cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.d0f3b/3
title: Benjamin single visit summary data

description: Summary data for single visits used to determine pollination service to blueberry flowers by different species groups. "Species Group" -- for details, see Benjamin, Reilly & Winfree (in press). Only pollen grains with tubes were included in this data set. Sample size refers only to the number of single visits used for each species group. Controls are not included.
DOI: 10.5061/dryad.ft612j0h.2
title: Data from: Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: the Latent Environmental Threshold Model
DOI: 10.5061/dryad.gg39253p/6
title: Santos_supermatrix_ML_tree
DOI: 10.5061/dryad.hd300/1
title: RatDemographics-ARLEQUIN

description: Genotype data from 146 trapped individuals formatted for Arlequin, with animals grouped by sampling site and year. "RatDemographics" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/2
title: RatDemographics-ARLEQUIN-PL8sep

description: Genotype data from 146 trapped individuals formatted for Arlequin, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/3
title: RatDemsPL8sep

description: Genotype data from 146 trapped individuals formatted for FSTAT, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/4
title: RatDemsPL8sep

description: Genotype data from 146 trapped individuals formatted for sex-biased dispersal tests in FSTAT, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/5
title: RatDemographics-GENECLASS-PL8sep

description: Genotype data from 146 trapped individuals formatted for Geneclass, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.kt3109v7/1
title: data
DOI: 10.5061/dryad.m3s84/1
title: softbots2013Config

description: HyperNEAT parameter file, HyperNEAT executable (usage: ./HyperNEAT -O [outputName] -I [parameterFileName] [optional: -R [random seed] -M [#ofMaterials] -P [penaltyType (key in parameter file)] -L [robotBoudingBoxLength]], Voxelize (usage: ./voxelyze -f [.vxa simulation file] [optional: -p (for print out during simulation)] - note: voxelize is not a GUI (VoxCAD is the GUI version, available online at www.voxcad.com - current for windows only)
DOI: 10.5061/dryad.m3s84/2
title: softbots2013Gen1000

description: Fully evolved creatures (at generation 1000).  Vxa files are to be imported as simulation into VoxCAD (available at voxcad.com) for viewing.
DOI: 10.5061/dryad.m3s84/3
title: softbots2013GenchampData

description: Txt data files describing the change over time for each evolutionary run.  Data is formatted into the following columns: (1) generation number, (2) original fitness of most fit individual, (3) penalty adjusted fitness of most fit individual, (4) original fitness of population average, (5) penalty adjusted fitness of population average
DOI: 10.5061/dryad.m3s84/4
title: softobts2013CodeREADME

description: Full source code for the project can be found at:http://jeffclune.com/codePublished/softbots2013Code.tgzSource code for voxelyze (non-GUI/library version of VoxCAD) can be found within: Voxel_Sim_noGui/VoxelyzeSource code for CPPN-NEAT can be found within: hyperneat/HperNEAT_v2_5/HyperNEAT/Hypercube_NEAT/src/Experiments/HCUBE_SoftbotsExperiment.cppUsages can be found in description of softobts2013Config.tgz
DOI: 10.5061/dryad.mm317th7/1
title: Accessible data spreadsheet

description: Microsatellite fragment lengths for 106 bobcats and GenBank accession numbers for two feline immunodeficiency virus gene fragments from 19 infected individuals.
DOI: 10.5061/dryad.q1v14ns0/1
title: BEAST file including sequence alignment, model parameters, and priors.
DOI: 10.5061/dryad.q1v14ns0/2
title: Morphologic matrix for 118 species and 30 variables (log-transformed morphometric data and square-root-transformed meristic data)
DOI: 10.5061/dryad.t5v58/2
title: genomes_beast_1

description: This file contains the consensus tree inferred on nuclear markers by BEAST with the topology fixed. External calibration only was used. Each time unit corresponds to 20 million years.
DOI: 10.5061/dryad.v1pr721v/1
title: matrix08REDUCEDBayes04

description: The combined molecular and morphological dataset analyzed using MrBayes.
DOI: 10.5061/dryad.v1pr721v/2
title: cynipoid_dating_all_calibrations

description: The molecular dataset analyzed using BEAST.
DOI: 10.5061/dryad.v5m8v/10
title: HOP_scores

description: Tab-delimited text file with MADL and z-scores for all approx. 1800 compounds tested in this study
DOI: 10.5061/dryad.v5m8v/7
title: HIP_scores-benomyl

description: Tab delimited text file with the data of all performed Benomyl experiments
DOI: 10.5061/dryad.v5m8v/8
title: HOP_scores-benomyl

description: Tab delimited text file with the data of all performed Benomyl experiments
DOI: 10.5061/dryad.v5m8v/9
title: HIP_scores

description: Tab-delimited text file with MADL and z-scores for all approx. 1800 compounds tested in this study
DOI: 10.5061/dryad.vq542/1
title: Recruitment in relation to paternal coloration

description: Father ID: identity of the father; Mother ID: identity of the mother; Year when experiment carried out; Treatment = brood size treatment; Father and mother color: from 5 (light melanic) to 1 (dark melanic); Mass Fledgling: mean body mass of fledglings; Nb recruits: number of fledglings that were recruited in the local breeding population
DOI: 10.5061/dryad.vq542/3
title: Tawny owl color-specific reproductive success Year1

description: Male ring: identity of the breeding male; Year: year when experiment carried out; Nb Fledglings: number of fledglings; Father and mother color: from 1 (dark melanic) to 5 (light melanic); Hatch date: hatching date in number of days to 1st January; BroodSizebefore: number of nestlings before treatment was applied; Treatment: brood size manipulation experiment
DOI: 10.5061/dryad.vq542/4
title: Tawny owl color-specific survival

description: Ring: identity of the breeding individual; Year: year when captured; Brood ID: identity of the nest where the individual bred; Treatment: Enlarged is for when we added nestlings to the brood, Reduced when we removed nestlings, N when no treatment was applied and absence of code is for non-breeding individuals; Coloration: between 1 (dark melanic) to 5 (light melanic); sex: sex of the individual
DOI: 10.5061/dryad.vq542/5
title: Reproductive success after having applied brood size manipulation experiment in two successive years

description: Male Ring: Identity of the breeding male; Year X2: second year of brood size manipulation experiment; N_Fledglings X2: number of fledglings in the second year; Hatch date X2: hatching date in the second year (number of days after 1st January); Treatment X1: brood size manipulation in the first year; Treatment X2: brood size manipulation in the second year; Class Treatment: 1 (reduced-reduced), 2 (enlarged-reduced), 3 (reduced-enlarge), 4 (enlarged-enlarged); Father color: color of the father (1 for dark melanic to 5 for light melanic)
DOI: 10.5061/dryad.vq542/6
title: Tawny owl Color-specific offspring body mass

description: Fledging Body Mass: mass at fledging (g); Year: Year when the experiment was performed; BroodID: identity of the nest where fledglings were raised; Hour: time of the day when weighed; Wing: wing length (mm); Sex: sex of the fledgling; Cross fostered: No is for when fledglings were raised by their biological parents and Yes is for when fledglings were raised by foster parents; Father and mother color: 1 for dark melanic to 5 for light melanic; Treatment: brood size manipulation experiment
DOI: 10.5061/dryad.100jc764/5
title: Supp Fig 3

description: Consensus tree from Bayesian analysis of the MUSK intron alone.
DOI: 10.5061/dryad.100jc764/6
title: Supp Fig 4

description: Consensus tree from Bayesian analysis of the Fibrinogen 5 intron alone.
DOI: 10.5061/dryad.100jc764/7
title: Supp Fig 5

description: Consensus tree from Bayesian analysis of the TGF5 intron alone.
DOI: 10.5061/dryad.30320/1
title: ThompsonHurdCrespi-SNPdata

description: Data for the three SNPs
DOI: 10.5061/dryad.3b87j/1
title: Fossil Mammal Occurrences and Localities

description: PBDB and NOW locality numbers by substages; mammal species by locality numbers.
DOI: 10.5061/dryad.3b87j/2
title: PaleoDB Refs
DOI: 10.5061/dryad.3b87j/3
title: Sampling Rate Variation OSX 0

description: Program for assessing distributions of per-collection sampling rates.
DOI: 10.5061/dryad.3b8k6/1
title: GDSseagrasses

description: Excel file containing Cymodocea nodosa (first sheet) and Posidonia oceanica (second sheet) datasets. First colums contain location identifiers (see Alberto et al., 2008 and Arnaud-Haond et al., 2007 for correspondencies), locus names are indicated in the first lines (see Albert et al., 2003 a&b) and genotypes matrix are filled without missing data and with 3digits per allele coprresponding to thei length on chromatograms. Full references are cited in the article
DOI: 10.5061/dryad.3t3n7/10
title: Compare mapping assemblies - Mapping 1

description: The quality of the mapping assemblies obtained after the consensus step is be evaluated.
DOI: 10.5061/dryad.3t3n7/11
title: Compare mapping assemblies - Mapping 2

description: The quality of the mapping assemblies obtained after the consensus step is be evaluated.
DOI: 10.5061/dryad.3t3n7/12
title: Differential expression analysis - baySeq

description: Differential expression analysis across the 2x10 libraries is performed using the Bioconductor package baySeq.
DOI: 10.5061/dryad.3t3n7/13
title: Differential expression analysis - edgeR

description: Differential expression analysis across the 2x10 libraries is performed using the Bioconductor packages edgeR
DOI: 10.5061/dryad.3t3n7/14
title: Evaluation of differential expression analysis

description: This script performs some evaluation of the output from the differential expression analyses, e.g. it generates FPR's and TPR's.
DOI: 10.5061/dryad.3t3n7/15
title: Create data for zebra finch.

description: Steps 1 and 2 are accomplished by running 1_2_create_datasets.sh for the zebra finch dataset.
DOI: 10.5061/dryad.3t3n7/16
title: ZebraFinchData

description: Zebra finch CDS downloaded from Biomart (Ensembl Version 61) with 100 bp 5' UTR and 400 bp 3' UTR per gene.
DOI: 10.5061/dryad.3t3n7/17
title: Distributions

description: Simuated read distributions per expression category.
DOI: 10.5061/dryad.3t3n7/8
title: Compare de novo assemblies

description: The quality of de novo assemblies can be evaluated using the scripts available on the GAGA website when alternative splicing is not being simulated. Step 5 consists of 7 sub-steps, each with its own script.
DOI: 10.5061/dryad.3t3n7/9
title: Compare de novo assemblies - Steps 1 to 7
DOI: 10.5061/dryad.42sh717m/1
title: DRYAD-microsat data
DOI: 10.5061/dryad.4dp71437/1
title: dataFig1a

description: Average equilibrium percentage of sexual females in dependence of maximum consumption rate epsilon (simulated electronically), here no migration is allowed, i.e., migration rate eta=0
DOI: 10.5061/dryad.4dp71437/2
title: dataFig1b

description: Average equilibrium percentage of sexual females in dependence of intrinsic growth rate of resources G (simulated electronically), here no migration is allowed, i.e., migration rate eta=0
DOI: 10.5061/dryad.4dp71437/3
title: dataFig1c

description: Average equilibrium percentage of sexual females in dependence of mortality strength 1/n (simulated electronically), here no migration is allowed, i.e., migration rate eta=0
DOI: 10.5061/dryad.4dp71437/4
title: dataFig1d

description: Average equilibrium percentage of sexual females in dependence of resource diversity L (simulated electronically), here no migration is allowed, i.e., migration rate eta=0
DOI: 10.5061/dryad.6gr7t/34
title: Car_mel_intragenomic_SNP_indel_variation_from_1200bp+_contigs.filtered

description: Variant call format (VCF) file containing potential single nucleotide polymorphisms (SNPs) and indels variation extracted from nucleotide contigs &gt;=1,200 bp assembled from 133,681,136 100 bp pair end (PE) reads from an Illumina HiSeq 2000 using Ray v2.0.0 for Caranx melampygus. The following filters were applied with the program vcf-annotate: –f +/c3,10/Q=20/d=15/D=25. This file contains ONLY SNPs and indels that DID pass filtering.
DOI: 10.5061/dryad.7f327q53/2
title: Chronogram Tree file 1

description: Chronogram, UCLD_exp0.01, gamma_root, medianheight
DOI: 10.5061/dryad.7f327q53/3
title: Chronogram Tree file 2

description: Chronogram, UCLD_exp0.01, uniform_root, medianheight, mrc tree file
DOI: 10.5061/dryad.7f327q53/4
title: gekko_final.ucld.gamma100_exp0.01.clocktree.runs1234.medianh.mrc

description: Chronogram, UCLD_gamma100_exp0.01, medianheight, mrc tree file
DOI: 10.5061/dryad.7f327q53/5
title: MrBayes Consensus Tree

description: Consensus Tree from Bayesian analysis in MrBayes
DOI: 10.5061/dryad.7f327q53/6
title: RAxML Consensus Tree

description: 50% majority rule consensus tree from RAxML ML analysis
DOI: 10.5061/dryad.7f327q53/7
title: GARLI ML Tree

description: ML tree from Garli analysis
DOI: 10.5061/dryad.7f327q53/8
title: Garli ML Bootstrap Tree

description: 50% majority rule consensus tree from Garli analysis
DOI: 10.5061/dryad.7rm34/1
title: Assembly Files

description: These files correspond to the assemblies described in the manuscript.
DOI: 10.5061/dryad.8311n/1
title: A software for mapping QTL of seed traits

description: This software was developed by Qi, Tiang and Xu, Haiming, which could be used to mapping QTL of seed traits for several designs including biparental backcross design, IF2 designe, random mating or selfing of IF2. The mixed linear model based composite interval mapping is used in mapping QTL. The software can simultaneously analyze the QTL maternal effects and embryo or endosperm effects, as well as their interaction effects with environments
DOI: 10.5061/dryad.b45bm/1
title: Guiguenoetal_BiologyLetters2014_RawData

description: Data represent acquisition (tabs 1 & 2) and performance (tabs 3 - 6) of a cognitive laboratory task withg brown-headed cowbirds (Molothrus ater). The cognitive testing was performed at the Advanced Facility for Avian Research at the University of Western Ontario.
DOI: 10.5061/dryad.bs87m/1
title: Bird community presence-absence data

description: Presence-Absence data for all species modeled; 4 years with 3 visits each year at each sampling point.
DOI: 10.5061/dryad.bs87m/2
title: DayOfYearCoVar

description: Day of the year covariate
DOI: 10.5061/dryad.c62kd/1
title: Ulex parviflorus: AFLP and flammability, Valencia, Spain

description: Ulex parviflorus AFLP loci and plant flammability.COLUMNS: 382 columns=  376 AFLP loci, 2 PCA flammability scores, fire regime, site and individual, and an additional columns (the first column) indicating the 4 rows with loci usage information (see rows).ROWS: 174 rows= column header, 169 individuals, and the last 4 rows (171 to 174) indicates the loci used in each of the analysis indicated in column 1 (see Table S4 in Moreira et al.).
DOI: 10.5061/dryad.c6qm2/2
title: Data supplement 2

description: Data of body dimensions and feather traits of 52 blackcaps Sylvia atricapilla wintering in the Campo de Gibraltar area, Southern Spain.
DOI: 10.5061/dryad.ft612j0h.1
title: Data from: Assessing adaptive phenotypic plasticity by means of conditional strategies from empirical data: the Latent Environmental Threshold Model
DOI: 10.5061/dryad.ft612j0h.2/1.1
title: Data_LETM

description: This data file contains: a script for simulated data sets using R software (ScriptR_LETM_SIM.R), a script (ScriptR_LETM_SAT.R) to analyze data collected in the field (Data_SAT.RData) using R and OpenBUGS software.
DOI: 10.5061/dryad.g7qs2/1
title: kardos_HFC_ID_simModel_11September2013

description: R script for simulation used in our paper
DOI: 10.5061/dryad.gm005fg8/1
title: Thornhill_etal_DRYAD_datafile
DOI: 10.5061/dryad.h22n9/1
title: INDIV_DATA
DOI: 10.5061/dryad.h22n9/2
title: NB OCCUPATION_DATA
DOI: 10.5061/dryad.hd300/10
title: RatDemographics-STRUCTUREPL8sep

description: Genotype data from 146 trapped individuals formatted for STRUCTURE, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/11
title: RatMsat17LociClean-STRUCTURE

description: Genotype data from 146 trapped individuals formatted for STRUCTURE, with animals grouped by sampling site and year. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/12
title: RatDems-Clusters-LDNE

description: Genotype data from trapped individuals formatted for LDNe, with animals grouped by structure clusters. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex. Juveniles have been removed from datasets used in Ne analyses.
DOI: 10.5061/dryad.hd300/13
title: RatDems-Clusters-LDNE-POP NAMES

description: Population (cluster) names for the LDNe file of rat microsatellite genotypes.
DOI: 10.5061/dryad.hd300/14
title: RatDems-ML-RELATE-full

description: Genotype data from 146 trapped individuals formatted for ML-Relate. All 146 animals are included in this file to test for pairwise relatedness across animals from different sites. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/15
title: RatDems-ML-RELATE-PL1-V1

description: Genotype data from trapped individuals formatted for ML-Relate. Only animals captured in site 1 in Pau da Lima (valley 1) are included in this file to test for pairwise relatedness within the site. "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/6
title: RatDems-GENECLASS-POP NAMES-PL8sep

description: Population names for the Geneclass file of rat microsatellite genotypes.
DOI: 10.5061/dryad.hd300/7
title: RatDemographics-GENEPOP-PL8sep

description: Genotype data from 146 trapped individuals formatted for Genepop, with animals grouped by sampling site with Pau da Lima site 8 separated by sampling year (clustering analyses indicated the site does not show stable genetic patterns). "RatDemographics" or "RatDems" refers to the excel sheet this file was made from in CREATE. The original excel sheet has demographic data on rat age and sex.
DOI: 10.5061/dryad.hd300/8
title: RatDems-GENEPOP-POP NAMES-PL8sep

description: Population names for the Genepop file of rat microsatellite genotypes.
DOI: 10.5061/dryad.hd300/9
title: Cluster1RatMsatIBD

description: Matrices of pairwise Fst and distance in meters between sites in Pau da Lima with site 8 separated into two populations based on sampling year for use in Genepop to perform Mantel tests of isolation by distance (IBD).
DOI: 10.5061/dryad.hv75h/1
title: Velvet_Reference_protein_matching.txt

description: Sequences of our reference based on the Lucania parva velvet assembly (kmer=25) with a total of 24,781 contigs, combining 1,657 contigs from the L. goodei assembly (all unique contigs over 200bp) with L. parva contigs that had blast matches to any of the following: 1) related teleost proteomes (Atlantic killifish: Fundulus heteroclitus, Japanese medaka: Oryzia latipes, three-spined stickleback: Gasterosteus aculeatus), 2) Fundulus ESTs on the microarray, or 3) target genes of interest (osmoregulation and vision related genes).  Blast results from blastX searches against the uniprot proteomes were retained only if contigs had only 1-2 protein matches per species (blast score &gt; 100) to avoid inclusion of contigs that were misassembled from multiple genes.
DOI: 10.5061/dryad.hv75h/2
title: Popoolation_Fst_all

description: Results from Fst calculation in Popoolation2 (Kofler et al. 2011).  We calculated allele frequencies and Fst between all populations, using a minimum coverage of 8 reads per population (to exclude SNPs from transcripts expressed at low frequency), a pool size of 10, and a sliding window of 50bp. Columns show Fst for populations listed at top (for given 50bp SNP window), last column is average of all L. goodei and all L. parva comparisons. Contigs match velvet reference names. L. goodei populations: Upper Bridge (Wakulla River, Florida) and Everglades (26-Mile Bend, Florida).  Freshwater L. parva populations: Pecos (Pecos River, Texas), Lower Bridge (Wakulla River, Florida), Delks (Delk's Bluff, Oklawaha River, Florida).  Saltwater L. parva populations: Indian River (Atlantic Ocean, Florida Coast), St. Mark’s (Gulf of Mexico, Florida Coast), Bolivar Peninsula (Galveston Bay, Texas Coast).
DOI: 10.5061/dryad.kp826/1
title: Buzatto et al - Alternative phenotypes within mating systems - literature review

description: This file contains the list of articles covered by our literature review on alternative mating phenotypes (AMP) in insects. For our classification of AMPs: they can be conditional (C) or mendelian (Mend, pure genetic polymorphism); fixed (F) or reversible (R). We also included whether male morphology determines (D), influences (I) or is irrelevant (Irr) for the mating behaviour employed by individuals; and whether there is morphological dimorphism (Y for yes, N for no) among individuals. ? indicates uncertainty, whereas lack of information is omitted. Our review is based on a search of the literature (through Web of Science) using the key-words ‘alternative’, ‘mating’, ‘reproductive’, ‘tactic(s)’, ‘strategy(ies)’, and combinations thereof. Even though we focused here only in mating phenotypes, and not on other features of insect reproduction (such as oviposition strategies, for instance), we still included ‘reproductive’ in our keywords because the usage of the term ‘alternative reproductive tactics/strategies’ in the literature often encompasses AMPs. However, some studies describe the sort of intraspecific variation in mating phenotypes that falls under the umbrella of AMPs, without using any of the key-words mentioned above, and have likely been missed. Moreover, to restrict our literature search to studies on insects, we also used the keywords ‘insect(s)’ and ‘Insecta’, and we might have missed studies that only treated their focal species by a common name. We therefore anticipate that our review is somewhat incomplete, and AMPs are probably even more widespread than currently recognized. We wouldn’t be surprised if they were the rule, rather than the exception, in insect mating systems. Our review covered a total of 353 references, including journal articles and chapters in peer-reviewed books, published between 1934 and 2012.