing 764,885 probe sets from 28,132 genes (Ensembl) or from 19,734 putative full-length transcripts (GenBank and Ref Seq).
DOI: 10.5061/dryad.4823jr1/1
title: Data_First_Experiment

description: Data from first experiment. Legend included in file.
DOI: 10.5061/dryad.4823jr1/2
title: Data_Second_Experiment

description: Data from second experiment. Legend included in file.
DOI: 10.5061/dryad.53k260v/1
title: Morphology and coloration data

description: Morphology, pattern of coloration and coloration intensity variables (as described in Table S3) for morphological clustering
DOI: 10.5061/dryad.53k260v/2
title: Climatic Data Oophaga populations

description: High resolution (30 arc-seconds) environmental data from 19 bioclimatic variables (www.worldclim.org) along with altitude data (STRM901 http://srtm.csi.cgiar.org/) for climatic clustering analysis.
DOI: 10.5061/dryad.53vt348/1
title: Dryad_Flowering_period_E.japonica

description: Flowering period of Eurya japonica in 2014.
DOI: 10.5061/dryad.53vt348/2
title: Dryad_Inoculation_Experiments

description: Colony detection in yeast inoculation experiment into flowers
DOI: 10.5061/dryad.53vt348/3
title: Dryad_E.japonica_field_experiment

description: CFU of nectar microbes (bacteria and fungi) and nectar concentration (Brix) in Eurya japonica flowers
DOI: 10.5061/dryad.53vt348/4
title: Dryad_E.emarginata_field_experiment

description: CFU of nectar microbes (bacteria and fungi), association between bacteria and fungi, and nectar concentration (Brix) in Eurya emarginata flowers
DOI: 10.5061/dryad.553t5/1
title: Spin coated ellipsometry thickness measurements

description: These are ellipsometry thickness measurements for the spin coated films after they were spin coated for the PC71BM fullerene thin films after spin coating