cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.t03h0/1
title: Data for Taborsky, Guyer & Demus, J EvolBiol

description: There are three Excel Worksheets. Worksheet 'total length males females' gives the total lengths of undisturbed pairs measured in 2005 and 2006 under water in Lake Tanganyika (refers to the data used for supplementary Figure S3 if Taborsky et al., JEB). Worksheet 'total length & habitat quality' gives data of total length of males and females of 30 pairs and the stone cover present in the territories of these pairs (refers to analysis in section "Do larger fish occupy territories with more stone cover?" of the Results in Taborsky et al., JEB.Worksheet 'Habitat manipulation' gives the total lengths of original and final pairs and the stone cover data before and after manipulation of the habitat manipulation experiment (analysis in section "Does territory stone cover predict the size of settling fish?")
DOI: 10.5061/dryad.vr28vf67/1
title: Dataset

description: A database of diets of mammalian species was constructed from published accounts drawn from primary research with data obtained through analysis of stomach or cheek pouch contents or the contents of food stores, direct behavioral observation, or fecal analysis. Please see the ReadMe file for further details.
DOI: 10.5061/dryad.vr28vf67/2
title: References for dataset

description: This contains a list of every reference used to create the dataset.
DOI: 10.5061/dryad.0s96k/4
title: Data3_Matlab

description: Part 3 of sample data for the Matlab codes
DOI: 10.5061/dryad.12477/1
title: Data on individual biomass and root proliferation into nutrient patches

description: Aboveground biomass per individual and root proliferation into nutrient pathces at the moment of harvest.
DOI: 10.5061/dryad.1mh57/4
title: Aligned sequences of Internal Tanscribed Spacer (ITS2) from Altica (Coleoptera, Alticinae)
DOI: 10.5061/dryad.277g0/4
title: EcJME_R1-part2

description: This is part 2 of the forward raw reads from Illumina sequencing. Please download all three parts and recombine them using the following command in Terminal or Command Prompt: cat xaa xab xac &gt; EcJME_R1.fastqsanger
DOI: 10.5061/dryad.27d0g/2
title: trees

description: For each of the 473 families we inferred a gene topology G that maximizes the joint likelihood given by the product of the likelihood of observing the unrooted gene tree topology G according to the exODT model developed in the manuscript and the classic Felsenstein likelihood of the alignment. All trees are in Newick format.
DOI: 10.5061/dryad.2d5m8/1
title: Agglutination and lysis scores for all samples

description: These are the scores that MWB and ZRS calculated for each sample at all temperatures.
DOI: 10.5061/dryad.3b151/1
title: InjuryHealing_toDryad

description: Data are healing rates for injuries observed in wild baboons and metadata for each injury, including age, ordinal dominance rank, proportional dominance rank, whether the injury occurred in a wild or garbage-feeding group, season, and group size. Injury healing data are reflected in the days to heal or be censored and whether the record is censored. Censored records are injuries that failed to heal by the final observation. The injuries in this study were observed between 1982 and 2011. They were not clinical diagnoses; instead, observations were collected non-invasively by watching the animals at a distance of a few meters. Whenever a baboon displayed signs of injury (e.g., limping, bleeding from a wound), observers used an established protocol and data sheet to record the type of injury and whether it impaired the animal's locomotion. See manuscript for more details.
DOI: 10.5061/dryad.3b151/2
title: Female_MonthlyInjuryRisk_toDryad

description: Data are binomial incidences of injury for 18,256 female-months of observation. Data were collected from wild baboons in Amboseli National Park between 1982 and 2011. If a female was injured in a given month, the column 'injured?' records a 1, if no injury occurred, it lists a zero. Metadata are provided for each female-month, including the animal's identity, her age during the given year and month, her ordinal rank, her proportional rank, the season, whether her social group was fissioning, a log-transformed number of days she was present in the group, her reproductive state as cycling (C), pregnant (P), or lactating (L), and her group size. See manuscript for more information.
DOI: 10.5061/dryad.3b151/3
title: Periovulatory_DailyInjuryRisk_toDryad

description: Data are binomial incidences of injury for cycling female baboons on 179,001 female-days of observation. Data were collected from wild baboons in Amboseli National Park between 1982 and 2011. If a female was injured on a given day, the column 'injured?' lists a 1, if no injury occurred it lists a zero. Metadata are provided for each female-month, including the animal's identity, her age on that day, her ordinal rank, her proportional rank, the season, whether she was in the periovulatory phase, her group size, and the sex ratio in the group. See manuscript for more information.
DOI: 10.5061/dryad.3tc00/2
title: Input file for the analysis of chloroplastic trnC-pet1N sequences diversity of Afrostyrax lepidophyllus

description: List of individuals, geographical coordinates (decimal degrees), haplotypes and matrix of genetic distance between haplotypes.
DOI: 10.5061/dryad.3tc00/3
title: Input file for the analysis of chloroplastic trnC-pet1N sequences diversity of Erythrophleum suaveolens

description: List of individuals, geographical coordinates (decimal degrees), haplotypes and matrix of genetic distance between haplotypes.
DOI: 10.5061/dryad.3tc00/4
title: Input file for the analysis of chloroplastic trnC-pet1N sequences diversity of Greenwayodendron suaveolens subsp. suaveolens var. suaveolens

description: List of individuals, geographical coordinates (decimal degrees), haplotypes and matrix of genetic distance between haplotypes.
DOI: 10.5061/dryad.3tc00/5
title: Input file for the analysis of chloroplastic trnC-pet1N sequences diversity of Milicia excelsa

description: List of individuals, geographical coordinates (decimal degrees), haplotypes and matrix of genetic distance between haplotypes.
DOI: 10.5061/dryad.3tc00/6
title: Input file for the analysis of chloroplastic trnC-pet1N sequences diversity of Santiria trimera

description: List of individuals, geographical coordinates (decimal degrees), haplotypes and matrix of genetic distance between haplotypes.
DOI: 10.5061/dryad.3tc00/7
title: Input file for the analysis of chloroplastic trnC-pet1N sequences diversity of Scorodophloeus zenkeri

description: List of individuals, geographical coordinates (decimal degrees), haplotypes and matrix of genetic distance between haplotypes.
DOI: 10.5061/dryad.3tc00/8
title: Input file for the analysis of chloroplastic trnC-pet1N sequences diversity of Symphonia globulifera

description: List of individuals, geographical coordinates (decimal degrees), haplotypes and matrix of genetic distance between haplotypes.
DOI: 10.5061/dryad.4sd51d4b/1
title: Bik_etal_PLoSOne

description: "Dramatic shifts in benthic microbial eukaryote communities following the Deepwater Horizon oil spill" This Dryad data packet contains: Raw Data Files - Pooled from 3 independent 454 Runs (GS FLX Titanium; 2 full plates, plus one 1/16 plate). Clustered OTU data - Raw data was demultiplexed and quality filtered in both the QIIME and OCTUPUS pipelines, and subsequently clustered at 99% pairwise sequence identity (two independent clustering runs carried out in uclust in QIIME and the octu.pl script in OCTUPUS). Taxonomy assignments - carried out using the Megablast algorithm against GenBank's non-redundant nucleotide database in Summer 2011. Alpha and beta diversity analyses (raw outputs with log files) - carried out in the QIIME pipeline.
DOI: 10.5061/dryad.54722/3
title: Spigler_etalEVOL_DRYAD_FemaleGenotypes

description: Genotypic data for male sterile individuals (female and neuter individuals)
DOI: 10.5061/dryad.66h5g23t/2
title: Duenas-Decamp figure 3 data

description: Data set for figure 3
DOI: 10.5061/dryad.66h5g23t/3
title: Duenas-Decamp Additional figure 1 data

description: Data set for Additional figure 1
DOI: 10.5061/dryad.677v3/1
title: 1 Arlequin input file for DNA sequences Table S4
DOI: 10.5061/dryad.6kp30/4
title: gonadal size

description: Dataset used to analyze timing of gonadal cycle
DOI: 10.5061/dryad.842nm/1
title: Olfactory - auditory recognition in lemurs
DOI: 10.5061/dryad.9g40d/1
title: Copy of 10562_Stapleton_DataSheet1

description: Excel file containing phenotype measurements for each recombinant inbred line in each environment.
DOI: 10.5061/dryad.9r2h3/2
title: DIYABC_5POP

description: Data input file for DIYABC demographic modeling.
DOI: 10.5061/dryad.bc0v0/1
title: 33496_Ahyacinthus_CoralContigs.fasta

description: Contigs with putative Cnidarian origin from a de novo transcriptome assembly of Acropora hyacinthus. 16 individual A hyacinthus adult colonies were exposed to control and elevated thermal exposures, mRNA was isolated and sequenced using the Illumina GA IIX platform, assembled, and resulting contigs were screened against known cnidarian databases for strong matches to isolate sequences likely to be coral in origin.
DOI: 10.5061/dryad.c32m0/1
title: PPL_1406_sm_AppendixS1

description: Construction of simulations, results of comparison of GLMC and composite interval mapping; details of GLM mixed model for QTL detection, and comparison of QTL detected with in pilot and full experiment and by GLMC and QTLNetwork composite interval mapping.
DOI: 10.5061/dryad.cq737/2
title: Data_and_scripts

description: Data from Avida runs, along with analysis and plotting scripts.
DOI: 10.5061/dryad.d0md6/1
title: annotated genes_proteins

description: 16,571 genes were annotated in the golden eagle genome, this fasta file describes the protein sequences (see readme.pdf for more information).  Corresponding file archived in fortress is kmer70_min10000_scaffolds_revisedassembly.all.maker.proteins.
DOI: 10.5061/dryad.d0md6/2
title: annotated genes_transcripts

description: 16,571 genes were annotated in the golden eagle genome, this fasta files describes the transcripts (see readme.pdf for additional information).  Corresponding file archived in fortress is kmer70_min10000_scaffolds_revisedassembly.all.maker.transcripts.
DOI: 10.5061/dryad.d0md6/3
title: mitochondrial genome_GE_MITObim_revised

description: Golden eagle mitochondrial genome sequence assembled with MITObim vs. 1.6 and MIRA MIRA 3.4.1.1.
DOI: 10.5061/dryad.d0md6/4
title: xenobiotic sequences_Golden_Eagle_BLASTN_output

description: blastn (DiaGrid)Input Options  Query File: GoldenEagle sequences with no significant match (E&lt;10-6) to chicken genome  Database Selection: nt  Custom Database Format: N  Expectation Value: 1.0E-6  Word Size: 28Search and Result Restriction Options  Max Target Seqs: 1000Output Formatting Options  Format: 6  Custom Selection: qseqid sseqid qstart qend sstart send evalue bitscore pident length mismatch gapopen staxids sscinames scomnames sblastnames sskingdoms stitle
DOI: 10.5061/dryad.dd65d/16
title: Mouse activity data P2C2_2100
DOI: 10.5061/dryad.dd65d/19
title: Mouse activity data P1C1_2841
DOI: 10.5061/dryad.dd65d/24
title: Mouse activity data P1C1_2066
DOI: 10.5061/dryad.dh5qs/1
title: SNP_Hr_astringente

description: Fasta file with assembled sequences used for SNP mining
DOI: 10.5061/dryad.f058c/8
title: Pop5

description: Standard Flowgram Format (sff) file that contains NGS reads for 16S and Cyt b amplicons from population-pool 5. Individuals that belong to population-pool 5 are listed in Table 1.
DOI: 10.5061/dryad.gd856/5
title: Seed-Masses and Seed Counts of Pods

description: Data for the starting population of seeds for all populations (collected in the field at their sites along the gradient)
DOI: 10.5061/dryad.h3s0r/11
title: Individual simulations, 1 day after perturbation

description: This RData file contains a table of all the simulations, 1 day after the perturbation. The columns encompass all parameters (prefixed with "p_") and all variables (prefixed with "v_"). The odd-numbered rows record the state of the model prior to the perturbation, and the even-numbered rows record the state of the model after the perturbation.
DOI: 10.5061/dryad.h3s0r/12
title: Individual simulations, 1 week after perturbation

description: This RData file contains a table of all the simulations, 1 week after the perturbation. The columns encompass all parameters (prefixed with "p_") and all variables (prefixed with "v_"). The odd-numbered rows record the state of the model prior to the perturbation, and the even-numbered rows record the state of the model after the perturbation.
DOI: 10.5061/dryad.h3s0r/13
title: Individual simulations, 4 weeks after perturbation

description: This RData file contains a table of all the simulations, 4 weeks after the perturbation. The columns encompass all parameters (prefixed with "p_") and all variables (prefixed with "v_"). The odd-numbered rows record the state of the model prior to the perturbation, and the even-numbered rows record the state of the model after the perturbation.
DOI: 10.5061/dryad.j015n/15
title: fish-genetree-bootrep-results-from-cloudforest.tar.gz

description: Gene tree bootstrap replicates generated by CLOUDFOREST.
DOI: 10.5061/dryad.jh8j7/2
title: Raw Filter Coloration Measurements

description: The first tab of this data file contains the raw "eye dropper" values collected for each of 13 concentric circular grid points in the CMYK color mode. Each "area" measurement describes which of 13 grid points was measured. Data was collected from each of seven different individuals from five different groups. The second tab of this data file contains the raw triplicate and averaged measures of darkness for the same seven individuals from five different groups indicated above.
DOI: 10.5061/dryad.k7d00/5
title: remating day

description: Remating days in the P2 experiment. Column abbreviations: id = female id, trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25),line = the line male originated from, Fthorax = female thorax lentgh, M2thorax = 2nd male thorax lentgh, remday = remating day, copdur2 = duration of the second copulation
DOI: 10.5061/dryad.k7d00/6
title: single-mating-productivity

description: Offspring production during ten days after single mating. Column abbreviations: trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25), Maleth = male thorax lentgh, Femaleth = female thorax lentgh, Mfamoforig = Male line of origin (within treatment), progeny = number of eclosed offspring, fday = day as a factor
DOI: 10.5061/dryad.k7d00/7
title: spermcounts 60min after 2nd copulation started

description: Sperm counts in 60 min ASM treatment. Column abbreviations: ID = female id, trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25), Fthorax = female thorax lentgh, M2thorax = 2nd male thorax lentgh, bursagr = 1st male sperm in bursa, bursared = 2nd male sperm in bursa, prSRgr = 1st male sperm in proximal SR (seminal receptacle), prSRred = 2nd male sperm in proximal SR, distSRgr = 1st male sperm in distal SR, distSRgr = 2nd male sperm in distal SR, SPT1gr = 1st male sperm in spermatheca (SPT) 1, SPT1red = 2nd male sperm in spermatheca 1, SPT2gr = 1st male sperm in spermatheca 2, SPT2red = 2nd male sperm in spermatheca 2, duct1gr = 1st male sperm in spermathecal duct 1, duct1red = 2nd male sperm in spermathecal duct 1, duct2gr = 1st male sperm in spermathecal duct 2, duct2red = 2nd male sperm in spermathecal duct 2, SRtotred = 2nd male sperm in SR, TOTred = total number of 2nd male sperm, SPTtotred = total number of 2nd male sperm in SPT, STOREDred =total number of 2nd male sperm in SR and SPT, remday = remating day, copdur = copulation duration, totgr = total number of first male sperm
DOI: 10.5061/dryad.k7d00/8
title: sperm counts 5h after 2nd copulation started

description: Sperm counts from 5 h ASM treatment. Column abbreviations: ID = female id, trt = treatment: aob = outbred (f =0), ib = highly inbred (f = 0.5), sib = moderately inbred (f = 0.25), Fthorax = female thorax lentgh, M2thorax = 2nd male thorax lentgh, bursagr = 1st male sperm in bursa, bursared = 2nd male sperm in bursa, prSRgr = 1st male sperm in proximal SR (seminal receptacle), prSRred = 2nd male sperm in proximal SR, distSRgr = 1st male sperm in distal SR, distSRgr = 2nd male sperm in distal SR, SPT1gr = 1st male sperm in spermatheca (SPT) 1, SPT1red = 2nd male sperm in spermatheca 1, SPT2gr = 1st male sperm in spermatheca 2, SPT2red = 2nd male sperm in spermatheca 2, duct1gr = 1st male sperm in spermathecal duct 1, duct1red = 2nd male sperm in spermathecal duct 1, duct2gr = 1st male sperm in spermathecal duct 2, duct2red = 2nd male sperm in spermathecal duct 2, SRtotred = 2nd male sperm in SR, TOTred = total number of 2nd male sperm, SPTtotred = total number of 2nd male sperm in SPT, STOREDred =total number of 2nd male sperm in SR and SPT, remday = remating day, copdur = copulation duration, totgr = total number of first male sperm, S2SR = proportion of second male sperm in SR, asS2= acrsin sqrt transformed S2 value
DOI: 10.5061/dryad.kc6m8/3
title: BCMA heterologous expression
DOI: 10.5061/dryad.kc6m8/4
title: BCMA2 genotypes & linkage
DOI: 10.5061/dryad.kr62k/3
title: QG data positions

description: Quantitative genetic half-sib data for aphid positions on host plant as influenced by parasitoid wasp.
DOI: 10.5061/dryad.mg822/3
title: Egg data – Experiment 2

description: Average volume and number of eggs produced by Nicorphorus vespilloides females on mouse carcasses aged for seven days and on fresh carcasses, collected for Experiment 2 in the linked publication.  ‘History’ refers to the mother’s natal environment.  The weight of the female beetle (‘Mother_weight’) is also given.
DOI: 10.5061/dryad.mg822/4
title: Brood weight data – Experiment 3

description: Brood size and weight of cross-fostered Nicorphorus vespilloides broods, collected for Experiment 3 in the linked publication.  The foster mother prepared the mouse carcass and provided post-hatch care.  ‘Foster_mother history’ and ‘Genetic_mother history’ refer to the environment which the breeding females experienced as larvae.  The weights of the foster mother and of the mouse carcasses (which were fresh in all cases) are given.  The cross-fostered broods all consisted initially of 20 larvae (‘Start_number_larvae’).  Survival and brood weight were then recorded at 24 hours and at dispersal.
DOI: 10.5061/dryad.mn71g/1
title: Bulk Genotype Table

description: This file contains the allele counts (number of occurrences of an allele in a sequencing read) for each heterozygous site found in YJM311 from the YJM311 (parental), simple, intermediate, and complex se- quencing runs, and the G-statistic values at each of these sites for the pairwise comparisons between the simple, intermediate, and complex pools. Note that heterozygous sites where neither allele matched the reference sequence are very rare, so were excluded from these results. Each row in the file contains data on a single heterozygous site identified in YJM311. The coordinates are based on Saccharomyces Genome Database (SGD) release r62, (release date: February 18, 2009).
DOI: 10.5061/dryad.mn71g/2
title: Individual Segregant Phenotype and Genotype Table

description: This file compiles phenotype and genotype data collected on individual segregants from the Bulk Segregant Analysis. Each row in the file contains data on a single segregant.
DOI: 10.5061/dryad.ns341/6
title: f) Smith_Hendricks_SystBiol_pseudofossil_.tre files

description: The two tree files (generated in TNT using the matrix files available here) for the two pseudofossil analyses shown in Figure 4 (C. abbreviatus and C. flavidus).
DOI: 10.5061/dryad.p4356/2
title: Supp2_simulation_results

description: The complete raw data underlying all graphs and tables shown in the article. All data were produced using the simulation code that constitutes the other supplementary zip-archive.
DOI: 10.5061/dryad.q31f8/1
title: SampleID_list

description: List of individual samples with sampling locations and Genbank accession numbers for cytochrome-b and control region.
DOI: 10.5061/dryad.qq601/1
title: Damsel Data for Am Nat
DOI: 10.5061/dryad.rc628/6
title: Appendix 4 GHR 080612

description: Haplotype table nuclear DNA GHR sequences
DOI: 10.5061/dryad.rd240/1
title: 16SCimexlectualrius
DOI: 10.5061/dryad.t3cd2/1
title: DATA_JEB-2012-00203
DOI: 10.5061/dryad.t77nc/1
title: Partial compensation for siderophore cheating in Pseudomonas aeruginosa

description: Spreadsheet (.xls) containing raw lab data used to draw figures, Minitab & R output for key analyses and an extra figure to illustrate that a comparable effect to the one reported is shown in a different wild-type P. aeruginosa strain.
DOI: 10.5061/dryad.v8d05/1
title: R code for simulations

description: This .zip file contains R code and functions used for the landscape simulator in R and the source code for the implementation of FDIST2 in R.
DOI: 10.5061/dryad.vh36n/2
title: Fig1B

description: Microsoft excel file containing raw data for Fig1B.
DOI: 10.5061/dryad.vh36n/3
title: Fig3A

description: Microsoft excel file containing raw data for Fig3A.
DOI: 10.5061/dryad.0003s/1
title: Image Stack Movies_Pierce et al
DOI: 10.5061/dryad.0s96k/6
title: Data_C++

description: Sample data for the C++ codes
DOI: 10.5061/dryad.26530/4
title: Foth_Rauhut_CLUSTER-Topologies
DOI: 10.5061/dryad.309t3/1
title: auriniarawdata

description: The data file consists of microsatellite allele lengths for 9 loci described in the paper. The data file has individuals organized in rows, with the name of the population in the first column. The subsequent 18 columns correspond to microsatellite data (two columns per locus). Missing data are coded by zeros.
DOI: 10.5061/dryad.370nq/3
title: CMix
DOI: 10.5061/dryad.3ft19/1
title: Appendix1

description: Main algorithm
DOI: 10.5061/dryad.510sb/1
title: Cooper&Nunn_CountryParasiteSAC

description: This contains the data needed to plot parasite species accumulation curves for each country
DOI: 10.5061/dryad.54722/4
title: Spigler_etalEVOL_DRYAD_FemandHerm_MAPFILE

description: Maternal ("female") and paternal ("hermaphrodite") map files
DOI: 10.5061/dryad.5j129/1
title: Data_CoEvolutionary_Feedbacks

description: The folder contains all data simulated for the experimental set-ups described  in the article as well as the specific Java source code used for each set-up. Further a fully commented version of the source code is included.
DOI: 10.5061/dryad.7j564/1
title: ExecuteCode.R

description: ExecuteCode.R is the code used to run the model. Use this file to change parameters, run the model, and get outputs. It calls on PDDDModel_V2.R, SetupModel.R, and Functions.R. It produces various model outputs in a list and saves as an R object file, called output.Rdat, which can then be read back into R at a later date using the function ‘load’.
DOI: 10.5061/dryad.84gf5/1
title: Torres Dowdall et al. 11-0833 Standard Length data

description: Data use in the analysis of size at maturity.  Data correspond to size at maturity of lab-reared male guppies (Poecilia reticulata). Size was measured as standard length of the fish (length column). Drainage refer to the drainage from were wild fish used to generate second generation of lab-reared experimental fish were collected. Pred refers to the community from which the wild caught fish were collected. LP represent low predation risk, simple fish communities. HP refer to downstream complex communities where predation risk is higher. Family refers to the family lines used in the experiment. Cue refers to the two treatments used in our experiment. hp means that fish were reared in the presence of predator cues, lp means that they were raised in the absence of such cues. Only significant interactions between terms were kept in the final model.