cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6tn7c/3
title: Sequence read identifiers and CREST taxonomic assignments

description: This zipped archive contains 48 taxonomic assigment text files: one taxonomic assignment file (sequence identification number and taxonomy with tab separation) for each sample used in this study (24 copepod gut content samples and 24 filterable seawater plankton biomass samples). Taxonomic assignment of quality-trimmed sequences was performed using the CREST classifier with Silvamod reference database.
DOI: 10.5061/dryad.6tn7c/4
title: AmpliconNoise OTU table

description: This table summarizes OTU (98% cut-off) abundance in all sequence samples used for this study. Rows of the table are OTUs and columns of the table are samples. Column names consist of "TYPE_TreatmentDate". TYPE indicates sample type ("COP" - copepod gut content or "FIL" - filterable seawater plankton biomass). Treatment designations indicate mineral nutrient additions for each treatment: "blank" - Control mesocosms that received no mineral nutrients, "NP" - mesocosms that received N + P addition, "NPSi" - mesocosms that received N + P + Si addition, "fjord" - samples taken from the adjacent Raunefjorden. Dates indicate sampling date in March 2012.
DOI: 10.5061/dryad.6tn7c/5
title: Taxonomic assignments for AmpliconNoise OTUs

description: This file contains taxonomic assignments for AmpliconNoise-identified OTUs (98% cut-off). Taxonomic assignment of OTUs was performed using the CREST classifier with Silvamod reference database.
DOI: 10.5061/dryad.7ck7r.1
title: Data from: The last bastion? X chromosome genotyping of Anopheles gambiae species pair males from a hybrid zone reveals complex recombination within the major candidate ‘genomic island of speciation’
DOI: 10.5061/dryad.85b2f/1
title: Evolution of plant defences along an invasion chronosequence
DOI: 10.5061/dryad.9bv73/10
title: S1 Table

description: S1 Table. Oligonucleotide sequence used in this study.
DOI: 10.5061/dryad.9bv73/11
title: S2 Table

description: S2 Table. Strains and plasmids used in this study.
DOI: 10.5061/dryad.9bv73/4
title: Fig4

description: Fig 4. Fermentative capacity and the survival of OsMDHAR-expressing yeast cells during batch fermentation. (A) Fermentative capacity was analyzed by measuring the alcohol (AC) and residual glucose (RG) concentrations in YG medium after fermentation for 72 h at 30°C. Upward triangles, AC of WT cells; circles, AC of TC cells; squares, RG of WT cells; diamonds, RG of TC cells. (B) Time-dependent OsMDHAR expression during batch fermentation was evaluated by western blotting. Tubulin (Tub) was used as a loading control. (C) Growth kinetics during fermentation was assessed by measuring the OD600 at 2-h intervals for the indicated time. Squares, WT cells; circles, TC cells. (D) Cell viability during fermentation at 30°C was assessed by a spotting assay. Cells were harvested after 24 h (upper panel), 48 h (middle panel), and 72 h (lower panel) of fermentation and serially diluted to 10−9. A 5-µL aliquot of each diluted solution was spotted onto YPD agar plates. After incubation for 3 days, the plates were photographed. (E) Stress response to ethanol. Mid-log phase yeast cells (OD600 ≈ 2.0) were exposed to different concentrations of ethanol (0, 15%, and 20%) for 1 h, serially diluted, and spotted onto YPD agar plates. WT, yeast cells with an empty vector; TC, OsMDHAR-expressing yeast cells.
DOI: 10.5061/dryad.9bv73/5
title: S1_Fig

description: SI Fig. Stress sensitivity and redox state of por1△ yeast cells under oxidative stress. (A) Growth kinetics was observed in YPD medium containing 3.5 mM H2O2 by monitoring optical density at 600 nm at 2-h intervals for 32 h. Square, BY cells; circle, por1Δ cells. (B) Cell survival by streaking (upper panel) and spotting (lower panel) assays in both BY and por1Δ cells. For streaking assay, yeast cells were cultured until reaching early log-phase (A600 ≈ 1.0) and streaked onto YPD agar plates supplemented with 3.5 mM H2O2. For spotting assay, yeast cells (A600 ≈ 1.0) were exposed to 10 mM H2O2 for 1 h at 28ºC with shaking, serially diluted to 10−4 with YPD medium, and spotted onto YPD agar plates. (C) Cytosolic and mitochondrial redox states were analyzed using the indicator probes for DCFHDA and DHR 123, respectively. Yeast cells were pretreated with the probes for 20 min, washed twice with PBS, and treated with 10 mM H2O2 for 1 h with shaking. Probe intensity was visualized by fluorescence microscopy. (D) Stress sensitivity of por1Δ yeast cells to physiochemical stressors. Yeast cells (A600 ≈ 1.0) were streaked onto YPD agar plates containing various stressors as mentioned in Materials and Methods. BY, wild-type yeast cells without an empty vector; por1Δ, yeast cells in which the POR1 gene had been deleted.
DOI: 10.5061/dryad.9bv73/6
title: S2_Fig

description: S2 Fig. Exogenous effect of ascorbate and its analogue on the stress sensitivity of ara2Δ yeast cells. (A) Monitoring of the effect was performed by spotting assay. Yeast cells pretreated with 10 mM AsA and 10 mM IAA for 1 h were exposed to 20 mM H2O2 for 1 h. Five microliters of diluted solutions were spotted onto YPD agar plates. Exogenous AsA- and IAA-treated cells showed better survival compared to cells under normal conditions, suggesting that their concentrations were sufficient for detoxifying endogenous and exogenous ROS and enhanced cell proliferation. WT, yeast cells transformed an empty vector; TC, OsMDHAR-expressing yeast cells. (B) Stress sensitivity of ara2Δ yeast cells to oxidative stress. Yeast cells were treated with abiotic stressors for 1 h with shaking and spotted onto YPD agar plates. For heat shock, yeast cells were incubated for 5 min at 55ºC, and then spotted as described above. BY, wild-type yeast cells without an empty vector; ara2Δ, yeast cells in which the ARA2 gene had been deleted.
DOI: 10.5061/dryad.9bv73/7
title: S3_Fig

description: S3 Fig. Response of OsMDHAR-expressing yeast cells to abiotic stressors. Yeast cells (A600 ≈ 2.0) were challenged with various stressors, including 0.4 mM MD, 15 mM t-BOOH, 20 mM CuSO4, 40 mM FeCl2, 10 mM CdCl2, and 1% SDS, for 1 h at 28ºC with shaking. Stressed cells were serially diluted to 10−4 with YPD medium, spotted onto YPD agar plates, and then incubated for 3 days at 28ºC. WT, yeast cells transformed an empty vector; TC, OsMDHAR-expressing yeast cells.
DOI: 10.5061/dryad.9nv3b/19
title: Audio_Bird16
DOI: 10.5061/dryad.9nv3b/20
title: Audio_Bird17
DOI: 10.5061/dryad.bk225/1
title: DawrinCode records - Diptera

description: Specimens were collected at a site in Steel Creek, in Northwest Arkansas, using Malaise pitfall, colored pan, Lindgren funnel, and canopy traps.
DOI: 10.5061/dryad.cc3rb/1
title: figure3_A

description: This data is made available to support the paper “Optimal Geocentric/Egocentric Switching Strategies in Navigation”, by Orit Peleg and L. Mahadevan, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138,USA

Data description, corresponding to the manuscript’s figures:

% figure3_A.txt N, $theta^*$, reorientation interval $n$, cost $f$
DOI: 10.5061/dryad.f3kc0/1
title: Metadata for the chemical genomics plates.

description: Metadata for the plates used in the chemical genomics screen, including uid, image analysis filename, condition and concentration of antibiotic, source plate, flags, and plate opacity IQR.
DOI: 10.5061/dryad.f3kc0/2
title: Iris Image Analysis Fileset

description: Tar ball of all Iris files generated in the current screen, see the image key for associated metadata.
DOI: 10.5061/dryad.fj34d/2
title: RSEM filtered assembly
DOI: 10.5061/dryad.g41cj/1
title: Genepop Input File

description: Microsatellite allele sizes formatted for Genepop.
DOI: 10.5061/dryad.h0g89/1
title: Data connected to Cramer et al BES 2014

description: Included in this data set are four .csv files containing data, one .xlsx file with information on the naming of columns in the data files (information for each data file is in a separate tab in the .xlsx file), and R code. Note that one of the R packages used in this publication (languageR) is no longer functional, and so the R code does not completely replicate tests presented in the manuscript. However, this R script should be sufficient to understand exactly how analyses were performed.Justification for analysis decisions is indicated in the manuscript.
DOI: 10.5061/dryad.h6v7g.1
title: Data from: Macroevolution of specificity in cyanolichens of the genus Peltigera section Polydactylon (Lecanoromycetes, Ascomycota)
DOI: 10.5061/dryad.h6v7g.2/12.2
title: Matrix 3
DOI: 10.5061/dryad.h6v7g.2/13.2
title: Matrix 4
DOI: 10.5061/dryad.h6v7g.2/14.2
title: Matrix 5
DOI: 10.5061/dryad.h6v7g.2/15.2
title: Matrix 6
DOI: 10.5061/dryad.h6v7g.2/16.2
title: Matrix 7
DOI: 10.5061/dryad.jr67t/1
title: RAxML trees

description: Trees in nexus format
DOI: 10.5061/dryad.jr67t/2
title: Multiple species alignments 500kb "most reliable segments"

description: Alignment blocks of 500,000 bp sampled from all “most reliable segments”, totaling 426 blocks, FASTA
DOI: 10.5061/dryad.jr67t/3
title: Multiple_sequence_alignments_most_reliable_segments

description: 224 multiple sequence alignments "most reliable segments", FASTA
DOI: 10.5061/dryad.jr67t/6
title: Multiple_alignments_LGs

description: Multiple sequence alignments, all linkage groups, FASTA
DOI: 10.5061/dryad.nb304/1
title: EMENDSpider_data

description: Ground-dwelling spider species abundance after variable retention harvest two, five and ten years after harvest prescriptions in four forest cover-types in the mixedwood boreal forest of northwestern Alberta (Canada)
DOI: 10.5061/dryad.q7s54/1
title: Cost of resistance data and analysis

description: This folder contains the data and analysis scripts to recreate the results and figures in the manuscript titled "Fitness costs of herbicide resistance across natural populations of the common morning glory". There is a README file in the folder containing more information.
DOI: 10.5061/dryad.qb7t2/1
title: FinalSurveyData_Schade et al_PLOS ONE

description: Please refer to our survey questionnaire (uploaded as ReadMe file) which serves as the codebook
DOI: 10.5061/dryad.qr871/1
title: FlycatcherDryadData

description: R script, sperm velocity data, and sperm proportion motility data
DOI: 10.5061/dryad.r8h3n/1
title: OF experiment

description: Turning points of homing ants walking in a channel set-up. The ants were carried by a nest mate during outbound run. Collected in the field in Tunisia.
DOI: 10.5061/dryad.r8h3n/3
title: IT experiment

description: Turning points of homing ants walking in a channel set-up. The ants were blindfolded after carrying and before being tested in the channel. Collected in the field in Tunisia.
DOI: 10.5061/dryad.2dn85/1
title: Greenwayetal2016 Adaptive, but not condition-dependent, body shape differences contribute to assortative mating preferences during ecological speciation Evolution Data

description: Data used in analyses for the manuscript "Adaptive, but not condition-dependent, body shape differences contribute to assortative mating preferences during ecological speciation"
DOI: 10.5061/dryad.2pc43/1
title: Database of young and aged women- Slaoui Meriem
DOI: 10.5061/dryad.2td06/1
title: Abundances

description: Species identities and relative abundances of each species on each sampling point of each field.
DOI: 10.5061/dryad.3bc76/5
title: DoS

description: Direction of selection (DoS) script:
DOI: 10.5061/dryad.3dp50/1
title: Reference sequences for 5162 loci

description: Fasta file of the reference sequences used for calling 5162 SNPs for Nannoperca australis.
DOI: 10.5061/dryad.3dp50/2
title: SPPLG_263_5162.stru

description: Data in STRUCTURE input format for 263 individuals and 5162 SNP loci
DOI: 10.5061/dryad.3dp50/3
title: Environmental data

description: Environmental data for 40 variables at 25 Nannoperca australis sampling locations.
DOI: 10.5061/dryad.3dp50/4
title: Table_S8-S11

description: Supplementary tables S8-S11 describing the BLAST and annotation results.
DOI: 10.5061/dryad.3kq05/1
title: Yakub_Tiffin_GCB_full_data_3oct_2016

description: phenotypic data on individual plants
DOI: 10.5061/dryad.3mf45/1
title: JAPPL-2016-00231_data

description: A csv file containing plot and vine stock ID, number of attacked lures per vine stock, main bird community metrics and habitat heterogeneity variables
DOI: 10.5061/dryad.41m3s/1
title: Monitoring period

description: Data frame with start and stop for each monitoring session
DOI: 10.5061/dryad.41m3s/2
title: Temperature data

description: Temperature log during the monitoring period
DOI: 10.5061/dryad.41m3s/3
title: Bumblebee visits

description: Data frame with number of bumblebee visits per monitored hour-block
DOI: 10.5061/dryad.4f3f6/1
title: Senegalese sole data Ibarra-Zatarain et al., 2016
DOI: 10.5061/dryad.5k7b5/1
title: 3genelocusalignment

description: DNA sequences alignment
DOI: 10.5061/dryad.8b3h0/1
title: Diversity metric (SES and rank) against predictors

description: The file contains the data used to construct the linear model. It contains: the standard effect size of the multi-trait functional diversity (SES), its rank, the associated growing season length (scaled), the site and community identifiers, the scale at which it was sampled and the extent of the null model (0: site, 1: landscape)
DOI: 10.5061/dryad.8tk11/1
title: supplementary video V1 (backward homing)

description: Shown is an ant that is presented a large food item. It grasps immediately the booty and starts its homing journey in backward locomotion. The ant also drops the load and performs foodless search loops that are directed towards the fictive nest site. Note that the early performed foodless search loops tend to be even much shorter in length and time than the two foodless search loops seen in this video.
DOI: 10.5061/dryad.9r161.1
title: Data from: Genome-wide association study of insect bite hypersensitivity in Swedish-born Icelandic horses
DOI: 10.5061/dryad.9r161.2
title: Data from: Genome-wide association study of insect bite hypersensitivity in Swedish-born Icelandic horses
DOI: 10.5061/dryad.9r161.2/1.2
title: Genotypes_for_209_horses

description: This file contains genotype information on 54,602 SNPs for 209 horses. The genotypes are from Illumina 50K SNP chip.
DOI: 10.5061/dryad.9r161.2/2.2
title: SNP information

description: This file contains information on SNPs.
DOI: 10.5061/dryad.9r161.2/3.2
title: Information on samples

description: This file contains information on phenotype, gender, region, age, sire and dam for 209 horses.
DOI: 10.5061/dryad.cc3rb/2
title: figure3_B

description: This data is made available to support the paper “Optimal Geocentric/Egocentric Switching Strategies in Navigation”, by Orit Peleg and L. Mahadevan, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138,USA

Data description, corresponding to the manuscript’s figures:

% figure3_B.txt N, $theta^*$, n^{opt}
DOI: 10.5061/dryad.cc3rb/3
title: figure4_A

description: This data is made available to support the paper “Optimal Geocentric/Egocentric Switching Strategies in Navigation”, by Orit Peleg and L. Mahadevan, John A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138,USA

Data description, corresponding to the manuscript’s figures:

% figure4_A.txt and figure4_B.txt $N$, $theta^$, penalty $A\theta^$, detection_error, Optimal estimated $n$, optimal attention span $\tau$
DOI: 10.5061/dryad.cc3rb/4
title: figure4_B
DOI: 10.5061/dryad.f3kc0/3
title: imagefile

description: Tar ball of plate images, see image key for associated metadata
DOI: 10.5061/dryad.f3kc0/4
title: Input Metadata for Statistical Analysis

description: These files include the metadata for conditions and arrays used as input for the statistical analysis and generation of the fitness score.
DOI: 10.5061/dryad.f3kc0/5
title: 10C fitness-scores

description: Gene deletions identified by ECK number. Ranked list of fitness-scores at 10C.
DOI: 10.5061/dryad.f3kc0/6
title: COG assignments

description: COG category assignments for KEIO genes, for use in GSEA analysis
DOI: 10.5061/dryad.h4s6t/1
title: Data from: Does one model fit all? patterns of beech mortality in natural forests of three European regions
DOI: 10.5061/dryad.hr431/1
title: Bash command to remove potential chimeras

description: These bash commands were used to search for and remove any read containing the EcoRI and MspI recognition sites, which are potential chimeric sites formed during ligation.
DOI: 10.5061/dryad.hr431/2
title: Demultiplexed ddRADseq fastq files per specimen

description: This zip file contains the individual fastq files for each sea star in which ddRADseq was performed. The data was demultiplexed in STACKS as described in the manuscript.
DOI: 10.5061/dryad.k05qb/1
title: Supplemental Data 5

description: Reference tree. Topology revealed by the all-nrDNA matrix of concatenated sequences of ETS, ITS and matK. Branches with support below 50% bootstrap are collapsed.
DOI: 10.5061/dryad.k05qb/2
title: Supplemental Data 6

description: Query tree. Topology revealed by the all-sequences matrix constrained by the reference tree, using concatenated sequences of ETS, ITS and matK. Branches with support below 75% aLRT are collapsed.
DOI: 10.5061/dryad.ks53j/1
title: Plumage colour measurements for Dark-eyed juncos in the Selkirk Mountains

description: A combination of morphological and body condition data collected in the field, as well as LAB colour space data measured in Adobe Photoshop for head and dorsal regions.  Column heading abbreviations: FWS is the unique individual identifier; std.l, std.a, and std.b are the L*A*B* colour variables for a black standard colour chip included in each photo; head.l, head.a, head.b are the L*A*B* colour variables for the mantle; back.l, back.a, back.b are the L*A*B* colour variables for the dorsal region.
DOI: 10.5061/dryad.ks53j/2
title: Feather microstructure measurements for Dark-eyed junco in the Selkirk Mountains

description: A combination of body condition data and feather microstructure variables. Originally, all microstructure variables were measured twice on two separate feathers. After finding there was no difference between variables measured on separate feathers (P&gt;0.33), we pooled the variables within individual and the averaged values are depicted in this data set (i.e., one row per individual).  Column heading abbreviations: penn.length & plum.length are the linear measurements of the pennaceous and plumulaceous feather regions respectively; penn.barb is the number of pennacous barbs counted to measure density; penn.density.length is the length over which the barbs were counted; penn.density is penn.barb/penn.density.length; penn.barbules: this series is the same as the penn.barb columns but for barbule densities measured twice (on two separate barbs); barbule.length: measurements of individual barbule length from 5 randomly selected barbules on the section of the barb that barbule density was measured.
DOI: 10.5061/dryad.ks53j/3
title: Plumage reflectance data for Dark-eyed junco in the Selkirk Mountains

description: A combination of body condition data collected in the field and plumage reflectance data derived from the R package 'pavo' (Maia et al. 2013) which is based on Stoddard and Prum (2008)'s 'Tetracolourspace'. The data was generated using an average avian visual and achromatic cone system. Column heading abbreviations: u.p, s.p, m.p, l.p: proportion of ultra-violet, short wave, medium wave, and long wave reflectance, respectively; u.r, s.r, m.r, l.r: relative reflectance for each wavelength category; the remaining variables (x, y, z, h.theta, h.phi, r.vec, r.max, and r.achieved) were ultimately not used in the final analysis but serve to place individuals in a 3D Tetracolourspace and also allow calculation of variables such as brilliance and chroma which tend to be more important for carotenoid colours (see Stoddard and Prum 2008 for a more detailed description).
DOI: 10.5061/dryad.ms812/1
title: Laidre et al. glacier database

description: These data are the physical variables that describe the properties of each glacier front in NW Greenland, as used in Laidre et al. Biology Letters.
DOI: 10.5061/dryad.qj716/1
title: Hasenjager and Dugatkin 2016 Control Patch Diffusion Data

description: Provides the latency to first arrive at the control "patch" for each individual in each group. See main text for additional details.
DOI: 10.5061/dryad.qj716/2
title: Hasenjager and Dugatkin 2016 Food Patch Diffusion Data

description: Provides the latency to first arrive at the foraging patch for each individual in each group. See main text for additional details.
DOI: 10.5061/dryad.qj716/3
title: Hasenjager and Dugatkin 2016 Social Networks

description: Provides social networks for each group. Network links are weighted according to the frequency of distinct contact phases between each pair of individuals. See main text for additional details.
DOI: 10.5061/dryad.qj716/4
title: Hasenjager and Dugatkin 2016 Familiar Focal Follows

description: Focal follows were conducted on each fish in a group on three separate occasions. Focal follows lasted for four minutes, during which the nearest neighbor of the focal individual was recorded every ten seconds. An X indicates that no individuals were within four body lengths of the focal individual at that time.
DOI: 10.5061/dryad.qj716/5
title: Hasenjager and Dugatkin 2016 Mixed Focal Follows

description: Focal follows were conducted on each fish in a group on three separate occasions. Focal follows lasted for four minutes, during which the nearest neighbor of the focal individual was recorded every ten seconds. An X indicates that no individuals were within four body lengths of the focal individual at that time.
DOI: 10.5061/dryad.qj716/6
title: Hasenjager and Dugatkin 2016 Unfamiliar Focal Follows

description: Focal follows were conducted on each fish in a group on three separate occasions. Focal follows lasted for four minutes, during which the nearest neighbor of the focal individual was recorded every ten seconds. An X indicates that no individuals were within four body lengths of the focal individual at that time.
DOI: 10.5061/dryad.r8h3n/2
title: BF experiment

description: Turning points of homing ants walking in a channel set-up. The ants were blindfolded during carrying. Collected in the field in Tunisia.
DOI: 10.5061/dryad.rg22j/1
title: Additional_file_10
DOI: 10.5061/dryad.t2s33/1
title: File S1. Unrooted RAxML tree from REA data

description: File S1. This file contains the unrooted phylogeny estimated from the REA data using RAxML with outgroups excluded.
DOI: 10.5061/dryad.t2s33/2
title: File S2. PBW trees and output

description: File S2. This file contains the trees for all analyses of the PBW dataset, as well as the resulting PAUP* output. Individual files are described in the readme within the zip file.
DOI: 10.5061/dryad.t2s33/3
title: File S3. REA trees and output

description: File S3. This file contains the trees for all analyses of the REA dataset, as well as the resulting PAUP* output. Individual files are described in the readme within the zip file.
DOI: 10.5061/dryad.t8p51/1
title: Male - MI pair Associations for Within Period Analysis
DOI: 10.5061/dryad.t8p51/2
title: Male - MI pair Associations for Between Period Analysis
DOI: 10.5061/dryad.t8p51/3
title: Infant - Adult Male Dyadic Interaction Rates
DOI: 10.5061/dryad.1580p/1
title: Owen_et_al_mtDNA_nDNA

description: Nexus file that includes mtDNA and nDNA alignment with a partition block at the bottom of the file.
DOI: 10.5061/dryad.1580p/2
title: Owen_et_al_nDNAonly

description: Nexus file that contains only the nDNA alignment.  The file contains a partition block at the bottom of the file.