cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t80gj/39
title: Supplemental File S18

description: SIFT prediction results for the missense-annotated heterozygous EMS-induced SNPs in all the 586 sequenced individuals.
DOI: 10.5061/dryad.t80gj/40
title: Supplemental File S19

description: Summary statistics for the sequencing, mapping, variants prediction, filtering, annotation and classification for the detected EMS-induced variants in all 586 sequenced individuals.
DOI: 10.5061/dryad.t80gj/41
title: Supplemental File S20

description: Detailed classification, gene function description and annotation of the medium or high impact homozygous EMS-induced SNPs.
DOI: 10.5061/dryad.t80gj/42
title: Supplemental File S21

description: Detailed classification, gene function description and annotation of the medium or high impact heterozygous EMS-induced SNPs.
DOI: 10.5061/dryad.t80gj/43
title: Supplemental File S22

description: Detailed classification, gene function description and annotation of the medium or high impact EMS-induced indels.
DOI: 10.5061/dryad.t80gj/44
title: Supplemental File S23

description: The detailed attributes of gene transcripts, including number of SNPs, GC-content, sequence length, mononucleotide and dinucleotide counts, which were used in the linear correlation analysis.
DOI: 10.5061/dryad.t80gj/45
title: Supplemental File S24

description: The subset of BLAST ungapped global alignments for the 51nt sequence contexts of the error-prone SNP positions, randomly selected EMS-induced SNP positions and randomly selected genome positions.
DOI: 10.5061/dryad.t80gj/46
title: Supplemental File S25

description: Sample scripts for the variants detection and annotation pipeline.
DOI: 10.5061/dryad.tq1f7/1
title: Caclulating the finmarchicus index for Fig3

description: Caclulating the finmarchicus index for Fig3
DOI: 10.5061/dryad.10qj1/1
title: breve.group.revision.10

description: The Mesquite file used to infer gene trees for the five genes analyzed in the study.
DOI: 10.5061/dryad.10qj1/2
title: Beauti.breve.STACEY.6.500M

description: Input file used in STACEY species delimitation analysis as implemented in BEAST (file in readable by BEAUTI under the STACEY template option).
DOI: 10.5061/dryad.10qj1/3
title: Bembidion_aeruginosum_DNA3890_rDNA

description: Reference sequence of the ribosomal DNA cistron taken from a de novo assembly of the sister taxon to the breve group, Bembidion aeruginosum. This reference sequence was used in the read mapping analyses to produce copy number profiles of the rDNA.
DOI: 10.5061/dryad.10qj1/4
title: ReadMapping.LIB0208.B.laxatum.DNA4918

description: A SAM file with the results of mapping shotgun sequencing reads (available on SRA) from Bembidion laxatum (Maddison voucher DNA4918) to a reference sequence (included in this submission) of B. aeruginosum.
DOI: 10.5061/dryad.10qj1/5
title: ReadMapping.LIB0248.B.laxatum.DNA4149

description: A SAM file with the results of mapping shotgun sequencing reads (available on SRA) from Bembidion laxatum (Maddison voucher DNA4149) to a reference sequence (included in this submission) of B. aeruginosum.
DOI: 10.5061/dryad.10qj1/6
title: ReadMapping.LIB0249.B.ampliatum.DNA4245

description: A SAM file with the results of mapping shotgun sequencing reads (available on SRA) from Bembidion ampliatum (Maddison voucher DNA4245) to a reference sequence (included in this submission) of B. aeruginosum.
DOI: 10.5061/dryad.1f7sk/1
title: time series data for mesocosm experiment
DOI: 10.5061/dryad.1f7sk/2
title: traits data
DOI: 10.5061/dryad.1f7sk/3
title: R script for linear and path models
DOI: 10.5061/dryad.364qh/1
title: Supplementary Data

description: Data matrices, trees and related files, assembled transcriptomes, translated transcriptomes, HaMStR output, script, and RCFV and LB data.
DOI: 10.5061/dryad.457fc/12
title: SAMDCpromoters align MEG
DOI: 10.5061/dryad.457fc/13
title: SAMDCpromoters align
DOI: 10.5061/dryad.457fc/14
title: SAMDC1Vs3.rtf - Copy
DOI: 10.5061/dryad.457fc/15
title: SAMDC1Vs4.rtf - Copy
DOI: 10.5061/dryad.457fc/16
title: SAMDC2Vs4.rtf - Copy
DOI: 10.5061/dryad.457fc/17
title: SAMDC3Vs5genes.rtf - Copy
DOI: 10.5061/dryad.457fc/18
title: SAMDCgenes 1Vs2.rtf - Copy
DOI: 10.5061/dryad.457fc/19
title: SAMDC1Vs2GATA
DOI: 10.5061/dryad.457fc/20
title: SAMDC1Vs3
DOI: 10.5061/dryad.63kb3/1
title: BatTents_Project
DOI: 10.5061/dryad.7d60f/1
title: Mathematica script for reproducing all data

description: A full, editable Mathematica notebook containing all of the analysis used to produce the data shown in the main text and Appendix B.
DOI: 10.5061/dryad.7fh30/1
title: Mansfield et al. Track_Data-for_Dryad

description: Metadata, turtle, and drifter track files combined in one excel file with three worksheet tabs (one each for metadata, turtle track files, and drifter track files).
DOI: 10.5061/dryad.7t7ff/1
title: Raw read counts, GC content, and Mean Gene Length

description: This file contains the raw HT-seq read counts generated from raw fastq sequence reads after alignment to the domestic cat genome. The first two columns include the mean GC content and mean gene length for all genes, which were used for filtering and normalization.
DOI: 10.5061/dryad.7t7ff/2
title: SupplementaryTable_S1

description: File includes summaries of data processing (sequence counts data), and metadata (technical and biological traits) for each bobcat.
DOI: 10.5061/dryad.7t7ff/3
title: SupplementaryTable_S3

description: File contains Gene Symbol, linear model coefficients and q-values, and WGCNA module assignments
DOI: 10.5061/dryad.961t3/1
title: Nigella_AFLP

description: See README file
DOI: 10.5061/dryad.9rd5f/1
title: Phenotypic data

description: Phenotypic data from common gardens in Vercors and Lautaret
DOI: 10.5061/dryad.b0733/1
title: cyno_matk_10Jan2017
DOI: 10.5061/dryad.b0733/2
title: cyno_trnL_intron10Jan2017
DOI: 10.5061/dryad.b0733/3
title: cyno_trnl_spacer_10Jan2017
DOI: 10.5061/dryad.fg12f/1
title: 600 Bayesian trees

description: Systematic sample of Bayesian trees. Every 1,000th post-burnin tree from the four runs was included, for a total of 600 trees.
DOI: 10.5061/dryad.fg12f/2
title: Volvocine tree, ultrametric

description: Volvocine phylogenetic tree, created from the phylogram using a penalized likelihood function.
DOI: 10.5061/dryad.fg12f/3
title: Volvocine tree, phylogram

description: Bayesian phylogram of volvocine and outgroup taxa.
DOI: 10.5061/dryad.fg12f/4
title: Chloroplast data matrix

description: Data matrix for volvocine chloroplast phylogenetic tree.
DOI: 10.5061/dryad.fp954/1
title: Dataset_Low rates of hybridisation

description: This file contains all necessary data from the manuscript.
DOI: 10.5061/dryad.h2r4r/1
title: Devkota_Perception Survey_Data Set

description: Primary data, collected in the field. Data analysed using SPSS and transferred to XL
DOI: 10.5061/dryad.n41j7/1
title: Martínez-Camilo et al._Data
DOI: 10.5061/dryad.pc1b6/1
title: Verhoeven et al._Generational shift_All seen marked adults

description: Data on adult staging site use
DOI: 10.5061/dryad.pc1b6/2
title: Verhoeven et al._Generational shift_Juvenile Data

description: Data on staging site use young
DOI: 10.5061/dryad.pc1b6/3
title: Verhoeven et al._Generational shift_Parent and Offspring

description: Data on parent-offspring pairs (table S2)
DOI: 10.5061/dryad.pc1b6/4
title: Verhoeven et al._Generational shift_Brood succes females

description: Data on brood success of females in the Haanmeer polder
DOI: 10.5061/dryad.pc1b6/5
title: Verhoeven et al._Generational shift_Brood succes males

description: Data on brood success of males in the Haanmeer polder
DOI: 10.5061/dryad.pc1b6/6
title: Verhoeven et al._Generational shift_FigS1_Extremadura

description: Data on proportion resighted in Spain (Figure S1A)
DOI: 10.5061/dryad.q3b45/1
title: Model Evaluation Metrics

description: Evaluation metrics for ecological niche models
DOI: 10.5061/dryad.q3b45/2
title: Pollen Functional Group Layers

description: GIS Layers of Pollen Functional Groups in North America
DOI: 10.5061/dryad.q3b45/3
title: WorldClim Layers

description: GIS Layers of WorldClim variables in North America, derived from data available at . For a description of how these data were derived, please see the methods section of Sanín C and Anderson RP (2018) A framework for simultaneous tests of abiotic, biotic, and historical drivers of species distributions: empirical tests for North American wood-warblers based on climate and pollen. The American Naturalist.

NOTE: For any use of WorldClim data, please cite the original publication: Hijmans, R.J., S.E. Cameron, J.L. Parra, P.G. Jones and A. Jarvis, 2005. Very high resolution interpolated climate surfaces for global land areas. International Journal of Climatology 25: 1965-1978. http://dx.doi.org/10.1002/joc.1276
DOI: 10.5061/dryad.q3b45/4
title: Background Cells

description: Species-specific set of background cells for Ecological Niche Models
DOI: 10.5061/dryad.q3b45/5
title: eBird Presence Cells

description: Set of cell for which eBird has records for a species. Dataset consulted:
eBird Basic Dataset. Version: EBD_relNov-2014. Cornell Lab of Ornithology, Ithaca, New York. November 2014.
DOI: 10.5061/dryad.q3b45/6
title: Sampling Effort

description: GIS layer of number of eBird sampling events in the study area
DOI: 10.5061/dryad.q3b45/7
title: Species Movement Area

description: GIS layers describing the 'movement' component of the distribution of each of the species.
DOI: 10.5061/dryad.r21pc/1
title: Snow_goose_behaviours

description: Spreadsheet of proportion time spent on six (6) observed behaviours in lesser snow geese
DOI: 10.5061/dryad.rf500/1
title: Alignments_allopolyploid_arborea

description: Alignments after allele phasing and RDP (Recombination detection program) testing. Alignments from majority consensus sequences.
DOI: 10.5061/dryad.rf500/2
title: Arborea_alleles_Alignments_before_RDP

description: Alignments after phasing. Original files.
DOI: 10.5061/dryad.s8045/1
title: Columbian ground squirrel oxidative stress data

description: Data collected from a 2016 field study on Columbian ground squirrels conducted by Viblanc, Dobson and collaborators.
DOI: 10.5061/dryad.sq67g/10
title: all_mutations_rel606_global_rank_new_ecoli_remove_ip_space.dat

description: Mutation effect prediction with the independent site model
DOI: 10.5061/dryad.sq67g/4
title: MAE_MutL_MutationList
DOI: 10.5061/dryad.sq67g/5
title: MAE_MutT_MutationList
DOI: 10.5061/dryad.sq67g/6
title: REL606_QuantitativeGenicData
DOI: 10.5061/dryad.sq67g/7
title: K12_QuantitativeGenicData
DOI: 10.5061/dryad.sq67g/8
title: all_mutations_k12_global_rank_new_ecoli_remove_ip_space.dat

description: Mutation effect prediction with the independent site model
DOI: 10.5061/dryad.sq67g/9
title: all_mutations_k12_global_rank_new_ecoli_remove_space.dat

description: Mutation effect prediction with the DCA model
DOI: 10.5061/dryad.tq1f7/2
title: Figure3

description: Data used in Fig. 3
DOI: 10.5061/dryad.tq1f7/3
title: Length_and_Recruitment_anomaly_data_Fig1_and_Fig2

description: Data used in Figure 1 and 2
DOI: 10.5061/dryad.vr20p/1
title: Latrine_Cameras

description: We monitored animal activity at Coal Oil Point Reserve in Santa Barbara County, California using wildlife camera traps. We set camera traps (Moultrie models: MFH-DGS-M80XT, MCG-12594, MCG-12631) at raccoon latrines and latrine-adjacent habitat to examine wildlife contact rates with raccoon latrines and exposure risk to the raccoon parasite, Baylisascaris procyonis. We mapped latrines and then monitored animal behavior at latrines and paired latrine-adjacent sites from December 2012 through April 2015. We identified vertebrate animals in camera trap photos and recorded when animals were in contact with or foraging in latrines. The “latrine cameras” data set includes three sheets with (1) set data for each camera deployment, (2) animal observations from each camera, and (3) latrine habitat surveys.  Field attributes for each sheet are described in the “Metadata ReadMe” file. Contact S. Weinstein for access to original camera trap photos.
DOI: 10.5061/dryad.10qj1/10
title: ReadMapping.LIB0182.B.lividulum.Lectotype.DNA4889

description: A SAM file with the results of mapping shotgun sequencing reads (available on SRA) from the electrotype of Bembidion lividulum Casey 1918 (Maddison voucher DNA4889) to a reference sequence (included in this submission) of B. aeruginosum.
DOI: 10.5061/dryad.10qj1/7
title: ReadMapping.LIB0250.B.ampliatum.DNA3593

description: A SAM file with the results of mapping shotgun sequencing reads (available on SRA) from Bembidion ampliatum (Maddison voucher DNA3593) to a reference sequence (included in this submission) of B. aeruginosum.
DOI: 10.5061/dryad.10qj1/8
title: ReadMapping.LIB0245.B.lividulum.DNA4165

description: A BAM file with the results of mapping shotgun sequencing reads (available on SRA) from Bembidion lividulum (Maddison voucher DNA4165) to a reference sequence (included in this submission) of B. aeruginosum.
DOI: 10.5061/dryad.10qj1/9
title: ReadMapping.LIB0245.B.lividulum.DNA5032

description: A BAM file with the results of mapping shotgun sequencing reads (available on SRA) from Bembidion lividulum (Maddison voucher DNA5032) to a reference sequence (included in this submission) of B. aeruginosum.
DOI: 10.5061/dryad.1tq09/1
title: Sinclair-Waters_et_al_MEC_2017_8581_SNPs

description: Genepop file containing SNP array data for 141 Atlantic Cod (Gadus morhua) genotyped at 8,581 loci. All SNPs are referred to by their database of Single Nucleotide Polymorphisms (dbSNP) accession numbers (http://www.ncbi.nlm.nih.gov/SNP). Geographic coordinates of sample collection sites can be found in Table 1 of the associated publication.
DOI: 10.5061/dryad.38776/1
title: all_market_shares

description: This file contains all the market shares for all cryptocurrencies market starting from April 28th 2013 until May 14th 2017
DOI: 10.5061/dryad.38776/2
title: market_cap_evolution

description: This file contains the whole market market capitalization aggregated over 15 weeks. The data spans the period from April 28th 2013 until May 14th 2017
DOI: 10.5061/dryad.38776/3
title: bitcoin_data

description: This file contains Bitcoin market capitalization from April 28th 2013 until May 14th 2017.
DOI: 10.5061/dryad.457fc/21
title: SAMDC1Vs4
DOI: 10.5061/dryad.457fc/22
title: SAMDC3Vs4
DOI: 10.5061/dryad.457fc/23
title: SAMDCGATA
DOI: 10.5061/dryad.457fc/24
title: SAMDCGATAREF
DOI: 10.5061/dryad.484tt/1
title: Landscape affects pest and crop yield

description: This file contains the abundance and incidence of insect pest, parasitoid-host ratios, plant damage, and crop yield in cabbage fields located across a gradient of landscape complexity in the Finger lakes region, NY, USA. This data is associated with the publication: Perez-Alvarez R., B. Nault, and K. Poveda. (2018).  “Contrasting effects of landscape composition on crop yield mediated by specialist herbivores”. Ecological Applications.
DOI: 10.5061/dryad.4d9s2/1
title: Redondo_etal.2017_functional_traits_Phytophthora

description: The excel file contains two sheets. In the sheet one, we provide the results of the baiting in the rivers. In the first four columns, we provide information about the sampling plot. In the next columns, we present the count data (number of isolates) for each of the species. In the second sheet, we provide the information of the survey in the nurseries, anthropogenic forests and natural forests. The first two columns correspond to the site and the type of environment. In the rest of the columns, we present the count data (number of individuals) for each of the species. In this second sheet of the file, we present the individuals and not the isolates because for the survey in nurseries and forests, all diversity calculations are based on individuals.
DOI: 10.5061/dryad.4ts31/1
title: HEED1
DOI: 10.5061/dryad.4ts31/2
title: CND-TCNQ1
DOI: 10.5061/dryad.4ts31/3
title: CND-TCNQ2
DOI: 10.5061/dryad.5709n/1
title: DryadData

description: Data used for analysis.
DOI: 10.5061/dryad.5p414/1
title: Bacterial ASV phylogeny

description: Phylogenetic tree of all bacterial ASVs (based on DADA2 generated ASVs). PASTA (doi:10.1089/cmb.2014.0156) was used to generate phylogeny.
DOI: 10.5061/dryad.5p414/2
title: Phylogeny of host plant species

description: Phylogenetic tree of host plant species. We downloaded accessions of 3 genes (2 plastid and 1 nuclear) for each of our plant species from GenBank: ribulose-bisphosphate carboxylase (rbcL); maturase K (matK); and internal transcribed spacer (ITS) adjacent to the 5.8S ribosomal RNA gene. We aligned sequences in MEGA v. 6.0 using MUSCLE with default parameters, followed by manually checking alignments. We used BEAST v. 2.1.3 to build a Bayesian phylogenetic tree. For each locus we implemented a standard general time-reversible model (GTR + I + Γ) and an uncorrelated lognormal clock (UCLN) to determine the rate of nucleotide change.
DOI: 10.5061/dryad.5p414/3
title: ASV taxonomic assignments

description: Taxonomy assignments of each ASV generated from DADA2 using the RDP training set and the RDP classifier (implemented in DADA2; See SI Appendix, Materials and Methods). Saved as an RDS file to be read into R.
DOI: 10.5061/dryad.5p414/4
title: Host plant phenotypic traits

description: The mean and standard error of phenotypic traits measured for each host plant species. AGB = aboveground biomass; BGB = belowground biomass; RL = root length; RA = root angle; WATER = leaf % water content; SLA = specific leaf area; RHD = root hair density; SRL = specific root length. See SI Appendix Materials and Methods for more detail.
DOI: 10.5061/dryad.5p414/5
title: ASV table

description: Count table for ASVs generated from DADA2 from raw MiSeq reads. Rows are individual samples and columns are individual ASVs. This table underlies nearly all analyses. Can be loaded into R using read.RDS(). Generate phyloseq() object using the meta data, bacterial phylogeny, and bacterial taxonomy provided here.
DOI: 10.5061/dryad.5p414/6
title: Sample metadata

description: Metadata associated with each individual sample. Community: E (endosphere); R (rhizosphere); S (bulk soil); RT (rhizosphere toothpick); ET (endosphere toothpick); MOCK (mock community); PAO (pure culture of Psuedomonas aeruginosa); WATER (negative control). Species: refers to the host plant species (see host plant trait data for key to species' codes); code 600 (bare soil); code 700 (toothpick); code ST (not analyzed in this experiment). Replicate: refers to experimental blocking ID. Run - refers to individual MiSeq sequencing run. Treatment - refers to watering treatment (well-watered or drought).
DOI: 10.5061/dryad.5p414/7
title: Host plant phenotypic distance

description: Matrix of phenotypic distance between host plant species. To create a metric of phenotypic distance we normally standardized species’ mean trait values and calculated the multi-trait Euclidean distance between species.
DOI: 10.5061/dryad.6fm52/1
title: dataset_hamilton_evapotranspiration

description: The file “dataset_hamilton_evapotranspiration.xlsx” contains data on the water balance of the Augusta Creek catchment over a 50-yr period (1965-2014); including changes in land use, precipitation, stream discharge, and evapotranspiration at both the catchment scale (by inference from water balance) and from specific land cover types (by soil water content).
DOI: 10.5061/dryad.7f140/1
title: Northwestern Medicine BMI data

description: Northwestern Medicine (NU) data are stored in NU.csv comma separated values (CSV) format. This file contains five columns: year t, BMI in year t, BMI in year t + 1, age in year t, and gender. Note: When BMI in year t + 1 is unavailable then the entry in the third column is -1.
DOI: 10.5061/dryad.7f140/4
title: BRFSS BMI data

description: BRFSS data are stored in BRFSS BMI.csv in CSV format. This file contains two columns: year t, BMI in year t.
DOI: 10.5061/dryad.7f140/5
title: Self Reported NHANES BMI data

description: Self-reported NHANES data are stored in NHANES SR.csv in CSV format. This file contains five colums: year t, BMI in year t − 1 (i.e. year prior to the interview), BMI in year t (i.e. at time of interview), age in year t, and gender. Note 1: We associate NHANES data from survey 1999-2000 with t = 1999, from survey 2001-2002 with t = 2001, and so on. Note 2: Because self-reported NHANES data are only used for individual-level computations, NHANES SR.csv only records data from respondents who reported both (a) BMI at time of NHANES interview and (b) BMI one year prior to NHANES interview.
DOI: 10.5061/dryad.8m54b/1
title: Mate choice data for Peromyscus leucopus and P. gossypinus.

description: Two-way mate choice data for Peromyscus leucopus and P. gossypinus using an electronically-gated choice apparatus.  Contains trials where the test mice were raised with their own parents, cross-fostered to parents of the other species, or cross-fostered to unrelated parents of the same species.
DOI: 10.5061/dryad.9rd5f/2
title: Environmental data (all years)

description: Environmental data averaged over each year
DOI: 10.5061/dryad.9rd5f/3
title: Environmental data (total averaged)

description: Environmental data averaged over all years
DOI: 10.5061/dryad.9rd5f/4
title: RAD haplotypes

description: Data corresponding to the RAD-tags ("RAD haplotypes" in the article)
DOI: 10.5061/dryad.9rd5f/5
title: SNP data from ddRADseq

description: SNP data from ddRADseq
DOI: 10.5061/dryad.9rd5f/6
title: Position of the loci in the genome

description: Position of the different loci (haplo: RAD haplotypes; snp: SNP) within the genome.
DOI: 10.5061/dryad.bn628/1
title: Data files (5) for Tree Skink social behaviour & attributes

description: Please note this data, as well as the accompanying R code, can also be found within a public Bitbucket (git) repository at this link: https://julia_riley@bitbucket.org/julia_riley/e.-striolata-social-behavior-study.git

The following files are provided in the compressed  folder:
1. Group Data_long.csv - contains data on social association over our six month observations,

2. Group Data_short.csv - contains data on social association over our six week observations,

3. Lizard_Attributes_long.csv - contains lizard attribute data for the six month observations (N = 27 lizards),

4. Lizard_Attributes_short.csv - contains lizard attribute data for the six week observations (N = 28 lizards), &

5. personality_data_NArm.csv - contains laboratory sociability data for analyses.
DOI: 10.5061/dryad.c0v5r/1
title: Escitalopram and NHT Normalized Stress-Induced Anhedonia and Molecular Neuroadaptations in a Mouse Model of Depression
DOI: 10.5061/dryad.dm8m5/1
title: Alberta_Wildfire_Final-1996-2002

description: This file contains attributes of different wildland fires that occured in Alberta, Canada between 1996 and 2002.
DOI: 10.5061/dryad.dm8m5/2
title: Script_R

description: This file contains the R script used for this analysis.
DOI: 10.5061/dryad.fg12f/5
title: Dataset S1

description: Continuous colony size metrics and discrete character states for mating systems and associated references for volvocine taxa. For heterothallic species, only one strain of a mating pair has been given.
DOI: 10.5061/dryad.hc4bj/1
title: Fig. S1
DOI: 10.5061/dryad.hc63s/1
title: Lymbery_et_al_Multivariate_Selection_Data

description: Raw data used in multivariate selection analyses. These data include: experimental block number, male ID, number of successes (competitive fertilizations), number of failures (total fertilizations in block minus number successfully fertilized by the male), proportion of successful fertilizations, flagellum beat cross frequency (BCF), curvilinear velocity (VCL), path linearity (LIN), percentage of motile sperm, mean sperm head length and mean sperm flagellum length.
DOI: 10.5061/dryad.hg736/1
title: Raw data_Strickland & Frere

description: Raw spatial data used for all analysis described in article entitled "Predictable males and unpredictable females: repeatability of sociability in eastern water dragons".