cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.0f1m0/1
title: Claidiere et al Supplementary data

description: Data used in the analysis of the results presented in the article. The dataset analysed in the article is provided as a comma separated value file (.csv) in which the following columns can be found. TransChain: indicates the number of replications of the experiment, 1 to 6. Generation: indicates the number of generations, 1 to 12. TrialOrder: for each block of 50 trials, gives the order in which each trial was done by the baboon (number 1 was the first trial, 2 the second, etc). TrialName: 1 for all the random trials, 1 to 50 for transmission trials. For transmission trials, the number is fixed for a lineage of grid for each replication of the experiment. TestingPhase: either random or transmission trials. Name: name of the individual. Sex: sex of the individual. AgeMonth: age in month at the time of the experiment. Square1 to 16: color of the square numbered by row from left to right and starting at the top left corner. Touch1 to 4: Number of the square touched by the individual for each trial in order (Touch1 was the first square touched, Touch2 the second one, etc). Takes values 1 to 16. RT1 to 4: cumulative reaction times in milliseconds for the four responses (RT1 is the reaction time for Touch1, RT2 for Touch2, etc).
DOI: 10.5061/dryad.cb58n/1
title: data inbreeding paper Tetranychus urticae

description: This Excel file contains the data of the two-part experiment on inbreeding depression and purging in Tetranychus urticae. The data of the two parts are presented in separate worksheets, labels are provided above the columns with comments explaining the labels.
DOI: 10.5061/dryad.jh5h4/1
title: kinematic_and_kinetic_data

description: .mat files
DOI: 10.5061/dryad.qf1dp/4
title: Testes derived transcripts

description: Putative transcripts from testes tissue.
DOI: 10.5061/dryad.qf1dp/5
title: Pfam results

description: These are the results from the Pfam search against Pero.BLTK.fasta
DOI: 10.5061/dryad.qf1dp/6
title: 4Tissue.transcripts

description: This file contains the putative transcripts from all tissues, and serves as the basis for most of the downstream analyses.
DOI: 10.5061/dryad.qf1dp/7
title: Transcript expression

description: This file contains the expression data for all transcripts in the Pero.BLTK.fasta file.
DOI: 10.5061/dryad.qf1dp/8
title: Coding sequences

description: This file contains the predicted coding sequences
DOI: 10.5061/dryad.qf1dp/9
title: Analysis code

description: This file contains code used in the bioinformatic analyses.
DOI: 10.5061/dryad.16pj3/1
title: Genotypes from Hyla arborea families

description: Genotypes from 43 microsatellite loci and 1 SNP locus (Fryl) in 12 Hyla arborea families originating from 4 populations. Each family consists of a mother, a father, and from 24 to 30 offspring. NA: missing data, 0: non-amplifying alleles.
DOI: 10.5061/dryad.76670/1
title: Supplemental Table 1: Haplotype of Isolates
DOI: 10.5061/dryad.76670/2
title: Supp_Table2

description: Supplemental Table 2: Average ODs of negative control wells and fraction of control wells with an OD &gt; 0.1 for each 96 well plate assessed.
DOI: 10.5061/dryad.76670/3
title: Supp_Table3: Model fitting: detailed models
DOI: 10.5061/dryad.jd1cq/1
title: mate_choice_experiment_data
DOI: 10.5061/dryad.mb437/1
title: worldwide data

description: microsatellite data from 18 locations worldwide
DOI: 10.5061/dryad.s9227/1
title: Deeming & Ruta data

description: Excel document with coordinates, semi-landmark analysis scores and eigenvalue analysis scores
DOI: 10.5061/dryad.vs7v6/1
title: DatasetsMariette&Griffith

description: daily data set of pair synchrony between day 6 and 14 and mean data set per pair over that period. variable names are as described in the paper. a refrence ID allows to link the two data sets.
DOI: 10.5061/dryad.4k5st/1
title: Figure5_CnidarianTreeNetwick

description: Bayesian genealogy of ten cnidarian species studied, based on partial COI sequences (approx. 700 bp) in Newick format.
DOI: 10.5061/dryad.4k5st/2
title: CnidarianProtein

description: Protein alignment in Nexus format for the COI phylogeny. Includes Mr. Bayes block.
DOI: 10.5061/dryad.4k5st/3
title: ScirokoResultsAllforDryad
DOI: 10.5061/dryad.76670/4
title: Supp_Table4

description: Supplemental Table 4: Coefficients for each haplotype-by-spatial distance interaction, the corresponding p-value and the significance level
DOI: 10.5061/dryad.qn474/2
title: Chaetodipus baileyi spleen transcriptome

description: Transcriptome assembly from combined assembly Illumina reads. These reads were assembled first in Trinity and then fragmented and assembled in gsAssembler (see methods of manuscript for more details and rationale)
DOI: 10.5061/dryad.qn474/3
title: Heteromys desmarestianus spleen transcriptome

description: Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
DOI: 10.5061/dryad.qn474/4
title: D_spec_spleen_top_blast_data

description: These are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads and 454 reads pooled from 4 individual Dipodomys spectabilis spleen libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e&lt;1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. if contig 2 from the gsAssembler asembly was smaller than 100 bp and removed prior to blast annotation then the first two contigs are contig 1 and contig 3).
DOI: 10.5061/dryad.qn474/5
title: Heteromys_desmarestianus_spleen_top_blast_data

description: These are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads and 454 reads pooled from 4 individual Heteromys desmarestianus spleen libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e&lt;1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. if contig 2 from the gsAssembler asembly was smaller than 100 bp and removed prior to blast annotation then the first two contigs are contig 1 and contig 3).
DOI: 10.5061/dryad.3f60c/1
title: Defining the alloreactive T cell repertoire using high-throughput sequencing of mixed lymphocyte reaction culture
DOI: 10.5061/dryad.3gq6t/1
title: Zinc supplementation inhibits complement activation in age-related macular degeneration

description: Collected as part of a clinical trial.
DOI: 10.5061/dryad.3hk2v/1
title: White_2014_HBolina
DOI: 10.5061/dryad.6f64b/1
title: Lanes et al 2014 Acrocomia aculeata genetic data

description: Excel file containing microsatellite genotypes of accessions A. aculeata. Genetic data of 6 microsatellite for 77 accessions A. aculeata obtained from the Macaw Palm Germoplasm Bank (Brazil). The locus names are listed in the first line. The accessions are identified by code of genebank listed in the first column of the file.  The genotypes of each accessions are from columns 2 to 13. The allelic description of each accessions was determined by informative numerical codes. Missing genetic data are coded as "0".
DOI: 10.5061/dryad.qn474/1
title: Dipodomys spectabilis spleen transcriptome

description: Combined assembly of 454 reads and fragmented Illumina assembly (see methods of associated paper) in gsAssembler version 2.6.
DOI: 10.5061/dryad.qn474/6
title: Chaetodipus_baileyi_spleen_top_blast_data

description: These are the preliminary blast descriptions for contigs from the combined assembly of Illumina reads pooled from 4 individual Chaetodipus baileyi spleen libraries. Descriptions are from a BLASTx search of the Swiss-Prot database at e&lt;1x10^-6. The combined assembly was conducted in gsAssembler version 2.6 and contigs that were smaller than 100 bp have been removed. This accounts for the gaps in contig names (e.g. contig 2 from the gsAssembler asembly was 25 bp long and removed prior to blast annotation so the first two contigs are contig 1 and contig 3).
DOI: 10.5061/dryad.qn474/7
title: COI_Guide_TREE_Marked_H_desm

description: This is the tree that was used in codeml as a guide tree for the branch and branch-site tests (see text of methods). The tree is unrooted to as is required for these tests. The tropical lineage, Heteromys desmarestianus has been marked with #1 to indicate it as the foreground branches to be assigned a different rate than the rest of the tree. D_spec = Dipodomys spectabilis, C_bail = Chaetodipus baileyi, H_desm = Heteromys desmarestianus, M_musc = Mus musculus.
DOI: 10.5061/dryad.qn474/8
title: perl_script_for_alignments

description: This is the perl script that was used to produce the multiple sequence alignments necessary for the paper associated with this data package.  The script has been uploaded as was used for the analysis and therefore would need to be adapted slightly for custom analyses (this script is designed to take four fasta files and then conduct an msa on a set of 4 sequences, one from each of the four files in order.  This could be adjusted to accomodate additional or fewer taxa.  The script is commented and questions should be directed to Nicholas Marra regarding it.  To replicate the analysis conducted for this paper, the inputs to the script should be four files from a reciprocal best blast analysis that have been trimmed to the start and stop codons of a full cds region.  Alignments from the script were further analyzed in codeml of PAML 4.7 to assess selection and alignments that were significant were then visually inspected.  See paper for details, note in the paper the 4th taxa was Mus musculus and was necessary for obtaining cds information.
DOI: 10.5061/dryad.qn474/9
title: Spleen_R_commands_dryad

description: This file contains the R commands that were used to run DESeq for the differential expression analysis described in this paper. The program DESeq was introduced in the following paper:  Simon Anders and Wolfgang Huber. Differential expression analysis for sequence count data. Genome Biology, 11:R106, 2010.   The commands and information about the function of these commands largely derive from the manual and documentation of this program written by Simon Anders that is available through the bioconductor page for DESeq.
DOI: 10.5061/dryad.v4h76/1
title: Aggression rate by swollen state data set

description: Contains dyadic aggression rates during female swollen and non-swollen periods, used to test whether dyadic aggression rates changed between female swollen and non-swollen periods.
DOI: 10.5061/dryad.74922/2
title: Drosophila gene trees

description: Data downloaded from TreeFam (http://www.treefam.org/) and processed to represent all  drosophila gene families, as well as the input gene tree distributions created from them.This file was compressed with tar using the XZ format, that is, must be uncompressed with e.g. "tar Jxvf filename.txz"When uncompressed it will contain a README file with more information.
DOI: 10.5061/dryad.74922/5
title: Simulation Scripts

description: Contains the python scripts used to simulate the replicate data sets, as well as the R scripts for recreating the manuscript and supplementary figures.This file was compressed with tar using the XZ format, that is, must be uncompressed with e.g. "tar Jxvf filename.txz"  When uncompressed it will contain a README file with more information.
DOI: 10.5061/dryad.74922/6
title: Supplementary Figures

description: Supplementary Figures mentioned in the text as SF1 to SF6, merged into one PDF file.
DOI: 10.5061/dryad.bt52f/1
title: Hierarchical Linear Model - Flight Initiation Distance

description: This file contains flight initiation distance dat from all of our study locations. These data were used to construct models of FID.
DOI: 10.5061/dryad.bt52f/2
title: Autotomy data

description: This file contains field autotomy and laboratory autotomy dat from all of our study sites. These data were used to construct models of both field and laboratory autotomy.
DOI: 10.5061/dryad.bt52f/3
title: Detection Distance - Flight Initiation Distance

description: This data file contains detection distance data for analysis of flight initiation distance.
DOI: 10.5061/dryad.bt52f/4
title: Field Autotomy Sex Data

description: This data file contains field autotomy sex data for all of our study locations where we collected field autotomy data.
DOI: 10.5061/dryad.hg7p0/6
title: Analysis_Tb VO2 DEE

description: Analysis of differences in body temperature and energy expenditure between solitarily and socially hibernating Cheirogaleus medius.
DOI: 10.5061/dryad.v4h76/2
title: Regression analysis data set

description: Data set used for regression analysis to determine factors predicting both dyadic copulation rates and paternity odds.
DOI: 10.5061/dryad.33mh2/1
title: Appendix A
DOI: 10.5061/dryad.hg7p0/1
title: arousal_frequency_all

description: Analysis of frequency of arousals of all analysed hibernating Cheirogaleus medius.
DOI: 10.5061/dryad.hg7p0/3
title: pair cohesiveness

description: Analysis on how often social pairs spend the daily resting phase or hibernation days together or in separate tree hollows.
DOI: 10.5061/dryad.hg7p0/4
title: arousal_frequency_social

description: Analysis of frequency of arousals during hibernation in socially hibernating Cheirogaleus medius.
DOI: 10.5061/dryad.hg7p0/5
title: group sizes

description: Group sizes of Cheirogaleus medius during hibernation.
DOI: 10.5061/dryad.sr687/1
title: Microsatellite data to estimate molecular population divergence in Calopteryx splendens (Figure 2)

description: Microsatellite data for “Sex differences in developmental plasticity and canalization shape population divergence in mate preferences”. BayesAss results (presented in Figure 2 in Svensson et al. (2014), as well as FST-analyses, Structure analyses and Microchecker analyses are based on these microsatellite data. The file contains genetic data from 133 individuals from seven study populations and one outgroup consisting of 90 individuals inhabiting populations along the River Loire, France. The genotypes of all damselflies were assayed at 13 microsatellite loci previously isolated for this species (see e.g. J. D. Austin et al., 2011, Mol. Ecol. Resour. 11, 757). Information on population ecology (sympatry or allopatry) is presented in Supporting Table 1 in the Supporting Material (Svensson et al. 2014).
DOI: 10.5061/dryad.sr687/2
title: Population divergence in female mate preferences of Calopteryx splendens (Figure 3A)

description: Data for C. splendens female population divergence in mate preferences in sympatric (S) and allopatric (A) populations, as shown in Fig. 3A (Svensson et al. 2014). Female mate preferences have been normalized by dividing by the average female response to conspecific C. splendens males (indicated by line at ‘1’ in Fig. 3A). For statistical tests, see legend to Fig. 3A in Svensson et al. (2014).
DOI: 10.5061/dryad.sr687/3
title: Population divergence in male mate preferences of Calopteryx splendens (Figure 3B)

description: Data for C. splendens male population divergence in mate preferences in sympatric (S) and allopatric (A) populations, as shown in Fig. 3B (Svensson et al. 2014). Male mate preferences have been normalized by dividing by the average male response to conspecific C. splendens females (indicated by line at ‘1’ in Fig. 3B). For statistical tests, see legend to Fig. 3B in Svensson et al. (2014).
DOI: 10.5061/dryad.71mh5/1
title: Evolution-BSO_sparrows-Dryad
DOI: 10.5061/dryad.rp8d0/1
title: Data from "Use of RAD sequencing for delimiting species"

description: This compressed folder contains three subfolders with data from the study "Use of RAD sequencing for delimiting species" by Pante et al. accepted for publication in the journal Heredity. Details are listed in the file named "README_Pante_etal_2014_Heredity.txt"
DOI: 10.5061/dryad.sr687/4
title: Sex differences in mate responses towards con- and heterospecifics in relation to population ecology (Figure 3C)

description: Raw data (C. splendens males and females in different populations) for mixed-model analysis testing for sex differences in mate preference responses in allopatric vs. sympatric environments (Fig. 3C and Table S2 in Svensson et al. 2014). R-code for the analysis (nlme-package) is provided in a separate Dryad data-file. We used the normalized mate preferences (rightmost column) as the response variable in the analysis and “Population identity” (here “Pop”) was a random factor.
DOI: 10.5061/dryad.sr687/5
title: R-code for mixed-model analysis of sex differences in mate responses (Figure 3C)

description: R-code using the nlme-package for the statistical test of sex differences illustrated in Figure 3C (Svensson et al. 2014). To compare male and female mate preferences in relation to local ecology we performed a mixed model with “Sex” (males and females) and “Population Ecology” (allopatry vs. sympatry) and their interaction (“Sex × Population Ecology”) as independent fixed factors, and “Population identity” as a random factor (nested within the fixed factor “Population Ecology”)(Table S2). By including “Population identity” as a random factor, we adjusted for the fact all our populations contributed with multiple individuals to the analysis and hence our data points (individual mate responses) are not entirely statistically independent.
DOI: 10.5061/dryad.sr687/6
title: Within-individual mate responses of sexually naive Calopteryx splendens males in relation to con- and heterospecific females (Figure 4A)

description: Raw data (male mate responses) of Fig. 4B in Svensson et al. (2014). Data are within-male mate responses of sexually naïve C. splendens males from Klingavälsåns Naturreservat in 2012 and 2013, in relation to female species presented (conspecific C. splendens females or heterospecific C. virgo females). The columns represent male mate responses in relation to conspecifics (first column) and heterospecifics (second column) in relation male ID (third column). A paired t-test shows that these sexually naïve C. splendens males show significantly stronger response towards conspecific females, unlike the situation for female mate responses (Fig. 4B). See legend to Fig. 4A in Svensson et al. (2014) for test-statistics.
DOI: 10.5061/dryad.sr687/7
title: Mate responses of sexually naive Calopteryx splendens females in relation to con- and heterospecific males (Figure 4B)

description: Raw data (female mate responses) of Fig. 4B in Svensson et al. (2014). Data are mate responses of sexually naïve C. splendens females from two populations (Klingavälsåns Naturreservat or Höje Å), in relation to male species presented (conspecific C. splendens males or heterospecific C. virgo males). There is a significant effect of female origin (population), but no effect of male species among these sexually naïve females (see legend to Fig. 4B in Svensson et al. 2014 for test-statistics).
DOI: 10.5061/dryad.sr687/8
title: Mate responses of sexually naive Calopteryx splendens males and females in relation to heterospecific mates (Figure 4C)

description: Raw data (sexually naïve male and female mate responses towards heterospecifics) of Fig. 4C in Svensson et al. (2014). Mate responses have been normalized by dividing by the average response towards conspecifics mates within each sex. Data are from Klingavälsåns Naturreservat only. For statistical test of the sex difference in mate responses, see legend to Fig. 4C in Svensson et al. (2014).
DOI: 10.5061/dryad.18kv7/1
title: Raberg_data

description: File contains raw data with densities of dinoflagellates and sporozoites over time (day 2-16) for each flask.
DOI: 10.5061/dryad.5q33h/1
title: Plant biomass

description: Aboveground plant biomass harvested at the end of the experiment in each herbivory treatment to quantify grasshopper impact on plant biomass
DOI: 10.5061/dryad.5q33h/2
title: Grasshopper feeding niche

description: Grasshopper herbivory per plant species was observed at the end of the experiment within each cage to quantify the realized feeding niche of the six grasshopper species. This files contains the mean herbivory observed over the five blocks per grasshopper and plant species.
DOI: 10.5061/dryad.5q33h/3
title: Plant traits

description: Mean trait values per plant species observed in the grasshopper experiment
DOI: 10.5061/dryad.5q33h/4
title: Grasshopper traits

description: Mean trait value per grasshopper species
DOI: 10.5061/dryad.90n5f/1
title: DSSheltonZebrafishDataJCP
DOI: 10.5061/dryad.q4432/1
title: Amino acid dataset

description: This is the amino acid dataset used to infer the phylogeny presented in Figure 1. It contains 15,549 positions and was assembled from 79 proteins encoded in the chloroplast genomes of 63 green algae. The data set is in Phylip format.
DOI: 10.5061/dryad.q4432/2
title: Degen1_nucleotide_dataset

description: This is the Degen1 nucleotide dataset used to infer the phylogeny presented in Figure 4. It contains 46,404 positions and was assembled from 79 chloroplast genes of 63 green algae. The data set is in Phylip format and comprises all three codon positions that were degenerated using the Degen1.pl script of Regier et al. (Nature 2010 463:1079-1083).
DOI: 10.5061/dryad.np2r5/1
title: Life history measurements

description: This is the full data set of all life history measurements (size, phenology, fecundity, survival) for individual pupae used in the experiments. Pupae that survived the winter and those that did not are included here. The second tab contains metadata explaining each column.
DOI: 10.5061/dryad.np2r5/2
title: Survival summary

description: This file summarises the survival of each nest (reproductive output of a single female) over winter in each environment. This summary comes from the life history data, and results from summing the total number of pupae from each nest assigned to each environment, and the resultant number of moths emerging as adults. We have removed all nests that were not represented in each environment, and all nests that had zero survival in both treatments. The nest identifications correspond to the life history data set.
DOI: 10.5061/dryad.np2r5/3
title: Physiology measurements

description: Body composition measurements for pupae at the beginning (November) and end (April) of winter. ID column corresponds to that in Life History file. Metadata tab explains each column. See manuscript for details of measurement.
DOI: 10.5061/dryad.np2r5/4
title: Respirometry data

description: Respirometry data measured using flow-through respirometric measurement of CO2 production, and calculated metabolic rates.
DOI: 10.5061/dryad.q4432/3
title: Codon_positions_1+2_dataset

description: This is the nt1+2 nucleotide dataset used to infer the phylogeny presented in Figure 4. It contains 30,936 positions and was assembled from 79 chloroplast genes of 63 green algae. The data set is in Phylip format and comprises only the first two positions of the codons.
DOI: 10.5061/dryad.ts56p/1
title: Raw Wing Data

description: This file contains the coordinates of each landmark from the wing. See Supplementary information/appendix in paper for the position of landmarks on the wing.
DOI: 10.5061/dryad.ts56p/2
title: Pigmentation Data

description: Contains the score between 0 and 10 given for each tergite.
DOI: 10.5061/dryad.79gk4/1
title: Metriocnemus knabi microsatellite data

description: 10 loci, GenalEx format
DOI: 10.5061/dryad.v8j20/1
title: Supplementary Data
DOI: 10.5061/dryad.9qd51/1
title: canidae_topology_MCCT

description: Maximum clade credibility tree from topology-only Bayesian analysis of canid morphological data
DOI: 10.5061/dryad.9qd51/2
title: canidae_dated_MCCT

description: Maximum clade credibility tree from Bayesian tip-dating analysis of canid morphological data. Branch lengths are in units of millions of years