cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.25m47/1
title: R script and data files
DOI: 10.5061/dryad.26820/1
title: TE_FBD_Supplemental

description: Supplemental Tables and Figures for manuscript "Total-Evidence Dating under the Fossilized Birth-Death Process".
DOI: 10.5061/dryad.2752g/1
title: Hatchability of eggs in crosses between Samia cynthia ssp.

description: These are original dataset to Figure 2 and Supplementary Table S1. Hatchability of eggs in the control (C), parental (P) and F1 crosses, and backcrosses (B1) between Samia cynthia walkeri (SCW) and Samia cynthia pryeri (SCP).
DOI: 10.5061/dryad.2ss46/1
title: Online Appendix 1

description: AICC SCORES OF MODELS FIT TO EMPIRICAL DATASETS
DOI: 10.5061/dryad.2ss46/2
title: Online Appendix 2

description: BM SIMULATIONS UNDER VARYING MODEL PARAMETERS
DOI: 10.5061/dryad.2ss46/3
title: Online Appendix 3

description: SIMULATION EXPERIMENT DEMONSTRATING THE EQUIVALENCE BETWEEN THE CENSORED APPROACH (O’MEARA ET AL. 2006) AND THE RATE METHOD USING A DESIGN MATRIX FOR GROUP MEANS (THOMAS ET AL. 2006, 2009)
DOI: 10.5061/dryad.46qm6/1
title: AllData_Exp1

description: Behavioral data Exp.1 in .mat format
DOI: 10.5061/dryad.46qm6/2
title: AllData_Exp2
DOI: 10.5061/dryad.46qm6/3
title: AllData_Exp3
DOI: 10.5061/dryad.46sp7/1
title: cyprochromis dryad deposit

description: Microsatellite genotypes of mothers, fry and population samples used in paternity analyses
DOI: 10.5061/dryad.5d3s2/1
title: Data for depositing
DOI: 10.5061/dryad.5m30d/1
title: Nachusa_site_characteristics

description: Characteristics of each site in the study, including age, species richness, MPD and MNTD of plant community and seed mixture applied, summer precipitation in the first year of growth, and number of high-priority exotic plant species present.
DOI: 10.5061/dryad.5m30d/2
title: Nachusa_plant_communities

description: Presence/absence of plant species in each survey site.
DOI: 10.5061/dryad.5m30d/3
title: Nachusa_seed_mixes

description: Species included in seed mixes applied to 16 of 19 surveyed restoration sites.
DOI: 10.5061/dryad.6p566/2
title: Data from Marine fouling assemblages on offshore gas platforms in the southern North Sea

description: This data was collected to determine whether the composition and the abundance of species assemblages changes with depth and along a distance from shore gradient. The species assemblage on offshore gas platforms in the Dutch part of the North Sea was inventoried using ROV inspection footage. The dataset contains observations of 11 species on 5 of these platforms.
DOI: 10.5061/dryad.7b2s3/1
title: rabosky_evolution
DOI: 10.5061/dryad.7bq5t/1
title: Allografts in guppies
DOI: 10.5061/dryad.8428t/1
title: nematode fights data JEB
DOI: 10.5061/dryad.9r35r/1
title: Dataset - Harmon et al 2015

description: Excel Results file for Harmon et al 2015.
DOI: 10.5061/dryad.9v2g5/1
title: Genotype data

description: Microsatellite genotype of 869 Myriophyllum spicatum inviduals from 58 populations.
DOI: 10.5061/dryad.9v2g5/2
title: Bioclim data

description: Bioclim variables (Bio1-Bio19) for the 43 sites used in landscape genetic analysis.
DOI: 10.5061/dryad.b8d0g/2
title: Andersen PLoS One 2015

description: This file contains data used to generate the figures in this manuscript.
DOI: 10.5061/dryad.bn987/1
title: Dynamic Stability Measures and Demographics

description: Spreadsheet containing demographics of subjects and their dynamic stability measures over 2 sessions.
DOI: 10.5061/dryad.cq983/1
title: Worm counts

description: Counts of the number of each worm species remaining during the worm species interaction experiment.
DOI: 10.5061/dryad.cq983/2
title: Crayfish data for worm interaction experiment

description: Metadata for all crayfish used in symbiont interaction experiment.
DOI: 10.5061/dryad.cq983/3
title: SURVEY

description: Worms observed during field survey.
DOI: 10.5061/dryad.cq983/4
title: Crayfish survey

description: Metadata for crayfish collected during field survey.
DOI: 10.5061/dryad.cq983/5
title: behave_exp

description: Behaviors observed during behavior experiment.
DOI: 10.5061/dryad.cq983/6
title: cray_exp

description: Metadata for crayfish used during behavior experiment.
DOI: 10.5061/dryad.cr0mb/22
title: Fastq Files for H.erythrogramma, gastrula stage

description: These are fastq files for H.erythrogramma, gastrula stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.cr0mb/23
title: Fastq Files for H.erythrogramma, prism "early larva" stage

description: These are fastq files for H.erythrogramma, prism "early larva" stage. There are three replicates, two are 50 bp PE and one is 50 bp SE
DOI: 10.5061/dryad.cr0mb/24
title: S1_Data

description: Log2-transformed, normalized count data
DOI: 10.5061/dryad.cr0mb/25
title: S2_Data

description: Mfuzz Data for cluster generation in L. variegatus, c=7
DOI: 10.5061/dryad.cr0mb/26
title: S3_Data

description: Standardized, mean expression profiles of normalized, log2-transformed counts
DOI: 10.5061/dryad.cr0mb/27
title: S4_Data

description: Jump scores
DOI: 10.5061/dryad.cr0mb/28
title: S5_Data

description: Mfuzz Data for cluster generation in L. variegatus, c=5
DOI: 10.5061/dryad.cr0mb/29
title: S6_Data

description: Mfuzz Data for cluster generation in L. variegatus, c=9
DOI: 10.5061/dryad.d6rb0/1
title: Bean_Communication_Data
DOI: 10.5061/dryad.d6rb0/2
title: BeanCommAnalysis
DOI: 10.5061/dryad.f098g/1
title: Field experiment data, G3s
DOI: 10.5061/dryad.f098g/2
title: Germination data for field collected seeds

description: ID's are cross-listed with ID's from Field data file
DOI: 10.5061/dryad.g0m5s/1
title: EdwardsEtAl_Ecology&Evolution2015_ArchivedData

description: Transcriptome assembly .fasta file, SNP data .vcf, and shared genotype information used in Edwards et al. 2015
DOI: 10.5061/dryad.g1m27/1
title: BTBW_annual_data

description: Annual summaries of field data on black-throated blue warbler reproduction (1986-2010) gathered at the Hubbard Brook Experimental Forest in Thornton, NH, USA. Notes on column headings are as follows: prop.F.ASY = proportion older (ASY) females; Acsa.budburst = day of sugar maple (Acer saccharum) budburst (Day 1 = 01 January); Acsa.canopy = day of nearly complete (90%) expansion of sugar maple leaves; arrival.50 = median arrival date of male black-throated blue warblers; clutch.init.50 = median clutch initiation date of black-throated blue warblers; mean.cats = mean dry caterpillar biomass (mg/8000 leaves) across the whole season; ln.mean.cats = seasonal mean dry caterpillar biomass, natural log-transformed; mean.first.cats = mean dry caterpillar biomass (mg/2000 leaves) in the early season; ln.first.cats = mean dry caterpillar biomass (mg/2000 leaves) in the early season, natural log-transformed; high_day = day of the count with the highest caterpillar biomass; density = breeding black-throated blue warblers per 64ha; survival = daily nest survival rate; mean.fledged = average annual reproductive success (mean number of young fledged per pair per year).
DOI: 10.5061/dryad.gb905/1
title: Seabird distance sampling data

description: This .R file contains all data to repeat the community distance sampling case study on seabird abundance and distribution off the mid-Atlantic coast presented in the associated paper. The data are in the form of a R list object; the R script to read in and analyze the data are part of the Supplement 2, available with the paper. The ReadMe file contains a detailed description of the data.
DOI: 10.5061/dryad.jd6ff/1
title: SM dataset MS Ducatez et al. JEB
DOI: 10.5061/dryad.k6tq2/1
title: Binned Analyses

description: Results of ML analyses of matrices binned according to rate of locus evolution. Separate analyses were carried out for 60-, 108-, and 216-locus bins. The text files contain support for the topologies of interest.
DOI: 10.5061/dryad.k6tq2/2
title: Code

description: Scripts used in analyses and plotting selected figures. See also    https://github.com/marekborowiec/metazoan_phylogenomics/blob/master/gene_stats.R
DOI: 10.5061/dryad.k6tq2/3
title: Partition Statistics

description: Spreadsheet containing data for all of the partition-specific statistics used to construct the various matrices described in the paper.
DOI: 10.5061/dryad.mb580/6
title: galloprovincialis_19C_guanidine

description: SANS and USANS scattering data after subtraction for Mytilus galloprovincialis plaques created at 19C water temperature and subjected to guanidine hydrochloride treatment.
DOI: 10.5061/dryad.mb580/7
title: induced_plaque_scattering

description: SANS and USANS scattering data after subtraction for Mytilus californianus induced plaques created at room temperature via KCl injection at the pedal ganglion. For particular times of collection after first appearance of secretion and whether they were submerged in seawater or not, read the ReadMe file.
DOI: 10.5061/dryad.r4342/10
title: Assembly of BACs

description: Assembly of the BAC sequences with SPAdes assembler, removing the low coverage scaffolds.
DOI: 10.5061/dryad.r4342/11
title: Genome assembly of Lymnaea stagnalis

description: The genome of Lymnaea stagnalis assembled with SOAPdenovo using PE and MP libraries.
DOI: 10.5061/dryad.r4342/9
title: qPCR raw data

description: The data in this files relates to Figure 1, Figure S2a and text in the Supplementary Information. Further detail within the file.
DOI: 10.5061/dryad.r4691/1
title: 3D pdfs of specimens

description: Two 3D pdfs, one of DGUF-145 and one of DGUF-146. Both images may be rotated, and the bony matrix, teeth, and an individual tooth may be viewed separately.
DOI: 10.5061/dryad.r4691/2
title: DGUF145
DOI: 10.5061/dryad.r4691/3
title: DGUF146
DOI: 10.5061/dryad.rn931/1
title: GP_Pharmacy_Survey_Data_London

description: London General Practitioner and London Pharmacist responses to survey (questions given as Appendices in manuscript)
DOI: 10.5061/dryad.vh5ht/1
title: Rat & phantom MRI data

description: This file contains the raw data (not the k-space, but the reconstructed magnitude and phase data) of the MR measurements.
DOI: 10.5061/dryad.vm72v/1
title: Benthic_PAD-June2012_F230-BE_Dryad_submission
DOI: 10.5061/dryad.0tc6q/1
title: Microsatellite data of European moose from 16 localities

description: GenAlex input file, data of 14 microsatellite loci
DOI: 10.5061/dryad.2c088/1
title: Jiménez&Ornelas_IMa_BERYvsHYB_mt

description: BERY (Amazilia beryllina) populations west of the Isthmus of Tehuantepec versus HYBRID populations east of the IT (Amazilia beryllina and Amazilia cyanura), combining mitochondrial markers (ND2 and ATPase 6-8).
DOI: 10.5061/dryad.2c088/2
title: Jiménez&Ornelas_IMa_SAUCvsHIB_mt

description: SAUC (Amazilia saucerottei) populations south of the Nicaraguan Depression versus HYBRID populations between the Nicaraguan Depression and the Isthmus of Tehuantepec (Amazilia saucerottei and Amazilia cyanura), combining mitochondrial markers (ND2 and ATPase 6-8).
DOI: 10.5061/dryad.2c088/3
title: Jiménez&Ornelas_IMa_BERYvsSAUC_mt

description: BERY (Amazilia beryllina) populations west of the Isthmus of Tehuantepec versus SAUC (Amazilia saucerottei) populations south of the Nicaraguan Depression, combining mitochondrial markers (ND2 and ATPase 6-8).
DOI: 10.5061/dryad.2c088/4
title: Jiménez&Ornelas_Microsatellites_info

description: Microsatellite sizing for 145 hummingbirds samples genotyped at twelve autosomal microsatellite loci previously designed for Amazilia cyanocephala (A1-3-5, A1-4-1, A2-1-2 and A2-5-3; Molecular Ecology Resources Primer Development Consortium et al., 2013), Campylopterus curvipennis (Cacu1-10, Cacu4-8, Cacu13-1, Cacu13-7; Molecular Ecology Resources Primer Development Consortium et al., 2010) and Selasphorus platycercus (HumB1, HumB2, HumB3, HumB9; Oyler-McCance et al., 2011). Microsatellite sizing for each loci consists in 3 digits (e.g. 222  for 82442 at loci A1-3-5).Numbers of POP correspond to sampling localities. Refer Table S4 for sampling locality information. ID corresponds to individual identifiers of the samples worked in this study.Genbank accession numbers for mitochondrial information is available for each sample; samples with no Genbank accession number were not sequenced for mitochondria. Missing data code= 0
DOI: 10.5061/dryad.2c088/5
title: Jiménez&Ornelas_Morphology_info

description: Plumage color variation of 145 adult hummingbirds assessed using a qualitative index created by summing up the scores of 10 morphological characters (rufous patch on secondary feathers, rufous patch on primary feathers, undertail feathers, belly color, throat and chest color, wings, upper tail feathers, back color, tail color, rachis color on tail feathers).Sex: male; female.Collection number corresponds to individual identifiers of the samples worked in this study.Sex: male; female.Collection number corresponds to individual identifiers of the samples worked in this study.
DOI: 10.5061/dryad.2sq1r/1
title: A database of the size of all extant or extinct mammals from the Holocene or Late Pleistocene

description: An excel-sheet with the sizes and island status of all mammalian species. A full description is found in the first worksheet entitled Metadata
DOI: 10.5061/dryad.2ss46/4
title: Online Appendix 4

description: SIMULATION EXPERIMENT TO INVESTIGATE WHETHER R-PACKAGES OUWIE AND MOTMOT PROVIDE COMPARABLE PARAMETER ESTIMATES AND LIKELIHOOD SCORES
DOI: 10.5061/dryad.2ss46/5
title: Online Appendix 5

description: VARIATION IN EVOLUTIONARY RATES ESTIMATED BY DIFFERENT MODELS FIT TO DATA SIMULATED WHILE VARYING RELATIVE OPTIMA AND RELATIVE RATES PARAMETERS
DOI: 10.5061/dryad.2ss46/6
title: R-code

description: R-code used for all tree and phenotypic data simulations, and for fitting different models to the simulated data. Please see the ReadMe file for details.
DOI: 10.5061/dryad.2v462/1
title: All_birds_MaxCladeCredTree

description: Maximum Clade Credibility tree (MCC) from 1000 time-calibrated Bayesian posterior phylogenies of all birds evenly sampled from the Bayesian posterior distribution of trees provided by Jetz et al. (2012). Including the large Neotropical family Furnariidae (Derryberry et al. 2011). MCC tree was calculated in TreeAnnotator v 2.1.3 (implemented in BEAST; Heled and Bouckaert 2013) using median node ages.
DOI: 10.5061/dryad.2v462/2
title: Bayesian_sample_1000_posterior_trees

description: Bayesian sample of 1000 posterior phylogenies of all birds evenly sampled from the Bayesian posterior distribution of trees provided by Jetz et al. (2012). Including the large Neotropical family Furnariidae (Derryberry et al. 2011).
DOI: 10.5061/dryad.3ck0v/1
title: nuclear3

description: Three gene alignment of double-stranded RNA-specific editase, 1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase class I & II, and lysine-specific demethylase lid
DOI: 10.5061/dryad.46qm6/4
title: AllData_Exp4
DOI: 10.5061/dryad.4jr00/1
title: C:N ratio raw data from seagrass meadows in Kertinge Nor & Dalby Bay, Denmark

description: Raw data for calculation of C:N ratios of sediment, seagrass and algae
DOI: 10.5061/dryad.4jr00/2
title: Fish stomach content data from seagrass meadows in Kertinge Nor & Dalby Bay, Denmark
DOI: 10.5061/dryad.4jr00/3
title: Infauna & Epifauna from seagrass meadows in Dalby Bay & Kertinge Nor, Denmark

description: Abundance and biomass raw data for infaunal and epifaunal invertebrate species collected using sediment cores and 200 µm mesh bags for epifauna. Depth 2 meter.
DOI: 10.5061/dryad.4jr00/4
title: Sediment rawdata from seagrass meadows in Dalby Bay and Kertinge Nor, Denmark

description: Rawdata on density, water content, organic matter, sulphide concentration and ammonium concentration.
DOI: 10.5061/dryad.55f35/1
title: PLATT-OECOLOGIA-2016-OECO-D-15-00685_growth

description: Data on the age and size of female fish for six species of Blennidae from Guam
DOI: 10.5061/dryad.55f35/2
title: PLATT-OECOLOGIA-2016-OECO-D-15-00685_ovary

description: Data on the weight of ovarian tissue, reproductive status and size of female fish for six species of Blennidae from Guam
DOI: 10.5061/dryad.55f35/3
title: PLATT-OECOLOGIA-2016-OECO-D-15-00685_eggnumber

description: Data on the number of eggs and size of female fish for six species of Blennidae from Guam
DOI: 10.5061/dryad.55f35/4
title: PLATT-OECOLOGIA-2016-OECO-D-15-00685_eggsize

description: Data on the average size of eggs, development stage of those eggs and size of female fish for six species of Blennidae from Guam
DOI: 10.5061/dryad.5qr62/1
title: Bi-Weekly soil N in Kenya

description: Bi-weekly potassium chloride-extractable N in soils collected 0-15cm in field sites in Yala, Kenya. Data span 26-Apr-2012 to 4-Dec-2013.
DOI: 10.5061/dryad.5qr62/2
title: Bi-Weekly soil N in Tanzania

description: Bi-weekly potassium chloride-extractable N in soils (0-15cm) in Tanzania plots. Collection dates span 9-Nov-2012 to 2-Apr-2014.
DOI: 10.5061/dryad.5qr62/3
title: Initial soil data from depth profiles in Kenya and Tanzania

description: Initial soil NO3-N, NH4-N and pH from 0-400 cm depth profiles.
DOI: 10.5061/dryad.5qr62/4
title: Soil depth profile data from Kenya and Tanzania after 2 years of cultivation

description: Soil NO3-N, NH4-N, pH from maize trials in Kenya and Tanzania collected after 2 years of cultivation in unfertilized (0N) and fertilized (200 N) plots.
DOI: 10.5061/dryad.5qr62/5
title: Soil depth profile data from Tanzania after 2 years of cultivation (organic vs. inorganic comparison)

description: Soil NO3-N, NH4-N, and pH in Tanzania plots receiving either 75 kg of N as inorganic fertilizer or 75 kg N as organic fertilizer from Gliricidia sepium leaves. Depth profiles collected after 2 years of maize cultivation.
DOI: 10.5061/dryad.5qr62/6
title: Depth profile data from Kenya after 3 years of maize cultivation

description: Soil data from depth profiles collected in Kenya plots after 3 years of cultivation. Note that there are fewer depth categories. Also, plots were bulked by fertilizer treatment, so there is no replication in this data set. These data were used for qualitative comparison to the other profiles, but not in statistical analyses.
DOI: 10.5061/dryad.6n5s3/1
title: Exp1_DATA_FilterSize_PreFilter

description: Presence/absence data for filtration experiment 1 using 3, 10 and 20 um filters, with and without a prefiltering step.
DOI: 10.5061/dryad.6n5s3/2
title: Exp2_DATA_eDNAshedding

description: Initial tilapia eDNA concentrations in ng at the start of Exp 2 on degradation for all three treatments, 23, 29 and 35 degrees Celcius.
DOI: 10.5061/dryad.6n5s3/3
title: Exp2_DATA_TMP_Degredation

description: Presence/absence data for Exp 2 on degradation of tilapia eDNA for 3 treatments of temperature 23,29 and 35 degrees Celcius.
DOI: 10.5061/dryad.6n5s3/4
title: Exp3_DATA_Density_Time_Flow

description: Presence/absence data recorded as probability of detection for all qPCR replicates by day for all treatment pond densities (0,1,2,4,8,16,32, and up to 64 fish) for Experiment 3-Accumulation of tilapia eDNA.
DOI: 10.5061/dryad.7j908/1
title: dispersal data

description: Dispersal distance of immigrants
DOI: 10.5061/dryad.90329/1
title: Cacao_yield_fruit_arthropod_abundance_indonesia2011_12

description: The data was collected during a ant, bird and bat exclusion experiment in smallholder cacao cacao plantations in Central Sulawesi, Indonesia. Yield measurement, counted fruits and leaves are aggregated over the study duration (April 2011 - May 2012). The fruits were classified by size/development and presence/absence of pest and disease symptoms. The yield was separated for damaged and marketable yield. Abundances of arthropods were gathered through fogging (5% Malathion) the experimental trees at the end of the experiment. Moreover we provide data regarding cacao tree phenology and biotic as well as abiotic environmental conditions.
DOI: 10.5061/dryad.90cv2/1
title: Lizard capture mark recapture data

description: The first worksheet contains the capture history for each of the 5849 individual sleepy lizards in the sampled population throughout the 30-year study.  The raw capture data was pooled to an annual time period, therefore the capture histories are continuous, annual resolution data from 1982 - 2011.  Each row is the data from a different individual.  The first column contains the capture histories in Rmark multi-state format where each letter represents a capture event in a different 'tick exposure risk state': A = B. hydrosauri low, B = B. hydrosauri moderate, C = B. hydrosauri high, D = A. limbatum low, E = A. limbatum moderate, F = A. limbatum high.  A zero in the capture history means that the individual was not encountered at that period in the time series.  The second column contains the age of the individual *at first capture*.  The second sheet contains the annual environmental data that were used as covariates in the multi-state capture-mark-recapture models.
DOI: 10.5061/dryad.90cv2/2
title: BASELINE worst case RAMAS female only model

description: This is the RAMAS metapopulation model file for estimating the the baseline (current conditions) effect of 'hot and dry' and 'cool and wet' winter and spring conditions on the sleepy lizard study population.  The effect of these extreme conditions are based on the largest effect size estimated from the capture-mark-recapture models (i.e. worst case).
DOI: 10.5061/dryad.90cv2/3
title: POLICY worst case female only RAMAS model

description: This is the RAMAS metapopulation model file for estimating the the worst case effect of 'hot and dry' and 'cool and wet' winter and spring conditions on the sleepy lizard study population in the future.  The probabilities of extreme conditions are based on regional temperature and rainfall forecasts from an ensemble climate model under policy greenhouse gas emission scenarios.
DOI: 10.5061/dryad.90cv2/4
title: REFERENCE worst case female only RAMAS model

description: This is the RAMAS metapopulation model file for estimating the the worst case effect of 'hot and dry' and 'cool and wet' winter and spring conditions on the sleepy lizard study population in the future.  The probabilities of extreme conditions are based on regional temperature and rainfall forecasts from an ensemble climate model under reference greenhouse gas emission scenarios.
DOI: 10.5061/dryad.90cv2/5
title: BASELINE best case female only RAMAS model

description: This is the RAMAS metapopulation model file for estimating the the baseline (current conditions) effect of 'hot and dry' and 'cool and wet' winter and spring conditions on the sleepy lizard study population.  The effect of these extreme conditions are based on the smallest effect size estimated from the capture-mark-recapture models (i.e. best case).
DOI: 10.5061/dryad.90cv2/6
title: POLICY best case female only RAMAS model

description: This is the RAMAS metapopulation model file for estimating the the best case effect of 'hot and dry' and 'cool and wet' winter and spring conditions on the sleepy lizard study population in the future. The probabilities of extreme conditions are based on regional temperature and rainfall forecasts from an ensemble climate model under policy greenhouse gas emission scenarios.
DOI: 10.5061/dryad.90cv2/7
title: REFERENCE best case female only RAMAS model

description: This is the RAMAS metapopulation model file for estimating the the best case effect of 'hot and dry' and 'cool and wet' winter and spring conditions on the sleepy lizard study population in the future. The probabilities of extreme conditions are based on regional temperature and rainfall forecasts from an ensemble climate model under reference greenhouse gas emission scenarios.
DOI: 10.5061/dryad.92257/1
title: Data archive

description: Tar archive file that contains SALUS model, input and output files.
DOI: 10.5061/dryad.bp95q/1
title: Clupea harengus genotypes_Gulf of Riga

description: Individual genotypes for six herring samples from the Gulf of Riga