cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.00731/1
title: Main results file with counts

description: The file contains counts of species of each domain that compose the OG, the membrane-protein and signal-peptide classifications, plus evolutionary rates. The first row gives a brief description of the values in each column.
DOI: 10.5061/dryad.118j2/1
title: Janus particle perfusion foot print data 0.5 dyn/cm^2

description: Footprint data for Janus particle perfusion experiments. Used in experimental velocity calculations.
DOI: 10.5061/dryad.1255v/4
title: Pruned_pedigree_Vlieland_East

description: Pedigree for Vlieland East great tit population
DOI: 10.5061/dryad.3h5kv/1
title: ReadMe File

description: This file is a guide to the rest of the files associated with this manuscript.
DOI: 10.5061/dryad.3h5kv/2
title: Avida Configuration Files

description: This folder contains the Avida configuration files needed to replicate all but one of the experimental treatments in the paper.
DOI: 10.5061/dryad.3h5kv/3
title: Avida nopX Configuration Files

description: This file contains the Avida configuration files needed to run the "non-functional insertion" treatment experiments. "nopX" refers to the nop-X instruction added in this configuration.
DOI: 10.5061/dryad.3h5kv/4
title: Submission Files

description: This folder contains the scripts used to submit the Avida experiments to a computing cluster.
DOI: 10.5061/dryad.3h5kv/5
title: Figures Script

description: This python script creates all of the figures in the paper.
DOI: 10.5061/dryad.3h5kv/6
title: CSV Script

description: This python script created the final csv used to create the figures for the paper.
DOI: 10.5061/dryad.3h5kv/7
title: Rename Detail Files Script

description: This python script renamed the detail files from the Avida experiments in order to better use them in Avida's Analyze mode.
DOI: 10.5061/dryad.3h5kv/8
title: Data CSV

description: This csv file contains all of the data from the experiments used in the paper.
DOI: 10.5061/dryad.5gb67/1
title: Brain_size_raw
DOI: 10.5061/dryad.73c00/1
title: Copy_of___latepres_22_03_15_for uload

description: raw data of patients with very late presentation
DOI: 10.5061/dryad.73c00/2
title: interview with physicians for upload

description: interview with physicians regarding the reasons for not sending an HIV test
DOI: 10.5061/dryad.81jh5/1
title: Raw data on acoustic mimicry

description: Full data from acoustic recordings of insect sounds, body sizes of specimens used, field predation data under different sound stimuli, and latency to attack from chicks trained on different stimuli. See ReadMe for more details.
DOI: 10.5061/dryad.81jh5/2
title: High speed video of Bombus sound production

description: The video shows the animal immobilised as described in the methods for the acoustic recording. There are two distinct phases of sound production: (i) 0:01 – 0:26 the insect flies in a characteristic manner with high amplitude wing strokes that produce a waveform similar to that seen in Figure S2A; (ii) 0:32 – 1:03 the insect responds to the simulated predation by transitioning to the alarm sound with nearly static wings and bodily contractions. It is suggested that this involves the decoupling of wings from the flight muscles similar to the mechanism of wing whirring that is used as a thermoregulatory mechanism in this species.
DOI: 10.5061/dryad.8r3v0/1
title: TIme tree of bush frogs

description: A dated tree of bush frogs (Raorchestes) inferred in BEAST. See methods and supplementary information for details. The file can be read in FigTree for node level information on divergence times and 95% HPD.
DOI: 10.5061/dryad.8r3v0/2
title: Pruned Time tree of bush frogs (Raorchestes)

description: A pruned version of the time tree of bush frogs, Raorchestes, from Western Ghats, used in the ancestral reconstruction of elevation mid-points. Contains 65 lineages. The tree was inferred in BEAST.
DOI: 10.5061/dryad.8r3v0/3
title: Raorchestes_Midpoint_elevation_datafile

description: Contains, elevation mid-point  (column-Elevation_mid)for 65 Lineages of Raorchestes, sample size(N), Coded discrete sates used in the reconstruction. Column - Three_states_mid	 (0- 0 to 900, 1- 901 to 1800, 3 - 1801 - 2700 m). Column - Five_states_mid (0 - 401 to 900, 1- 901 - 1200, 2- 1201 - 1800, 3- 1801 - 2200, 4 - 2201 - 2700). Note no mid-points in the 0-401 m category. Use Likelihood method, in Mequite, to replicate the analyses. Associated pruned time tree used in the reconstruction is provided as a separate file.
DOI: 10.5061/dryad.ck3g3/1
title: Brain imaging data HEDOREX

description: This data file contains brain PET images obtained in growing pigs subjected to different olfactogustatory food stimulations.
DOI: 10.5061/dryad.dr130/1
title: GHANA_PLoS_upload

description: Raw data in Excel
DOI: 10.5061/dryad.gp4h2/1
title: Mélade et al PLOS ONE 2016 database

description: Neutralizing antibody titers recorded for each bat serum sample tested
DOI: 10.5061/dryad.h0h8d/1
title: Algerian sheep genotypes (.ped file)

description: Genotypes obtained with the Illumina OvineSNP50K Genotyping BeadChip  (genotype files) for eight Algerian sheep breeds in a Plink format.
DOI: 10.5061/dryad.h0h8d/2
title: Algerian sheep genotypes (.map file)

description: Genotypes obtained with the Illumina OvineSNP50K Genotyping BeadChip  (markers files by chromosomes) for eight Algerian sheep breeds in a Plink format.
DOI: 10.5061/dryad.j0r00/1
title: Data - The effect of movement tactic on twinning rate

description: Data used to analyze the effect of movement tactic on twinning rate.
DOI: 10.5061/dryad.j0r00/2
title: Data - shoulderheight and twinning

description: Data used to compare shoulderheight of resident and migrant female moose. And to test the effect of shoulderheight on the probabilty of having twins.
DOI: 10.5061/dryad.j0r00/3
title: Data - moose and altitude

description: Data used to examine if migrants and residents used different altitudes during the year.
DOI: 10.5061/dryad.j0r00/4
title: Data - summersurvivalcalves

description: Data used to analyze summer survival of calves in relation to their mothers movement tactic.
DOI: 10.5061/dryad.j0r00/5
title: Data - totalcalfsurvival

description: Data used to analyze first year survival of calves in relation to their mothers movement tactic.
DOI: 10.5061/dryad.jn400/1
title: all_lizard_partA.fasta

description: Fasta file containing the sequences for lizard fecal 16S rRNA V1-V3 region. Sequencing was performed on MiSeq platform, and fasta files are generated after QC. Sequence ID contains sampleID (see metadata file for details) followed by sequence number. This file needs to be combined with partB.
DOI: 10.5061/dryad.jn400/2
title: all_lizard_partB.fasta

description: Fasta file containing the sequences for lizard fecal 16S rRNA V1-V3 region. Sequencing was performed on MiSeq platform, and fasta files are generated after QC. Sequence ID contains sampleID (see metadata file for details) followed by sequence number. This file needs to be combined with partA.
DOI: 10.5061/dryad.jn400/4
title: lizard_metadata.xlsx

description: This is the metadata file contains information concerning the lizard samples used in analyses.
DOI: 10.5061/dryad.k17j5/1
title: Data of larger brains, small guts
DOI: 10.5061/dryad.m0hd2/1
title: Lupse etal 2016 data
DOI: 10.5061/dryad.m35k6/10
title: ModelSel_HEWA_2013_DynamicAll

description: AIC model selection table and associated coefficients for hermit warbler 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.m35k6/11
title: ModelSel_ORJU_2012_DynamicAll

description: AIC model selection table and associated coefficients for dark-eyed (Oregon) junco 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.m35k6/12
title: ModelSel_ORJU_2013_DynamicAll

description: AIC model selection table and associated coefficients for dark-eyed (Oregon) junco 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.m35k6/13
title: ModelSel_PAWR_2012_DynamicAll

description: AIC model selection table and associated coefficients for Pacific wren 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.m35k6/14
title: ModelSel_PAWR_2013_DynamicAll

description: AIC model selection table and associated coefficients for Pacific wren 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.m35k6/15
title: ModelSel_PSFL_2012_DynamicAll

description: AIC model selection table and associated coefficients for Pacific-slope flycatcher 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.m35k6/16
title: ModelSel_PSFL_2013_DynamicAll

description: AIC model selection table and associated coefficients for Pacific-slope flycatcher 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.m35k6/9
title: ModelSel_HEWA_2012_DynamicAll

description: AIC model selection table and associated coefficients for hermit warbler 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.mm4cc/1
title: 1. cranidia data

description: Excel file for cranidia measurements
DOI: 10.5061/dryad.mm4cc/2
title: 2. pygidia data

description: Excel fiel for pygidia measurements
DOI: 10.5061/dryad.mm4cc/3
title: 3. Average and SD of pygidia for grapher

description: Excel fiel of averages and standard deviations of pygidia measurements
DOI: 10.5061/dryad.mm4cc/4
title: Data matrix for TNT

description: Data matrix for TNT analysis(.tnt)
DOI: 10.5061/dryad.pb1d5/1
title: Clinical data of test and control group

description: Clinical data of test and control group
DOI: 10.5061/dryad.pk5sg/1
title: Morph assignment - offspring and parents

description: Morph assignment of offsprings, dams, and sires, from threshold values of percentage of colour (red and yellow) on throat.
DOI: 10.5061/dryad.r7s92/4
title: Supplementary figure 4

description: NMDS ordination of a double-standardized subsample of the total dataset comparing individual habitats along the depth- and salinity gradient for species and families using proportional abundances and presence/absence data. Environmental assignment of samples: estuarine intertidal – black points, estuarine subtidal – red squares, marine intertidal – green diamonds, marine subtidal – blue triangles.
DOI: 10.5061/dryad.r7s92/5
title: Supplementary figure 5

description: Effect of taxonomic aggregation and numerical transformation on NMDS ordination patterns in the total non-standardized dataset. Results for square-root and fourth-root transformed proportions were omitted for clarity and showed patterns intermediate between proportional and presence/absence data.  Environmental assignment of samples: estuarine intertidal – black points, estuarine subtidal – red squares, marine intertidal – green diamonds, marine subtidal – blue triangles.
DOI: 10.5061/dryad.r7s92/6
title: Supplementary figure 6

description: Distribution of p-values from PERMANOVA comparing molluscan assemblages along the depth- and salinity gradients at different levels of taxonomic aggregation and numerical resolution. A, In the total dataset (all four habitats considered) B, Along environmental gradients (pairwise comparisons of habitats). Filled points represent median P-values across 1000 subsampling iterations, thick lines denote interquartile range (IQR), whiskers (thin lines) encompass data points scattered less than 1.5 times the IQR from the lower and upper quartile and outliers are marked as empty points.
DOI: 10.5061/dryad.rq7t3/1
title: dataDroso - census data

description: Demographic transitions of Drosophyllum lusitanicum populations recorded in annual censuses (from 2011 to 2015) in five populations. These data are used to quantify vital rates of above-ground individuals.
DOI: 10.5061/dryad.rq7t3/2
title: dataDrosoSB - seed bank

description: Seed fates (in a binary format) inferred from two experiments. These data are used to quantify the transitions related to the seed bank and associated parameter uncertainties.
DOI: 10.5061/dryad.rq7t3/3
title: BayModel - Bayesian vital rate GLMMs

description: Executes and saves the results of a Bayesian model quantifying all vital rates; illustrates basic diagnostics that can be run on the results of an MCMC run (i.e., the posterior parameter distribution) to check for model convergence and autocorrelation of the posterior samples.
DOI: 10.5061/dryad.rq7t3/4
title: mcmcOUT - parameter samples

description: In case the reader wishes to forego the step of fitting the Bayesian models, we provided a mcmcOUT.csv file with 1000 posterior parameter values for each of the parameters estimated with Bayesian models using uninformative priors
DOI: 10.5061/dryad.rq7t3/5
title: makeIPM

description: Demonstrates how to construct IPMs including continuous and discrete (seed bank) transitions for (A) mean parameter values and (B) from the parameter distributions of the Bayesian models; saves IPMs for all parameters related to seed-bank ingression, stasis, and ingression. The code is based on the supporting material in Ellner and Rees (2006), Am. Nat., 167, 410-428
DOI: 10.5061/dryad.rq7t3/6
title: perturbVR - vital rate perturbations

description: Demonstrates how to construct IPMs from perturbed vital rates. Each IPM is obtained by (a) perturbing a vital rate by its mean or standard deviation (see makeVRmu.R on constructing mean vital-rate kernels) and (b) constructing a new IPM kernel incorporating the perturbed vital rate
DOI: 10.5061/dryad.s13rt/5
title: zebra_phenotypes
DOI: 10.5061/dryad.v7g7d/2
title: Table S2 - Temperature-development data

description: This file contains an extensive synthesis of temperature-development records from laboratory experiments involving the rearing of Syrphidae. Contained within the Excel file are (i) a spreadsheet with the data extracted from the papers, (ii) a metadata worksheet with definitions of the columns, and (iii) a full bibliography of the studies involved.
DOI: 10.5061/dryad.v7g7d/3
title: Table S3 - HRS species specific data

description: Table S3: Full dataset of relationships between temperature, date, and flight periods in hoverflies derived from the Hoverfly Recording Scheme.
DOI: 10.5061/dryad.v7g7d/4
title: Table S4 - Phenology shifts vs zero

description: Table S4: Results of statistical analysis to test for a difference between samples of phenological responses (PC=Pearson correlation, Reg=regression coefficient) of different parts of the flight period (5=5th percentile, 50=50th percentile, 95=95th percentile) and zero. Results are all from generalised least squares analysis with a floating intercept, fitted without phylogenetic autocorrelation ("Uncontrolled") and using two different hoverfly phylogenies.
DOI: 10.5061/dryad.v7g7d/5
title: Table S5 - All traits analysis

description: Table S5: Results of statistical analysis to test for an effect of species traits on phenological responses (Pearson correlations between annual temperature or year). Results are all from generalised least squares analysis with a floating intercept, fitted without phylogenetic autocorrelation ("Uncontrolled") and using two different hoverfly phylogenies. "--" indicates no data due to the presence of only one trait value in that dataset. Significant results are highlighted in bold.
DOI: 10.5061/dryad.v7g7d/6
title: Table S6 - Owen species specific data

description: Table S6: Full dataset of relationships between temperature, date, and flight periods in hoverflies derived from standardised recording (see main text for details).
DOI: 10.5061/dryad.00731/2
title: Protein sequences for the selected orthologs in OMA

description: For each ortholog group (OG) in OMA, we selected only one ortholog per species. For example, there are dozens of E. coli strains in OMA, so if an OG had multiple E. coli orthologs, we picked only one of these and ignored the others. We did this to avoid oversampling and guarantee a wider phylogenetic distribution. We only kept OGs with orthologs from 3 or more separate clades. That is, if an OG was composed of, say, orthologs from 4 different E. coli strains and 2 from B. subtilis strains, we ignored it, since there were only 2 strains represented in total.
DOI: 10.5061/dryad.1s27n/1
title: Setchell et al data Behav Ecol June 2016

description: This data file includes the raw data that we used to perform our analyses in a single Excel file.
DOI: 10.5061/dryad.27m63.2
title: Data from: Vascular patterns in iguanas and other squamates: blood vessels and sites of thermal exchange
DOI: 10.5061/dryad.27m63.2/1.2
title: CT scan data of green iguana, Iguana iguana OUVC 10445

description: This zip file contains DICOM images from an x-ray microcomputed tomography (µCT) scan of an injected Iguana iguana (OUVC 10445). 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.27m63.2/2.2
title: CT scan data of green iguana, Iguana iguana OUVC 10603

description: This zip file contains DICOM images from an x-ray microcomputed tomography (µCT) scan of an injected Iguana iguana (OUVC 10603). 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.2pm97/1
title: Dataset

description: Dataset
DOI: 10.5061/dryad.32kc7/1
title: Dryad data Fayet et al 2016 JAE

description: GLS light and activity data, and metadata. See ReadMe file for details.
DOI: 10.5061/dryad.37rt1/1
title: Lewanzik_Voigt_2016_data
DOI: 10.5061/dryad.5q1h4/1
title: Fig. 2 Olfactory receptor phylogeny estimation (RAxML)

description: Phylogenetic analysis of Ors in Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) using a Maximum Likelihood method. Evolutionary history was inferred using a Maximum Likelihood method based on the JTT matrix-based model (Jones et al. 1992). The tree was constructed using RAxML under the JTT model of substitution with NNI topology search (Stamatikis 2014), based on an amino acid alignment by MUSCLE (Edgar 2004). Branch support was estimated using 500 bootstrap replications. The tree is rooted with Orco.
DOI: 10.5061/dryad.5q1h4/2
title: Fig. 3 Gustatory receptor phylogeny estimation (RAxML)

description: Phylogenetic analysis of Grs in Drosophila suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) using a Maximum Likelihood method. Evolutionary history was inferred using a Maximum Likelihood method based on the JTT matrix-based model (Jones et al. 1992). The tree was constructed using RAxML under the JTT model of substitution with NNI topology search (Stamatikis 2014), based on an amino acid alignment by MUSCLE (Edgar 2004). Branch support was estimated using 500 bootstrap replications. The tree is rooted with Gr21a.
DOI: 10.5061/dryad.5q1h4/3
title: Ors_alignment file (Muscle)

description: Olfactory receptor peptide sequences of D. suzukii (Dsuz), D. biarmipes (Dbia), D. takahashii (Dtak) and D. melanogaster (Dmel) ≥ 360 aa in length were multiply aligned using MUSCLE v3.8.31 (Edgar 2004).