cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t60n5/2
title: 2_mutation_effect_ANOVA

description: R Script to perform ANOVA to: (i) examine variation in effect of each mutations over strains, (ii) examine variation in average effect of mutations per strain, and (iii) determine average effect of each mutation
DOI: 10.5061/dryad.t60n5/3
title: 2a_Recipient strains on Broad phylo

description: R Script to identify engineered strains in context of broader E. coli phylogeny
DOI: 10.5061/dryad.t60n5/4
title: 3_PLSregression_&_correlations

description: Script to perform ANOVA testing for mutation effect variation over different recipient strains and to perform partial least squares (PLS) regression and plot contribution of independent variables to each component
DOI: 10.5061/dryad.t7rb4/1
title: Scent choice data

description: All datafiles contain the time (in seconds) a mite (continuously numbered in the column "repeat"; the instar and sex can be found in the column "mite": f - adult female, m - adult male, l - larva, pn - protonymph, dn - deutonymph) spend in the respective sector of the olfactometer. The sectors with the respective treatments (extract of phoretic vectors or controls) can be found in the column headings. For all olfactometer experiments four sectors (with four scents) were used. Therefore, the tables from the dual choice experiments contain each two columns with the same header.
DOI: 10.5061/dryad.td03h/5
title: South_Acoustic_Data_a

description: South Cave Acoustic Files: First half of experimental days
DOI: 10.5061/dryad.td03h/6
title: South_Acoustic_Data_b

description: South Cave Acoustic Files: Second half of experimental days
DOI: 10.5061/dryad.td03h/7
title: Data File Information

description: Information about the data
DOI: 10.5061/dryad.074r6/1
title: Dataset

description: This Excel file reports data from a field experiment. The first 8 columns (A-H) report conditions established at the beginning of the experiment. In column F, cri = crinita, bar = barbata; com = compressa. Columns K to L report the percentage cover of Caulerpa cylindracea, Cystoseira compressa, Cystoseira barbata and Cystoseira crinita in experimental plots at the end of the experiment.
DOI: 10.5061/dryad.14sg2/1
title: Input files for capture histories of individuals

description: These are basic input files without station or covariate information, for each of the species in the manuscript.
DOI: 10.5061/dryad.15264/1
title: Data_PER_LearningAcquisition

description: Proboscis extension response (PER) data of 10 CS-US trials for honeybees and bumblebees.
DOI: 10.5061/dryad.15264/2
title: Data_PER_Responsiveness_UnrewardedAndMemoryTest

description: Responsiveness to sugar stimulus test, unrewarded test and memory test data for honeybees and bumblebees.
DOI: 10.5061/dryad.15264/3
title: Data_SugarConsumptionCollection

description: Sugar water consumption/collection data for honeybees and bumblebees.
DOI: 10.5061/dryad.1536g/1
title: França_et_al_SelectiveLogging_BrazilianAmazon_DungBeetle_13032016

description: This dataset results from the PhD research “Ecological Impacts of selective logging in the Amazon: lessons from dung beetles” developed by Filipe França to understand the impacts of selective logging in the Brazilian Amazon on the dung beetle diversity, physiology and associated ecological functions. For dataset descriptions see the file 'README.docx'.
DOI: 10.5061/dryad.22p7r/10
title: Rhode Island - Food webs with habitat modification effects by cordgrass removed

description: This file contains all matrices from which we removed species dependent on habitat modification by cordgrass.
DOI: 10.5061/dryad.22p7r/11
title: Rhode Island - Food webs with trophic effects by ribbed mussels removed

description: This file contains matrices from which we removed ribbed mussels (Geukensia demissa) and any species and species exclusively feeding on it.
DOI: 10.5061/dryad.22p7r/12
title: Rhode Island - Food webs with trophic effects by cordgrass removed

description: This file contains matrices from which we removed cordgrass (Spartina alterniflora) and any species and species exclusively feeding on it.
DOI: 10.5061/dryad.22p7r/13
title: Rhode Island - Food webs with trophic effects by the most highly connected species removed

description: This file contains matrices from which we removed the most highly connected species and any species exclusively feeding on it.
DOI: 10.5061/dryad.22p7r/14
title: Rhode Island -  Relative effects of habitat modifiers and the most highly connected species

description: File summarising the relative effects of non-trophic facilitation by habitat modifiers and trophic effects by the most highly connected species on food web metrics.
DOI: 10.5061/dryad.22p7r/8
title: Rhode Island - Masterfile

description: This file contains the trophic and non-trophic interaction data from all sampling stations (bare, colonising and established) at Rhode Island (salt marshes).
DOI: 10.5061/dryad.22p7r/9
title: Rhode Island - Food webs with habitat modification effects by ribbed mussels removed

description: This file contains all matrices from which we removed species dependent on habitat modification by ribbed mussels.
DOI: 10.5061/dryad.40494/10
title: intact replicate 4 prior to reagent
DOI: 10.5061/dryad.40494/11
title: intact replicate 4 after reagent
DOI: 10.5061/dryad.40494/12
title: intact replicate 4 recovery
DOI: 10.5061/dryad.40494/6
title: Intact replicate 2_recovery
DOI: 10.5061/dryad.40494/7
title: Intact replicate 3_prior to reagent
DOI: 10.5061/dryad.40494/8
title: Intact replicate 3_after reagent
DOI: 10.5061/dryad.40494/9
title: Intact replicate 3_recovery
DOI: 10.5061/dryad.5d8jv/1
title: SCGMT et al - Rest
DOI: 10.5061/dryad.5d8jv/2
title: SCGMT et al - Stand
DOI: 10.5061/dryad.7cs0p.2/14.2
title: A.flav_sample_data

description: Sample and site information including morphological measurements, sampling date and sex for A. flavipes.
DOI: 10.5061/dryad.7cs0p.2/15.2
title: P.brev_sample_data

description: Sample and site information including morphological measurements, sampling date and sex for P. breviceps.
DOI: 10.5061/dryad.7cs0p.2/16.2
title: P.norf_sample_data

description: Sample and site information including morphological measurements, sampling date and sex for P. norfolcensis.
DOI: 10.5061/dryad.7cs0p.2/17.2
title: A.flav_microsatData

description: Microsatellite dataset for A. flavipes
DOI: 10.5061/dryad.7cs0p.2/18.2
title: P. norfolcensis_microsatData

description: Microsatellite dataset for P. norfolcensis
DOI: 10.5061/dryad.7cs0p.2/19.2
title: P.brev_microsatData

description: Microsatellite dataset for P. breviceps
DOI: 10.5061/dryad.7cs0p.2/5.2
title: Pbrev_coords

description: Sample geographic coordinates for P. breviceps
DOI: 10.5061/dryad.7cs0p.2/6.2
title: Roussets_matrix_A.flav

description: Roussets a genetic distance matrix for A. flavipes
DOI: 10.5061/dryad.7kn53/1
title: Simkin_et_al_2016_data_from_PNAS_Diversity_and_N_deposition

description: Each row in the "Simkin_et_al_2016_data_from_PNAS_Div_and_N_dep.csv" dataset represents one of 15,136 sites, and each of the 16 columns is a separate variable. The "README.csv" file contains descriptions corresponding to the 16 column header names, including the site coordinates (latitude and longitude), the response variable (species richness), the environmental variables (niitrogen deposition, precipitation, temperature, and pH), the output variables (critical loads of nitrogen with 95% confidence interval, as well as corresponding exceedance values), and assorted vegetation classification and data source variables. The "README.csv"  also has further details about the multiple vegetation data sources corresponding to the abbreviated values in the "proj_orig" variable. The description of vegetation data sources is a text file adaptation of Table S1 in the Supplemental Material of Simkin et al. 2016 in the PNAS paper.
DOI: 10.5061/dryad.8kn8c.2
title: Data from: A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them
DOI: 10.5061/dryad.9h9q2/2
title: Worldview-2 image for Le Cesine site acquired on 2013-11-07

description: Worldview-2 satellite image of Le Cesine site acquired on 2013-11-07. RGB-Visual composition. Spatial resolution: 2 meters. - VHR satellite data were provided through the European Space Agency  (ESA) Data Warehouse Policy within the framework of the FP7/SPA.2010.1.1-04 EU project titled "BIOdiversity multi-source monitoring system: from Space tO Species (BIO_SOS)", www.biosos.eu -
DOI: 10.5061/dryad.9h9q2/3
title: Land Cover map for Le Cesine in FAO-LCCS taxonomy

description: Land Cover map for Le Cesine in FAO-LCCS taxonomy. Spatial resolution: 2 meters. The README file contains the look-up.
DOI: 10.5061/dryad.9h9q2/4
title: Habitat Map for Le Cesine

description: Habitat Map for Le Cesine site produced applying pattern zonation rules as Expert Knowledge. Spatial Resolution: 2 meters. The README file contains the look-up
DOI: 10.5061/dryad.b9765/1
title: Input and output files.

description: Input and output files for Network, FSTAT, BAPS, TESS and POPTREE.
DOI: 10.5061/dryad.d136v/1
title: Spider Abundance

description: Spider abundances for the three studied species (Dictyna, Aculepeira, and Tetragnatha) across three sites on simulated invasion and control plots.  Spider abundance was observed three times each year (June, July, August) over the two-year study (2011-2012).
DOI: 10.5061/dryad.d136v/2
title: Spider Mechanisms

description: Potential mechanisms (web size, prey captures, and reproduction) leading to web spider community reassembly following Centaurea stoebe invasion.  These mechanisms were experimentally evaluated in three focal web spider species (Dictyna, Aculepeira, Tetragnatha) over two summers (2011-2012) across three sites by comparing responses on simulated invasion and control plots.
DOI: 10.5061/dryad.d136v/3
title: Web size 2011

description: Web sizes for Dictyna and Aculepeira across three sites over three sampling periods (June, July, August) in 2011.  These data were used to evaluate if web size differed temporally and to justify pooling of web size data within a given year.
DOI: 10.5061/dryad.d136v/4
title: Juveniles 2012

description: The number of juvenile spiders (Dictyna, Aculepeira) observed across three sites on simulated invasion and control plots during 2012.  These data were used to calculate recruitment (= # juveniles present in August 2012 / # reproductive females June 2012).
DOI: 10.5061/dryad.d63t5/1
title: Dryad

description: Two amino acid alignments (ClustaX and Mafft), a PAL2NAL translated nucleotide alignment based upon the ClustalX amino acid alignment and a nucleotide tree and amino acid (ClustalX alignment) tree.
DOI: 10.5061/dryad.d67h6/1
title: eois_glassmire_gprobs

description: This file contains the genotypes at 20,458 SNPs in 155 Eois encina Dognin individuals.
DOI: 10.5061/dryad.j4r56/1
title: Concatenated alignment of exonic sequence data

description: Concatenated alignment (1195 loci) of exonic sequence data used to fit branch length on summary-coalescent species tree
DOI: 10.5061/dryad.j4r56/2
title: Morphological dataset

description: Phenotypic measurements used to infer morphological evolution
DOI: 10.5061/dryad.j5n06/10
title: multilocus_bootstraps

description: Multilocus bootstraps for each dataset (734 loci, 10 PI dataset, and 20PI dataset) using either PhyML or RAxML.
DOI: 10.5061/dryad.j5n06/11
title: piranga_supp_table

description: Summary information and statistics for each sample, including barcodes used for RAD sequencing, number of RAD tags, coverage of RAD loci, adapters used in UCE library prep, UCE sequencing coverage, number of recovered UCEs, and length of UCEs.
DOI: 10.5061/dryad.j5n06/5
title: uce_raxml

description: Results of species tree analyses (both bootstraps and summarized tree) using RAxML gene trees as input. Output is shown for three UCE datasets, including all 734 loci, only loci with 10 or more parsimony informative sites, and only loci with 20 or more parsimony informative sites.
DOI: 10.5061/dryad.j5n06/6
title: uce_beast_input

description: Input files for *BEAST with each of the three UCE datasets, including all loci, only those with 10 or more parsimony informative sites (PI), and only loci with 20 or more PI sites.
DOI: 10.5061/dryad.j5n06/7
title: rad_snapp_trees

description: Output of two runs of SNAPP using the RAD-seq SNP data.
DOI: 10.5061/dryad.j5n06/8
title: rad_species_input

description: Input nexus files from the RAD-seq dataset for SNAPP and SVDquartets.
DOI: 10.5061/dryad.j5n06/9
title: Piranga Trees

description: Pictures of species trees for all RAD-seq and UCE analyses used in this study. Descriptions in the PDF.
DOI: 10.5061/dryad.m3p7d/1
title: Informations concerning the samples and positive and negative controls multiplexed in the two MiSeq runs

description: This XLSX file contains the run names, the sample IDs, the sample types, the PCR IDs, the PCR replicate numbers, the localities, the rodent species and the fastq file names for each of the 1560 PCR products multiplexed in the two Illumina MiSeq runs.
DOI: 10.5061/dryad.m3p7d/2
title: MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 1 to 4)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
DOI: 10.5061/dryad.m3p7d/3
title: MiSeq raw sequences (Run 1) of the V4 region 16S rRNA gene from the spleens of 355 murinae from Senegal and 21 positive and negative controls (part 2 to 4)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual in duplicate or triplicate using the MiSeq platform (Run 1). The 823 multiplexed PCR products were indexed using both forward and reverse indices. The list of the 355 multiplexed samples and the 21 positive and negative controls are provided in the following XLSX file titled: Information concerning the samples multiplexed in the MiSeq Run 1 & 2.
DOI: 10.5061/dryad.m730b/1
title: S1 Blad thickness for male

description: Bladder thickness for juvenile, male and female oyster toadfish
DOI: 10.5061/dryad.m730b/2
title: S2 Thickness rostroacaudal and dorsal, side and ventral  transects

description: Bladder thickness in dorsal, side ventral and in rostral caudal transects in the oyster toadfish
DOI: 10.5061/dryad.m730b/3
title: S3 Stress, strain and modululs

description: Stress, strain and modulus of bladder wall in 0 and 90 degree pulls (circuluar and longitudinal
DOI: 10.5061/dryad.t60n5/5
title: 4_Phylo_contrasts

description: R script to perform phylogenetic regression and calculate statistics of phylogenetic signal
DOI: 10.5061/dryad.t60n5/6
title: biolog

description: Biolog profiles of engineered strains
DOI: 10.5061/dryad.t60n5/7
title: fitness_estimates

description: Fitness estimates of engineered strains
DOI: 10.5061/dryad.t60n5/8
title: growth_rates

description: Growth rate estimates of parent strains
DOI: 10.5061/dryad.326fv/1
title: Sample 2 - Injection 1 Orbitrap-Ion Trap

description: Sample 2 - Injection 1
DOI: 10.5061/dryad.3db6p/1
title: Singh et al. Data

description: The four sheets of the file contain data from the assays done in four experiments as described in the manuscript.
DOI: 10.5061/dryad.40494/13
title: Intact replicate 5 prior to reagent
DOI: 10.5061/dryad.40494/14
title: Intact replicate 5 after reagent
DOI: 10.5061/dryad.40494/15
title: Intact replicate 5 recovery
DOI: 10.5061/dryad.40494/16
title: Isolated replicate 2 prior to reagent
DOI: 10.5061/dryad.40494/17
title: Isolated replicate 2 after reagent added
DOI: 10.5061/dryad.40494/18
title: Isolated replicate 2 recovery
DOI: 10.5061/dryad.40494/19
title: Isolated replicate 3 prior to reagent
DOI: 10.5061/dryad.40494/20
title: Isolated replicate 3 after reagent
DOI: 10.5061/dryad.40494/21
title: Isolated replicate 3 recovery
DOI: 10.5061/dryad.41db8/1
title: data

description: Times of the fish moving out of cover ("M") and returning to cover ("W").
DOI: 10.5061/dryad.51j89/1
title: Full dataset

description: All variables measured are in this table.
DOI: 10.5061/dryad.6kn23/1
title: Sequence data details and alignments for dataset A and B.

description: Contains (1) table with accession numbers, isolate names, cell passage history, publication details, country/location of sampling, sampling dates and (2) Fasta format sequence alignments of datasets A and B.
DOI: 10.5061/dryad.6kn23/2
title: Epidemiological Data: Numbers of suspected ZIKV cases and suspected microcephaly cases per state and per epidemiological week.

description: Contains 1) CSV file with number suspected ZIKV cases from January 2015 to the end of December 2015; 2) CSV file with number of suspected microcephaly cases from January 2015 to the first week of January 2016. Numbers correspond to suspected microcephaly cases at week 20 of pregnancy; 3) CSV file with codes of state of residence and municipality of residence in Brazil; and 4) R scripts for correlation analysis described in SI Section 1.5.
DOI: 10.5061/dryad.6kn23/3
title: BEAST XML input file used for genetic analysis.

description: BEAST XML input file used to generate Figure 3 under a strict clock model, a Bayesian skyline coalescent prior and a CTMC prior on the clock rate.
DOI: 10.5061/dryad.7cs0p.1
title: Data from: Dealing with uncertainty in landscape genetic resistance models: a case of three co-occurring marsupials
DOI: 10.5061/dryad.7cs0p.2/1.2
title: simulation_script
DOI: 10.5061/dryad.7cs0p.2/20.2
title: data_set_up

description: R code for constructing fractal landscapes for the simulations.
DOI: 10.5061/dryad.7cs0p.2/21.2
title: functions

description: R functions for constructing resistance surfaces
DOI: 10.5061/dryad.7cs0p.2/22.2
title: grid_search

description: R Code for conducting the grid search approach for estimating resistance parameters
DOI: 10.5061/dryad.7cs0p.2/23.2
title: optim_search

description: R code for conducting the optimisation search method for estimating landscape resistance parameters.
DOI: 10.5061/dryad.8kn8c.1
title: Data from: A draft fur seal genome provides insights into factors affecting SNP validation and how to mitigate them
DOI: 10.5061/dryad.8kn8c.2/1.2
title: submission.assembly.ArcGaz001_AP3.fasta

description: Draft fur seal genome v1.0
DOI: 10.5061/dryad.8kn8c.2/2.2
title: Seal_assay_SNPs.csv

description: List of pre-validated fur seal SNPs plus variables used for modeling SNP validation success.
DOI: 10.5061/dryad.8kn8c.2/3.2
title: crossvalidation.R

description: R script to perform the k-fold cross-validation.
DOI: 10.5061/dryad.b754g/1
title: Bird movement data in response to playbacks, Fagan et al. 2016

description: This file contains the data for the experimental playback trials with four species of birds, as described in Fagan et al. 2016.  See the readme for more details.  If you want the control data for the subset of birds that responded to playbacks, please contact the author.
DOI: 10.5061/dryad.b9765/2
title: Ion torrent data

description: Raw Ion Torrent reads in FASTQ format; scripts associated with the bioinformatics pipeline; BWA alignments in SAM format; raw SNP reports in VCF and BCF format; the filtered SNP report used to construct consensus sequences; an overview of the number of reads in total and per marker and/or individual; nuclear DNA data in genotypic format; nuclear DNA sequence alignments.
DOI: 10.5061/dryad.c6b40/1
title: Brachyrhaphis endurance and kinematics

description: This file contains endurance and kinematics measures for species and populations of Brachyrhaphis fishes (Poeciliidae) from different predation environments.
DOI: 10.5061/dryad.c6b40/2
title: Brachyrhaphis burst speed and mesocosm

description: This file contains the results of a mesocosm experiment with species of Brachyrhaphis fishes (Poeciliidae) from different predation environments. This file also includes burst speed measurements and a measure of relative body shape.
DOI: 10.5061/dryad.d136v/5
title: Prey abundance 2012

description: Invertebrate prey was sampled via sweep netting in July 2012.  These data show the total number of invertebrate prey per sweep net sample at three sites on simulated invasion and control plots.  These data were used to evaluate the amount of available prey between plots.
DOI: 10.5061/dryad.dd0b3/1
title: SI 1 Additional methods and data

description: Contains age ranges, supertree construction details, mode of life details, and the environmental parameters used.
DOI: 10.5061/dryad.dd0b3/2
title: SI 2 JK croc occs

description: Raw occurrence files including metadata for Jurassic/Cretaceous crocodyliforms
DOI: 10.5061/dryad.dd0b3/3
title: SI 3 additional methods 2

description: Additional details on the time binning schemes, subsampling protocol, model-fitting procedure, and supertree building methods.
DOI: 10.5061/dryad.dd0b3/4
title: SI 4 Diversity, extinction and origination results

description: Complete results for biodiversity, extinction, and origination rates.
DOI: 10.5061/dryad.dd0b3/5
title: SI 5 Correlation results

description: Complete results of model-fitting procedure
DOI: 10.5061/dryad.dd0b3/6
title: SI Genus tree

description: Genus level supertree
DOI: 10.5061/dryad.dd0b3/7
title: SI Species tree

description: Species level supertree
DOI: 10.5061/dryad.ff051/1
title: All summarized flow cytometry data and strain information

description: This csv contains the summarized flow cytometry data for each cross (each row is a different cross). The descriptions of the columns are included in the readme file.
DOI: 10.5061/dryad.ff051/2
title: Images of crosses for perithecia counting

description: This zip file contains images of all crosses along with the imageJ .xml files corresponding to each cross in which perithecia are marked for counting.
DOI: 10.5061/dryad.ff051/3
title: Spore Flow Cytometry (fcs) files

description: These are the raw flow cytometry data files. See readme for description of contents.
DOI: 10.5061/dryad.j5n06/12
title: piranga_uce_snapp

description: Files associated with SNAPP analysis of UCE SNPs. Input nexus file, and output of two SNAPP runs. Output includes posterior sampling of all trees (.trees files), tree summaries (.tre) and pictures of the output trees (.pdf).
DOI: 10.5061/dryad.m3p7d/10
title: OTU table of raw abundance

description: This XLSX file contains the number of reads obtained for the Operational Taxonomic Units (OTU ≥ 100 reads due to file size limits for Excel) of the two MiSeq runs and each PCR product before the data filtering.
DOI: 10.5061/dryad.m3p7d/11
title: Table of presence and absence for the twelve pathogenic OTUs in the 704 analysed rodents

description: This XLSX file shows the presence (1) or absence (0) for the twelve pathogenic OTUs in the spleen of the 704 analysed rodents after the data filtering.
DOI: 10.5061/dryad.m3p7d/12
title: Sequence alignment file of the 16S rRNA PCR primers and 41,113 sequences from 79 bacterial zoonotic genera

description: This FASTA file contains  41,113 sequences of the V4 hypervariable region from 79 bacterial zoonotic genera extracted from the Silva SSU database v119, and the forward and reverse primers used in our 16S rRNA amplicon sequencing experiment.