cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.r1478/1
title: Data and code

description: This zip file contains an R project file, data, and code to reproduce analyses and simulations.  Note that some simulations are commented out in the R code due to the long run time - the code instead reads in saved .csv files with simulation outputs from the "output data" folder.
DOI: 10.5061/dryad.rq3sp/1
title: Species_Orthologs.tar.gz

description: Archive containing files for target species-to-Drosophila melanogaster pairwise ortholog models. Each file maps ids from a transcriptome assembly to D. melanogaster flyabase IDs. Methods for orthology assignment and references for each transcriptome assembly available in Ragland and Keep, and in the 'MetaData' data file also contained in this archive.
DOI: 10.5061/dryad.rq3sp/2
title: MetaDataDryad

description: Meta data for transcriptomic data sets used in the comparative analysis to generate gene expression matrix 'UnFilteredExpressionAllOrthos' also included in this archive.
DOI: 10.5061/dryad.rq3sp/3
title: UnFilteredExpressionAllOrthos.txt.gz

description: Matrix of diapause expression data across included insect species. Each row of expression data is associated with a single gene orthologous across all species, designated with the flyabase id for the gene in Drosophila melanogaster. Each data value is a log2 fold change: log2(diapause) - log2(non-diapause) for each included species. See Ragland and Keep for methods. Species codes are described in the first metadata line of the file.
DOI: 10.5061/dryad.s91p4/1
title: CaraDonna_Interaction_Turnover_All_Years_RMBL

description: Data from Table S4. Beta-diversity (turnover) values for each week-to-week transition for all turnover metrics (including Bray-Curtis interaction turnover) for each year of study. All notation is included in the main text of the manuscript.
DOI: 10.5061/dryad.s91p4/3
title: CaraDonna_Interaction_Turnover_simulation_models_and_observed_All_Years_RMBL

description: Data generated from probability-based simulation models to explore potential ecological factors that may constrain within-season interaction turnover. Details of simulation models and subsequent analyses are provided in the main text of the manuscript.
DOI: 10.5061/dryad.03f4f/1
title: Manson_Extraversion-Openness-LHS_data

description: Participants: 93 UCLA students. Procedure: Ps wore the Electronically Activated Recorder for 72 hours, generating one 30-sec audio recording every 12.5 min from 0600-2400. Ps also kept an hour-by-hour event diary. Based on the audio clips and event diaries, research assistants described Ps' personalities using the California Adult Q-sort (CAQ). Column R contains the correlation (r-to-z transformed) of each P's CAQ profile with the Slow Life History CAQ template. Columns S-X contain the CAQ-profile-based scores on each FFM model dimension (neuroticism, extraversion, openness, agreeableness, and conscientiousness), based on McCrae et al (1986). Column V contains the openness scores after improving inter-item reliability by dropping CAQ items 007, 041, and 062. After the audio sampling phase of the study, Ps completed the Arizona Life History Battery (column C contains the overall K-factor, the mean of the standardized scale scores excluding the mini-K) and the HEXACO-60 (columns D-I contain standardized scores of the major HEXACO dimensions, while columns J-Q contain the standardized scores of the four Extraversion facet scales and the four Openness facet scales).
DOI: 10.5061/dryad.0j67t/1
title: Wood density of trees in savannas of the northern Brazilian Amazon

description: The file contains the wood density values (g cm-3), classes of diameter (cm), geographical position (UTM) and altitude (meters above sea level) of eight typical savanna tree species found in Roraima, northern Brazilian Amazonia (225 wood samples). Wood density values were estimated taking into account the oven dry mass (g) divided by fresh volume (cm3) of samples derived from three classes of diameter (1-5 cm = twigs; 5-10 cm = branches; &gt; 10 cm = main stem).
DOI: 10.5061/dryad.192f1/1
title: Microsatellite genotypes for the black rhinoceros (Diceros bicornis)

description: Microsatellite dataset used in this study. This file includes the genotypes for 11 microsatellite loci for both historic and modern black rhinoceros samples. Individuals represent 12 populations and are numbered from 1-560.
DOI: 10.5061/dryad.1c394/1
title: Publications on weather and bird migration in the 20th and 21st century

description: This file contains a list of all peer-reviewed publications which we used for our review of weather and bird migration literature. Publications were selected based on criteria described in the Materials and Methdods section of our paper. To produce Figure 1 we categorized publications according to the main method used for studying birds´ responses to weather on migration.
DOI: 10.5061/dryad.2f050/1
title: Chinook_Genotypes_11759SNPs

description: Chinook salmon genotypes for 11,759 SNPs (GenePop format)
DOI: 10.5061/dryad.2f050/2
title: Brook_Genotypes_13522SNPs

description: Brook charr genotypes for 13,522 SNPs (GenePop format)
DOI: 10.5061/dryad.31dj3/10
title: Channelrhodopsin Cell 15: 120626 C1
DOI: 10.5061/dryad.31dj3/11
title: Channelrhodopsin Cell 16: 120906 C2
DOI: 10.5061/dryad.31dj3/12
title: Neurons 1-8 morph
DOI: 10.5061/dryad.31dj3/13
title: Rebounds set 1
DOI: 10.5061/dryad.31dj3/14
title: Neurons 9-13 morph + extra neurons
DOI: 10.5061/dryad.31dj3/15
title: Neurons 14-16 morph
DOI: 10.5061/dryad.31dj3/16
title: 5 Neurons
DOI: 10.5061/dryad.31dj3/17
title: 4 Neurons
DOI: 10.5061/dryad.31dj3/18
title: 3 Neurons
DOI: 10.5061/dryad.31dj3/9
title: Channelrhodopsin Cell 14:120628 C1
DOI: 10.5061/dryad.65vs3/2
title: PME_JEcol_myco_data

description: Root mycorrhizal colonisation data. Root materials were field-collected along the Jurien Bay dune chronosequence in Western Australia in 2013. Arbuscular mycorrhizal fungi root colonisation were determined using gridline-intersect method at 200× magnification, while all viable root tips were scored for ectomycorrhizal fungi root colonisation or non-mycorrhizal colonisation. This PME_JEcol_myco_data.csv file was created using Microsoft Excel 2013. See readme file for descriptions of (abbreviated) column headings.
DOI: 10.5061/dryad.7832m/2
title: Fig1

description: Figure 1
DOI: 10.5061/dryad.7832m/3
title: Fig2

description: Figure 2
DOI: 10.5061/dryad.7832m/4
title: Fig3

description: Figure3
DOI: 10.5061/dryad.7832m/5
title: Fig4

description: Figure 4
DOI: 10.5061/dryad.7832m/6
title: Supplemental data

description: Table of supplemental data
DOI: 10.5061/dryad.83f17/1
title: Genotype calls and genetic divergence from bulk segregant analysis of survivorship.

description: We show results of the analysis of Bulk Segregant Analysis (BSA) of survivorship in reciprocal transplants between sand dune and rocky headland environments at Lennox Head (NSW, Australia) as performed with the Popoolation2 software. RADseq genotypes were mapped the a genome draft. For each SNP (defined by the position along the genomic contig where it was mapped) and genomic comparison between two pools of survivors from contrasting environments we show the identity and read counts for the major allele (maa) in the two populations (i.e. pop1 is the pool of sand dune survivors and pop2 is the pool of headland survivors). We also show the value of Fst, as calculated by Popoolation2, as well as the p-value of a fisher exact test of allelic differentiation (FET). Finally, in the last column we show if the SNPs had outlier Fst values (i.e. upper 5% tail of the distribution) and presented significantly different allelic frequencies in the FET (Bonferroni corrected p-value lower than 5%). Survivors from each environment where included in three different pools which were sequenced individually. Therefore we had three different comparisons between pools of survivors (i.e. F8-A-S-Dune_vs_F8-A-S-Headland, F8-B-S-Dune_vs_F8-B-S-Headland, and F8-C-S-Dune_vs_F8-C-S-Headland).
DOI: 10.5061/dryad.8qp4n/2
title: Gzipped tar archive of contig files

description: This tarball contains all 402 draft- and complete genomes compared within this study.
DOI: 10.5061/dryad.8v38v/1
title: Data for Figures 3D and 4A

description: Quantification of AAV-GFP DNA and vector plasmid by droplet-digital PCR (Fig 3D).  Quantification of AAV capsids and GFP DNA in rAAV purified from yeast (Fig 4A).
DOI: 10.5061/dryad.8v38v/2
title: Codon optimized sequences

description: AAP and Rep coding sequences from AAV2, codon optimized for expression in Saccharomyces cerevisiae.
DOI: 10.5061/dryad.8vs6h/1
title: Pedigree of the southern Quebec tree swallow population

description: Genetic pedigree constructed with Cervus based on 6 microsatellite loci.
DOI: 10.5061/dryad.8vs6h/2
title: Dataset of southern Quebec tree swallow nestlings

description: Dataset used to estimate selection and quantitative genetic parameters. Column headings are nestling ids (ID), farm ids (FARM), year (YEAR), brood ids (BROOD), hour of measurement (HOUR), Julian day (JDAY),  age (AGE), survival (FLEDG, 0 or 1), body mass (MASS) and feather length (WL).
DOI: 10.5061/dryad.9677h/1
title: baboon_metadata_alpha_diversity

description: Metadata, number of reads, estimated sample coverage, and alpha diversity metrics (Shannon's diversity index and OTU richness) for each vaginal sample included in this study.
DOI: 10.5061/dryad.9677h/2
title: unrarefied_OTU_table

description: Unrarefied OTU table with taxonomic classifications in the last column. All OTUs that occurred in only one sample are not included.
DOI: 10.5061/dryad.9g54r/1
title: thylacine_smithsonian

description: Structural images and outputs from BEDPOSTX and DTIFIT for the Smithsonian thylacine brain (USNM 125345).
DOI: 10.5061/dryad.9g54r/2
title: thylacine_sydney

description: Structural images and outputs of BEDPOSTX and DTIFIT for the Australian Museum thylacine brain (M18411). Contains very high resolution structural (0.1 x 0.1 x 0.2 mm).
DOI: 10.5061/dryad.9g54r/3
title: devil_smithsonian

description: Structural images and outputs from BEDPOSTX and DTIFIT for the Smithsonian Tasmanian devil brain (USNM 142598).
DOI: 10.5061/dryad.ch4p5/1
title: Phenotype_data_FINAL

description: see readme
DOI: 10.5061/dryad.dh250/10
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17 -Supplemental Table 9

description: Histopathology evaluation at necropsy 14 days following dosing/SNI surgery, SNITX1 study
DOI: 10.5061/dryad.dh250/4
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17  -Supplemental Table 3

description: Clinical laboratory assessments of female rats at Day 3 and 30 in the ADY-TX2 study
DOI: 10.5061/dryad.dh250/5
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17 -Supplemental Table 4

description: ADY-TX2 study, Functional observation battery results, pre-dose and 4h post-dosing of Day 3 animals
DOI: 10.5061/dryad.dh250/6
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17 -Supplemental Table 5

description: Histopathology analysis of lumbar spinal cord of female rats in the ADY-TX2 study
DOI: 10.5061/dryad.dh250/7
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17 -Supplemental Table 6

description: Summary of Total AYX1 (full length + metabolites) toxicokinetics in the CSF and plasma of male and female rats in the ADY-TX2 study
DOI: 10.5061/dryad.dh250/8
title: Mamet et al, 2017 - Toxicological Sciences - 05 25 17 -Supplemental Tables 7abc

description: Irwin Test, SNITX1 study
DOI: 10.5061/dryad.dh250/9
title: Mamet et al, 2017 - Toxicological Sciences - 05 28 17 -Supplemental Table 8

description: Clinical laboratory assessments at study Day 14 in the ADY-SNITX1 study
DOI: 10.5061/dryad.g0b2c/1
title: data_MS_ECE-2016-11-01203

description: Full data used for the analyses
DOI: 10.5061/dryad.g1372/1
title: Thermal tolerance traits of temperate and tropical aquatic insects

description: This dataset includes critical thermal max and min data along with thermal breadths measured for a variety of aquatic insects from low, mid, and high elevation temperate and tropical streams. Each individual was assigned to a species using DNA barcoding (Taxon) and the taxonomic order is indicated (Order). The elevations (in meters) and latitudes (0 = Colorado, 1 = Ecuador) from which the insects were collected are provided. Dry weights are provided along with critical thermal limits (CTmax and CTmin) and their differences where applicable (Thermal Breadth). Stream temperature range is also provided (Range).
DOI: 10.5061/dryad.g370c/1
title: Supplementary Material - model code

description: The Netlogo code for the program used to run the simulations. This program was developed using NetLogo 5.0 (http://ccl.northwestern.edu/netlogo). The program is free of use for research and education. If you use this program or model for your own research, please refer to our paper “Pim Edelaar, Roger Jovani & Ivan Gomez-Mestre 2017. Should I change or should I go? Phenotypic plasticity and matching habitat choice in the adaptation to environmental heterogeneity. The American Naturalist”.
DOI: 10.5061/dryad.g370c/2
title: Am Nat - plasticity and MHC - NetLogo model online v. 45

description: The model code in Netlogo format. Download (http://ccl.northwestern.edu/netlogo) and install NetLogo for free, and you can open and run the model directly.
DOI: 10.5061/dryad.g7h7n/57
title: SV Pond 8 dates

description: SV Pond 8 210Pb dates using CRS dating method
DOI: 10.5061/dryad.g7h7n/58
title: West Lake dates

description: West Lake 210Pb dates using CRS dating method
DOI: 10.5061/dryad.g7h7n/59
title: SV Ponds 14C dating

description: SV Pond 5 and 8 14C dates and types of microfossils dated
DOI: 10.5061/dryad.g7h7n/60
title: Hills N2 script

description: Hill's N2 R script used to calculate Hill's N2 and rarify species count data (using pre-made packages)
DOI: 10.5061/dryad.hh435/1
title: Bird communities in woody pastures, Sweden

description: Data on bird communities collected in the field from April to June 2014, data on environmental variables (incl. tree communities) collected in the field 2013. Landscape forest cover was digitized using aerial photos. All data has been compiled using Microsoft Excel and R. Please see datasheet "META" for details on column headings, and please see publication for more information on data collection.
DOI: 10.5061/dryad.m1s4p/1
title: Patient EBUS 01

description: Patient 01 - CT and Ultrasound
DOI: 10.5061/dryad.m1s4p/2
title: Patient EBUS 02

description: Patient 02 - CT and Ultrasound
DOI: 10.5061/dryad.m1s4p/3
title: Patient EBUS 03

description: Patient 03 - CT and Ultrasound
DOI: 10.5061/dryad.m1s4p/4
title: Patient EBUS 04

description: Patient 04 - CT and Ultrasound
DOI: 10.5061/dryad.n54g4/1
title: Glucocorticoid_primary data_faecal samples

description: The feces of individual meerkats were collected in the field. Hormones were extracted and a 3a,11ß- assay conducted to measure glucocorticoid metabolites. 3a,11ß (ng/g faeces) represent the glucocorticoid metabolite concentrations for organic matter or the entire feces.
DOI: 10.5061/dryad.n54g4/2
title: Meanacousticsstructure_for correlation_FGC

description: Shows the call structural parameters and the median fecal glucocorticoid metabolite levels. IPI:Interpluse Interval, F0: Fundamental Frequency.
DOI: 10.5061/dryad.n54g4/3
title: rate_primarydata

description: Shows the data collected for close call rate of individual meerkats.
DOI: 10.5061/dryad.n77r3/1
title: lane3276_CGATGTTT_54re_L006_trimmed_tophat

description: RNA-seq data embryo #54
DOI: 10.5061/dryad.n77r3/2
title: lane3276_TGACCACT_93re_L006_trimmed_tophat

description: RNA-Seq data embryo #93
DOI: 10.5061/dryad.n77r3/3
title: lane3276_TTAGGCAT_60re_L006_trimmed_tophat

description: RNA-Seq data embryo #60
DOI: 10.5061/dryad.n77r3/4
title: lane3277_ACAGTGGT_94re_L007_trimmed_tophat

description: RNA-Seq data embryo #94
DOI: 10.5061/dryad.n77r3/5
title: lane3277_ACTTGATG_191re_L007_trimmed_tophat

description: RNA-Seq data embryo #191
DOI: 10.5061/dryad.p12q4/1
title: Yoder and Tiffin (2017) supporting information

description: This archive provides configuration files for forward population genetic simulations of local adaptation, scripts to perform analysis on their results, and a copy of data produced by this pipeline. See README file for detailed description and annotation.
DOI: 10.5061/dryad.q1j50/5
title: Supplementary Movie 5. Invadopodia formation in SGEF KD cells.

description: SUM159 cells stably expressing SGEF targeting shRNA were infected with mCherry-cortactin adenovirus as in Supp Movie 1. At indicated times cells were stimulated to form invadopodia with PDBu. Images were captured at 15 sec intervals for the duration of the movie.
DOI: 10.5061/dryad.q1j50/6
title: Supplementary Movie 6. Invadopodia formation in RhoG KD/rescue cells.

description: RhoG KD SUM159 cells were co-infected with adenoviruses encoding mCherry-cortactin and shRNA resistant mycRhoG. At indicated times cells were stimulated to form invadopodia with PDBu. Images were captured at 15 sec intervals for the duration of the movie.
DOI: 10.5061/dryad.q1j50/7
title: Supplementary Movie 7. Invadopodia formation in SGEF KD/rescue cells.

description: SGEF KD SUM159 cells were co-infected with adenovirus encoding mCherry-cortactin and shRNA resistant mycSGEF. At indicated times cells were stimulated to form invadopodia with PDBu. Images were captured at 15 sec intervals for the duration of the movie.
DOI: 10.5061/dryad.qj195/1
title: Laguna Larga
DOI: 10.5061/dryad.qj195/2
title: LaMina dataset
DOI: 10.5061/dryad.rm7dd/1
title: Lung Cancer Epigenomics Data_MEOX2/RNA Pol II_ratio_peaks

description: Identification of Fluorescence peaks derived from the MEOX2 and RNA POL II Immuno-precipitation assays, derived from lung carcinoma patients, using gene promoter tiling microarrays (NIMBLEGEN Platform, 3X720K format). Shown peak ID, chromosome, start and end of peaks, score and FDR, and Access number.
DOI: 10.5061/dryad.s3tc6/1
title: Lionfish preying upon undescribed species

description: During a submersible dive off the coast of Curacao in 2015, researchers from the Smithsonian Deep Reef Observation Project (DROP) observed an invasive lionfish preying on an undescribed species of deep-reef fish. The species is a member of the family Gobiidae (gobies), and the genus Palatogobius. It occurs in large schools on deep reefs at depths of 88-200 m. It is currently being formally described in a scientific journal by the Smithsonian team. This species is one of many new species recently discovered through exploratory submersible diving in the Caribbean.
DOI: 10.5061/dryad.s8n05/1
title: benthic survey of Cockles and American Razor clams

description: Benthic survey of Cockles (Cerastoderma edule) and American razor clams (Ensis directus) in the Balgzand area, Wadden Sea, The Netherlands. Aimed at assessing the available food stock for Oystercatchers at a high spatial resolution. Contains over 3000 sampling points on 15 sampling grids of 50 meter resolution. Survey was performed autumn 2011, and repeated in spring 2012.
DOI: 10.5061/dryad.s8n05/2
title: C code to calculate ideal free distribution for a generalised functional response

description: This is a library written in the C programming language, for solving the ideal-free distribution for a generalised functional response with exponential interference function. This library can be called from R, to speed up model fits using Bayesian MCMC methods.
DOI: 10.5061/dryad.tj4p2/1
title: Attribute table

description: Derived data used for analysis
DOI: 10.5061/dryad.tj4p2/2
title: Planning units

description: ESRI shape file, planning units
DOI: 10.5061/dryad.vn707/2
title: Marked plant and spore deposition data

description: Excel file with 5 data sheets:  1)All marked adults.  This mark recapture data for each individual in the adult-plant demography study.  Columns Qx, Qy, dx, dy, and coin are all identifying information on the location of the plants.  Status codes:  D=diseased, H= healthy, X=dead, V=vegetative, HH=healthy hermaphrodite, MS or HMS = healthy male-sterile.  Columns marked ‘present’ indicate survival (1=surv, 0=dead). Columns marked ‘flwr’ indicate whether or not a plant flowered (1=flowered, 0=did not flower). Columns marked ‘infl’ indicate the number of inflorescences produced.
2) Subset used for aster.  This is the subset of the marked plants used for aster analyses.  Only individuals that were present in 2009, had complete data (e.g. no ‘lost’ or ‘missing’ years) and did not change disease status were included.
3) Implant data.  This the complete data for the transplanted 1-year old plants in the implant experiment. 
4) Spores on sticky traps.  Spore counts from sticky traps laid out around 4 diseased plants, with three strips (A,B, and C) per plant.
5) Spore on flowers.  Spore counts from sampled healthy flowers in transect 1.
DOI: 10.5061/dryad.017v9/1
title: Signal lag data

description: Signal lag data for predation tag testing. Indicates time between consumption of the tag and the first detected transmission in the 'post-predation' state. PRED = Individual Largemouth Bass,TAG_ID_BEF = Acoustic Tag ID before predation. All length measurements in mm, weights in grams.
DOI: 10.5061/dryad.017v9/2
title: Tag Retention Data

description: Tag retention data for predation tag transmitters. Represents the time from the predation event until the tag was evacuated from the predator (Largemouth Bass). PRED = Individual Largemouth Bass,TAG_ID_BEF = Acoustic Tag ID before predation. All length measurements in mm, weights in grams.
DOI: 10.5061/dryad.017v9/3
title: R-script for analysis of signal lag data

description: R-script for analysis of signal lag data.
DOI: 10.5061/dryad.017v9/4
title: R-script for analysis of predation tag retention data

description: R-script for analysis of predation tag retention data.
DOI: 10.5061/dryad.136bm/1
title: Yates_et_al_2016_dataset

description: Data associated with quantitative synthesis examining Nb/Nc relationships among three salmonid fishes
DOI: 10.5061/dryad.1n1kj/1
title: Pmuralis_sexratio_polymorphism

description: Colour morph diversity in Podarcis muralis' Pyrenean populations
DOI: 10.5061/dryad.202fn/1
title: Miao et al_elife 2017
DOI: 10.5061/dryad.26v0g/1
title: Release of pedicellariae following simulated attacks

description: The number of pedicellariae released after simulated fish attack by five species of sea urchin found in the Coffs Harbour region. Fish attack was simulated mechanically by touching and tapping the test with forceps, and control sea urchins were undisturbed.
DOI: 10.5061/dryad.26v0g/2
title: Palatability of pedicellariae to fish when in an artificial diet

description: The proportion (count) of artificial diet (1:10 ratio of pureed squid mantle to 0.45 µm filtered seawater, and 5% sodium alginate) with and without pedicellariae consumed by Chromis atripectoralis and Pseudanthias hypselosoma in a laboratory feeding assay.
DOI: 10.5061/dryad.26v0g/3
title: Palatability of pedicellariae to fish when in an artificial diet in the field

description: The weight (g) and percent of biomass of artificial diets with and without pedicellariae consumed by Scorpis lineolatus in the field.
DOI: 10.5061/dryad.26v0g/4
title: Palatability of pedicellariae to fish

description: The proportion (count) of pedicellariae with venom and with venom extracted consumed by Chromis atripectoralis and Pseudanthias hypselosoma in a laboratory feeding assay.
DOI: 10.5061/dryad.26v0g/5
title: Do pedicellariae act as a pursuit-deterrent cue?

description: The response of Chromis atripectoralis and Pseudanthias hypselosoma to water-borne cues from the sea urchin Tripneustes gratilla before and after it has been induced to release pedicellariae, and to seawater with no cue. When no sea urchin was present some fish individuals preferred one side of the flume over another (&gt;60% of time in one channel). The data with a cue thus indicate time (%) spent in treatment water when the sea urchin was on their preferred side.
DOI: 10.5061/dryad.31dj3/19
title: 3 Neurons
DOI: 10.5061/dryad.31dj3/20
title: 7 Neurons
DOI: 10.5061/dryad.31dj3/21
title: 5 Neurons