cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.23p42/2
title: Species level sexual dichromatism

description: Species-level sexual dichromatism for Australian passerines and parrots.
DOI: 10.5061/dryad.2br2b/1
title: databaseS1

description: Seed-dispersal networks, species traits and avian functional/ phylogenetic distance matrices
DOI: 10.5061/dryad.2jd45/1
title: fastsimcoal2 template file for the best model

description: Template file for fastsimcoal2 describing the model of "speciation from a hybrid population at Python Island". This is the model with the highest likelihood among all models tested.
DOI: 10.5061/dryad.2jd45/2
title: fastsimcoal2 estimation file for the best model

description: Fastsimcoal2 input file describing the parameter distributions for the model of "speciation from a hybrid population at Python Island". This is the model with the highest likelihood among all models tested.
DOI: 10.5061/dryad.2sk24/4
title: Proteroctopus in coleoid evolution supplementary material

description: The supplementary material includes CT scan data acquisition, table of measurements, phylogenetic analysis data, characters list, list of synapomorphies and 2 figures (tree with nodes and image of the gills).
DOI: 10.5061/dryad.3861f/1
title: Duthie_Reid_2016_AmNat.tar

description: This compressed directory contains the 44 files needed to compile the code underlying the paper and run all simulations. Parameter values for simulations are set in the InMult.c file. This code is also publicly available, with additional documentation, on Brad Duthie's GitHub repository: https://github.com/bradduthie/Inbreeding
DOI: 10.5061/dryad.410fc/1
title: Size-at-age data

description: Size at ages 35 d - 200 d
DOI: 10.5061/dryad.52b22/4
title: Mating System Genotypes 2012

description: Genotypes used to estimate mating system from the 2012 sampling of populations.
DOI: 10.5061/dryad.52b22/5
title: R Code

description: R Code in markdown format.
DOI: 10.5061/dryad.5h17h/1
title: Mreukaufii amino acid transporters aligned with Clavispora lusitaniae and Saccharomyces cerevisiae homologs

description: Alignment file created in Geneious 8.0 using Blosum62 cost matrix
DOI: 10.5061/dryad.5h17h/2
title: Mreukaufii_transporters_GAP1&PUT4 aligned to homologs from Clavispora lusitaniae and Saccharomyces cerevisiae

description: Protein sequence alignment created in Geneious 8.0 using the BLOSUM62 cost matrix and manually curated.
DOI: 10.5061/dryad.66f6m/1
title: One fly to rule them all: all data behind analyses
DOI: 10.5061/dryad.6c7p5/1
title: X. riversiana microsatellite genotypes

description: Microsatellite genotypes for Xantusia riversiana for the publication "Historical environment is reflected in modern population genetics and biogeography of an island endemic lizard (Xantusia riversiana reticulata)"
DOI: 10.5061/dryad.6mr8n/1
title: Southern Gulf of St. Lawrence winter skate transcriptome

description: Southern Gulf of St. Lawrence winter skate transcriptome. Assembled unannotated contigs from 454 sequencing reads.
DOI: 10.5061/dryad.6mr8n/2
title: Scotian Shelf Winter Skate transcriptome

description: Scotian Shelf Winter Skate transcriptome. Assembled unannotated contigs from 454 sequencing reads
DOI: 10.5061/dryad.6mr8n/3
title: Scotian Shelf Winter Skate assembled consensus transcriptome contigs

description: Scotian Shelf Winter Skate assembled consensus transcriptome contigs from 454 sequences
DOI: 10.5061/dryad.6mr8n/4
title: Southern Gulf of St. Lawrence Winter Skate consesnus assembled transcriptome contigs

description: Southern Gulf of St. Lawrence Winter Skate consesnus assembled transcriptome contigs from 454 sequencing
DOI: 10.5061/dryad.6mr8n/5
title: Scotian_Shelf_Winter Skate_Longest_ORF

description: Scotian_Shelf_Winter Skate_Longest_ORF nucleotide contigs from 454 sequence data
DOI: 10.5061/dryad.6mr8n/6
title: Scotian_Shelf_Winter Skate_Longest_ORF_Translated

description: Scotian_Shelf_Winter Skate_Longest_ORF_Translated from 454 sequence data
DOI: 10.5061/dryad.9rb13/11
title: Middle Miocene dataset

description: Middle Miocene dataset used for the R code "Indo-Pac_figs.R".
DOI: 10.5061/dryad.9rb13/12
title: Modern dataset

description: Modern dataset used for the R code "Indo-Pac_figs.R".
DOI: 10.5061/dryad.9rb13/13
title: R code for supplementary figs

description: The R code used for supplementary figures, "Indo-Pac_figs.R".
DOI: 10.5061/dryad.b1q15/1
title: El Nagar & MacColl stickleback parasite data

description: In order, the four worksheets contain: (1) Data on the occurrence of parasites in CHRU and OBSM in years 2011 and 2013; (2) Diplostomum abundance and hepatosomatic index of individual wild fish from CHRU; (3) Gyrodactylus counts from artificially infected, lab-raised fish of different cross types ('Day 28' = count of parasites on the 28th day following infection; 'AUC28' = sum of all counts to day 28; 'Max' = maximum count during the whole infection period.
DOI: 10.5061/dryad.bq68f/6
title: m32_PCA_Structure

description: Structure from the m32 pyRAD analysis file used for PCA.
DOI: 10.5061/dryad.bq68f/7
title: m32_SNPs

description: SNPs file from the m32 pyRAD analysis
DOI: 10.5061/dryad.cm586/1
title: Days with temperatures above 32 degrees C

description: The dates and maximum temperatures at the Magic Mountain SNOTEL site when temperatures reached 32 degrees C between 1989 and 2015.
DOI: 10.5061/dryad.cm586/2
title: Basal area of lodgepole pine at 67 locations in South Hills

description: This file contains the data used to estimate basal area at 67 locations in the South Hills, Idaho in 2002 and 2013. The first column is plot identifier, then its latitude, longitude, numbers of lodgepole pine within a 20-m radius in 2002 and 2013, the mean DBH of the these trees, and estimated basal areas.
DOI: 10.5061/dryad.cm586/3
title: distance data, crossbill density estimates 2003-2015

description: These data were used to estimate the density of crossbills between 2003 and 2015. The first 4 columns represent the raw data: year of survey, plot identifier, distance to the nearest group of crossbills, and the number of South Hills crossbills in the group; blanks indicate no crossbills were observed). Columns 6-9 represent estimates of crossbill densities from the data in the first 4 columns (year, mean, lower 95% confidence limit, and upper 95% confidence limit). Columns 10 and 11 represent the mean annual and spring temperatures for the preceding year using data from the Magic Mountain SNOTEL site in the South Hills, Idaho.
DOI: 10.5061/dryad.cm586/4
title: Annual cone production data

description: The first 17 columns represent the raw cone data, whereas columns 19-22 represent the summary data shown in figure 7. Column 1 is the tree identifier, column 2 is the branch number (5 branches were sampled from each tree), and columns 3-17 represent the number of cones from each year on each branch.
DOI: 10.5061/dryad.cm586/5
title: Cone opening temperatures

description: This file provides the mean cone opening temperatures for 1-11 year-old cones from 30 trees (column 2), and the mean cone opening temperatures for 15-20 year-old cones from 32 trees (column 3). These are the data used to produce the inset in figure 9.
DOI: 10.5061/dryad.cr7s6/1
title: Behavioral level and incubation behavior plasticity in marsh tits (Poecile palustris) and oriental tits (Parus minor) in response to pulsed and prolonged risks of nest predation

description: Nest ID; Species (MATI = marsh tit; ORTI = oriental tit); Nestbox type (SMALL = control; ENLARGED = treatment; prolonged risk); Playback stimulus (DOVE = non-predator sound; MAGPIE = nest predator sound; pulsed risk); Clutch size (number of eggs per nest); Incubation period (days; clutch completion = day 1 of incubation); Nest predation (0 = fledged; 1 = depredated); Ambient temperature (ºC); Nest attentiveness (%); Male incubation feeding trips / hr; Female foraging trips / hr; Detected numbers of corvids (within 50 m for 5 mins); Vigilance time (%)
DOI: 10.5061/dryad.d1s39/2
title: Transect data

description: The zip file contains the raw pictures taken along each transect. Transects are numbered following Table S1. Each folder contains all used pictures. Added are the MATLAB scripts used to calculate the relative sand cover within each quadrant. Resulting Sand cover estimates are included in the respective text files.
DOI: 10.5061/dryad.f0h49/1
title: raw_data_salmon_microbiome

description: Salmon salar gut microbiome sequences. Samples are identified by their "FLD0001.****_R1.fastq"  code in the samples' name.
DOI: 10.5061/dryad.fb1fq/1
title: Ritchie_TreePrior_OnlineAppendix

description: Online Supplementary Information for "The Impact of the Tree Prior on Molecular Dating of Heterogeneous Inter- and Intraspecies Data Sets".  Contains Table S1, Figures S2-S4.
DOI: 10.5061/dryad.fj0qj/1
title: E8.5 mouse embryo_1

description: Data of DNA microarray analysis of E8.5 mouse embryo (whole body)
DOI: 10.5061/dryad.fj0qj/2
title: E8.5 mouse embryo_2

description: Data of DNA microarray analysis of E8.5 mouse embryo (whole body)
DOI: 10.5061/dryad.fj0qj/3
title: E8.5 mouse embryo_3

description: Data of DNA microarray analysis of E8.5 mouse embryo (whole body)
DOI: 10.5061/dryad.h3tc2/1
title: This file contains additional figures, table and information that could not be included in the main paper or supplementary information due to space limitations

description: This file contains additional figures, table and information that could not be included in the main paper or supplementary information due to space limitations. List of content:Figure 1. A ML tree from seven concatenated nuclear lociFigure 2. Details of the genome assemblyFigure 3. BEAST Divergence time estimates among sampled giraffe subspecies Table 1: ID, subspecies and locations of all 141 own samples used in this studyTable 2: Microsatellite loci in the giraffe genomeTable 3: Percentages of mobile DNA elements in the giraffe genome
DOI: 10.5061/dryad.j2t44/1
title: Analysis Codes

description: Codes used in our analyses.
DOI: 10.5061/dryad.j2t44/2
title: Bacterial loads in non-virgin female flies (Major Experiment)

description: Bacterial loads in non-virgin female flies (Major Experiment)
DOI: 10.5061/dryad.j2t44/3
title: Bacterial loads in non-virgin male flies (Major Experiment)

description: Bacterial loads in non-virgin male flies (Major Experiment)
DOI: 10.5061/dryad.j2t44/4
title: Bacterial loads in virgin males (follow-up experiment)

description: Bacterial loads in virgin males (follow-up experiment)
DOI: 10.5061/dryad.j2t44/5
title: Bacterial loads in virgin females (follow-up experiment)

description: Bacterial loads in virgin females (follow-up experiment)
DOI: 10.5061/dryad.k0p2b/1
title: Seedling Characteristics

description: Characteristics of Eucalyptus pilularis seedlings in high- and low-nutrient treatments.
DOI: 10.5061/dryad.k0p2b/2
title: Experiment 1: Behavioural response to seedling odour

description: Visits and investigations by swamp wallabies (Wallabia bicolor) and eastern grey kangaroos (Macropus giganteus) of buried vials in three treatments: no seedling, cut high-nutrient seedling and cut low-nutrient seedling.
DOI: 10.5061/dryad.k0p2b/3
title: Experiment 2: Browsing patterns as a function of seedling odour and visual cues

description: Time to browsing of high- and low- nutrient seedlings (Eucalyptus pilularis) by swamp wallabies (Wallabia bicolor). Seedlings were presented both in the normal upright position and pinned to the ground (reducing visual cues). All 160 seedlings were periodically inspected for browsing damage, and a subset of 40 were also monitored by motion-triggered cameras.
DOI: 10.5061/dryad.n5m81/1
title: Trait measurements and cumulative fecundity of 173 bryozoans growing in either shallow or deeper waters

description: Each row represents one colonial bryozoan, its trait values for five life history traits (onset of senescence, growing edge width, early module size, intermediate module size, and late module size) and cumulative fecundity (number of eggs). These bryozoans naturally settled on to different panel stacks (one panel in 1 m water depth and one panel at 4 m per stack).
DOI: 10.5061/dryad.qp1nd/2
title: Data matrices
DOI: 10.5061/dryad.qp1nd/3
title: Resulting trees
DOI: 10.5061/dryad.s1m40/1
title: Leung & Koprivnikar JAE 2016 Dryad data

description: Excel file
DOI: 10.5061/dryad.s866f/1
title: Database of unique Lytocarpia brevirostris unique MLGs per population

description: Tab delimited text. On each line is represented a unique MLG, with haplotypes for 10 loci used in all analyses of the publication.
DOI: 10.5061/dryad.ts544/1
title: Introgression data

description: The file was produced using the command 'save()' from the R software. This resulted in the file “introgression.RData”, which includes two dataframes: (1) intro.rates.paper and (2) tree.data. The first dataframe comprises the empirical introgression rates recorded by Bialozyt et al. (2012).  The columns are the individual tree number followed by the percentage of introgression for year 2006 and 2007 respectively. The second dataframe (tree.data) comprises the name, coordinates, sex and taxa of all trees used in the simulation. In the column 'SEX' females are coded '0' and males are coded '1'. In the column 'SPECIES'  Populus nigra are coded '0' and the hybrids (Populus × canadenis) are coded '1'.
DOI: 10.5061/dryad.vb322/1
title: Edwards et al., (2016) tracking data

description: Geolocator and GPS data used in the double-tagging experiment and pre-laying exodus analysis described in Edwards et al., (2016). Data are arranged in folders and there is a short readme file associated with the double-tagging study.
DOI: 10.5061/dryad.05qs7/1
title: McAllister_Miller_Andropogon_gerardii_UNEAK_SNPs

description: Zipped VCF file containing SNPs called using UNEAK bioinformatic pipeline in 190 Andropogon gerardii accessions
DOI: 10.5061/dryad.05qs7/2
title: McAllister.Miller.all.mergedRefGuidedSNPs.vcf

description: Zipped VCF file containing SNPs called via alignment of GBS reads from 190 Andropogon gerardii accessions to the Sorghum bicolor genome.
DOI: 10.5061/dryad.05qs7/3
title: McAllister_Miller_Locality_Ploidy_Info

description: This file includes locality and ploidy level inforomation for each specimen included in both SNP files in this dataset
DOI: 10.5061/dryad.10f4p/3
title: NMR-Spectra-036-059

description: 1H NMR spectra in raw Bruker format. Part 2 / 5.
DOI: 10.5061/dryad.10f4p/4
title: NMR-Spectra-060-080

description: 1H NMR spectra in raw Bruker format. Part 3 / 5.
DOI: 10.5061/dryad.10f4p/5
title: NMR-Spectra-081-104

description: 1H NMR spectra in raw Bruker format. Part 4 / 5.
DOI: 10.5061/dryad.10f4p/6
title: NMR-Spectra-105-125

description: 1H NMR spectra in raw Bruker format. Part 5 / 5.
DOI: 10.5061/dryad.2g3s4/1
title: Simulated data: comparing allele frequencies with FST
DOI: 10.5061/dryad.2jd45/3
title: observed four-dimensional SFS

description: Observed four-dimensional SFS of four whole-genome sequenced individuals each from P. pundamilia and P. nyererei at Makobe Island and from P. sp. "pundamilia-like" and P. sp. "nyererei-like" at Python Island.
DOI: 10.5061/dryad.2jd45/4
title: Maximum likelihood parameters of the best model

description: File with model specification and maximum likelihood parameters of the model with highest likelihood among all models tested ("speciation from a hybrid population at Python Island").
DOI: 10.5061/dryad.41r54/1
title: supplementary material 1

description: Results of eight canonical discriminant analyses (CDA 1–CDA 8, fig. 8) based on morphological characters measured/scored on 19 specimens and eight body segments of Lasiochernes cretonatus, L. jonicus and L. pilosus. Values of the total canonical structure listed in the table express correlations of characters with canonical axes (Can 1 and Can 2) in each CDA. Higher total canonical structure values are in bold type.
DOI: 10.5061/dryad.68mp3/1
title: MIGRATE output_maxLiklihood

description: This file contains the output from our microsatellite gene flow analyses in the program MIGRATE..
DOI: 10.5061/dryad.68mp3/2
title: Sprint speeds

description: Estimates of lizard sprint speeds at each of six temperatures.
DOI: 10.5061/dryad.68mp3/3
title: Operative temperature data

description: Temperature data from iButton data loggers.
DOI: 10.5061/dryad.6mr8n/10
title: sGSL Winter Skate transcriptome Consensus Annotation

description: Southern Gulf of St. Lawrence Winter Skate transcriptome Consensus Annotation in a  Genbank-like format
DOI: 10.5061/dryad.6mr8n/11
title: sGSL Winter Skate_Up-regulated_GO-Terms

description: sGSL Winter Skate Gene Ontogeny Terms for up-regulated genes &gt;1 Fold Change in RPKM
DOI: 10.5061/dryad.6mr8n/12
title: sGSL Winter Skate_Down-regulated_GO-Terms

description: sGSL Winter Skate Gene Ontogeny Terms for Down-regulated genes
DOI: 10.5061/dryad.6mr8n/13
title: Scotian Shelf Winter Skate_Down-regulated_GO-Terms

description: Scotian Shelf Winter Skate_Down-regulated_Geno Ontology-Terms
DOI: 10.5061/dryad.6mr8n/14
title: Scotian Shelf Winter Skate_UP-regulated_GO-Terms

description: Scotian Shelf Winter Skate_Down-regulated_Geno Ontology-Terms &gt;1 fold change in sequencing RPKM
DOI: 10.5061/dryad.6mr8n/7
title: sGSL_Winter Skate_Longest_ORF

description: Southern Gulf of St. Lawrence_Winter Skate_Longest_ORF nucleotide contigs from 454 sequence data
DOI: 10.5061/dryad.6mr8n/8
title: sGSL_Winter Skate_Longest_ORF_Translated

description: sGSL_Winter Skate_Longest_ORF_Translated contigs from 454 sequencing data
DOI: 10.5061/dryad.6mr8n/9
title: Scotial Shelf Winter Skate transcriptome Consensus Annotation

description: Scotial Shelf Winter Skate transcriptome Consensus Annotation in a genebank-like format
DOI: 10.5061/dryad.77971/1
title: RIL_DataForSelectionAnalyses3yrs

description: Contains RIL mean flowering time, fitness components, and fitness.
DOI: 10.5061/dryad.77971/2
title: ReadMe_QTLMappingFiles

description: Read me file for files associated with QTL mapping.
DOI: 10.5061/dryad.77971/3
title: MapQTL_F09IT_DTFF

description: Example R script for mapping QTL using R/qtl.
DOI: 10.5061/dryad.77971/4
title: geno

description: File of RIL genotypes, formatted for R/qtl.
DOI: 10.5061/dryad.77971/5
title: pheno

description: Phenotype file for RILs, formatted for R/qtl
DOI: 10.5061/dryad.93fv2/2
title: yohheiBrickner.fastq
DOI: 10.5061/dryad.c3318/1
title: Filtered SNP genotype data set for Brazil, Massachussets and Florida

description: This is a genepop formatted file (.gen) with SNP data for the three populations examined in this study (Porto Allegre, Brazil, Panama city beach FL, and Agawam river MA, USA). File contains data for 2,783 SNPs which were filtered for HWE, LD, and coverage. Genotype data was exported from the Stacks pipeline v. 1.34 or higher.
DOI: 10.5061/dryad.c3318/2
title: Full SNP dataset for 2 North American populations

description: This file contains SNP genotype data in genepop format (.gen) for 9864 loci from two blue crab populations : Agawam river MA (AR populatioN) and Panama City Beach, FL (PCB population). Genotype data were filtered for coverage and &gt;85% genotypes called for individuals, and HWE,  but not for linkage disequilibrium (LD). Data were exported from Stacks v.1.34 or above.
DOI: 10.5061/dryad.cd546/74
title: Concatenated nuclear alignment, 70 taxa
DOI: 10.5061/dryad.cd546/75
title: Concatenated nuclear tree, unpartitioned
DOI: 10.5061/dryad.cd546/76
title: Concatenated nuclear tree, partitioned by gene
DOI: 10.5061/dryad.cd546/77
title: Concatenated nuclear tree, partitioned by splice site
DOI: 10.5061/dryad.cm586/6
title: Cone temperatures

description: These are the maximum surface temperatures of cones from one tree in the South Hills, Idaho recorded in June 2015. The date, the time, the maximum temperature on the cone surface, and the corresponding temperature at the nearby Magic Mountain SNOTEL site are provided. These data are shown in figure 9.
DOI: 10.5061/dryad.cv03k/1
title: Bohaiornithid_SOM
DOI: 10.5061/dryad.cv03k/2
title: Bohaiornithid CT

description: A video of the computed tomography (CT) scan of the new bohaiornithid specimen from the Early Cretaceous Jiufotang Formation, near Lamadong Village, Jianchang County, Liaoning Province, China.
DOI: 10.5061/dryad.fb1fq/2
title: Cetacea_TreePriors_Analyses

description: Alignment and BEAST files for analysis of tree prior impact on Cetacean date estimates.
DOI: 10.5061/dryad.fb1fq/3
title: Coregonus_TreePriors_Analyses

description: Alignments and analysis files for investigation of tree prior impact on whitefish (Coregonus) date estimates.
DOI: 10.5061/dryad.fb1fq/4
title: Phocid_TreePriors_Analyses

description: Alignments and BEAST analysis files for investigation of tree prior impact on phocid date estimates.
DOI: 10.5061/dryad.fb1fq/5
title: All Simulation Data

description: LARGE FILE. Alignments, true tree files, phylograms showing branch rates, and BEAST analysis files for all simulated analyses. The analysis number in the filename refers to the index of the true tree in the relevant .trees file.
DOI: 10.5061/dryad.fj0qj/4
title: E9.5 mouse embryo_1

description: Data of DNA microarray analysis of E9.5 mouse embryo (whole body)
DOI: 10.5061/dryad.fj0qj/5
title: E9.5 mouse embryo_2

description: Data of DNA microarray analysis of E9.5 mouse embryo (whole body)
DOI: 10.5061/dryad.fj0qj/6
title: E9.5 mouse embryo_3

description: Data of DNA microarray analysis of E9.5 mouse embryo (whole body)
DOI: 10.5061/dryad.fj0qj/7
title: E10.5 mouse embryo_1

description: Data of DNA microarray analysis of E10.5 mouse embryo (whole body)
DOI: 10.5061/dryad.fj0qj/8
title: E10.5 mouse embryo_2

description: Data of DNA microarray analysis of E10.5 mouse embryo (whole body)
DOI: 10.5061/dryad.fj0qj/9
title: E10.5 mouse embryo_3

description: Data of DNA microarray analysis of E10.5 mouse embryo (whole body)
DOI: 10.5061/dryad.gt78n/1
title: Data for figures 1 & 3

description: Relationship between shear force, adhesive force, peel angle, and crack propagation speed for the adhesive organs of stick insects (Carausius morosus)
DOI: 10.5061/dryad.j2t44/6
title: Weights of males and females

description: Weights of males and females
DOI: 10.5061/dryad.j2t44/7
title: Survivorship data

description: Survivorship data
DOI: 10.5061/dryad.j2t44/8
title: Mating history bacterial load data (follow-up experiment)

description: Mating history bacterial load data (follow-up experiment)
DOI: 10.5061/dryad.n21f4/1
title: Sample and sequence data information for Awaous stamineus

description: Excel file including sample data information for the 2229 cytochrome-b sequences (512bp) of Awaous stamineus from Hawaii analyzed in Alda et al. Sample ID, Year of collection, Watershed, Islands, Hawaiian Division of Aquatic Resources (DAR) Code, Sequence name.
DOI: 10.5061/dryad.n6g99/1
title: Tdobrogicus_input_files

description: Input files for PopArt, Arlequin, BAPS, Geneland, Genepop and Structure.
DOI: 10.5061/dryad.nr6bf/1
title: koweps_fn
DOI: 10.5061/dryad.r4d09/3
title: R Script

description: The R script with all code and instructions for running the analyses. Requires the .RData image.
DOI: 10.5061/dryad.r4d09/4
title: Data Tables and Model Outputs

description: This is an .RData image with the data tables used in the statistical models. It also includes the model output objects. This is to be used alongside the R script.
DOI: 10.5061/dryad.t4j06/1
title: Supplementary data

description: Brains and Behavior