cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5fh23/3
title: Data 2

description: Laboratory inoculation experiment data used for Figure 3
DOI: 10.5061/dryad.5fh23/4
title: Data 1

description: Laboratory inoculation experiment data used for Figure 2.
DOI: 10.5061/dryad.5fh23/5
title: Metadata

description: Metadata for all four datasets within this package.
DOI: 10.5061/dryad.6t3dn/1
title: genotype and phenotype information
DOI: 10.5061/dryad.6t3dn/2
title: female_pheno_info

description: Female Phenotype information. Column names: female_ID = female's ID, total_eggs_laid = number of eggs laid by a female, Pronotum_length_mm = female Pronotum length (mm), N_spdoses = number of spermatodoses found in a female
DOI: 10.5061/dryad.71425/11
title: WT14h_Final

description: Mean Cp values and Normalized Enrichment Ratio (Interaction frequencies) + standard deviation for WT yeast, time point 14h (late)
DOI: 10.5061/dryad.74mn5/10
title: Crotalus atrox

description: Crotalus atrox tree file
DOI: 10.5061/dryad.74mn5/11
title: Trimorphodon

description: Trimorphodon tree file from Beast
DOI: 10.5061/dryad.74mn5/12
title: Crotalus molossus

description: Crot molossus tree file from Beast
DOI: 10.5061/dryad.74mn5/13
title: Crotalus scutulatus

description: Crot scutulatus tree file from Beast
DOI: 10.5061/dryad.74mn5/14
title: masticophis flagellum

description: Mast. flagellum tree file from Beast
DOI: 10.5061/dryad.74mn5/7
title: lampropeltis getula

description: Lamp. getula tree from Beast
DOI: 10.5061/dryad.74mn5/8
title: Hypsiglena torquata

description: Hypsiglena torquata tree file from Beast
DOI: 10.5061/dryad.74mn5/9
title: thamnophis marcianus

description: thamnophis marcianus tree file from Beast
DOI: 10.5061/dryad.76p82/1
title: Pipefish PRR data

description: Data from Gotland 2012 (and some from the Swedish west coast 1987 for comparison), along with the statistical tests performed
DOI: 10.5061/dryad.7j21m/1
title: COPD in Oomuta Japan
DOI: 10.5061/dryad.8r8sj/1
title: Rito et al 2016_JEcol

description: Data were collected in the Caatinga vegetation of the Catimbau National Park, Pernambuco state, Brazil (8º24'00'' and 8º36'35'' S; 37º0'30'' and 37º1'40'' W). We sampled all shrubs and trees with diameter at soil height (DAS) ≥ 3 cm and total height ≥ 1 m. We measured the DAS and total height to calculate the stem density and total plant aboveground biomass per plot. Total aboveground biomass was calculated using an allometric equation for Caatinga vegetation (Biomass kg =0.173 DAS cm2.295) as proposed by Amorim, Sampaio & Araújo (2005), which is based on basal area and height.
DOI: 10.5061/dryad.9pf75/33
title: additional_samples/CrossModal_raw.hdf

description: Sample based data set for Cross Modal experiment
DOI: 10.5061/dryad.9pf75/34
title: additional_samples/CrossModal2_raw.hdf

description: Sample based data set for Cross Modal 2 experiment
DOI: 10.5061/dryad.9pf75/35
title: additional_samples/EEG_raw.hdf

description: Sample based data set for EEG experiment
DOI: 10.5061/dryad.9pf75/36
title: additional_samples/FaceDiscrimination_raw.hdf

description: Sample based data set for Face Discrimination experiment
DOI: 10.5061/dryad.9pf75/37
title: additional_samples/FaceLearning_raw.hdf

description: Sample based data set for Face Learning experiment
DOI: 10.5061/dryad.9pf75/38
title: additional_samples/Filtered_raw.hdf

description: Sample based data set for Filtered experiment
DOI: 10.5061/dryad.9pf75/39
title: additional_samples/Gap_raw.hdf

description: Sample based data set for Gap experiment
DOI: 10.5061/dryad.9pf75/40
title: additional_samples/Head_Fixed_raw.hdf

description: Sample based data set for Head Fixed experiment
DOI: 10.5061/dryad.bq124/1
title: TEMPUS AT ms_MasterData v022317
DOI: 10.5061/dryad.bq124/19
title: S1 Figure
DOI: 10.5061/dryad.cf6n0/1
title: CO2 traces for pupae 1 - 24

description: Zip file contains 24 individual files, one for each pupa in Figure 2 (pupal IDs 1 - 24). Data are parts per million CO2 in air, with flow rate 300 ml per minute (STP) and measurements made at room temperature (21 - 23 degrees C). Although original data were sampled at 1 Hz, here they are uploaded at 0.5 Hz so that we produce files of reasonable size. Recording durations were 24 or 48 hours.
DOI: 10.5061/dryad.cf6n0/2
title: Lactate concentrations in post-immersion pupae

description: Data used to construct Figure 5. An Excel file.
DOI: 10.5061/dryad.d1nm3/1
title: Koen_global_data

description: Average network closeness for 7 groups of female white-tailed deer in southern and central Illinois, USA. Data include proportion of forest, agriculture, and forest-agriculture edge (and the average current density obtained from program Circuitscape for each of those classes) for each study area. Notes in the column headings in the .xls data file describe each column.
DOI: 10.5061/dryad.d1nm3/2
title: Koen_local_data

description: Summarized data from GPS-collared female white-tailed deer in southern and central Illinois, USA. Data include, for each individual deer (by study area and season), social network characteristics (degree, average edge weight), home range overlap, and the proportion of forest, agriculture, and forest-agriculture edge (and the average current density obtained from program Circuitscape for each of those classes) within each home range (95% kernel density contour). Notes in the column headings in the .xls data file describe each column.
DOI: 10.5061/dryad.d28j8.2
title: Data from: Ecophysiological limits to aerobic metabolism in hypoxia determine epibenthic distributions and energy sequestration in the northeast Pacific ocean
DOI: 10.5061/dryad.g0n2d/42
title: Fig S9D
DOI: 10.5061/dryad.g0n2d/43
title: Fig S10A
DOI: 10.5061/dryad.g0n2d/44
title: Fig S10B
DOI: 10.5061/dryad.g0n2d/45
title: Fig S10C
DOI: 10.5061/dryad.g0n2d/46
title: Fig S11A
DOI: 10.5061/dryad.g0n2d/47
title: Fig S11B
DOI: 10.5061/dryad.g0n2d/48
title: Fig S13A
DOI: 10.5061/dryad.g0n2d/49
title: Fig S13B
DOI: 10.5061/dryad.g0n2d/50
title: Fig S13C
DOI: 10.5061/dryad.hq6c7/1
title: qPCR_data_MolEcol_Feb2017

description: The Bt density and TC009881 expression data as determined by qPCR
DOI: 10.5061/dryad.n95k3/1
title: Accession numbers for NCBI Short Read Archive

description: Table providing accession numbers for samples used in RNAseq analyses.
DOI: 10.5061/dryad.n95k3/2
title: Pedigree used in animal model analyses

description: Individual ID numbers with sire and dam ID numbers
DOI: 10.5061/dryad.n95k3/3
title: Size data for quantitative genetic analyses

description: Data used for animal model analyses of size and mass across 6 age classes
DOI: 10.5061/dryad.n95k3/4
title: Growth rates for quantitative genetic analyses

description: Rates of instantaneous growth in length and mass across 5 age intervals for use in animal model analyses
DOI: 10.5061/dryad.n95k3/5
title: Growth curve parameters for quantitatvie genetic analyses

description: Parameters estimated from Von Bertalanffy growth trajectories for use in animal model analyses
DOI: 10.5061/dryad.n95k3/6
title: ReadMe file explaining data in other files
DOI: 10.5061/dryad.n95k3/7
title: Normalized expression data for juveniles and subadults

description: Normalized counts per million for transcriptome comparisons of juvenile and subadult males and females
DOI: 10.5061/dryad.n95k3/8
title: Normalized expression data for juveniles with testosterone treatment

description: Normalized counts per million for transcriptome data from juvenile males and females with a control implant (blank) or a testosterone implant (T)
DOI: 10.5061/dryad.nk1b8/1
title: Individual behavior of injected animals

description: This file contains information on the number of nest boxes focals visited, the time spent inside those boxes and the number of times they passed through the entrance of the boxes. Data are provided for a night previous to injection (a.pre) and for the night of injection (b.inj). ID corresponds to the animal identification number, which is equivalent in the three datasets submitted here.
DOI: 10.5061/dryad.nk1b8/2
title: Focal animal ID, sex, injection treatment, date, mass and social group

description: This dataset contains information on the injection treatment received by the focal animals, the date of injection, mass at injection and social group. ID corresponds to the animal identification number, which is equivalent in the three datasets submitted here.
DOI: 10.5061/dryad.nk1b8/3
title: Encounter data

description: These dataset contains the nest box meetings of all animals during the nights of testing over the study period. "Box" corresponds to the box number (box ID) in which encounters took place. "IDA" corresponds to the ID of the animal that was inside the box first for a set of encounters. "sexA" and "sexB" correspond to the sex of animals with IDA or IDB, respectively. "IDB" corresponds to the ID of the animal that arrived inside the box after IDA for a set of encounters. "number_encounters" and "time_together" reflect the number of encounters and time spent together for IDA and IDB in that box. "date_obs" concerns the night during which the data were collected. IDA and IDB correspond to the animal identification number, which is equivalent in the three datasets submitted here.
DOI: 10.5061/dryad.nk1b8/4
title: InfectionModel

description: The R code exemplifies how to implement the simulation model used in our study. Further description in the code.
DOI: 10.5061/dryad.p6b5m/1
title: Cooperative antipredator behavior in the presence of a same-sex social partner

description: Excel file with the raw data for cooperative antipredator behavior of focal and partner fish (male-male and female-female pairs) interacting together in the presence of a predator. Each focal fish interacts twice each with two different social partners for a total of four behavioral trials. Fish from four pairs of high and low predation populations (Aripo, Guanapo, Lopinot, and Turure Rivers, Trinidad and Tobago) are represented.
DOI: 10.5061/dryad.rk07d/3
title: Measurement data

description: All direct measurement data used for statistical and ratio analysis.
DOI: 10.5061/dryad.rp13h/1
title: concatenated input to MrBayes

description: Nexus file used for Bayesian phylogeny of the concatenated dataset
DOI: 10.5061/dryad.rp13h/2
title: ITS input to MrBayes

description: ITS dataset prepared for MrBayes (in Nexus formate)
DOI: 10.5061/dryad.rq56t/1
title: data used in the manuscript and script to reproduce tables and figures.

description: The zip file contains three data sets used in the study. data.striders.complete.sihetal.csv provides the activity and mating activity of individuals at each observation. data.striders.mating.durations.sihetal.csv provides the durations, individual identities, and other data associated with each mating observed. data.striders.mating.frequencies.sihetal.csv provides information on the number of mating of each individual each day. Each data set is also associated with a text meta-data file describing the meaning of the variables and the structure of the data. The zip file also contains the R script used to produce tables and figures in the manuscript. See the read me file for more information.
DOI: 10.5061/dryad.s3vq7/1
title: Sukhum_Energeticcostsdata

description: This file contains all the raw data, including dissection weights, behavior videos, and EOD recordings, as well as all R code for analyses used in the paper.
DOI: 10.5061/dryad.s3vq7/2
title: Hypoxia Brevimyrus
DOI: 10.5061/dryad.s3vq7/3
title: Hypoxia_Brienomyrus
DOI: 10.5061/dryad.s3vq7/4
title: Hypoxia_Campys
DOI: 10.5061/dryad.s3vq7/5
title: Hypoxia_Gnathonemus
DOI: 10.5061/dryad.s3vq7/6
title: Hypoxia_Pollimyrus
DOI: 10.5061/dryad.s3vq7/7
title: README
DOI: 10.5061/dryad.01c3t/10
title: reproductive pfam

description: Pfam database matches annotation file for transcriptome (generated by dammit).
DOI: 10.5061/dryad.01c3t/11
title: reproductive rfam

description: Rfam database matches annotation file for transcriptome (generated by dammit).
DOI: 10.5061/dryad.01c3t/12
title: reproductive dammit

description: Complete annotation file for transcriptome, which includes annotations from all five searched databases generated by dammit.
DOI: 10.5061/dryad.01c3t/13
title: reproductive uniref

description: UniRef90 database matches annotation file for transcriptome (generated by dammit).
DOI: 10.5061/dryad.01c3t/14
title: epi.tpm.plus.ncRNA

description: Epididymis matches to the ncRNA Database.
DOI: 10.5061/dryad.01c3t/7
title: transdecoder.cds

description: Transdecoder .cds format output file for predicted protein coding regions for annotated transcriptome.
DOI: 10.5061/dryad.01c3t/8
title: transdecoder.bed

description: Transdecoder .bed format output file for predicted protein coding regions for annotated transcriptome.
DOI: 10.5061/dryad.01c3t/9
title: transdecoder.mRNA

description: Transdecoder .mRNA format output file for predicted protein coding regions for annotated transcriptome.
DOI: 10.5061/dryad.255hj/10
title: Watterson's θ for 10Kbp windows for six L. pustulata populations

description: Watterson's θ (θw) output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.
DOI: 10.5061/dryad.255hj/2
title: Allele coverage counts for differentially fixed SNPs

description: We provide here the Sync file of allele coverage counts for the 4,170 SNPs for six populations of Lasallia pustulata that were differentially fixed between the low (1 to 4) and high-altitude (6) population clusters. 

Used populations and abbreviations:
1 =&gt; Population 1, 176 m a.s.l.
2 =&gt; Population 2, 297 m a.s.l.
3 =&gt; Population 3, 588 m a.s.l.
4 =&gt; Population 4, 842 m a.s.l.
5 =&gt; Population 5, 1,125 m a.s.l.
6 =&gt; Population 6, 1,303 m a.s.l.

Output of the Sync file (for format specification see Kofler et al., PoPoolation2: identifying differentiation between populations using sequencing of pooled DNA samples (Pool-Seq). Bioinformatics 2011;27:3435-3436):

col1: scaffold number
col2: SNP position on scaffold
col3: reference character
col4: allele frequencies of population number 1
col5: allele frequencies of population number 2
coln: allele frequencies of population number n

The allele frequencies are in the format A:T:C:G:N:del, i.e: count of bases 'A', count of bases 'T', etc. , and deletion count in the end.
DOI: 10.5061/dryad.255hj/3
title: Aligned DNA sequences for six genetic markers

description: Aligned DNA sequences in fasta format for six genetic markers (linked to Additional file 3).
DOI: 10.5061/dryad.255hj/4
title: Annotated features for genic and promoter SNPs

description: Annotated features for genic and promoter SNPs in the Lasallia pustulata genome.
DOI: 10.5061/dryad.255hj/5
title: GO terms for 5,742 genes of Lasallia pustulata

description: The complete list of GO terms for 5,742 genes of the lichen-forming fungus Lasallia pustulata.
DOI: 10.5061/dryad.255hj/6
title: Lasallia pustulata genome annotation

description: Lasallia pustulata genome annotation file in GTF format.
DOI: 10.5061/dryad.255hj/7
title: Input for Migrate-N

description: Data input file for Migrate-N analysis.
DOI: 10.5061/dryad.255hj/8
title: π for 10Kbp windows for six L. pustulata populations

description: π output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.
DOI: 10.5061/dryad.255hj/9
title: Tajima's D for 10Kbp windows for six L. pustulata populations

description: Tajima's D output for 10Kbp windows for six populations of Lasallia pustulata along an elevational cline. "na" indicates windows that fail the coverage criteria.
DOI: 10.5061/dryad.2j420/1
title: Elevation

description: Raster (.tif) - Digital Surface Model of Port Lockroy on the Western Antarctic Peninsula. Created through Structure from Motion using Agisoft Photoscan. Projection EPSG: 3031 (Antarctic Stereographic).
DOI: 10.5061/dryad.2j420/2
title: Cost Distance Raster

description: Raster (.tif) - Cost weighted distance from water for Port Lockroy. Cost of movement through each cell is given by slope of that cell. Projection EPSG: 3031 (Antarctic Stereographic).
DOI: 10.5061/dryad.2j420/3
title: Flow Accumulation

description: Raster (.tif) - Flow accumulation for Port Lockroy generated from SfM derived elevation, using ArcGIS. Projection EPSG: 3031 (Antarctic Stereographic).
DOI: 10.5061/dryad.2j420/4
title: Flow Accumulation 4x scale

description: Raster (.tif) - Flow accumulation for Port Lockroy generated from SfM derived elevation, using ArcGIS at 4x scale. Projection EPSG: 3031 (Antarctic Stereographic).
DOI: 10.5061/dryad.2j420/5
title: Flow Accumulation 16x scale

description: Raster (.tif) - Flow accumulation for Port Lockroy generated from SfM derived elevation, using ArcGIS at 16x scale. Projection EPSG: 3031 (Antarctic Stereographic).
DOI: 10.5061/dryad.2j420/6
title: Nest Locations

description: CSV - Locations of Gentoo nests at Port Lockroy, Western Antarctic Peninsula. Positions are given in EPSG:3031  (Antarctic Stereographic).
DOI: 10.5061/dryad.31g05/1
title: breveGroupContextAnalyses

description: The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the breve species group (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
DOI: 10.5061/dryad.31g05/2
title: LionephaContextAnalyses

description: The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the genus Lionepha (Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
DOI: 10.5061/dryad.31g05/3
title: obscuripenneGroupContextAnalyses

description: The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in the obscuripenne species group (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
DOI: 10.5061/dryad.31g05/4
title: TrepanedorisContextAnalyses

description: The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in subgenus Trepanedoris (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
DOI: 10.5061/dryad.31g05/5
title: NotaphusContextAnalyses

description: The NEXUS file written for Mesquite which was used to assess accuracy of sequences obtained from Illumina sequencing of historical specimens in subgenus Notaphus (Bembidion, Carabidae) through phylogenic analysis alongside sequences from non-historical specimens. The file contains matricies for seven genes and the trees produced by the analyses.
DOI: 10.5061/dryad.31g05/6
title: DNA3890 de novo assembly

description: List of contigs generated from the de novo assembly in CLC Genomics Workbench
DOI: 10.5061/dryad.31g05/7
title: DNA3782 de novo assembly

description: List of contigs generated from the de novo assembly in CLC Genomics Workbench
DOI: 10.5061/dryad.31g05/8
title: DNA4233 de novo assembly

description: List of contigs generated from the de novo assembly in CLC Genomics Workbench
DOI: 10.5061/dryad.34hq1/1
title: Vázquez-Miranda et al. color data

description: raw color reads, residuals on date of collection, and PC scores
DOI: 10.5061/dryad.34hq1/2
title: LCTH_wCOOR_reduced

description: raw morphological data from Jay Sheppard
DOI: 10.5061/dryad.34hq1/4
title: ima data sets

description: IMA data sets
DOI: 10.5061/dryad.45q7h/1
title: Syngnathid brain size

description: The file consists of three parts. First, the data for brain mass and body length for 339 individuals across 23 species are presented. Then, head shape of 23 species as described with 12 homologous landmarks are presented in NTS format. Finally, a nexus format description of molecular-morphological phylogeny (see paper for details) is provided. Uses needs to separate these three parts of this file with appropriate file extensions (.txt, .NTS and .nex) to repeat the analyses presented in the paper. Questions will be answered by Masahito Tsuboi (masa.tsuboi@gmail.com).
DOI: 10.5061/dryad.6528d/1
title: Sweet_Burns_2017
DOI: 10.5061/dryad.74mn5/15
title: Salvadora hexalepis

description: Sal. hexalepis tree file from Beast
DOI: 10.5061/dryad.86309/1
title: Response to selection

description: Sheet 1: Raw data of survival and their phenotypic variance (standard deviation) for each population, sex, generation combination. Sheet 2: model fitted to test for response to selection, note that we nest generation in treatment.  Sheet 3: mean survival for each population and generation combination, Grand means for each treatment for each generation, as presented in Fig 1 and supplementary table 1.  "Parental" represent the survivial data of moscafut mass reared strain tested at F7 (not included on the model).
DOI: 10.5061/dryad.86309/2
title: Heritability

description: Sheet 1: Raw data of resistance, selection intensities and response to selection by sex.  Sheet 2: Final data based on a population level (mean intensity on population) and the estimated response for each selection event. Final variables are "selection cumulative" and "response cumulative". Note that response are corrected by mean control resistance on each generation. Sheet 3: Using the data on sheet 2 , we present the full model to asses the heritabilitty. Note that model are fixed to the origin (no selection have no response).
DOI: 10.5061/dryad.86309/3
title: Demography - life tables

description: Sheet 1: Raw data of demography (dialy survival and fecundity) for each population (C1-C5, D1-D5). Sheet 2-11: demography and estimated demography parameters for each population. Sheet 12 Mean of estimated parameters by treatment. Sheet 13-14: pool demography by treatment. Sheet 15 : Cumulative survival and reproduction by treatment as presented on figure 3.
DOI: 10.5061/dryad.86309/4
title: transition matrices

description: Sheet 1: transition matrices for each population. symbols: p= survival (transition) ; f= fecundity ;  C= control population; D= desiccation or selected population; 1-5= number of replica population. Note: see Rockwood 2006 to see details of construction of Px and Fx  from a life table. Life tables of each population are presented on a separated file. For LTRE analysis, mean transition matrices per treatment was used. See "popbio" library of R for details of LTRE analysis and lambda estimation.
DOI: 10.5061/dryad.86309/5
title: Size water and lipids

description: For the analysis of Size, water and lipids contain on selected and control treatments the raw data and the data for each population are presented. Sheet 1: Raw data for each fly, on desing we proyected 15 fly per sex of each population. Sheet 2: Data of each population by sex, was constructed using mean of individual values. Full factorial was used to analyzed the response to selection.
DOI: 10.5061/dryad.86309/6
title: Pupal stage duration

description: We present the duration of pupal stage, in hrs, of individuals flies for each population and replica. Sheet 1: Raw data of time to emerge of each fly. Sheet 2: parametric survival model of time to emerge and the estimated time were 50% of the flies had emerged from the pupa. Note that some factors are nested and data are presented per replica. Sheet 3: estimated mean time to emerge by replica, then, mean of replicas by population and, then, mean of populations to obtain treatment means.
DOI: 10.5061/dryad.86309/7
title: Sexual Competitiveness

description: Sheet1: we present the frequency of copulas per treatment for each of the 18 field cages. Sheet 2: Analysis : chi squared test for competitiveness between selected and control males.