cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q0m8/9
title: Raw variant calls from alignment files

description: VCF files created using GATK UnifiedGenotyper from alignment files
DOI: 10.5061/dryad.65fr2/1
title: Data and analyses for "Minimal effects of latitude on present-day speciation rates in New World birds"

description: Includes: BAMM settings, BAMM results, raw data (phylogenies + taxonomy + latitude for NW birds), and scripts to analyze results in R using the BAMMtools R package
DOI: 10.5061/dryad.65th6/1
title: PairwiseLD

description: This file contains estimates of pairwirse linkage disequilibrium (r^2) for all 623 SNPs significantly associated with gender in mapping population T52.
DOI: 10.5061/dryad.65th6/2
title: chr19_tree_ML

description: Newick tree file for Figure 3 panel b (concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107)
DOI: 10.5061/dryad.65th6/3
title: chr19

description: Fasta aligment of concatenated Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107, used for divergence estimates presented in Table 3. This file also includes transcript sequences used to infer which positions in the alignment were in coding regions for estimates of silent and replacement substitutions.
DOI: 10.5061/dryad.b1d63/1
title: Supplemental_Data_1

description: Measurements and relevant locality data for all specimens examined in the paper.
DOI: 10.5061/dryad.d95j4/2
title: EzoSal.transcriptome.annotation

description: An Annotation file of de novo assembled contigs
DOI: 10.5061/dryad.d95j4/3
title: Ezosal.transcriptome.Trinity_components.counts

description: Counting data of each library which is an input file of DEG analysis
DOI: 10.5061/dryad.d95j4/4
title: DEG.piarwise.output

description: Raw output files of pairwise DEG analysis
DOI: 10.5061/dryad.f4v0s/1
title: ATR list of fresh and achived spores

description: List of fresh and archived spores for ATRspectraArchivedSpores.txt spectra
DOI: 10.5061/dryad.f4v0s/2
title: ATR list of Fresh Pollen and Spores

description: ATR list of Fresh Pollen and Spores for ATRspectraFreshPollenSpores.txt
DOI: 10.5061/dryad.f4v0s/3
title: ATRspectraArchivedSpores

description: ASCII file containing absorbance values of 192 FTIR spectra of fresh and archived spores (see list in ATR list of fresh and archived spores); spectral wavenumbers are in Wavenumbers.txt
DOI: 10.5061/dryad.f4v0s/5
title: Wavenumbers

description: Spectral wavenumbers for files ATRspectraArchivedSpores.txt and ATRspectraFreshPollenSpores.txt
DOI: 10.5061/dryad.h360q/1
title: Synalpheus dimorphism_all mature individuals

description: Sex, gonad maturity and size of each mature individual
DOI: 10.5061/dryad.h360q/2
title: Synalpheus dimorphism_statistics by colony

description: sex ratio, percentage maturity and eusociality index for each colony.
DOI: 10.5061/dryad.h360q/3
title: Synalpheus dimorphism_statistics by species

description: Sex ratio, allometry, proportion maturity and eusociality index of each species
DOI: 10.5061/dryad.j01j0/2
title: DRB alignment file

description: All NZSLs, MHC DRB clustal omega alignment file
DOI: 10.5061/dryad.j01j0/3
title: Microsatellite genotypes

description: NZSL microsatellite genotypes for pups used in MHC study
DOI: 10.5061/dryad.jj3tp/1
title: Ferrari etal-SupplMaterial
DOI: 10.5061/dryad.k22kg/4
title: population size

description: Data obtained through genetic analysis software to estimate population size through genotype rarefaction curve (Gimlet input and output files)
DOI: 10.5061/dryad.kg943/1
title: ME_opinionRdata_tidy

description: This is an excel csv file that contains summary information concerning the public data archiving of genetic, geographic and temporal information for articles published in Molecular Ecology from 2009 to 2013
DOI: 10.5061/dryad.p31j8/2
title: set of high quality SNPs used in the analysis

description: SNPs were identified by pooling the allele counts acrosss all libraries and requiring a minium base quality of 40 and a minimum allele count of 3; contains SNPs for D.melanogaster and D.simulans separately
DOI: 10.5061/dryad.p31j8/3
title: allele counts for all sites, all libraries and all experiments (PoPoolation2 data)

description: for detail see the attached readme file
DOI: 10.5061/dryad.pc5j0/1
title: Supplementary materials (including SFig 1-33, STable 1)

description: Accepted topologies and lists of species for species-tree discordance test, lists of species for minimum duplication test, supplementary table 1, and supplementary figures 1 to 33.
DOI: 10.5061/dryad.pc5j0/2
title: Raw data of enriched species discordance, minimum duplication test, and simulation study

description: Alignment and trees associated with enriched species-tree discordance test, minimum duplication test, and simulation study.
DOI: 10.5061/dryad.pc5j0/3
title: Raw data of Ensembl Compara analyses

description: Alignment and trees associated with Ensembl compara data and pipeline.
DOI: 10.5061/dryad.pc5j0/4
title: Genome list

description: List of genomes used in the study, including source and release number.
DOI: 10.5061/dryad.r5303/1
title: NpNaInput_MPE

description: The file contains microsatellites genotypes coming from individuals trees of all populations sampled in the study. Species genotypes are provided in two different sheets.
DOI: 10.5061/dryad.t2682/1
title: Habitat cover, connectivity, and forest restoration potential in an Atlantic forest region

description: This dataset includes a set of indices to characterize forest cover and connectivity dynamics, which are used to evaluate various aspects of forest restoration potential for the 5000-ha focal landscapes distributed across a 1,970,000-ha study site in southern Bahia, Brazil for years 1990 and 2002. Refer to the corresponding article for a thorough explanation of the indices included in this dataset. Both restoration and conservation candidates are included.
DOI: 10.5061/dryad.tc8j2/1
title: Foraging behavior of northern elephant seals and mercury concentrations in blood and muscle

description: We quantified variables for the full foraging trip (short and long foraging trip) to describe foraging behavior of northern elephant seals, using geography, diving behavior, and stable isotopes (carbon and nitrogen). Most seals were weighed upon recovery. If not, then RecoveryMassEstimated was recorded as 1, meaning that the recovery mass was estimated using body composition and morphometric measurements. The ToppID is the unique ID for the individual and the foraging trip that would link with the full diving and tracking file, housed at the University of California, Santa Cruz. The Seal_ID is an ID that corresponds to each seal in this study and links with their individual histories, also housed at the University of California, Santa Cruz.
DOI: 10.5061/dryad.tv179/1
title: Data from Ross et al., 2015

description: Data from: Ross CL, Falter JL, Schoepf V, McCulloch MT (2015) Perennial growth of hermatypic corals at Rottnest Island, Western Australia (32°S), PeerJ
DOI: 10.5061/dryad.1771t/1
title: Capture data of raccoons and striped skunks in Montérégie and Estrie regions

description: Capture data of raccoons and striped skunks during wildlife surveys in Montérégie and Estrie regions, Québec, Canada. These data were used to illustrate the resampling method in the case study. The columns “X_METER” and “Y_METER” are X and Y projected coordinates (in meters) of live-trap locations. The locations were projected into UTM Zone 18N coordinates with NAD 1983 datum.
DOI: 10.5061/dryad.2451q/1
title: Shi_Rabosky_2015_Evolution.tar

description: The data include the following sections: (1) PHLAWD alignments per locus and Genbank identifiers/metadata, (2) RAxML input/output and RogueNaRok output for phylogeny construction, (3) treePL input/output for both bootstraps and the ML phylogeny, (4) BAMM input/output for both bootstraps and the ML phylogeny, and (5) code for our phylogeneitc imbalance simulations.
DOI: 10.5061/dryad.3216c/2
title: Potential methane oxidation, production, organic matter compositon, gene copies, and environmental data

description: In early June 2011, 48 experimental plots (50 × 50 cm) were established in lawn (n = 24) and hummock microhabitats (n = 24) in a Sphagnum-dominated ombrotrophic peatland in the Store Mosse National Park, Sweden (57°17’54 N, 14°00’39 E). In both microhabitats, the vascular plant functional type (PFT) composition was manipulated by removing (clipping) ericoids (–Eric), graminoids (–Gram), or both. A set of control plots remained intact. One year later, peat samples (c. 20 g. f. wt) were collected from all plots (n =48) at the aerobic/anaerobic boundary (10 – 30 cm below the peat surface, microhabitat dependent). These samples were used to measure potential methane production, potential methane oxidation, organic matter chemistry, pmoA gene copies, and environmental data.
DOI: 10.5061/dryad.3216c/3
title: Ecosystem respiration

description: To asses the effect of vascular plant removal in aforementioned experiment, one year after the start of the experiment, we measured carbon dioxide respiration rates on 10 cm diameter collars using an automated soil CO2 flux system (LI-8100, LI-COR Biosciences, USA). We compare the fluxes from the vascular plant removal plots with respiration rates from comparable areas in the control plots with little or no vascular plant cover, and assessed the relationship with the amount of removed biomass.
DOI: 10.5061/dryad.3p147/2
title: Matrices

description: Variance/covariance matrices used in this study, separated by species. The BSFG G-matrix is named G_Bayes. The BSFG P-matrix is named P_Bayes.
DOI: 10.5061/dryad.3p147/3
title: Posterior_and_matrices_Gnoise

description: BSFG model priors and posterior distributions, when estimating G based on random noise. File names follow the convention established by the BSFG model (Runcie & Mukherjee, 2013).
DOI: 10.5061/dryad.3p147/4
title: Species_and_node_information

description: Information on species' trait means and branch lengths used when estimating rate of morphological evolution. Branch names correspond to the names reported in the main text.
DOI: 10.5061/dryad.45ds3/1
title: Effect of H. pylori Infection on Cytokine Profiles and Oxidative Balance in Subjects with Chronic Alcohol Ingestion
DOI: 10.5061/dryad.47bm8/1
title: morphologic comparision of the T. turcica with related species
DOI: 10.5061/dryad.47bm8/2
title: Figure 1

description: habit and holotype of Tragopogon turcicus
DOI: 10.5061/dryad.545tv/1
title: Solomon Islands_Ngella_cross-sectional study 2012

description: The file contains the epidemiological data used for the analysis and results presented in the associated manuscript.
DOI: 10.5061/dryad.5r776/1
title: Data of Artemisia C:N:P stoichiometry

description: In August to early September 2012, 48 species of Artemisia and their close relatives (Ajania, Filifolium, Hippolytia, Neopallasia and Seriphidium) were collected from 65 sites of natural vegetation across China.  C and N were analyzed using an element analyzer, and P concentrations were determined using the Thermo Scientific iCAP 6300.
DOI: 10.5061/dryad.65th6/10
title: 40024_sanger_nousat_fortree_ML

description: Newick tree file for Figure S2 panel c (Chr19 Amplicon1:Chr19:40024, all P. tremuloides clones included)
DOI: 10.5061/dryad.65th6/11
title: 40024_sanger_nousat_fortree

description: Fasta alignment for Figure S2 panel c (Chr19 Amplicon1:Chr19:40024, all P. tremuloides clones included)
DOI: 10.5061/dryad.65th6/4
title: chr19_tree

description: Fasta aligment of concatenated  Amplicon1:Chr19:40024, Amplicon2:Chr19:41515 and Amplicon3:Chr19:44107, used for generating phylogenetic tree on Figure 3b.
DOI: 10.5061/dryad.65th6/5
title: sanger_7690067_oneclone_ML

description: Newick tree file for Figure 3 panel a (Amplicon1:Chr09:7690067)
DOI: 10.5061/dryad.65th6/6
title: sanger_7690067_anno

description: Fasta aligment of Amplicon1:Chr09:7690067, used for divergence estimates presented in Table 3. This file also includes transcript sequences used to infer which positions in the alignment were in coding regions for estimates of silent and replacement substitutions.
DOI: 10.5061/dryad.65th6/7
title: sanger_7690067_oneclone

description: Fasta aligment of Amplicon1:Chr09:7690067, used for generating phylogenetic tree on Figure 3a.
DOI: 10.5061/dryad.65th6/8
title: sanger_7690067_ML

description: Newick tree file for Figure S2 panel a (Amplicon1:Chr9:7690067, all P. tremuloides clones included)
DOI: 10.5061/dryad.65th6/9
title: sanger_7690067

description: Fasta aligment of Amplicon1:Chr9:7690067 with all P. tremuloides clones included used for generating phylogenetic tree on Figure S2 panel a
DOI: 10.5061/dryad.6hk4h/1
title: CPUE data and complete model results

description: This Excel document contains 4 tabs: 1) "Models-7 year analyses" - mixed-model repeated measures analysis of BPUE and mean length estimates for each MPA. 2) "Models-Network analyses" - mixed-model repeated measures analysis of BPUE and mean length estimates across all MPAs. 3) "CCFRP_CPUE_by_gridcell_07-13" - raw data of CPUE for each grid cell each year. 4) "Species codes" - A key for 3 letter codes used for fishes in CPUE table.
DOI: 10.5061/dryad.6pr21/6
title: Experimental MR Signal Contrast Dynamics Magnitude Data Set 6

description: MR Signal Magnitude Image Data Contrast Dynamics Experiment No. 6
DOI: 10.5061/dryad.6pr21/7
title: Experimental MR Signal Contrast Dynamics Magnitude Data Set 7

description: MR Signal Magnitude Image Data Contrast Dynamics Experiment No. 7
DOI: 10.5061/dryad.8265h/1
title: Microsatellite genotypes

description: This file contains raw genotypes for 17 microsatellite loci for two species of Rattus- R. rattus and R. satarae sampled in seven locations in Western Ghats.
DOI: 10.5061/dryad.bt703/1
title: Optical Imaging Data Sets

description: Six data sets with optical imaging sequences from Manduca sexta and Cydia pomonella.
DOI: 10.5061/dryad.c15ph/1
title: Timing of elk births and abortions
DOI: 10.5061/dryad.ct528/10
title: Porites_australiensis_dryad
DOI: 10.5061/dryad.ct528/6
title: Acropora_Hyacinthus_dryad
DOI: 10.5061/dryad.ct528/7
title: Acropora_Sarmentosa_dryad
DOI: 10.5061/dryad.ct528/8
title: Acropora-florida_dryad
DOI: 10.5061/dryad.ct528/9
title: Pocillopora_species_complex_dryad
DOI: 10.5061/dryad.d0h7s/1
title: GLS tracking locations + time-matched front metrics

description: All original GLS tracking locations, plus associated 7-day front thermal and chlorophyll-a front metrics (Thermal metrics = thermal front density, Tdens5; thermal front gradient density, Tgdens5; thermal front persistence, Tpfront; distance to closest thermal front (km), Tdist; side of thermal front, Tside; Chlorophyll-a metrics = chl-a front density, Cdens5; chl-a front gradient density, Cgdens5; persistence of chl-a front, Cpfront; distance to closest chl-a front, Cdist; side of chl-a front, Cside).
DOI: 10.5061/dryad.d95j4/5
title: DEG.GLM.output

description: Raw output files of GLM DEG analysis
DOI: 10.5061/dryad.d95j4/6
title: Morphological.measurements

description: Data of morphological measurements
DOI: 10.5061/dryad.d95j4/7
title: Transcriptome assembly of Hokkaido salamander
DOI: 10.5061/dryad.f4v0s/4
title: ATRspectraFreshPollenSpores

description: ASCII file containing absorbance values of 417 FTIR spectra of fresh and archived spores (see list in ATR list of fresh and archived spores); spectral wavenumbers are in Wavenumbers.txt
DOI: 10.5061/dryad.h0d12/1
title: Raw hemolymph, egg-laying, and paraquat survival data

description: Data from: Egg-laying and paraquat survival data, and hemolymph data for phenoloxidase activity, protein content, and glutathione concentration
DOI: 10.5061/dryad.kt69d/1
title: Phenotypic data
DOI: 10.5061/dryad.kt69d/2
title: bash command file used for data analysis
DOI: 10.5061/dryad.p1p29/1
title: Roitberg_et_al_svl_data

description: Data for adult body size (snout-vent length, SVL)Abbreviations of characters/columns (if not clear from their designations):No, this column is for technical purposes of the author;No_inv, inventary number (in the museum or in the working protocols of the primary researcher);ssp, subspecies/clade: 1 L. a. agilis, 3 L. a. exigua;reg3, code of the study sample as in Roitberg et al., 2015, Table 1;sta, "stages": ad adult, gr gravid, m junger adult, sub subadult, j (=juv) juvenile;NB: subadults and juveniles, as well as unsexed individuals, were excluded from all analyses in Roitberg et al. 2015; sex: 1 males, 2 females, 3 unsexed;Num , individual (study subject) number in the author's extended data base.filter_adults: 1 individuals considered as "adults" in Roitberg et al. (2015), 2 other individuals.Abbreviations of museums:mkhar, Museum of Nature, Kharkiv National Karazin University;mkiev, National Museum of Natural History Kyiv;mtd, Senckenberg Natural History Collections Dresden;zfmk, Zoological Research Museum A. Koenig Bonn;zmb, Humboldt Natural History Museum Berlin;zmh, Zoological Museum Hamburg;zsm, Zoological State Collections Munich.Comment 1.  The codes “mkhar” and “mkiev” do not represent established abbreviations of the corresponding museums and used for simplicity.Comment 2. This data table does not include Sample 3 (South Sweden) and Sample 9 (Russia, Ciscaucasia 1) because for these samples we used published mean values (respectively, Olsson, 1988 and Ushkalova, 1976).Comment 3. SVL-values for Sample 4 (Poland) were obtained by extracting log(SVL)-values from published scatterplots (Borczyk & Paśko, 2011: Fig. 1, A,B) and subsequent re-calculating the raw values using the exponent function.Comment 4. SVL-values for Sample 10 (Russia, Ciscaucasia 2) and Sample 11 (Russia, Ryazan Region) were obtained from published histograms (respectively, Lukina, 1966: Fig. 22 and Zharkova, 1973: Fig. 4).Comment 5. SVL-values for the other samples are original data of the authors.
DOI: 10.5061/dryad.p1p29/2
title: Roitberg_et_al_repro_data

description: Data for female reproductive output and maternal body size: 

Abbreviations of characters/columns (if not clear from their designations):

No, this column is for technical purposes of the author;

No_inv, inventary number (in the museum or in the working protocols of the primary researcher);

ssp, subspecies/clade: 1 L. a. agilis, 3 L. a. exigua;

reg3, code of the study sample as in Roitberg et al., 2015, Table 1;

data: "real",  usual data, which relate to real individuals;  "sur", surrogate data which were generated for those samples where only mean values and standard deviations were available; these artificial samples were used in ANOVA/ANCOVA models (see Roitberg et al. 2015 for details and references);

svl, maternal snout-vent length;

cs_t, egg stage: 1 'enlarged follicles', 2 'oviductal eggs', 3 'corpora lutea', 4 'laid eggs';

cs, clutch size;

m2, post-oviposition female mass;

cm, clutch mass (the total mass of the freshly deposited eggs);

rcm, relative clutch mass (in %);

egg_m, mean egg mass per clutch;

hm, mean hatchling mass per clutch ;

Num, individual (study subject) number in the author's extended database.

ln_rcm, natural logarithm of  rcm.

Abbreviations of museums:
mkhar, Museum of Nature, Kharkiv National Karazin University;           
mkiev, National Museum of Natural History Kyiv;             
mtd, Senckenberg Natural History Collections Dresden;
zfmk, Zoological Research Museum A. Koenig Bonn;
zmb, Humboldt Natural History Museum Berlin;
zmh, Zoological Museum Hamburg;
zsm, Zoological State Collections Munich.

Comment 1.  The codes “mkhar” and “mkiev” do not represent established abbreviations of the corresponding museums and used for simplicity.

Comment 2.  Sample 3 (South Sweden) should actually include some additional values which could not be extracted from the scatterplot (Olsson, 1993: Fig. 1) because the corresponding points were superimposed. The resulting bias is obviously minor, however: the published values for mean maternal SVL, mean clutch size, and the maternal SVL-clutch size correlation (Olsson, 1993; Olsson & Shine, 1997a) are close to those of Sample 3.


See Roitberg et al. (2015) for important comments to our study traits.
DOI: 10.5061/dryad.p1p29/3
title: Roitberg_et_al_physical_characteristics_of_study samples

description: Data for geographic coordinates and climateAbbreviations of characters/columns (if not clear from their designations):ID, code of the study sample as in Roitberg et al. 2015, Table 1;reg3 (as ID);tmin1 – tmin12, monthly means of minimal temperatures;tmax1 – tmax12, monthly means of maximal temperatures;tmax1 – tmax12, monthly means of maximal temperatures;prec1 – prec12, monthly sums of precipitation;PC1-clim – PC2-clim, first two principal components of geographic variation for the above 36 climatic variables (see Roitberg et al. 2015 for explanations);bio1 – bio19, the so called bioclimatic variables:bio1, Annual Mean Temperature;bio2, Mean Diurnal Range (Mean of monthly (max temp - min temp));bio3, Isothermality (BIO2/BIO7) (* 100);bio4, Temperature Seasonality (standard deviation *100);bio5, Max Temperature of Warmest Month;bio6, Min Temperature of Coldest Month;bio7, Temperature Annual Range (BIO5-BIO6);bio8, Mean Temperature of Wettest Quarter;bio9, Mean Temperature of Driest Quarter;bio10, Mean Temperature of Warmest Quarter;bio11, Mean Temperature of Coldest Quarter;bio12, Annual Precipitation;bio13, Precipitation of Wettest Month;bio14, Precipitation of Driest Month;bio15, Precipitation Seasonality (Coefficient of Variation);bio16, Precipitation of Wettest Quarter;bio17, Precipitation of Driest Quarter;bio18, Precipitation of Warmest Quarter;bio19, Precipitation of Coldest Quarter.Note that for most study samples, values for longitude, latitude, and climatic variables are average values for several sites from which the study animals were collected; sites which provided relatively small amount of data were not considered for computing these average values. Specifically, for Sample 16, most study animals come from surroundings of Nizhnyaya Neninka (Soltonskiy district); for Sample 17, most study animals were collected near Yailyu (Turochakskiy district). These localities were taken as reference sites for the corresponding samples.
DOI: 10.5061/dryad.rq3ng/1
title: Zip-file containing data and metadata

description: This zip-file contains several data files - as well as their metadata - that are used for the analyses
DOI: 10.5061/dryad.th441/2
title: 2011 wings v body data

description: Data from observations of _Papilio glaucus_ butterflies foraging on _Rhododendron calendulaceum_ flowers in the field. Showing contact between butterfly wings and an anther & stigma versus contact between butterfly's body and an anther & stigma. Observed contact = 1, absence of contact = 0. Note that these data should not be used to draw any conclusions about which visits had BOTH wings and bodies contact anthers and stigmas. Data collected June 2011.
DOI: 10.5061/dryad.vj64m/1
title: Microsatellite genotypes
DOI: 10.5061/dryad.vj64m/2
title: SNP genotypes
DOI: 10.5061/dryad.18b29/1
title: H2O2 production in NADPH-oxidase mutants

description: Production of ROS in Arabidopsis NADPH-oxidase mutants upon aphid interactions. Confocal JPEG files and 8 bits ImageJ converted images. Leaves of Col-0, the atrbohD-3 and atrbohF-3 mutant lines after exposure to aphids species Myzus persicae (Mp), M. cerasi (Mc) and Rhopalosihpum padi (Rp) and were collected after 3 and 24 hours. 3 replicates, R1, R2 and R3.
DOI: 10.5061/dryad.18b29/2
title: H2O2 production in Col0

description: Production of ROS in Col-0. Confocal JPEG files and 8 bits ImageJ converted images. Col-0 leaves after exposure to aphid species Myzus persicae (Mp), M. cerasi (Mc) and Rhopalosihpum padi (Rp) and  collected after 3, 6,12 and 24 hours. 2 replicates, R1 and R2.