cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5q1h4/4
title: Grs_aligment file (Muscle)

description: Gustatory receptor peptide sequences of D. suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) ≥ 340 aa in length were multiply aligned using MUSCLE v3.8.31 (Edgar 2004).
DOI: 10.5061/dryad.5tp75/1
title: Rashid et al Science 2016- Data for Figs 1-4, S1-S9

description: Excel file with all data presented in manuscript (each sheet corresponds to specific figures as indicated).
DOI: 10.5061/dryad.631kf/1
title: Rc NEW filter data  aligment used in contruct ML tree and TCS analysis  but no subsitute Het by question mark FOR DYR submittion

description: The full alignment of Rc gene for constructing ML tree
DOI: 10.5061/dryad.6jd59/1
title: Gilfillan et al. Raw Data

description: Raw data for the response of lions to the cross-modal playback experiments.
DOI: 10.5061/dryad.6r12h/1
title: Dataset ITS-B (alignment and phylogenetic trees used for analyses)

description: Nexus file containing sequence alignment of nuclear ITS sequences and 4,500 phylogenetic trees (obtained using BEAST) used for chromosome number reconstruction
DOI: 10.5061/dryad.6r12h/2
title: Dataset ITS-MB (alignment and phylogenetic trees used for analyses)

description: Nexus file containing sequence alignment of nuclear ITS sequences and 4,500 phylogenetic trees (obtained using MrBayes; out-groups removed) used for chromosome number reconstruction
DOI: 10.5061/dryad.6r12h/3
title: Dataset matK-B (alignment and phylogenetic trees used for analyses)

description: Nexus file containing sequence alignment of plastid matK sequences and 4,500 phylogenetic trees (obtained using BEAST) used for chromosome number reconstruction
DOI: 10.5061/dryad.6r12h/4
title: Dataset matK-MB (alignment and phylogenetic trees used for analyses)

description: Nexus file containing sequence alignment of plastid matK sequences and 4,500 phylogenetic trees (obtained using MrBayes; out-groups removed) used for chromosome number reconstruction
DOI: 10.5061/dryad.8r3v0/4
title: Raorchestes_Area_datafile

description: Distribution of Raorchestes lineages across broad areas used in the ancestral area reconstruction. A - Sri Lanka, B - South of Palghat Gap, C - North of Palghat Gap and eastern regions, D - North-east part of India and SE Asia. Use the 89TAX_PRIOR6_R1R2_NAMESUPDATED.tre for analyses. Need to be pruned before analyses.
DOI: 10.5061/dryad.g2c8c/1
title: FigureData

description: This is the numerical data from the all graphs in the paper.
DOI: 10.5061/dryad.hm872/1
title: Hirtella datasets
DOI: 10.5061/dryad.j32cb/1
title: AllFourSubjects_NasoPressure

description: Figure 6 of article. Steady-state nasopharyngeal pressure for all four subjects used in the study.
DOI: 10.5061/dryad.j32cb/2
title: WSS_2LPM

description: Wall shear stress data in Figure 5 compare with literature.
DOI: 10.5061/dryad.j32cb/3
title: NormalSubjec1_3PL
DOI: 10.5061/dryad.j32cb/4
title: preop_3PL
DOI: 10.5061/dryad.j32cb/5
title: PostopSubj2b_3PL
DOI: 10.5061/dryad.j32cb/6
title: DrillOut_Subject3
DOI: 10.5061/dryad.m35k6/17
title: ModelSel_RBNU_2012_DynamicAll

description: AIC model selection table and associated coefficients for red-breasted nuthatch 2012 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/18
title: ModelSel_RBNU_2013_DynamicAll

description: AIC model selection table and associated coefficients for red-breasted nuthatch 2013 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/19
title: ModelSel_STJA_2012_DynamicAll

description: AIC model selection table and associated coefficients for Steller's jay 2012 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/20
title: ModelSel_STJA_2013_DynamicAll

description: AIC model selection table and associated coefficients for Steller's jay 2013 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/21
title: ModelSel_SWTH_2012_DynamicAll

description: AIC model selection table and associated coefficients for Swainson's thrush 2012 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/22
title: ModelSel_SWTH_2013_DynamicAll

description: AIC model selection table and associated coefficients for Swainson's thrush 2013 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/23
title: ModelSel_VATH_2012_DynamicAll

description: AIC model selection table and associated coefficients for varied thrush 2012 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/24
title: ModelSel_VATH_2013_DynamicAll

description: AIC model selection table and associated coefficients for varied thrush 2013 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.m35k6/25
title: ModelSel_WETA_2012_DynamicAll

description: AIC model selection table and associated coefficients for western tanager 2012 for all models combined. Column names for the model coefficients use the following notation: coefficient = parameter(covariate) and standard error = SEparameter(covariate). Parameter abbreviations are p = detection probability, psi = initial occupancy, col = colonization/settlement, ext = extinction/vacancy.  Parameter(Int) refers to the intercept. ‘nPars’ is the number of parameters estimated in the model. Each model is ranked by its AIC score, which represents how well the model fits the data. A lower ∆AIC (delta) value is indicative of a better model. The probability that the model (of the models tested) would best explain the data is indicated by AICwt.
DOI: 10.5061/dryad.mb605/1
title: Dataset1_HBD

description: Dataset1_HBD contains individual observations of CO2 and time, along with categorical or integer identifiers for day, vegetation type, plot, session (group). DayN = day since 1/1/2006; Datecode = unique integer ID for each measurement date; Min = minutes after chamber closure; Veg = vegetation treatment ID (1 = vegetated; 2 = herbicide); Plot = plot ID; Group = chamber session ID; CorrCO2 = corrected CO2 concentration (ppm); SoilT = soil temperature (celcius) in/near temperature in surface layer.
DOI: 10.5061/dryad.mb605/2
title: Dataset2a_HBD

description: Dataset2a_HBD contains the integer identifiers for date, vegetation type, and plot associated with each chamber session; dateID, vegID, and PlotID are the same as Datecode, Veg, and Plot in Dataset1_HBD, but each row in Dataset2a_HBD corresponds to the chamber session ID (i.e., Group in Dataset1_HBD).
DOI: 10.5061/dryad.mb605/3
title: Dataset2b_HBD

description: Dataset2b_HBD contains various constants and sample size information required for the the HBD (hierarchical Bayesian diffusion model). This includes Tmtcode, which is a list of 30 values giving the treatment ID associated with each of the 30 plots (ordered by plot #), where 1 = ct, 2 =  cT, 3 = Ct, 4 = CT, 5 = ctd, and 6 = cts, for c = ambient CO2, C = elevated CO2, t = ambient temperature, T= warmed, d = deep irritation, and s = shallow irrigation. This dataset also contains Ctrt, denoting the CO2 treatment level associated with each of the 6 treatments; 1 = ambient CO2 and 2 = elevated CO2.
DOI: 10.5061/dryad.mb605/4
title: Dataset3_HBD

description: Dataset3_HBD contains soil water content data for every plot and date. SWC_DSM1[r,c] is the soil water content associated with day = r and plot ID = c. Plot ID (columns) correspond to Plot in Dataset1_HBD; r = 1 (row #1) corresponds to 12/21/2006 or day 355 from 1/1/2006, with rows ordered by date (no missing days).
DOI: 10.5061/dryad.mb605/5
title: Dataset4_HBD

description: Dataset4_HBD contains atmospheric pressure data for every date, with row #1 corresponding to 3/1/2007 (i.e., day 425 since 1/1/2006). Rows are ordered by day (no missing dates).
DOI: 10.5061/dryad.mb605/6
title: ModelCode_HBD_SI

description: OpenBUGS / JAGS model code that uses Dataset1_HBD.txt, Dataset2a_HBD.txt, Dataset2b_HBD.txt, Dataset3_HBD.txt, and Dataset4_HBD.txt
DOI: 10.5061/dryad.mb605/7
title: Initials_HBDa_SI

description: Initials (starting) values for first MCMC chain, to be used with the OpenBUGS / JAGS model code (ModelCode_HBD_SI.txt).
DOI: 10.5061/dryad.mb605/8
title: Initials_HBDb_SI

description: Initials (starting) values for second MCMC chain, to be used with the OpenBUGS / JAGS model code (ModelCode_HBD_SI.txt).
DOI: 10.5061/dryad.p3nt7/1
title: Bill size and diet in reed buntings
DOI: 10.5061/dryad.rq7t3/10
title: sLambdaRmpi - stochastic simulations on parallel processors

description: Implements the simulations of the stochastic population growth rate using parallel processing, where simulations are split into different processors of a supercomputer to greatly speed up computational time.
DOI: 10.5061/dryad.rq7t3/7
title: makeIPMmu

description: function to constructs IPMs for average environments
DOI: 10.5061/dryad.rq7t3/8
title: makeVRmu

description: functions to constructs vital-rate kernels for average environments.
DOI: 10.5061/dryad.rq7t3/9
title: sLambdaSimul - stochastic lambda simulations

description: Runs simulations, based on different fire return intervals, of the stochastic population growth rate using IPMs constructed (A) from mean parameter values, (B) from perturbed vital rates, and (C) for each posterior sample of the parameters describing seed-bank ingression (goSB), stasis (staySB) and egression (outSB); calculates the stochastic population growth rate, its elasticities, and the probability of quasi-extinction at time t. The structure of the code is based on Tuljapurkar et al. (2003), Am. Nat., 162, 489-502 and Trotter et al. (2013), Methods Ecol. Evol., 4, 290-298.
DOI: 10.5061/dryad.s13rt/6
title: environmental_data
DOI: 10.5061/dryad.sd6jq/1
title: Aruajo et al. Biology Letters Data

description: Behavioral data for larval wood frog exposed to ranavirus during disease trials. The data is separated into focal animals, infected with a lethal dose of ranavirus, and non-focal animals that were exposed to the focals for 24 hour transmission trials. Non-focal animals were monitored for survival until metamorphosis.
DOI: 10.5061/dryad.sv71c/1
title: Supplementary Fig. 1. Species-level phylogenetic hypothesis for early Pliensbachian ammonites

description: Species-level phylogenetic hypothesis for early Pliensbachian ammonites (after Hardy et al., 2012) and the 29 clades used inthis study (red stars).
DOI: 10.5061/dryad.sv71c/2
title: Supplementary Fig. 2. Correspondence analyses calculated made at the species/locality and clade/cluster levels for the western Tethys for each chronozone of the early Pliensbachian

description: Correspondence analyses made at the species/locality (A-C) and clade/cluster (D-E) levels for the western Tethys for each chronozone of the early Pliensbachian, in order to determine if the biogeographical partitioning detected at the species level still exists at the clade level. The polygons represent the 95% convex hull of the MED assemblages (in orange) and NWE assemblages (in blue). Eigenvalues are indicated for each axes. Only localities with at least 4 species and clusters with at least 3 clades are considered in these analyses.
DOI: 10.5061/dryad.sv71c/3
title: Supplementary Fig. 3. SDD calculated at the locality/species level for the NWE province and the MED province for each chronozone of the early Pliensbachian, after grouping the species according to the volume of their shell

description: Similarity distance decay calculated at the locality/species level for the NWE province (A-F) and the MED province (G-L) for each chronozone of the early Pliensbachian, after grouping the species according to the volume of their shell (V = ln(volume) in mm3), in order to determine if there is a relationship between shell size and long-distance dispersal. For each province, the lower graphs represent the small species and the upper graphs the large ones. The black lines are the Ordinary Least-Square linear regressions and the SDD rates are the values of their slopes.
DOI: 10.5061/dryad.sv71c/4
title: Supplementary Fig. 4. SDD calculated at the cluster/species level for the NWE province and the MED province for each chronozone of the early Pliensbachian, after grouping the species according to the volume of their shell

description: Similarity distance decay calculated at the cluster/species level for the NWE province (A-F) and the MED province (G-L) for each chronozone of the early Pliensbachian, after grouping the species according to the volume of their shell (V = ln(volume) in mm3), in order to determine if there is a relationship between shell size and long-distance dispersal. For each province, the lower graphs represent the small species and the upper graphs the large ones. Only clusters with at least 3 species are considered in these analyses. The black lines are the Ordinary Least-Square linear regressions and the SDD rates are the values of their slopes.
DOI: 10.5061/dryad.sv71c/5
title: Supplementary Fig. 5. SDD calculated at the locality/species level for the NWE province and the MED province for each chronozone of the early Pliensbachian, after grouping the species according to the relative whorl height of their shell

description: Similarity distance decay calculated at the locality/species level for the NWE province (A-F) and the MED province (G-L) for each chronozone of the early Pliensbachian, after grouping the species according to the relative whorl height of their shell (H / D, H = last-whorl height, D = shell diameter), in order to determine whether a relationship between shell shape and long-distance dispersal exists. For each province, the lower graphs represent the most evolute species and the upper graphs the most involute ones. The black lines are the Ordinary Least-Square linear regressions and the SDD rates are the values of their slopes.
DOI: 10.5061/dryad.v6q77/1
title: Tropheus moorii microsatellite genotypes

description: File in genepop format
DOI: 10.5061/dryad.v6q77/2
title: Simochromis diagramma microsatellites genotypes

description: File in genepop format
DOI: 10.5061/dryad.v6q77/3
title: Tropheus moorii and Simochromis diagramma - miscellaneous data

description: phenotypic data, parasite data and MHC genotypes
DOI: 10.5061/dryad.v9p27/1
title: validation_constant_10C

description: Target and actual temperatures logged for a 10 degrees Celsius constant-temperature validation scheme. We logged actual chamber temperatures every minute for 30 days.
DOI: 10.5061/dryad.v9p27/2
title: validation_constant_13C

description: Target and actual temperatures logged for a 13 degrees Celsius constant-temperature validation scheme. We logged actual chamber temperatures every minute for 30 days.
DOI: 10.5061/dryad.v9p27/3
title: validation_constant_16C

description: Target and actual temperatures logged for a 16 degrees Celsius constant-temperature validation scheme. We logged actual chamber temperatures every minute for 30 days.Add new data file
DOI: 10.5061/dryad.202t3/1
title: Pairs_archive

description: Summary data on each pair of adults involved in the swap experiment.
DOI: 10.5061/dryad.202t3/2
title: Visitrate_archive

description: Summary data for each observation session on each individual subject int he swap experiment
DOI: 10.5061/dryad.202t3/3
title: Rawvisits_archive

description: Data on each trip by each subject in the swap experiment
DOI: 10.5061/dryad.27c8s/1
title: Citizen science reports of amphibian mortality events in the UK between 1991 and 2010

description: This a csv file where each record relates to a citizen science report of amphibian mortality in the UK between 1991-2010. The fields cover georeference data and data on the mortality event (numbers of affected animals and signs of disease observed).
DOI: 10.5061/dryad.27c8s/2
title: Nexus alignment of UK ranaviruses plus viruses which provide global context

description: This nexus alignment was used to construct the phylogeny in figure 5 of the attached publication. It is a concatenated alignment of seven partial open reading frames detailed in Price et al. (2014). The resulting phylogeny visualises relationships of UK ranaviruses in a global context.
DOI: 10.5061/dryad.27m63.1
title: Data from: Vascular patterns in iguanas and other squamates: blood vessels and sites of thermal exchange
DOI: 10.5061/dryad.27m63.2/3.2
title: CT scan data of green iguana, Iguana iguana OUVC 10611

description: This zip file contains DICOM images from an x-ray microcomputed tomography (µCT) scan of an injected Iguana iguana (OUVC 10611). The arteries were injected with a latex and barium solution and scanned on a GE eXplore Locus in vivo Small Animal MicroCT scanner (90µm slice thickness at 80kV and 450 µA) at the Ohio University µCT Scanning Facility.
DOI: 10.5061/dryad.27m63.2/4.2
title: CT scan data of green iguana, Iguana iguana OUVC 10612

description: This zip file contains DICOM images from an x-ray microcomputed tomography (µCT) scan of an injected Iguana iguana (OUVC 10612). The veins were injected with a latex and barium solution and scanned on a GE eXplore Locus in vivo Small Animal MicroCT scanner (90µm slice thickness at 80kV and 450 µA) at the Ohio University µCT Scanning Facility.
DOI: 10.5061/dryad.27m63.2/5.2
title: CT scan data of green iguana, Iguana iguana OUVC 10709

description: This zip file contains DICOM images from an x-ray microcomputed tomography (µCT) scan of an injected Iguana iguana (OUVC 10709). The arteries were injected with a latex and barium solution and scanned on a GE eXplore Locus in vivo Small Animal MicroCT scanner (90µm slice thickness at 80kV and 450 µA) at the Ohio University µCT Scanning Facility.
DOI: 10.5061/dryad.27m63.2/6.2
title: 3D-PDF of green iguana, Iguana iguana
DOI: 10.5061/dryad.48nv3/1
title: 1918 Pandemic Influenza Mortality, Chicago USA

description: Point location and week of epidemic of 8,031 influenza and pneumonia deaths recorded during the 1918 Spanish flu pandemic within the city of Chicago. Data was digitized from 1920 City of Chicago Department of Health annual reportDate last modified: 25-10-2016.  Fields include: ID (FID), indicator of pneumonia (0 or 1, 0 indicates an influenza death, 1 an influenza and pneumonia death), x and y coordinates (with units in meters), and week (sequential week of epidemic).  See paper for more details.
DOI: 10.5061/dryad.48nv3/2
title: Fine-scale sociodemographics of Chicago, USA, 1920

description: Socio-demographic data (including population size, illiteracy, unemployment) of 496 census tracts within the City of Chicago. Data was collected from the 1920 national census.
DOI: 10.5061/dryad.48nv3/3
title: Shapefile of census tract boundaries in Chicago in 1920

description: Shapefile of census tract boundaries in Chicago in 1920.  File included in zip file include IL_tract_a.dbf, IL_tract_a.prj, IL_tract_a.sbn, IL_tract_a.sbx, IL_tract_a.shp, IL_tract_a.shp.xml, IL_tract_a.shx
DOI: 10.5061/dryad.61dr5.2
title: Data from: Avian cephalic vascular anatomy, sites of thermal exchange, and the rete ophthalmicum