cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.j1t67/1
title: Immune Responses Saccostomus mearnsi

description: Immunity parameters from Saccostomus mearnsi collected in Kenya Long Term Exclosure Experiment. Eartag1/Eartag2 = unique eartags applied to each animal.  Species = species ID, always Saccostomus mearnsi (SAME).  Sex = sex (always male, M).  condition = reproductive status (always scrotal, S).  Weight = mass in g.  Number fleas = number of fleas on one side of the animal (data not used in analysis).  CPUE = catch per unit effort (trap success per plot and season).  Site = KLEE site used (North, South or Central represented by N, S, C; Exclosure = 0, Control = MWC).  Capture date = date animal captured.  Rainfall = Rainfall for the period preceding that trapping date.  Trapping period = the period in which that animal was trapped.  Neutrophil, Eosinophil, Basophil, Monocyte, Lymphocyte = number of cells of each type counted out of the "Total Count" column. Pre1_score = HA score prior to antigen exposure, Pre2_score = replicate of HA score prior to antigen exposure.  Post1_score = HA score post antigen exposure.  Post2_score = HA score post antigen exposure. Sheep = HA score for control (sheep). BKA1, BKA2, BKA3 = number of colonies present in BKA for three different plates.  pos1,pos2,pos3 = number of colonies from positive control (no blood) in BKA for three plates.
DOI: 10.5061/dryad.j81m5/1
title: Data file for condition-dependent expression of carotenoid- and melanin-based plumage colour of northern flicker nestlings revealed by manipulation of brood size

description: Excel document with three tabs.
DOI: 10.5061/dryad.kq230/1
title: RH2B in situ hybridization probe sequence
DOI: 10.5061/dryad.kq230/2
title: RH2Aα in situ hybridization probe sequence
DOI: 10.5061/dryad.kq230/3
title: LWS in situ hybridization probe sequence
DOI: 10.5061/dryad.kq230/4
title: Cichlid opsin expression plasticity qPCR data

description: Cone opsin expression levels determined by qPCR relative to GNAT2.
DOI: 10.5061/dryad.kq230/5
title: Microsatellite Genotypes

description: Microsatellite marker genotypes of sires, dams, and their offspring that were reared in the Red Inverted treatment and examined by fluorescent in situ hybridization. Letters represent genotypes (different lengths) of the specified microsatellite. Based on breeding groups we knew Sire 32 and Dam 33 contributed to one brood together and to no other broods, while the remaining sires and dams had the opportunity to breed in any combination.
DOI: 10.5061/dryad.kq230/6
title: Parentage Based on Microsatellites

description: Parentage of Red Inverted individuals examined by fluorescent in situ hybridization, based on microsatellite analysis. The Dam of RI7 could have been Dam 3 (believed to be the same individual as Dam 7) or Dam 5.
DOI: 10.5061/dryad.pb74r/1
title: Kamilar&Tecot-AppendixS1

description: Data used in analyses
DOI: 10.5061/dryad.pm37b/4
title: Call Frequency Raw Data

description: Raw data for female responses to the call frequency stimuli
DOI: 10.5061/dryad.pm37b/5
title: Call Duration Preference Function data

description: Descriptive measurements for female preference functions measured in response to the call duration stimuli
DOI: 10.5061/dryad.pm37b/6
title: Call Period Preference Function Data

description: Descriptive measurements for female preference functions measured in response to the call period stimuli
DOI: 10.5061/dryad.pm37b/7
title: Call Frequency Preference Function Data

description: Descriptive measurements for female preference functions measured in response to the call frequency stimuli
DOI: 10.5061/dryad.0m09h/1
title: Stimulus WAVE Files used in localization task

description: Stimuli consisted of bi-syllabic Children’s Spondees that have been previously used for studies on spatial unmasking of speech in children with NH [14], and with BiCIs[15], recorded with a male voice at a sampling rate of 44 kHz. The speech corpus had 25 words. On each trial one of the words was randomly chosen from the list, with replacement. Thus, on any given trial the stimulus was unpredictable, thereby reducing the availability of reliable spectral cues that might be used in the computation of sound source location. Stimuli were balanced for loudness using equal root-mean-square levels for all words. Stimuli were amplified and sent to the loudspeakers via Tucker Davis Technologies System III hardware. Stimulus levels averaged 60 dB SPL, with a random variation between 56 and 64 dB SPL (±4 dB) from trial to trial to minimize the availability of overall level cues.
DOI: 10.5061/dryad.0m09h/2
title: MatLab code used to calculate and plot Localization Sensitivity

description: Analyses of localization sensitivity employed a statistical non-parametric Kruskal-Wallis test to examine the relative independence of responses to each stimulus location, given a single response to an unknown stimulus. For each pair of locations in the loudspeaker array, the two response groups were analyzed using pairwise localization sensitivity index (LSI) values based on the z-scores from the p-value obtained bythe non-parametric Kruskal-Wallis test. The analysis produces a matrix of LSIs in coordinates of response locations. For N=15 target locations, the total number of LSI values was 105 [15*(15-1)/2=105]. The matrix is symmetrical about the diagonal. The matrixwas interpolated via the MATLAB contour function to find a contour of LSI with a z score of 1.65 (the 95th confidence level as the statistical threshold indicative of two locations being perceptually differentiated). We defined the contour of LSI = 1.65 as the sensitivity threshold. The overall localization sensitivity (LS) was characterized for individuals by averaging LSIs in the LSI matrix.
DOI: 10.5061/dryad.15jj2/1
title: tomita_database
DOI: 10.5061/dryad.23d0f/1
title: SF2 input files

description: Frequencies of European human SNPs and fixed differences (x=n) to chimpanzee that was used as input file for SweepFinder2. Original data from: Drmanac R, Sparks AB, Callow MJ et al. (2010) Human genome sequencing using unchained base reads on self-assembling DNA Nanoarrays. Science, 327, 78–81.
DOI: 10.5061/dryad.23d0f/2
title: Recombination rates

description: Sex-averaged pedigree-based human recombination rates from deCODE Genetics that was used as input file for SweepFinder2. Original data from: Kong A, Thorleifsson G, Gudbjartsson DF et al. (2010) Fine-scale recombination rate differences between sexes, populations and individuals. Nature, 467, 1099–1103.
DOI: 10.5061/dryad.23d0f/3
title: input_Bvalues

description: B-value map that was used as input file for SweepFinder2. Original data from: McVicker G, Gordon D, Davis C, Green P (2009) Widespread genomic signatures of natural selection in hominid evolution. PLoS Genet, 5, e1000471. Note that the positions correspond to the positions of the recombination rate and frequency files.
DOI: 10.5061/dryad.23d0f/4
title: Human-chimpanzee site frequency spectrum

description: Whole-genome site frequency spectrum (SFS) that includes the proportion of sites that are fixed to chimpanzee (x=n). This file was used as background SFS for SweepFinder2.
DOI: 10.5061/dryad.29gb5/1
title: Fox et al_Evidence of aggregative mating in a socially monogamous marine fish Siganus doliatus

description: Detection sequences recorded on acoustic receivers for 8 individuals of the species Siganus doliatus at Pioneer Bay, Orpheus Island, Australia
DOI: 10.5061/dryad.2q3qh/1
title: Simulated Data for COLONY analysis

description: This zipped file, SimuData.Zip, contains 5 folders, named as “Allele”, “Dup”, “Err”, “Loci”, “Robust”. Each folder contains a number of simulated input files for COLONY analysis, as described in detail in the ReadMe file.
DOI: 10.5061/dryad.2r732/1
title: A set of input tree dataset inferred using RaxMl overlapping on 443 prokaryotic genera taxon set.

description: This is a directory containing 5 input tree datasets in newick format. Prok_dataset: is composed of input trees overlapping on 443 prokaryotic genera taxon set. Prok_MinusRogue_dataset: The same as Prok dataset except the taxa that were identified as unstable by a concatabomination analysis have been pruned out. Eubac_dataset: Also a subset of Prok, this time with the archaebacterial taxon set pruned out. Eubac_MinusRogue_dataset: A subset of Eubac_dataset with the unstable taxa pruned out. Finally Arc_dataset: Another subset of Prok, this time with all the eubacterial taxon set pruned out.
DOI: 10.5061/dryad.2r76f/1
title: killer toxin mRNA, complete cds

description: 1. Saccharomyces cerevisiae M1 killer toxin mRNA, complete cds. 2.Saccharomyces paradoxus M1 killer toxin mRNA, complete cds 3. Saccharomyces paradoxus M28 killer toxin mRNA, complete cds
DOI: 10.5061/dryad.33ps4/1
title: iWiW_town_network

description: The data is stored in two csv files. 1. iWiW_town_nodes.csv includes characteristics of 2558 towns. The file is structured into 7 coloumns as follows: “id” – key to match node characteristics into edgelist.“town” – name of towns.“user” – number of registered iWiW users in the town.“pop” – number of inhabitants in the town.“latitude” – geo-coordinates (latitude) of the town.“longitude” – geo-coordinates (longitude) of the town.“code” – unique identifier of the town in databases of the Hungarian Statistical Office. This key can be used to match the data with further town characteristics.2. iWiW_town_edges.csv includes “id1” – identifier of town i, which can be used as a key to match node characteristics into edgelist.“id2” – identifier of town j, which can be used as a key to match node characteristics into edgelist. “connect” – the number of friendship ties between towns i and j.
DOI: 10.5061/dryad.373mg/1
title: Kumordzi et al. 2015_dataF
DOI: 10.5061/dryad.47jp0/1
title: HMcGregor et al_video collar data

description: Microsoft Excel spreadsheets, including details of the 23 video-collar deployments on cats and all hunting events witnessed on camera.
DOI: 10.5061/dryad.4hg2p/10
title: NP122-alignment

description: Aligned sequences of NP122 gene fragment from 293 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/11
title: NDHC_TRNV-alignment

description: Aligned sequences of NDHC_TRNV gene fragment from 306 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/12
title: TRNP_RPL33-alignment

description: Aligned sequences of TRNP_RPL33 gene fragment from 306 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/13
title: Structure_input_file
DOI: 10.5061/dryad.4hg2p/6
title: GBSS-alignment

description: Aligned sequences of GBSS gene fragment from 294 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/7
title: NP23-alignment

description: Aligned sequences of NP23 gene fragment from 294 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/8
title: NP39-alignment

description: Aligned sequences of NP39 gene fragment from 293 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.4hg2p/9
title: NP81-alignment

description: Aligned sequences of NP81 gene fragment from 293 individuals of Oryza nivara and O. rufipogon and two individuals of O.barthii used as outgroup.
DOI: 10.5061/dryad.50125/1
title: 454 raw sequences of the V4 region 16S rRNA gene from the spleens of 190 bank voles

description: This FASTA file contains 78,087 raw sequences produced using 454 GS-FLX pyrosequencing. The 190 multiplexed amplicons were tagged using both forward and reverse primers. The list of the 190 multiplexed samples and associated tags are provided in the following CSV file titled: Information concerning the samples multiplexed in the 454 run.
DOI: 10.5061/dryad.9b30b/1
title: Fitness_Assay_Data

description: Fitness data for evolved Sindbis virus populations. Fitness is measured as viral titer (pfu/mL) on each cell type (BHK and CHO). Each virus population was assayed in triplicate on each host type. The ancestral Sindbis virus used to found experimental Sindbis lineages was assayed nine times on each host.
DOI: 10.5061/dryad.bj042/1
title: PGENETICS_TEL1_ReCombine_data

description: Processed sequencing and microarray data from analysis of meiotic recombination in Saccharomyces cerevisiae. Genotypes analyzed are wild type, tel1, sgs1, zip3, msh4, tel1 zip3, and sgs1 zip3.
DOI: 10.5061/dryad.bj042/2
title: Simulation scripts

description: Python scripts used to simulate crossover and DSB interference in Figure 6B.
DOI: 10.5061/dryad.c3g80/10
title: B_pubescens_only_pairwise_geographical_distance

description: Geographical distances among B. pubescens populations used for Mantel test
DOI: 10.5061/dryad.c3g80/11
title: Betula_ssp_pop_marker_frq__1primer

description: AFLP marker frequencies per population based on the combined AFLP matrix . Used as inputfile for NJ-analyses among populations
DOI: 10.5061/dryad.c3g80/12
title: Betula_pubescens_and ref_pop_marker_frq__3primers

description: AFLP marker frequencies per population based on the original B pubescens AFLP matrix (3 primers). Used as inputfile for NJ-analyses among populations
DOI: 10.5061/dryad.c3g80/13
title: trnS_trnG_Alignment_58seq

description: Alignment file for trnS-trnG region based on plastid sequences used to generate haplotypes
DOI: 10.5061/dryad.c3g80/14
title: trnQ-rsp16_Alignment

description: Alignment of plastid sequences trmQ-rsp16
DOI: 10.5061/dryad.c3g80/7
title: Betula_pubescens_only_303_132_structure-input

description: Input file to the software program structure based on the aflp matrix only including populations of B. pubescens, 3 primers, 303 ind and 132 markers
DOI: 10.5061/dryad.c3g80/8
title: Betula_nana_only_structure-input

description: Input file to the software program STRUCTURE based on the AFLP matrix only including B.nana ind(528) and 115 markers, 3 primer combinations
DOI: 10.5061/dryad.c3g80/9
title: B_nana_only_pairwise_geographical_distance

description: Geographical distances among B. nana populations used for Mantel test
DOI: 10.5061/dryad.d4g4n/6
title: GIS file for CFP (SHP)

description: This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs.
DOI: 10.5061/dryad.d4g4n/7
title: GIS file for CFP (SHX)

description: This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs.
DOI: 10.5061/dryad.d4g4n/8
title: GIS file for CFP (SBX)

description: This file is part of a set of files describing the border of the California Floristic Province in western North America. When included in a directory with the other "CFP_GIS" files, the GIS layer is openable in most standard GIS programs.
DOI: 10.5061/dryad.fc40s/1
title: Fig1_Behavioral_Data

description: Accuracy data (%) related to Figure 1
DOI: 10.5061/dryad.fc40s/2
title: Fig2_Time_Frequency_Data_Control

description: Time-Frequency data of the control group, related to Figure 2
DOI: 10.5061/dryad.fn7gv/2
title: sequences_Hminckleyi&cyanoguttatus

description: Aligned sequences of mtDNA control region for individuals of H. minckleyi and H. Cyanoguttatus included in this study
DOI: 10.5061/dryad.nf27r/1
title: growth and development of final-instar Pieris napi larvae
DOI: 10.5061/dryad.s6764/1
title: Kamath et al_Yellowstone grizzly bear data

description: This data file contains genotypes and life history data  for Yellowstone grizzly bears (n=729) born between 1962 and 2010. Bears were genotyped at 20 microsatellite loci and associated life history parameters include sex, birth year, oldest known year, and death year.
DOI: 10.5061/dryad.s6764/2
title: Kamath et al_Yellowstone grizzly bear input files

description: Input files used to evaluate grizzly bear recent trends in diversity, generation interval and effective population size.
DOI: 10.5061/dryad.ts351/2
title: SNP FST file

description: This is the pairwise fst output for individual snps. The non-informative sites have been suppressed, so all the rows are the SNPs that meet the coverage criteria.the columns are:col1: scaffold numbercol2: SNP position on scaffoldcol3: number of snps in window (because the window size was set to 1 to get individual SNP estimates, all values should be 1)col4: fraction of the window covered (more relevant for sliding window analyses)col5: mean coverage at SNP over all four populationscol6: pairwise Fst for Tac-C:Tac-Scol7: pairwise Fst for Tac-C:Puy-Ccol8: pairwise Fst for Tac-C:Puy-Scol9: pairwise Fst for Tac-S:Puy-Ccol10: pairwise Fst for Tac-S:Puy-Scol11: pairwise Fst for Puy-C:Puy-Spopulation codes: 1=Tac-C, 2=Tac-S, 3=Puy-C, 4=Puy-SNote that the Fst values that are 0.000000000 are not polymorphic SNPs for a given pairwise comparison. For example, snp 'NW_006799939.1  19911'has an Fst of 0.00000000 in the Tac-C:Tac-S comparison because it is not polymorphic between Tac-C and Tac-S. From the sync file:NW_006799939.1  19911   A       21:0:0:0:0:0    21:0:0:0:0:0    39:0:0:2:0:0    37:0:0:5:0:0you can see that Tac-C and Tac-S are fixed for the A allele (21 counts in each). The only reason it is included as a SNP in the .fst file is because it is polymorphic in the Puy-C & Puy-S populations (and polmorhic in the comparison across Tac & Puy).
DOI: 10.5061/dryad.ts351/3
title: Fisher's exact test data

description: This is the fisher's exact test output for each SNP, in each pairwise comparison. The same SNP definition ws used as for the .fst output, so these are the FET results for the same snps included in the Fst output.The structure of the file is the same as for Tac-C_Tac-S_Puy-C_Puy-S.fst. Instead of Fst values, the numbers are -log10 P-values.
DOI: 10.5061/dryad.ts351/4
title: 1kb window FST

description: This file contains the output of the 1000bp sliding window Fst analysis. Structure of the output file is similar to Tac-C_Tac-S_Puy-C_Puy-S.fst:col1: reference contig (chromosome)col2: mean position of the sliding windowcol3: number of SNPs found in the window (not considering sites with a deletion)col4: fraction of the window which has a sufficient coverage (min. coverage &lt;= cov &lt;= max. coverage) in every population;col5: average minimum coverage in all populationscol6: 1:2 the pairwise Fst for population 1 and 2col7: 1:3 the pairwise Fst for population 1 and 3....
DOI: 10.5061/dryad.ts351/5
title: Puy-C Tajima's D

description: Tajima's D output for 1000bp windows for Puy-C. There is no option in the script to suppress the non-informative windows, so there are lots of windows with "na" that fail the coverage criteria so no calculation is made.
DOI: 10.5061/dryad.v4t80/1
title: JS Database

description: Estimates of selection on juvenile size traits, compiled by Njal Rollinson and Locke Rowe in September 2013. These data are are described as the "J-S Database" in the main text. Both the data included in our formal selection analyses as well as data omitted from formal analyses are included in this dataset.
DOI: 10.5061/dryad.v4t80/2
title: Genetic & Phenotypic Correlations

description: Genetic (rA) and phenotypic (rP) correlations between size and number of offspring collected from the literature.
DOI: 10.5061/dryad.11r1j/1
title: Individual Based Male Data from the Wild

description: Monthly individual guppy data on color, survival and reproductive success from the Upper and Lower La Laja introduction experiments. March 2008-2009.
DOI: 10.5061/dryad.11r1j/2
title: Common Garden F2 Male Data

description: Color data on F2 common garden males from ancestral (Guanapo HP) and derived (La Laja) populations one year after introduction.
DOI: 10.5061/dryad.43kf3/1
title: Relatedness_Populations

description: Relatedness data at the population level. It relates to Fig. 2 in the manuscript
DOI: 10.5061/dryad.43kf3/2
title: Relatedness_Individuals

description: Relatedness at the individual level. Relates to Fig 2 in the manuscript
DOI: 10.5061/dryad.43kf3/3
title: Virulence

description: Waxmoth virulence data. Relates to Fig 6 in the manuscript
DOI: 10.5061/dryad.43kf3/4
title: Signal_Interference

description: Signal interference data. Fig 5 in paper
DOI: 10.5061/dryad.43kf3/5
title: Relatedness_Responsiveness

description: SIgnal responsiveness data. Fig 4 in paper
DOI: 10.5061/dryad.43kf3/6
title: Relative_Fitness

description: Relative fitness data. Fig 4 in paper
DOI: 10.5061/dryad.50125/2
title: Information concerning the samples multiplexed in the 454 run

description: This CSV file contains the sample names, the forward and reverse tag sequences, the forward and reverse primer sequences, the gene name, the species name and the population name for each of the 190 samples multiplexed in the 454 pyrosequencing run.
DOI: 10.5061/dryad.50125/3
title: MiSeq raw sequences of the V4 region 16S rRNA gene from the spleens of 190 bank voles (part 1)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual using the MiSeq platform. The 190 multiplexed amplicons were indexed using both forward and reverse indexes. The list of the 190 multiplexed samples and associated indexes are provided in the following CSV file titled:  Information concerning the samples multiplexed in the MiSeq run.
DOI: 10.5061/dryad.50125/4
title: MiSeq raw sequences of the V4 region 16S rRNA gene from the spleens of 190 bank voles (part 2)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual using the MiSeq platform. The 190 multiplexed amplicons were indexed using both forward and reverse indexes. The list of the 190 multiplexed samples and associated indexes are provided in the following CSV file titled:  Information concerning the samples multiplexed in the MiSeq run.
DOI: 10.5061/dryad.50125/5
title: MiSeq raw sequences of the V4 region 16S rRNA gene from the spleens of 190 bank voles (part 3)

description: This ZIP file contains the FASTQ files of the paired-end reads (R1: reads 1; R2: reads 2) produced for each individual using the MiSeq platform. The 190 multiplexed amplicons were indexed using both forward and reverse indexes. The list of the 190 multiplexed samples and associated indexes are provided in the following CSV file titled:  Information concerning the samples multiplexed in the MiSeq run.
DOI: 10.5061/dryad.50125/6
title: Information concerning the samples multiplexed in the MiSeq run

description: This CSV file contains the sample names, the forward and reverse index names and the forward and reverse index sequences for each of the 190 samples multiplexed in the Illumina MiSeq run.
DOI: 10.5061/dryad.50125/7
title: Contigs of sequences of the HiSeq RNA sequencing from the spleens of 190 bank voles

description: This FASTA file contains 5,338 contigs of sequences produced using HiSeq2000 RNAseq sequencing. These contigs result from the de novo assembly of HiSeq reads. They were assigned to bacteria via successive sequence alignment using the non-redundant nucleotide and protein databases from NCBI and the BLAST algorithm.