cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.ft511/1
title: Quantitative genetics of Cd survival time of two natural populations of Gammarus fossarum

description: Survival time to Cd exposure of juveniles of Gammarus fossarum with a known pedigree. Mothers and fathers of each juveniles are recorded in this data file that allowed both full-sib and half-sib analyses. This data file is associated with a publication in which full information is given (section "Breeding design for sib analysis and estimation of genetic parameters" of the materials and methods).
DOI: 10.5061/dryad.jg613/1
title: data of occupancy

description: data for analysis in Presence format. First part : presence-absence. Second part : covariates. Third : id/cells
DOI: 10.5061/dryad.kc470/1
title: data

description: Bird survey data (abundance, foraging rate/success, and activity budgets along with anonymised socioeconomic data for saltpans and aquaculture ponds in the Inner Gulf of Thailand. For further information see Green et al. "The ecology and economics of shorebird conservation in a tropical human-modified landscape". Journal of Applied Ecology.
DOI: 10.5061/dryad.t0k5k/1
title: Airfield Vegetation Community Composition

description: Plot-level community composition data of 80 plots of vascular vegetation data from a site of anthropogenic disturbance on Ellesmere Island, Nunavut, Canada. Please refer to Becker & Pollard, 2015 for more information.
DOI: 10.5061/dryad.t0k5k/2
title: Airfield Plot Metadata

description: Corresponding metadata of plot environmental variables matching 80 plots of vascular vegetation data from a site of anthropogenic disturbance on Ellesmere Island, Nunavut, Canada. Please refer to Becker & Pollard, 2015 for more information.
DOI: 10.5061/dryad.th547/12
title: Fig.9_LAAO_Jalview

description: Primary multiple sequence alignment of Fig.9 (LAAO) performed with MUSCLE program using Jalview software.
DOI: 10.5061/dryad.th547/13
title: Fig.10_Vespryn_Jalview

description: Primary multiple sequence alignment of Fig.10 (Vespryn) performed with MUSCLE program using Jalview software.
DOI: 10.5061/dryad.th547/14
title: Fig.11_PLA2_Jalview

description: Primary multiple sequence alignment of Fig.11 (PLA2) performed with MUSCLE program using Jalview software.
DOI: 10.5061/dryad.th547/15
title: Fig.12_CVF_Jalview

description: Primary multiple sequence alignment of Fig.12 (CVF) performed with MUSCLE program using Jalview software.
DOI: 10.5061/dryad.vp530/1
title: Fungal colonisation

description: This file contains data for roots hyphal colonisation, based on roots that have been cleared and stained with ink-vinegar. Metadata included.
DOI: 10.5061/dryad.vp530/2
title: Pathogen table

description: This file contains records for each genus identified by 454 and whether they have been recorded as a pathogen. Metadata included.
DOI: 10.5061/dryad.vp530/3
title: Plant dry weights

description: This file contains the dry weights of roots, shoots, and pods. These data were used in the models to assess V. rossicum biomass growing in soils from different invasion periods. Metadata included.
DOI: 10.5061/dryad.vp530/4
title: Site by species matrix from 454 pyrosequencing

description: This file contains the site by species matrix of the Genome Quebec pyrosequencing data. Metadata provided.
DOI: 10.5061/dryad.1dd0m/1
title: Microsatellite data of Ch. montanus and Ch. parallelus

description: In 2009 and 2010, 1159 specimens were sampled from 16 localities in the Hunsrueck Mountains, Rhineland-Palatinate, Germany. All individuals were genotyped at ten polymorphic microsatellite loci. Six microsatellite markers were designed for Ch. parallelus (BF1, BD5, BH5, BD7, BF9, CD6; Molecular Ecology Resources Primer Development Consortium et al. 2009), four were developed for Ch. montanus prior to this study (Additional file 1).
DOI: 10.5061/dryad.1n6s9/4
title: Partitioning scheme (ribosomal; 52 taxa)

description: Partitioning scheme for 3 gene ribosomal dataset of 52 taxa.
DOI: 10.5061/dryad.1n6s9/5
title: Alignment file (ribosomal; 52 taxa)

description: Phylip alignment file of 3 gene ribosomal dataset for 52 taxa
DOI: 10.5061/dryad.1n6s9/6
title: Partitioning scheme (combined; 52 taxa)

description: Partitioning scheme for combined dataset
DOI: 10.5061/dryad.1n6s9/7
title: Alignment file (combined; 52 taxa)

description: Phylip alignment file for combined dataset of 52 taxa
DOI: 10.5061/dryad.1n6s9/8
title: Bootstrap Trees for each gene for STAR

description: Zip file of 370 rooted bootstrap gene trees. Each file contains 100 bootstrap replicates of each gene. Gene ID's in file names correspond to those listed Gene regions file which correspond to positions in the Phylip file.
DOI: 10.5061/dryad.1n6s9/9
title: GeneID and partition in alignment

description: The make up of the concatenated alignment file by Gene ID (as in STAR gene trees).
DOI: 10.5061/dryad.31733/104
title: SNP_rice_HET50-MINFREQ-15

description: n calling SNP on Oryza glaberima (enriched, genomic and LRPCR libraries) with Mpileup -Bg and Varscan (min_freq_for_hom =0.5 and --min-var-freq 15 )
DOI: 10.5061/dryad.4ht07/3
title: Captive Pathogen Load and Eye Scores

description: Sampling data from captive transmission experiment, including eye scores (visible pathology) and pathogen load.
DOI: 10.5061/dryad.4ht07/4
title: Time Spent on Feeder by Week - Captive Experiment

description: Time each individual house finch in our captive experiment spent on the feeder by week.
DOI: 10.5061/dryad.4ht07/5
title: Disease and RFID Behavior Data - Field Study

description: Disease status data and social behavior data gathered via radio-frequency identification for wild house finches included in the field study.
DOI: 10.5061/dryad.4ht07/6
title: Eye Score vs. Pathogen Load - Field Study

description: Eye scores (visible pathology) and pathogen loads for wild house finches included in the field study.
DOI: 10.5061/dryad.4ht07/7
title: Group by Individual Matrix for Networks - Field Study

description: Presence/absence of each wild PIT-tagged house finch within foraging groups detected via radio-frequency identification.
DOI: 10.5061/dryad.67n7n/11
title: Mybaits M18

description: Mybaits datafile. Sample M18
DOI: 10.5061/dryad.67n7n/12
title: Mybaits M19

description: Mybaits datafile. Sample M19
DOI: 10.5061/dryad.67n7n/13
title: Mybaits M20

description: Mybaits datafile. Sample M20
DOI: 10.5061/dryad.67n7n/14
title: Amplicon Sequencing Files

description: All 12 samples. Amplicon Sequencing data zipped together.
DOI: 10.5061/dryad.67n7n/15
title: Table results

description: Table showing the results in read counts between samples and methods
DOI: 10.5061/dryad.67n7n/16
title: Sanger Sequencing Reads COI

description: Sanger sequencing of some missing species. Name in Fasta file. Species names are unknown.
DOI: 10.5061/dryad.67n7n/17
title: Sample file explanation

description: Samples are referred to by there number and type of lab prep in the sample files. I.e. RS4 has a A4 (amplicon) and M4 mybaits samples associated with it in the sample files
DOI: 10.5061/dryad.67n7n/18
title: MMCI biomass calculation

description: Spreadsheet with the details regarding the biomass calculations included.
DOI: 10.5061/dryad.67n7n/19
title: Reference databases

description: Two files zipped together. One fasta file contains all the genes associated with the Mayflies, Stoneflies and Caddisflies. These three groups had the additional genes used in the mapping protocol. The second fasta contains the sequences for all other species (only COI sequences).
DOI: 10.5061/dryad.67n7n/9
title: Mybaits M16

description: Mybaits datafiles. Sample M16
DOI: 10.5061/dryad.6d5h2/1
title: Data Submission
DOI: 10.5061/dryad.74jt1/4
title: Seed-set by experimental crosses

description: To estimate the potential ability to produce seeds at each site (ridge, slope, and valley), we conducted artificial pollination experiments within and nearby the quadrats over 2 years (2010 and 2011). The total numbers of pin and thrum plants pollinated were 78 and 77 during 2010 and 59 and 81 during 2011, respectively. The plants were covered with fine-meshed nylon nets to exclude insect visitors. For each plant, one target flower bud was emasculated just before opening, and other flowers were removed. After opening of the target flowers, hand pollination was conducted by legitimate pollen grains collected from a single pollen donor growing at least 5 m away from the recipient plant. All fruits derived from the pollination treatments were harvested just before dehiscence, and the number of seeds and undeveloped seeds or ovules were counted using a microscope.
DOI: 10.5061/dryad.74jt1/5
title: Seed-set under natural conditions

description: To estimate the number of ovules and the seeds per fruit under natural conditions at each site (ridge, slope, and valley), we examined the plants growing within and nearby the quadrats over 2 years (2010 and 2011). The total number of pin and thrum plants examined was 78 and 79 during 2010 and 170 and 157 during 2011, respectively. We collected several fruits from each plant (2.8 on average) during 2010, and one fruit per plant during 2011. The total number of fruits collected from the pin and thrum plants was 233 and 204 during 2010 and 170 and 157 during 2011, respectively. The fruits were collected just before dehiscence, and the number of seeds and undeveloped seeds or ovules were counted using a microscope.
DOI: 10.5061/dryad.74ms0/1
title: Mussel shell growth data

description: Mussel shell growth data for figures 2, 3 and 4. The first worksheet entitled 'Mussel shell growth' lists all growth measurements for individual mussel shells used for mussel shell growth (mean ± SD) during 9 months of experimental culture (n=4 per treatment) used for figure 2. Shells were grown at 380, 550, 750 and 1000 μatm CO2 at ambient temperature and 750 and 1000 μatm CO2 ambient temperature + 2°C. The second worksheet entitled 'Aragonite_Calcite thickness' list all shell aragonite and calcite thickness measurements for individual mussels to calculate mussel shell calcite and aragonite in new growth (mean ± SD) (n=4 per treatment) used for figure 3. Aragonite and calcite in mm and the ratio of aragonite/ calcite. Shells were grown at 380, 550, 750 and 1000 μatm CO2 at ambient temperature and 750 and 1000 μatm CO2 ambient temperature + 2°C. The third worksheet entitled 'STI' lists all measurements taken to calculate Shell Thickness Index (STI) for mussel shells grown under experimental conditions for 9 months (n=4 per treatment) used for figure 4. Measurements for weight (g), height (mm), length (mm) and width (mm) of shell are provided for use of calculating STI. A higher shell thickness index indicates a thicker shell. Shells were grown at 380, 550, 750 and 1000 μatm CO2 at ambient temperature and 750 and 1000 μatm CO2 ambient temperature + 2°C, treatments were labelled as CO2 μatm and temperature in the spreadsheet.
DOI: 10.5061/dryad.74ms0/2
title: mussel380_001

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/3
title: mussel380_002

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.74ms0/4
title: mussel380_003

description: Mussel shape analysis data for figures 1 and 5. There are four .obj files per treatment, one for each individual mussel as titled. The .obj file is a matrix of points in 3d (x,y,z) that make up the mussel with a color attached to each point. A simple triangulation of these 3d points creates the visualized surface of the mussel. These individual .obj files were compared across the experimental condition populations 380, 550, 750 and 1000 μatm pCO2, and 750 and 1000 μatm pCO2 + 2°C (n=4 per treatment). Each file name refers to the treatment, the .obj files are labelled for each individual mussel as mussel’treatment’_oo# where # represents the number of the individual mussel, and treatment is the CO2 concentration. The files were produced by Dimensional Imaging OBJ exporter http://www.di3d.com.
DOI: 10.5061/dryad.8pd11/1
title: EnvironmentalSurvey.tar.gz

description: Analysis commands and results of environmental surveysby 454 massively parallel 18S amplicon sequencingof eukaryote community sampled at Monbetsu.
DOI: 10.5061/dryad.8pd11/2
title: EstimationOfPCRSuccessRates.tar.gz

description: Analysis commands and results for estimating PCR success rates and amplicon sequence variability.
DOI: 10.5061/dryad.8pd11/3
title: EstimationOfEffectiveNumberOfSequences.tar.gz

description: Analysis commands and results of estimation of effective number of registered sequences.
DOI: 10.5061/dryad.9fg8m/6
title: Zebra finch sperm numbers data

description: Data on the number of sperm reaching the ovum after natural (high) and artificial (low) inseminations in the zebra finch. Data include only eggs that were reached by at least one sperm.
DOI: 10.5061/dryad.bq4t8/1
title: 06_16_15-fastqs.tar.gz_replace
DOI: 10.5061/dryad.f47f6/1
title: Thompsonetal_Genotypedata

description: This file includes all the genotypic data for all individuals used in the analyses for this publication.
DOI: 10.5061/dryad.gq883/1
title: chimera_ID

description: This script sorts capture sequences that hit to non-closest-relative (NCR) MMA probes.
DOI: 10.5061/dryad.gq883/10
title: Dryad_ModernSquirrelDemux

description: This file contains the 454 barcode information to demultiplex the samples from the two 454 sff files.
DOI: 10.5061/dryad.gq883/11
title: pero_in.454.fasta

description: This file contains 454 generated fastq reads for the Peromyscus samples used for the probe development. Both individuals included in the concatenated reference sequence are within this file, with USNM 569292 represented as 92. Sample USNM 569298 is represented as reads ID'd as 98.
DOI: 10.5061/dryad.gq883/2
title: combiner-2.0

description: The FASTA file is sequences from MMA capture. The Blast output is the output of blasting those sequences against the MMA probeset, minus closest relative to the target species (non-closest-relative, or NCR, probeset). This program appends the length of the query sequence (found in the FASTA file) onto the end of that sequence's line in the blast table so that the chimera detection decision rules can be followed in chimera_ID.py
DOI: 10.5061/dryad.gq883/3
title: sequenceGetter-4.0

description: This script gets a subset of a FASTA file based on a CSV file of BLAST hits.
DOI: 10.5061/dryad.gq883/5
title: AllProbes_good

description: This file contains all 8,178 probes used for RNA bait synthesis.
DOI: 10.5061/dryad.gq883/7
title: H3FTPWM01

description: 454 Sequencing reads for some of newly generated mitogenomes, a text file is provided with demultiplexing information and for this run.
DOI: 10.5061/dryad.gq883/8
title: H3HWW5Q01

description: Second 454 run containing novel mitogenomes. Details for demultiplexing are provided in a separate text file.
DOI: 10.5061/dryad.gq883/9
title: WMG_Alignment26Ind_FINAL01.09.14

description: All mitochondrial genomes used for array design. 16 are published sequences and 10 are novel mitogenomes.
DOI: 10.5061/dryad.j5r51/1
title: Simulated laminar recordings for input intensity 0.5 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/2
title: Simulated laminar recordings for input intensity 1.0 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/3
title: Simulated laminar recordings for input intensity 1.5 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/4
title: Simulated laminar recordings for input intensity 2.0 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/5
title: Simulated laminar recordings for input intensity 2.5 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/6
title: Simulated laminar recordings for input intensity 3.0 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.j5r51/7
title: Simulated laminar recordings for input intensity 6.0 sp/ms

description: Simulated recordings (10101 ms) of the LFP generated by the 3D network described in the paper, computed from LFPy. Each row is a different depth. Input intensity is reported in the title.
DOI: 10.5061/dryad.k797r/1
title: Ranavirus_eDNA_Hall_et_al_2015

description: This file includes raw data included in figures and tables of this manuscript. Each row contains data of one pond visit, such as GPS location, ranavirus die-off, date, dipnet survey, amphibian density, amphibian presence/absence, date of die-off, average log 10 ranavirus eDNA titer, average log 10 ranavirus larvae titer, respective standard errors, and any notes.
DOI: 10.5061/dryad.p0372/1
title: RCC data for Dryad

description: This file conatins all the data files for the submission. The cohort data file is provided both as a SPSS file and as an excel file where varibales have been specifiec in the column headers. There is also a list file explaining sample lanes in the WB images. The file folder is compressed.
DOI: 10.5061/dryad.p0372/2
title: Additional data

description: Additional data.
DOI: 10.5061/dryad.pb271/1
title: Moore 2015 Final Data

description: Soil respiration, soil carbon pools, and enzyme activities. The first row is a header and units of measurement are included in this row. In "exclusion group", R=roots and M= mycorrhizae. In "carbon label", C=control (water-only) and L=labeled starch addition.
DOI: 10.5061/dryad.qm7gg/1
title: Survival data

description: Survival of ants fed on either control or ROS diet, and afterwards being exposed to either Fungus or Control.
DOI: 10.5061/dryad.qm7gg/2
title: Spore Viability

description: Viability of spores after being in contact with varying concentrations of ROS. Spores were counted as either alive or dead in one 'field of view'.
DOI: 10.5061/dryad.qm7gg/3
title: Food choice

description: Results of the diet choice of either control or infected ants. The column 'time' depicts hours after treatment.
DOI: 10.5061/dryad.qm7gg/4
title: ROS concentration in body

description: ROS concentration measurements. Note that these are the raw values straight from the spectrophotometer.
DOI: 10.5061/dryad.qm7gg/5
title: R scripts

description: R scripts used for final analysis of the data.
DOI: 10.5061/dryad.s0054/1
title: R analyses

description: File of all analyses carried out on opsin expression data.
DOI: 10.5061/dryad.v13m6/1
title: ha13_176a_FineScaleTagData

description: Time-series data of northern bottlenose whale subject in the study.
DOI: 10.5061/dryad.v13m6/2
title: ha13_176a_FineScaleMahalanobisDistance

description: Mahalanobis distance time series from the whale subject.
DOI: 10.5061/dryad.v13m6/3
title: DiveParameters

description: Measured dive parameters from tagged northern bottlenose whales
DOI: 10.5061/dryad.v13m6/4
title: NBW_visual_and_acoustic_detections

description: Visual and acoustic detection of northern bottlenose whales before and after the experiment
DOI: 10.5061/dryad.v13m6/5
title: splData

description: Modelled sound pressure levels of by distance and azimuth of the source location
DOI: 10.5061/dryad.v13m6/6
title: vesselTrack_Sverdrup2

description: GPRMC string of navigation data of the research vessel before and after the experiment
DOI: 10.5061/dryad.v2890/1
title: 2014adultslon - dryad

description: raw data on fitness and cort
DOI: 10.5061/dryad.v7g2k/1
title: 73 gene data set for 112 asterids

description: 73 plastid genes for 112 accessions of asterids focusing on the lamiids
DOI: 10.5061/dryad.v7g2k/2
title: Gene partitions

description: List of the starting and stopping positions of the concatenated 73 plastid genes.
DOI: 10.5061/dryad.vd7bf/1
title: Maximum posterior probability triggerfish tree

description: Nexus file for the maximum posterior probability triggerfish tree that was used in this study for phylogenetic analyses of shape diversification.
DOI: 10.5061/dryad.vd7bf/2
title: Cranial shape landmark data

description: .tps file with (x,y) coordinates for 44 cranial landmarks digitized on 79 specimens. Landmarks correspond to those listed in the caption of Figure 1a.
DOI: 10.5061/dryad.vd7bf/3
title: Triggerfish jaw biomechanics

description: Species mean measurements of each adductor mandibulae in-levers, out-levers, mechanical advantage (MA), effective mechanical advantage (EMA).
DOI: 10.5061/dryad.0h82m/2
title: S1 Fig. Evolutionary analyses of 52 strains of B. anthracis based on 29906 chromosomal SNPs.

description: S1 Fig. Evolutionary analyses of 52 strains of B. anthracis based on 29906 chromosomal SNPs. Phylogenetic relationships were inferred using the Maximum Likelihood method (A), the Maximum Parsimony method (B), the Neighbor-Joining method (C) and the UPGMA method (D). Bootstrap values (100 iterations) higher than 70% are shown next to the branches. All evolutionary analyses were conducted in MEGA6 [28]. The maximum likelihood tree with the highest log likelihood (0.000) is shown in A. Tree #1 out of 2 most parsimonious trees (length = 7469, consistency index = 0.815, retention index = 0.947) is shown in B. The optimal neighbour-joining tree with the sum of branch length = 0.251 is shown in C. The optimal UPGMA tree with the sum of branch length = 0.239 is shown in D. The later tree is drawn to scale, with branch lengths in the same units as those of the evolutionary distances used to infer the phylogenetic tree.