cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g33s9/3
title: J.haematoloma development times (F1 2014, F2 2014, F1 2013)

description: Development time from hatching to adulthood for J.haematoloma combined from 3 experiments. Column heading interpretation: Number=individual identifier (unique between experiments); Family=maternal identifier: NOT unique across experiments (explained in more detail below); bug.pop=location, city or island name, from which the individuals parents or grandparents were collected; host.pop=location, city or island name, from which natal host seeds were collected (not available for K.elegans in 2013); pophost=host species from which parents or grandparents were collected in the field; nathost=host species on which the individual was reared; hatch date=date an individual hatched (not available for 2013 data); eclosion date=date an individual reached adulthood (not available for 2013 data); sex=M is male, F is female; Dvpt.time=number of days after hatching before an individual reached adulthood; Experiment=which experiment the individual is from (F1 2014, F2 2014, or F1 2013); mate=identifier (Number) of the individual with whom each F1 2014 individual was mated (some individuals did not have suitable mates available or died before they became available; not applicable for F2 2014 or F1 2013 experiments). FAMILY elaboration: The family number for individuals in the F2 2014 experiment indicates the Number of the mother, all of whom were members of the F1 2014 experiment. Paternal identifiers can be determined from the mate of the mother. Family identifiers were reused between experiments.
DOI: 10.5061/dryad.j909k/1
title: West & Capellini NComm Male care dataset

description: The data file contains data on the presence/absence of male parental care behaviours, allocare, social monogamy, life history traits, and citation counts in mammalian species, at the global scale. Here we provide basic details of the variables included in the data file. The full description of the data and data collection protocols for all behavioural and life history traits can be found in the Methods section of the Nature Communications paper. The total sample size of species in this dataset is 529 mammals, although not all species have data for all variables.
DOI: 10.5061/dryad.k44f0/1
title: Evolutionary relationship of the Acinetobacter baumannii strains based on 16SrRNA sequences.

description: The evolutionary history was inferred using the Neighbor joining method. 1000 bootstrap re-samplings were done to estimate the consensus tree. The optimal tree with a sum of branch length = 0.5833 is shown. The tree is drawn to scale with branch lengths in same units as those of evolutionary distances used to infer the phylogenetic tree. The evolutionary distances were computed using the maximum composite likelihood method and are in the units of the number of base substitutions per site. A) Illustrates the complete phylogenetic tree of all the included strains and B) shows the enhanced view of the selected clads. The strains like A. baumannii AYE, A. baumannii A1, A. baumannii 307-0294 all belonging to IC I fall in the same clade, indicating phylogenetically closeness to their clonal strains. A. baumannii D1279779 expressed as a separate branch of the tree, validating the unique properties of this strain in between IC I and IC II. Similarly strains belonging to IC II appeared in single clad, showing their close phylogenetic relationships.
DOI: 10.5061/dryad.mm6jc/1
title: Zhang et al 2016 JAE repository data

description: Life-history, physiology and stoichiometry data of Daphnia magna from different time period (pre-fish or fish period) reared under different temperature (20 and 24 degrees celsius) and predation risks (presence or absence). For life history traits, maturity days, fecundity and intrinsic population growth rate were measured. For physiology, organismal protein, total sugar and total fat were measured. For stoichiometry, the C%, N%, P% and their ratios were tested. See manuscript and Supporting Information on the publisher's website for more guidance.
DOI: 10.5061/dryad.n2g80/13
title: figures_theropod_06-17-16

description: R script which, if executed from within the saved R environment, produces all figures in the manuscript and supplemental.
DOI: 10.5061/dryad.n2g80/14
title: makeBEAST2_majRule_02-05-16

description: An R script for obtaining half-compatibility trees with posterior probabilities on the edges from BEAST2 treelogs, albeit without branch lengths.
DOI: 10.5061/dryad.n2g80/15
title: mass_data_for_PCMs_BensonEtal14_10-27-14

description: Datafile of mass estimates for taxa, as obtained from the dataset supplied by Benson et al., 2014.
DOI: 10.5061/dryad.n2g80/16
title: MrBayesSA_100treeSample_burn03

description: The Posterior tree sample from MrBayes analysis.
DOI: 10.5061/dryad.n2g80/17
title: MrBayesSA_input_script

description: NEXUS input with MrBayes block for our MrBayes analysis.
DOI: 10.5061/dryad.n2g80/18
title: MrBayesSA_majrule_burn03

description: Half-compatibility summary for the MrBayes analysis
DOI: 10.5061/dryad.n2g80/19
title: MrBayesSA_mcc_burn03

description: Maximum clade compatibility summary for the MrBayes analysis
DOI: 10.5061/dryad.n2g80/20
title: theropod_tree_LeeWorthy2011_RAXML_02-01-16

description: NEXUS file containing an unscaled topology matching the RAXML tree presented in Lee & Worthy, 2011.
DOI: 10.5061/dryad.p51q8/1
title: Nectar availability in flowers of Heliconia spathocircinata

description: Availability of nectar in flowers uninfested with dipteran larvae and those infested, with two samples of nectar taken per flower from 70 flowers (at 8 a.m. and 11 a.m., n = 140) of unbagged and bagged inflorescences. In the bagged inflorescences, floral visitors were excluded to prevent the extraction of nectar.
DOI: 10.5061/dryad.p51q8/2
title: Floral visits by hummingbirds in Heliconia spathocircinata

description: Hummingbirds floral visits in Heliconia spathocircinata. Number of visits to flowers uninfested with dipteran larvae and those infested per two-hour period of monitoring (6 a.m. to 4 p.m.).
DOI: 10.5061/dryad.q530s/5
title: aligned_pseudomyrmex_genomes.tar

description: Six species of Pseudomyrmex were assembled based on alignments to the P. gracilis reference.
DOI: 10.5061/dryad.q530s/6
title: aligned_pseudomyrmex_genes.tar

description: Gene alignments for the seven Pseudomyrmex species sequenced. Genes that did not pass quality controls are not included.
DOI: 10.5061/dryad.1597g.2
title: Data from: Downscaled and debiased climate simulations for North America from 21,000 years ago to 2100AD
DOI: 10.5061/dryad.1597g.2/2.2
title: CCSM3 NA Climates 22ka-0ka, PET & AET

description: Downscaled and debiased paleoclimatic simulations from CCSM3 (Liu et al. 2009). Downscaled to 0.5deg lat/lon and decadal resolution for North America for 22,000 years ago to 20th century. Variables: potential evapotranspiration, actual evapotranspiration.
DOI: 10.5061/dryad.1597g.2/3.2
title: CCSM3 NA Climates 22ka-0ka, Precipitation

description: Downscaled and debiased paleoclimatic simulations from CCSM3 (Liu et al. 2009). Downscaled to 0.5deg lat/lon and decadal resolution for North America for 22,000 years ago to 20th century. Variables: mean total monthly precipitation
DOI: 10.5061/dryad.1597g.2/31.2
title: CCSM3 NA Climates 22ka-0ka, Min & Max Temperature

description: Downscaled and debiased paleoclimatic simulations from CCSM3 (Liu et al. 2009). Downscaled to 0.5deg lat/lon and decadal resolution for North America for 22,000 years ago to 20th century. Variables: mean minimum daily temperature, mean maximum daily temperature
DOI: 10.5061/dryad.1597g.2/4.2
title: CCSM3 NA Climates 22ka-0ka, Growing Degree Days

description: Downscaled and debiased paleoclimatic simulations from CCSM3  (Liu et al. 2009). Downscaled to 0.5deg lat/lon and decadal resolution for North America for 22,000 years ago to 20th century. Variables: growing degree days, 5C & 0C.
DOI: 10.5061/dryad.1597g.2/5.2
title: CCSM3 NA Climates 22ka-0ka, Net Downward Longwave Radiation

description: Downscaled and debiased paleoclimatic simulations from CCSM3  (Liu et al. 2009). Downscaled to 0.5deg lat/lon and decadal resolution for North America for 22,000 years ago to 20th century. Variable: mean monthly net downward longwave radiation at surface
DOI: 10.5061/dryad.1597g.2/6.2
title: CCSM3 NA Climates 22ka-0ka, Downward Shortwave Radiation

description: Downscaled and debiased paleoclimatic simulations from CCSM3  (Liu et al. 2009). Downscaled to 0.5deg lat/lon and decadal resolution for North America for 22,000 years ago to 20th century. Variable: mean monthly downward shortwave radiation at surface.
DOI: 10.5061/dryad.1597g.2/7.2
title: CCSM3 NA Climates 22ka-0ka, Upward Shortwave Radiation

description: Downscaled and debiased paleoclimatic simulations from CCSM3  (Liu et al. 2009). Downscaled to 0.5deg lat/lon and decadal resolution for North America for 22,000 years ago to 20th century. Variable: mean monthly upward shortwave radiation at surface.
DOI: 10.5061/dryad.24v57/1
title: Table 1 MC1R and ASIP genotype in total population

description: Genotype of the MC1R and ASIP gene in 328 samples from Creole sheep breed classified in color groups.
DOI: 10.5061/dryad.24v57/2
title: Table 2 MC1R and ASIP genotype in Quantification experiment

description: Genotype of MC1R and ASIP gene, color group classification and Real Time PCR Ct in 82 samples from expression quantification experiment.
DOI: 10.5061/dryad.24v57/3
title: Table 3 Colorimetric parameters in total population

description: Colorimetric parameters data in CIELAB color space in 115 wool samples from Creole sheep breed.
DOI: 10.5061/dryad.24v57/4
title: Table 4 Colorimetric parameters in quantification experiment

description: Colorimetric parameters in CIELAB color space in 82 wool samples from expression quantification experiment
DOI: 10.5061/dryad.24v57/5
title: Aligment MC1R gene total samples

description: Sequence alignment from MC1R gene in 328 samples from Creole sheep breed.
DOI: 10.5061/dryad.2v1p6/10
title: Dataset S6

description: Voucher numbers, locality information, and genetic cluster assignment of sampled specimens.
DOI: 10.5061/dryad.2v1p6/11
title: Dataset S7

description: Distribution records used in species distribution models of A. punctatus and A. ortonii.
DOI: 10.5061/dryad.2v1p6/12
title: Dataset S8

description: Atlantic Forest specimens used in spatial demographic models.
DOI: 10.5061/dryad.2v1p6/13
title: Table S1

description: Posterior distributions of parameters estimated in spatial demographic models.
DOI: 10.5061/dryad.2v1p6/15
title: Fig S1

description: Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (Atlantic Forest I).
DOI: 10.5061/dryad.2v1p6/16
title: Fig S2

description: Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (Atlantic Forest II).
DOI: 10.5061/dryad.2v1p6/17
title: Fig S3

description: Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (eastern Amazonia).
DOI: 10.5061/dryad.2v1p6/18
title: Fig S4

description: Plots of the posterior distributions of parameters and PCA from population-level demographic analyses (western Amazonia).
DOI: 10.5061/dryad.2v1p6/19
title: Fig S5

description: Plots of the posterior distributions of parameters and PCA from multi-population demographic analyses based on the aSFS.
DOI: 10.5061/dryad.32s2t/1
title: Temperature data for gardens

description: Data for climate from three common garden sites, Ephraim, Majors Flat, and Orchards.
DOI: 10.5061/dryad.32s2t/2
title: Three garden survival

description: Data for survival of Artemisia tridentata (Big Sagebrush) from three common garden sites.
DOI: 10.5061/dryad.32s2t/3
title: Population climate data

description: Climate data from 55 source populations.
DOI: 10.5061/dryad.3813d/1
title: Wagner et al_patch_adjustments

description: This file contains data on the number of patches by which each replicate was "adjusted" in each generation. See the treadmill metaphor of the main text.
DOI: 10.5061/dryad.3813d/2
title: Wagner et al_raw data

description: Raw data on beetle densities in each patch for each replicate in each generation.
DOI: 10.5061/dryad.3813d/3
title: Wagner et al_treatment_assignments

description: Source population composition of each replicate.
DOI: 10.5061/dryad.69bj8/2
title: Survival of butterflies

description: Parasite treatment: 1- yes; 2-no; Plant species: 1, asperula; 2, curassavica; 3, incarnata; 4, linaria; 5, perennis; 6, physocarpa; 7, incarnata pulchra; 8, tuberosa
DOI: 10.5061/dryad.70628/1
title: Supplementary data and figures

description: This file contains an annotated list of independent origins of parasitism in Animalia, derived from an extensive search of available literature.  Monophyletic parasite groups for which the closest free-living relatives are known are listed in an additional table, including species and genera counts and estimated age of divergence for each pair. The file also contains the approximately 300 references used to identify parasite clades and compare species diversity between parasite and free-living sister groups.
DOI: 10.5061/dryad.7b191/1
title: 2012_common garden data

description: two tabs provide data collected in 2012 from two common garden experiments
DOI: 10.5061/dryad.7qv72/22
title: concat_cut

description: see readme_align.txt
DOI: 10.5061/dryad.7qv72/23
title: Fig2A_FigS3A_Dikary39.NOcal_lnrootP_sample.chronogram

description: Tree file underlying Fig2A. See readme_align.txt
DOI: 10.5061/dryad.7qv72/24
title: Fig2B_Fig3B_RAxML_bipartitions.cystos_130316_correct_names

description: Tree file underlying Fig. 2B. See readme_align.txt
DOI: 10.5061/dryad.7qv72/25
title: FigS4_Dikary39.1calConcat_lnrootP_sample.chronogram

description: Tree file underlying Fig. S4. See readme_align.txt
DOI: 10.5061/dryad.7qv72/26
title: FigS5_Dikary39.4cal_lnrootP_sample.chronogram

description: Tree file underlying Fig. S5. See readme_align.txt
DOI: 10.5061/dryad.7qv72/27
title: FigS12_RAxML_bipartitions.cystosITS_120316_correct_names.test

description: Tree file underlying Fig. S12. See readme_align.txt
DOI: 10.5061/dryad.7qv72/28
title: FigS13_RAxML_bipartitions.cystosLSU_120316_correct_names.test

description: Tree file underlying Fig. S13. See readme_align.txt
DOI: 10.5061/dryad.7qv72/29
title: FigS14_RAxML_bipartitions.cystosSSU_120316_correct_names.test

description: Tree file underlying Fig. S14. See readme_align.txt
DOI: 10.5061/dryad.7qv72/30
title: MLSuperMatrix.wIC.75BTSP.CONSENSE

description: Alignment used for internode uncertainty analysis
DOI: 10.5061/dryad.c5h4p/1
title: Data files

description: Data to analyse occupancy rate
DOI: 10.5061/dryad.c5h4p/2
title: hoopoe_chicknumber

description: Data to analyse effect of molecrickets on current reproductive success
DOI: 10.5061/dryad.d0m4r/1
title: Diversification_butterfly_Dryad

description: R Code for diversification rate analyses using published chronograms of Neotropical butterflies
DOI: 10.5061/dryad.d0m4r/2
title: Tree_simulation_Dryad

description: R Code for simulated phylogenies, diversification rate analyses, and LTT plots
DOI: 10.5061/dryad.f9k77/1
title: Annotated seedhead images

description: Zip file containing multiple Powerpoint files, each containing images of sunflower heads with parastichies overlaid and counted
DOI: 10.5061/dryad.f9k77/2
title: JS annotations for MSF007_Countdata

description: Summary of parastichy counts made by author when photoreviewing images in associated Powerpoint file
DOI: 10.5061/dryad.g0v02/1
title: DNA sequence alignments per superfamily

description: Cox1 and 28S DNA sequence alignments of each superfamily of shelled gastropods and brachyuran crabs analyzed in the study. Cox1 alignments include only haplotypes. Cox1 datasets were supplemented with DNA sequences from Canadian marine shelled gastropods and North East Pacific brachyuran crabs available on BOLD. Cox1 and 28S alignments include an outgroup. Alignments were generated using MAFFT v. 7 (Katoh et al. 2002; Katoh & Toh 2010) with the FFT-NS-I option. Alignments were used to generate Maximum Likelihood implementations.
DOI: 10.5061/dryad.g0v02/2
title: Tree figures

description: Figures of the phylogenetic trees produced in this study using Cox1 and 28S datasets. For each superfamily are represented the ML tree based on 28S dataset, and the PTP and GMYC trees produced using Cox1 datasets. Trees were built using Maximum Likelihood (ML) implementations using the GTR+GAMMA model of rate substitution (the most inclusive model) inferred using RAxML HPC2 (Stamatakis 2006) on Teragrid v.7.2.7, implemented in the Cyber Infrastructure for Phylogenetic Research (CIPRES) portal v.3.1. (Miller et al. 2011). One hundred independent searches, each starting from distinct random trees, were conducted. Robustness of the nodes was assessed using nonparametric bootstrapping (Felsenstein 1985) with 1000 replicates. For Cox1 datasets, the resulting tree served as input for the PTP model. For GMYC, the ML trees were made ultra-metric using r8s (Sanderson 2003). Trees were calibrated using divergence time and absolute rate of substitution between roots (fixed to have an arbitrary age of 1.0) and all unfixed nodes. Calibrations were reconstructed using the Langley-Fitch method and Powell’s algorithm (Sanderson 2003). PTP and GMYC analyses were both run using the ETE package (Huerta-Cepas et al. 2010).
DOI: 10.5061/dryad.g0v02/3
title: Presence-absence matrices

description: Six presence-absence matrices generated to detect non-random species co-occurrence patterns using EcoSim (Gotelli & Entsminger 2004). Rows correspond to the species sampled in this study. Columns correspond to the sampled sites analyzed.
DOI: 10.5061/dryad.g33s9/4
title: Simulated development time code

description: This file includes: 1) Code for data extraction of development times from Figure 3 of Carroll et al 1997; note that the exact pixel values will differ depending on how you size and crop the image. 2) Code for simulating 1000 (or however many you want) datasets using the means and standard deviations of 1988 and 2013-2014 data. 3) Code for statistical comparison of all 1000 datasets for the complete dataset and within each host plant. Code for model selection is not included (but could be added if requested).
DOI: 10.5061/dryad.gr6t5/1
title: Reciprocal translocation experiment

description: Data from a reciprocal translocation experiment on hatching success and viability of hatched larvae through the yolk sac phase for pike eggs that were artificially fertilized and then reared in cages using a split-brood design such that half were planted at ’home’ in their native and half were transplanted and reared ’away’ in a foreign spawning habitat. Data is provided for 2466 individual eggs that were produced by females representing two different subpopulations from the Baltic Sea. The file includes information on population origin, spawning habitat location, family ID, translocation treatment, hatching status, and survival.
DOI: 10.5061/dryad.gr6t5/2
title: Data on female reproductive investment in pike from two subpopulations

description: Data on body size and reproductive investment for 46 female pike from two anadromous populations in the Baltic Sea. The file includes information on population, fish ID, date of capture, body length, somatic mass, egg mass, and gonad dry mass.
DOI: 10.5061/dryad.hb34s/1
title: Data from: The efficacy and safety of bevacizumab plus erlotinib versus bevacizumab or erlotinibalone in the treatment of non-small-cell lung cancer: a systematic review and meta-analysis
DOI: 10.5061/dryad.n2g80/21
title: theropod_tree_XuEtAll2011_FigS6_02-01-16

description: NEXUS file containing an unscaled topology matching the tree presented in Figure S6 of Xu et al., 2011.
DOI: 10.5061/dryad.n2g80/22
title: timeList_sorted_asIs_theropods_DWB_11-05-14

description: A timeList object for these taxa, structured as is necessary for use with paleotree, describing their stratigraphic ranges in discrete intervals.
DOI: 10.5061/dryad.n2g80/23
title: TNT_most_parsimonious_trees

description: Sample of 100 most parsimonious trees taken from our TNT analysis.
DOI: 10.5061/dryad.pn8mn/1
title: SI_factorial

description: Data from comprehensive screen.
DOI: 10.5061/dryad.pn8mn/2
title: SI_reactivity_screen

description: Data from reactivity screen.
DOI: 10.5061/dryad.t1d8k/1
title: Alligator gar daily age data

description: Data from daily age estimates, including precision, accuracy, and relations between otolith and fish size for hatchery-reared Alligator Gar. The excel file contains 3 tabs, each labeled descriptively.
DOI: 10.5061/dryad.t1d8k/2
title: CT Xray images 1of2

description: 1 of 2 zip file archives of CT x-ray scans of the head of an Alligator Gar. Images are in 16bit TIFF format: Scan parameters: NSI scanner.  Feinfocus source, high power, 150 kV, 0.18 mA, no filter, Perkin Elmer detector, 0.5 pF gain, 2 fps (499.893 ms integration time), no binning, no flip, source to object 293.346 mm, source to detector 1066 mm, continuous CT scan, no frames averaged, 0 skip frames, 3600 projections, 6 gain calibrations, 15 mm calibration phantom, data range [-1.671085, 8.845427], beam-hardening correction = 0.1. Voxel size = 0.066 mm. Slices = 1-942 in this archive.
DOI: 10.5061/dryad.t1d8k/3
title: CT Xray images 2of2

description: 2 of 2 zip file archives of CT x-ray scans of the head of an Alligator Gar. Images are in 16bit TIFF format: Scan parameters: NSI scanner. Feinfocus source, high power, 150 kV, 0.18 mA, no filter, Perkin Elmer detector, 0.5 pF gain, 2 fps (499.893 ms integration time), no binning, no flip, source to object 293.346 mm, source to detector 1066 mm, continuous CT scan, no frames averaged, 0 skip frames, 3600 projections, 6 gain calibrations, 15 mm calibration phantom, data range [-1.671085, 8.845427], beam-hardening correction = 0.1. Voxel size = 0.066 mm. Slices = 942-1883 in this archive.
DOI: 10.5061/dryad.v286m/1
title: Traits and characteristics of fish

description: This table present the traits (sex, body size, weight, origin, ID, offspring number) and experimental treatment of brown trout spawners used for the experiment described in the associated reference. The experimental treatment is flow manipulation (constant versus stochastic), and fish originate from two rivers (Bastan, France, and Urumea, Spain).
DOI: 10.5061/dryad.091v0/1
title: 3-D cranial landmark dataset for Macaca fuscata

description: Excel spreadsheet with 61 3-D cranial landmarks for 181 specimens of Macaca fuscata with specimen numbers and division into five groups: infant, juvenile, subadult, adult female and adult male.  Data described in detail in Goswami and Polly (2010)
DOI: 10.5061/dryad.127fg/1
title: Tree ring and competiton data from northeast Washington, USA

description: Data collection methods are described in Methods. Tree-level completion data was collected in the field and tree ring data was measured in laboratory using standard techniques. Year = Calendar year of tree ring; ST_ID = Unique ID for each subject tree; Canopy_Class = Canopy position of subject tree, either dominant (DO) or intermediate (IN); ST_DBH = diameter at breast height of subject tree; HCI = Hegyi's Competition Index; DIB = Diameter inside bark; Comp_Class = Categorical grouping based on HCI; SW = avg. distance (cm) of sapwood on increment cores; Age = age at breast height when tre was sampled; Stand_ID = Unique ID for each stand; PLW_Class = Categorical grouping based on PLW; BAI = Basal area increment; BAI.rwi = Index based on BAI; EWA = Earlywood area increment; EWA.rwi = Index based on EWA; LWA = Latewood area increment; LWA.rwi = index based on LWA; PDSI = Palmer Drought Severity Index for NCDC WA Div 9; PLW = Proportion of latewood