cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.2d6h4/10
title: ground vegetation

description: Inventory data for species numbers of the ground vegetation as well as associated climate and tree vegetation. Inventories were conducted in the Austrian Alps (FLORALP database).
DOI: 10.5061/dryad.35jt8/1
title: Grouse MHC class IA sequences

description: Grouse MHC class IA sequences. Aligned fasta file.
DOI: 10.5061/dryad.39k32/1
title: Saproxyic beetle data from two forest areas the Czech Republic in 2007 & 2008

description: This file contains information on saproxylic beetles that where caught in a lowland forest area along the lower Dyje (Thaya) and Morava (March) rivers in southern Moravia and a montane forest area in the Moravian-Silesian Beskids (Beskydy) in the years 2007 and 2008, respectively. The file contains a species-abundance list of all the species caught in the study, as well as a list with further information (saproxylic status, feeding guild, red list status, indicator species) on the beetle species themselves.
DOI: 10.5061/dryad.422sh/1
title: STEPS data PLOS ONE
DOI: 10.5061/dryad.52504/8
title: Input file used for BAPS analyses

description: Input file used for Bayesian analyses of genetic structure implemented in the program BAPS.
DOI: 10.5061/dryad.52504/9
title: Input files used for Mantel tests

description: Input files for Mantel tests performed using the program ZT. These files include two indexes of niche overlap (D and I) between each pair of species and different estimates of interspecific genetic differentiation (Fst, Reynolds distance, G`st and Jost`s D) calculated for 16 nuclear (nuSSR) and 5 chloroplast (cpSSR) simple sequence repeat loci.
DOI: 10.5061/dryad.52582/5
title: Close et al. TNT input and output files

description: Input and output files for phylogenetic analyses using TNT
DOI: 10.5061/dryad.52582/6
title: CT scan of Palaeoxonodon ooliticus NMS G. 2015.17.10

description: X-Ray Computed Tomographic (CT) Scan of Palaeonxonodon ooliticus NMS G. 2015.17.10 in DICOM format
DOI: 10.5061/dryad.53j96/1
title: KERGUELEN data

description: Long–term dataset of capture–mark–recapture of feral cats collected at three sites in the Grande Terre Island of the Kerguelen archipelago (sub-Antarctic). The excel files contains three sheets. The first sheet contains the begining and the end of capture sessions and the population in which the capture session is performed. The second sheet contains variables that vary in time and between the populations. Here the only such variable is the Normalized Difference Vegetation Index (NDVI). Date stands for the year in which the NDVI is estimated. The last sheet contains information about captured individuals: identifier (ind), population (pop), sex (0 for females, 1 for males), age (in months), physical condition (PC) and the date of capture.
DOI: 10.5061/dryad.55610/1
title: Life history data of lizards of the world

description: Life is defined by a capacity for reproduction, yet the ways in which animals reproduce vary tremendously among species. Reproductive life histories are complex phenomena influenced by a variety of factors, such as physical condition of individuals, food supply, bauplan, and phylogenetic history, which are often correlated. Understanding life histories is crucial in evolutionary ecology because they represent different strategies that evolved to maximize individual fitness. Variation in life history can be attributed to both historical (= phylogenetic) and non-historical (= environmental) causes. We compiled a large dataset on lizard life history variables. Our dataset consists of life history data for 737 lizard populations, representing 337 species in 33 families from 280 study sites globally. About 64% of these data were collected directly by the authors. Regarding data collected by authors, we sexed lizards by dissection and direct examination of gonads. Females were considered reproductive if vitellogenic follicles or oviductal eggs were present. We regarded the simultaneous presence of enlarged vitellogenic follicles and either oviductal eggs or corpora lutea as evidence for the sequential production of more than one clutch of eggs per year. We considered clutch size as the number of vitellogenic follicles or oviductal eggs in mature females. For each population, we recorded the following variables, if available: adult female mass (g), adult female SVL (mm), female SVL at maturity (based on SVL of smallest reproductive female), offspring SVL (based on hatchling size or smallest individual in population), clutch or litter size (number of offspring per clutch or litter for all reproductive females in the population), total number of clutches or litters per year, clutch frequency (single- or multiple-brooded), relative clutch or litter mass [total volume of eggs or embryos (cc) divided by adult female mass (g)], reproductive mode (oviparous or viviparous), foraging mode (sit-and-wait or active), distribution (tropical or temperate), and preferred habitat type (aquatic, arboreal, bromelicolous, fossorial, psammophilous, saxicolous, semi-arboreal, or terrestrial). These data are valuable to test various life history hypotheses, including phylogenetic design constraints and effects of ecology and climate on reproductive tactics.
DOI: 10.5061/dryad.57433/1
title: Female size, clutch size, and mean egg mass.

description: This file contains data on body size, clutch size, and mean egg mass for females in the "Late" and "Early" treatments.  The columns are as follow: "treatment" (Early or Late), "pair" is a unique identifier for replicates within treatment, "carcass_mass" is the mass of the breeding carcass in grams, "female_family" identifies the family that the female was derived from, "female_pronotum" is the width of the female's pronotum in mm, "clutch_size" is the number of eggs laid, "mean_egg_mass(g)"  is the mean mass of eggs in grams.
DOI: 10.5061/dryad.57433/2
title: Breeding success data

description: This file contains data on breeding success from females in the "Late" or "Early" treatment.  The columns are as follow: "treatment" Late or Early, "pair" is a unique identifier of replicate within treatment, "carcass_mass" is the mass of the breeding carcass in grams, "female_family" is the family the female was derived from, "female_pronotum" is the females pronotum width in mm, "success" is whether the breeding attempt produced at least one dispersing larvae (1 = yes, 0 = no), "larvae" is the number of larvae at dispersal, "total_brood_mass" is the mass (in grams) of the entire brood at dispersal, "mean_larval_mass" is the mean mass (in grams) of larvae from each brood.
DOI: 10.5061/dryad.5t5s1/1
title: Combined full-length OTUs
DOI: 10.5061/dryad.5t5s1/2
title: Combined OTUs
DOI: 10.5061/dryad.5t5s1/3
title: metagenomic-cox1
DOI: 10.5061/dryad.6rg10/1
title: zhou&fuller_malecomp

description: Behavioral and chromatic data for male E. spectabile
DOI: 10.5061/dryad.78250/1
title: brix_robbingplots

description: Brix readings for flowers sampled from robbing treatment plots, "zc"=closed from all visitors, unrobbed, "ao"=open to all visitors, unrobbed, "er"=robbed, open to all visitors.
DOI: 10.5061/dryad.78250/2
title: ov_glmm_nozero

description: Nectar volume data from Oreocallis grandiflora flowers sampled in robbing treatment plots. "ind"= individual tree, "group"=plot, "treat"= robbing treatment ("zc"=closed to all visitors, unrobbed, "er"=open to visitors, robbed, "ao"=open to visitors, unrobbed), "ov" = nectar volume in microliters.
DOI: 10.5061/dryad.78250/3
title: visitation_robbedplots

description: Records of visits by different hummingbird species to flowers in nectar robbing treatment plots. "ind"=individual tree, "group"=plot, "treat"= treatment ("ao"=open, unrobbed, "er"=open, robbed), "day"=day since flower opening, "visits"=total number of visits per day, "duration"= time in hours that flower was observed, "bin"= presence/absence of visits, "agcu"=Aglaeactis cupripennis, "boma"=boissonneaua matthewsii, "coco"=Colibri coruscans, "covi"= Coeligena violifer, "heam"=Heliangelus amethysticollis, "mety"= Metallura tyrianthina, "unk"= unidentified hummingbird species.
DOI: 10.5061/dryad.78250/4
title: maternal reproduction

description: Seed set, mass, and seed length from Oreocallis grandiflora under different nectar robbing treatments. Treatments as follows: "c"=closed to visitors, unrobbed, "er"=open to visitors, robbed, "o"=open to visitors, unrobbed.
DOI: 10.5061/dryad.7b76q/1
title: Bergia_Montenegroetal2015

description: Zip file containing the full size, masked and concatenate alignments used for the phylogenetic reconstructions presented in Montenegro et al. (2015).
DOI: 10.5061/dryad.7dj7t/1
title: CRC GWAS data

description: We performed a genome-wide association studies (GWAS) and replicated the findings in seven independent samples from China. In the GWAS stage, 2,364 samples were enrolled from the Cancer Center of Nanjing Medical University. Genotyping for the GWAS stage was conducted using Illumina Human Omni ZhongHua Bead Chips for 900,015 SNPs. Individual-level genotype calls are in original file format as PLINK binary format.
DOI: 10.5061/dryad.84751/1
title: Sample information and microsatellite data or Lichenostomus melanops cassidix and L.m. cassidix.
DOI: 10.5061/dryad.857dd/1
title: Data For Depository Felton et al

description: Worksheet 1 contains observations of daily food intakes of six captive moose individuals included in the feeding experiment, which included 5 different treatments. The weight measurements are translated into nutrient intakes and displayed separately for pellets and browse items. Worksheet 2 contains daily data on individuals' browse and pellet intake per metabolic body weight, matched with the browse species offered, air temperature and browse availability.
DOI: 10.5061/dryad.8p0g8/1
title: Mortality, reproduction and body mass data used in paper

description: The reproduction tab has reproduction data. The mortality tag has mortality data. The weight tab has body mass data.
DOI: 10.5061/dryad.8s6n7/1
title: Diameter measurements for D. discoideum gametes and vegetative cells
DOI: 10.5061/dryad.9fp8k.1
title: Data from: A tool for determining duration of mortality events in archaeological assemblages using extant ungulate microwear
DOI: 10.5061/dryad.9fp8k.2/3.2
title: Background with boundaries and error probability

description: Boundary lines with the error probability (heat map) based on SD and CV values of microwear data used for the classification of samples into short events (region 1​), long-continued events (region 2), or two separated short events (region 3​).
DOI: 10.5061/dryad.9fp8k.2/4.2
title: g12.dat

description: Boundary between region 1 (short mortality events) and region 2 (longer mortality evens). The coordinates x (CV) and y (SD) of the points belonging to the curve have been calculated numerically for x in [0:1] and y in [0:10] and are reported in two columns with a space as separator.
DOI: 10.5061/dryad.9fp8k.2/5.2
title: g23.dat

description: Boundary between region 2 (longer than seasonal mortality events) and region 3 (two separated mortality evens). The coordinates x (CV) and y (SD) of the points belonging to the curve have been calculated numerically for x in [0:1] and y in [0:10] and are reported in two columns with a space as separator. Since the curve is not continuous, there is a blank line separating the two branches.
DOI: 10.5061/dryad.9fp8k.2/6.2
title: var.dat

description: Error probability in the range CV=[0:1],  SD=[1:10]. The values have been calculated numerically and are reported in three columns (CV, SD and the error probability value, respectively) with a space as separator. The step separating the values of CV is dCV=0.01 and that of SD is dSD=0.01.
DOI: 10.5061/dryad.9fp8k.2/7.2
title: Boundaries with transparent grid

description: ​Transparent grid to be superimposed to the heat map for positioning new samples according the SD and CV values.
DOI: 10.5061/dryad.c0s22/1
title: dataset

description: This zip file includes the raw datasets (Beijing and London street networks) and graphs created in the primal and dual space for Beijing, London, ERPG, and GRID. The raw datasets are ArcGIS shapefile format and the graphs are ‘pajek’ format.
DOI: 10.5061/dryad.c509n/1
title: Measurements of Rhagoletis pupae

description: Length and width measurements and hemispherical cylinder volume calculations of Rhagoletis fly pupae. These measurements represent field collected populations of apple-, blueberry-, and hawthorn-associated Rhagoletis fly pupae. We photographed the pupae and then processed all images with ImageJ to measure the pupae length and width. These measurements were used to calculate a hemispherical cylinder volume of each pupae.
DOI: 10.5061/dryad.c509n/2
title: Female D. alloeum body character measurements

description: Body character measurements of apple-, blueberry-, and hawthorn-associated populations of Diachasma alloeum wasps. These wasps were reared in the lab from field collected, Rhagoletis-infested apple, blueberry and hawthorn fruits. We used a Leica IC80HD camera attached to a Leica M125 dissecting microscope to photograph the wasps and then processed all images with ImageJ to measure the wasp body size characters.
DOI: 10.5061/dryad.d15v3/5
title: 26genes-less-85

description: 26 coding genes with the sequence identity less than 85%
DOI: 10.5061/dryad.d15v3/6
title: 10genes_less_80

description: 10 coding genes with sequence identity less than 80%
DOI: 10.5061/dryad.d15v3/7
title: concatenated_non_coding_95genes

description: 95 non-coding regions
DOI: 10.5061/dryad.d76mm/1
title: Am Nat data

description: Spring testosterone, corticosterone, fat, cp, gonad mass, and hydrogen isotope data from sympatric migrant and resident juncos.
DOI: 10.5061/dryad.dt059/1
title: Stable isotopic values of jaegers and their prey used in Ruffino et al. 2015 Ecography

description: Stable isotope values of long-tailed and parasitic jaegers' chick feathers in nothern Fennoscandian tundra. Values are arranged by year and study area. There were three study areas, scattered along a coast (Altafjord) - inland (highland tundra plateau of Joatka Reserch Area) gradient (see Figure 1 in Ruffino et al. 2015 in Ecography for details of study areas). Year 2011 was a rodent outbreak year (both Norwegian lemmings and voles) in our study areas, while in 2012 rodent abundances declined sharply. Values have been obtained after lipid extraction - Analyses were made at the Stable Isotope Laboratory of Environment Canada, Saskatoon, Canada. See also the supplementary files of Ruffino et al. 2015 for further details on how the stable isotopic analyses were conducted.
DOI: 10.5061/dryad.n7hc4/1
title: nest visits in focal and nearby pairs

description: Treatment effects on nest visits in focal and neighbouring pairs. Repeated measures model, type II approach. Predicted values in neighbouring nests during sparrowhawk presentation calculated in relation to mobbing latency in focal nests.
DOI: 10.5061/dryad.np600/1
title: Stickleback

description: This file contains the primary data underlying the publication, that is, three-spined stickleback brain (and body size) measurements. The second tab in sheet contains some explanations for abbreviations used in the header columns.
DOI: 10.5061/dryad.p4s57/1
title: chicken.all_samples.galGal3.tpm.refgene.osc

description: Data for the analysis of the chicken chromosome Z. FANTOM5 chicken libraries consisted of 25 CAGE libraries including: chicken aortic smooth muscles, hepatocytes, mesenchymal stem cells, leg buds, wing buds, embryo extra-embryonic tissue (day 7 and day 15), and whole body developmental time course (from 5 hours 30 minutes to 20 days). The number of available datapoints to which TPM was normalized was limited by the number of annotated chicken RefSeq transcripts (which was approximately six times smaller than human, N = 4,426 on autosomes, and N = 241 on chromosome Z). Consequently, the cutoff for a gene to be classified as “on” was adjusted six times higher to 60 TPM.
DOI: 10.5061/dryad.p4s57/2
title: human.tissue.hCAGE.hg19.tpm.refgene.osc

description: The FANTOM5 dataset for human tissue. CAGE tags were mapped to RefSeq transcripts +/-500 base pairs (bps) from their TSSes and normalized to tags per million (TPM), as previously described [37,45]. The signal of ten TPM was chosen as the cutoff for a gene to be classified as “on” (this cutoff was accepted as the standard for human data throughout the consortium). FANTOM5 is the most comprehensive expression dataset ever generated, including 952 human and 396 mouse tissues, primary cells and cancer cell-lines. FANTOM5 is based on cap analysis of gene expression (CAGE) a unique technology that characterizes TSSes across the entire genome in an unbiased fashion and at a single-base resolution level [21]. CAGE automatically sums expression levels of all transcripts beginning at a given transcription start site.
DOI: 10.5061/dryad.p4s57/3
title: human.primary_cell.hCAGE.hg19.tpm.refgene.osc

description: The FANTOM5 dataset for human primary cells.
DOI: 10.5061/dryad.p4s57/4
title: human.cell_line.hCAGE.hg19.tpm.refgene.osc

description: The FANTOM5 dataset for human cancer cell-lines.
DOI: 10.5061/dryad.qh0h1/2
title: Chronic diseases in older outpatients in German general practices (2014)

description: File includes 10,000 patients with following variables: an anonymous patient ID (1-10,000), age (years), gender (1 for male, 0 for female), diagnoses (1 for yes, 0 for no): hypertension, heart failure, chronic kidney disease, lipid metabolism, osteoporosis, COPD, CHD, cancer
DOI: 10.5061/dryad.rg58m/2
title: sections_250

description: This file contains the complete dataset of en-face sections at a resolution of 250x250 pixels. This file contains one dataset called 'sections' - this is a three dimensional array of uint8 values. The first axis is individual sections in the dataset. The second and third axes are the rows and columns of intensity values of that section.
DOI: 10.5061/dryad.s630c/1
title: Fasta alignment files for all genetic loci used

description: FASTA alignment files of the sequences for each molecular marker used in the current study. The number of individuals is indicated in the file name (e.g. N=122). Information concerning choice of loci, primers used and alignment optimisation is described in section 2.2 of the paper (2.2 DNA extraction & PCR), in Table S2 and section 2.3 Sequencing & alignments. The alignment files provided (and used in the paper) are the optimised alignments (i.e. sites in the alignment which consisted of one or a few individuals having a 1bp insertion were typically highlighted a bad following T-COFFEE analysis and were removed). The original sequences are available on GenBank (see Table S1).
DOI: 10.5061/dryad.s630c/2
title: Maximum likelihood tree files

description: Maximum likelihood tree files generated using RAXML for each nuclear intron and mtDNA and 6-nuclear intron partition.  Please see the ReadME file for the full data package for further information.
DOI: 10.5061/dryad.s630c/3
title: PAML MCMCTREE dated phylogeny

description: PAML MCMCTREE dated phylogeny based on the Bayesian 6-nuclear topology generated in BEAST. Please see the ReadME file for the full data package for further information.
DOI: 10.5061/dryad.s630c/4
title: Bayesian tree files - Gene Trees

description: Tree files for the Bayesian analysis (NEXUS format). All Bayesian analysis were conducted in BEAST v. 1.8. This is described in section 2.4 of the paper (2.4 Phylogenetic reconstruction). The files were generated using the software associated with BEAST: LogCombiner and TreeAnnotator as described in section 2.4. The LogCombiner files contain all trees generated from 3 independent runs with burn-in removed for each analysis (i.e. 27,000 trees); here called ‘LogC’ files. The TreeAnnotator files contain a single consensus topology generated from these 27,000 trees (a maximum clade credibility tree, keeping target node heights); here called ‘TAn’ files. ‘P’ in the file name simply stands for ‘partitioned’; however all phylogenetic analyses with more than one locus were partitioned whether this is stated in the file name or not. See Readme file section 3 for more information
DOI: 10.5061/dryad.sr8g0/1
title: Pérez i de Lanuza & Font_JEB2016_conspicuous_lizard_pattern

description: Presence/absence of both ventral and lateral conspicuous patches in lacertids
DOI: 10.5061/dryad.t87f0/1
title: PLOSONEdata
DOI: 10.5061/dryad.vn8km/1
title: List of chromosomes and crossover positions for the wt population

description: This is a tab-delimited text files with the format     .
DOI: 10.5061/dryad.vn8km/2
title: List of crossover positions for the recq4a mutant population

description: This is a tab-delimited text file with the format     .
DOI: 10.5061/dryad.vs4d3/1
title: Koopetal_Matlabcode

description: File contains MatLab code necessary for running model simulations.
DOI: 10.5061/dryad.vs4d3/2
title: Koop_DryadDataSubmission

description: File contains raw data used to calculate most model parameters.
DOI: 10.5061/dryad.vv804/1
title: Arabidopsis_data_279accessions_20jan16
DOI: 10.5061/dryad.06g12/1
title: Database Malagasy bats

description: Description of bats collected in Madagascar
DOI: 10.5061/dryad.0vm0s/1
title: Figure 2 data

description: Excel data file for results depicted in Figure 2 of Auge et al. (2016) paper.
DOI: 10.5061/dryad.0vm0s/2
title: Figure 3 data

description: Excel data file supporting the results depicted in Figure 3 of Auge et al. (2016) paper.
DOI: 10.5061/dryad.0vm0s/3
title: Figure 4 data

description: Excel data file supporting the results depicted in Figure 4 of Auge et al. (2016) paper.
DOI: 10.5061/dryad.0vm0s/4
title: Figure 5 data

description: Excel data file supporting the results depicted in Figure 5 of Auge et al. (2016) paper.
DOI: 10.5061/dryad.0vm0s/5
title: Table 1 data

description: Excel data file supporting the results depicted in Table 1 of Auge et al. (2016) paper.
DOI: 10.5061/dryad.19923/1
title: microsat_flanking_regions_for_networks

description: Alignments of phased sequences (in FASTA) at two microsatellite flanking regions used in constructions of median-joining networks.
DOI: 10.5061/dryad.19923/2
title: mitochondrial_alignment_for_starbeast

description: An alignment of concatenated Cyt-b and COI genes (in FASTA) used in a *BEAST analysis for inferring the divergence processes within the Murina gracilis complex. The XML input file of *BEAST is also provided.
DOI: 10.5061/dryad.19923/3
title: microsat_flanking_regions_for_starbeast

description: Alignments of phased sequences (in FASTA) at ten microsatellite flanking regions used in *BEAST analyses for inferring the divergence processes within the Murina gracilis complex. Prior to *BEAST analyses, all alignments except for that for the locus A122-2 are trimmed to be free from recombination. XML input files of *BEAST separately prepared for analyses with different demographic models are also provided.
DOI: 10.5061/dryad.19923/4
title: IMa2_input

description: The input of multi-taxon IMa2 which is used to infer the divergence processes within the Murina gracilis complex.
DOI: 10.5061/dryad.1sm6c/1
title: Jacquet_C.imicola_Efa_alignment.nex

description: Sequences of the nuclear gene Elongation factor alpha (Efa) of Culicoides imicola. Sequences were phased using the option phase implemented in DNASP v5.10 software. The two first letters of each sequence name, correspond to the location code described in Table 1.
DOI: 10.5061/dryad.1sm6c/2
title: Jacquet_C.imicola_microsatellite_data
DOI: 10.5061/dryad.1sm6c/3
title: Jacquet_C.imicola_COI_alignment.nex
DOI: 10.5061/dryad.1sm6c/4
title: Jacquet_C.imicola_Cytb_alignment
DOI: 10.5061/dryad.1sm6c/5
title: Jacquet_C.imicola_SamplesID
DOI: 10.5061/dryad.310nt/1
title: Datasets

description: The datasets include text files (z-position of thorax morphology), an R script file for visualization and sample reconstructed images (bmp, avi and webGL).
DOI: 10.5061/dryad.35jt8/2
title: Grouse MHC class II BLB sequences (all)

description: Grouse MHC class II BLB sequences (BLB1 and BLB2 locus). Aligned fasta file.