cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.247st/4
title: Birth death multitype model initialization file, HA segment

description: xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) with 1 MCMC chain of 10 million iterations.  Set-up for analysis of 85 aligned whole segment sequences of the hemagglutinin (HA) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.
DOI: 10.5061/dryad.247st/5
title: Birth death multitype model initialization file, PB2 segment

description: xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 MCMC chain of 10 million iterations.  Set-up for analysis of 85 aligned whole segment sequences of the Polymerase Subunit (PB2) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.
DOI: 10.5061/dryad.247st/6
title: Birth death multitype model initialization file, M segment

description: xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations.  Set-up for analysis of 85 aligned whole segment sequences of the matrix (M) gene of isolates from the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.
DOI: 10.5061/dryad.247st/7
title: Birth death multitype model initialization file, HA segment wild birds

description: xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations.  Set-up for analysis of 38 aligned whole segment sequences of the hemagglutinin (HA) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.
DOI: 10.5061/dryad.247st/8
title: Birth death multitype model initialization file, PB2 segment wild birds

description: xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations.  Set-up for analysis of 38 aligned whole segment sequences of the polymerase subunit (PB2) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.
DOI: 10.5061/dryad.247st/9
title: Birth death multitype model initialization file, M segment  wild birds

description: xml file created from the BEAUTI template for the birth-death multi type model (https://github.com/denisekuehnert/bdmm) to implement Bayesian estimation of phylodynamic parameters in BEAST v2.4.3 (available from www.BEAST2.org) from 1 chain of 10 million iterations.  Set-up for analysis of 38 aligned whole segment sequences of the matrix (M) gene of isolates from wild birds during the 2014-2015 highly pathogenic avian influenza HA clade 2.3.4.4 outbreak in North America.
DOI: 10.5061/dryad.30tg8/1
title: Survival seedlings

description: Survival seedlings
DOI: 10.5061/dryad.30tg8/2
title: Survival saplings

description: Survival saplings
DOI: 10.5061/dryad.30tg8/3
title: PFE

description: data of Fig.1 and Table 3
DOI: 10.5061/dryad.30tg8/4
title: MA and PAH

description: data of Fig.2, Fig.3 and Table 3
DOI: 10.5061/dryad.3n08c/1
title: Data

description: zip-folder containing the data sets for the simulated and recorded data
DOI: 10.5061/dryad.3n08c/2
title: Scripts

description: zip-folder containing the scripts to process the raw data in the folder Data.zip
DOI: 10.5061/dryad.3n08c/3
title: Scripts - readme

description: The file "Scripts - readme.txt" explains which MATLAB scripts are the main files and how the parameters in the header need to be set to obtain the diagrams in the paper, based on the supplied data files.
DOI: 10.5061/dryad.3rd6f/1
title: Hydrosense_SoilMoisture

description: Soil moisture measurements in 2012 & 2013 from rain-out shelters and control plots using Hydrosense soil moisture probe.
DOI: 10.5061/dryad.3rd6f/2
title: Decagon_SoilMoisture

description: Hourly soil moisture measurements in 2013 from five rain-out shelters and control plots using Decagon soil moisture probe.
DOI: 10.5061/dryad.3rd6f/3
title: Demography Data 2012

description: Plant demographic data collected in 2012 monsoon season.
DOI: 10.5061/dryad.3rd6f/4
title: Demography Data 2013

description: Plant demographic data collected in 2013 monsoon season.
DOI: 10.5061/dryad.3rd6f/5
title: Species Biomass

description: Data for size-biomass relationships.
DOI: 10.5061/dryad.3s57p/1
title: Land use and drought effects on grassland C dynamics

description: Data were collected from a common garden drought experiment in the Austrian Central Alps using intact vegetation-soil monoliths from an extensively managed meadow and a nearby abandoned grassland. The monoliths were installed in summer 2013 on the meadow site and pre-incubated until drought simulation was started in early summer 2014. The effects of land use on the response of plant C allocation and plant-microbial C transfer to drought and rewetting were studied by conducting two 13C pulse-chase labelling campaigns. A description of all data and abbreviations used in the excel file can be found in tab "0-README".
DOI: 10.5061/dryad.44m2h/1
title: data for SSI specialization index

description: Heritability, CVa and Heterozygosity of wild bird populations associated with SSI specialization index.
DOI: 10.5061/dryad.49vj1/1
title: FeederWatch interactions

description: The 7,685 interspecific displacements used in our Behavioral Ecology paper to create a dominance hierarchy of North American feeder birds.
DOI: 10.5061/dryad.6r6pn/1
title: Temperature and soil moisture data climate manipulation

description: Temperature and Soil moisture data of a peat core that was exposed to experimental climate manipulation by placement into a modified Tullgren setup
DOI: 10.5061/dryad.6r6pn/2
title: Collembola community data climate manipulation

description: Collembola community data of peatcores exposed to climate manipulation by placement into a modified Tullgren setup
DOI: 10.5061/dryad.789pv/10
title: Rhinella jimi Ribossomal 16S DNA

description: Cyb alignment of Rhinella jimi before bGMYC analysis. Information on the lineage used in this study can be found in the Excel file.
DOI: 10.5061/dryad.789pv/11
title: Vanzosaura multiscutata Cytochrome-b

description: Complete Cyb alignment of Vanzosaura multiscutata before bGMYC analysis. Data first published by Recoder et al 2015, Zool J Linn Soc, 171, 206-225. Information on the lineage used in this study can be found in the Excel file.
DOI: 10.5061/dryad.789pv/12
title: Excel sheet

description: This Excel file contains information only for the populations used in the study. The sheet contains locality, GPS, voucher and genbank accession numbers. Some sequences were not deposited in Genbank up to June of 2017.
DOI: 10.5061/dryad.789pv/7
title: Philodryas nattereri Cytochrome oxydase 1

description: Complete COI alignment of Philodryas nattereri before bGMYC analysis. Information on the lineage used in this study can be found in the Excel file bellow.
DOI: 10.5061/dryad.789pv/8
title: Phyllomedusa nordestina Cytochrome-b

description: Complete Cyb alignment of Phyllomedusa nordestina before bGMYC analysis. Information on the lineage used in this study can be found in the Excel file bellow.
DOI: 10.5061/dryad.789pv/9
title: Phyllopezus pollicaris Cytochrome-b

description: Complete Cyb alignment of Phyllopezus pollicaris before bGMYC analysis. Data first published by Werneck et al 2012, Evolution, 66, 3014–3034. Information on the lineages used in this study can be found in the Excel file.
DOI: 10.5061/dryad.7p7n2/1
title: ddRADSeq Data Files

description: We include the output haplotypes.tsv file resulting from the populations module of Stacks, our custom filtered haplotypes files, and the resulting input files generated for various programs from the filtered haplotypes file. The filtering and input files were generated as part of the pipeline developed for processing ddRADseq data, available at https://github.com/dportik/Stacks_pipeline.
DOI: 10.5061/dryad.7p7n2/2
title: Arlequin Data Files and Results

description: We include all input files for the mtDNA and SNPs data sets to perform various partitioning schemes of AMOVA. The commands for running Arlecore are included, along with a results folder for each input file.
DOI: 10.5061/dryad.8424c/1
title: Female_manipulation_2017
DOI: 10.5061/dryad.84b09/3
title: Gunter2017_landmark_covarSL

description: Landmarks of geometric morphometric measurements of the lower pharyngeal jaws of various cichlid species, as specified in tpsDig. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD).
DOI: 10.5061/dryad.84b09/4
title: sliders

description: Landmarks of geometric morphometric measurements of the lower pharyngeal jaws of various cichlid species, as specified in tpsDig. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD).
DOI: 10.5061/dryad.84b09/5
title: Gunter2017_geneexpression

description: Gene expression measurements of the lower pharyngeal jaws of various cichlid species, which are specified in column A.  Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD), specified in column B. Standard length of each fish is recorded in mm in column E. Gene expression values are derived from qRT-PCR experiments using 13 candidate genes, with values scaled against 3 housekeeping genes and normalised.
DOI: 10.5061/dryad.90d2g/1
title: Abiotics

description: Snow depth over and soil temperatures in manipulated and unmanipulated non-sorted-circles. Snowdepths have been measured from west to east at every 50 cm, at three dates in the springs of 2013 and 2014. Soil temperatures measured in the center of non-sorted circles at approximately -1 cm in the autumn-spring of 2012-2013, and autumn-mid summer 2013-2014. 'ctrl' plots are unmanipulated, 'fleece' plots were covered with gardening fleeces, and 'snow' plots had snow added by use of a stone wall catching snow.
DOI: 10.5061/dryad.b3k81/1
title: Buchanan et al_Oikos_Metaanalysis data

description: This data file is an excel file containing three worksheets. (1) "Table of contents" defines the column names for the remaining worksheets; (2) "Data extracted from papers" contains values and descriptors for each non-consumptive effect response for each of the 62 papers used in the analysis. Descriptors include information about the paper (e.g., type of study, where in the paper the data was found) and the study species used in the paper (e.g., species names and characteristics); (3) "Collapsed data and effect sizes" contains the same descriptors as worksheet (2), but also includes (i) effect sizes (log response ratios) and variance as calculated by MetaWin , and (ii) values averaged within a single paper where inclusion of multiple separate data points from a single paper would have resulted in psuedoreplication. Data contained in worksheet (3) "Collapsed data and effect sizes" is the data used in the meta-analysis and reported in the manuscript.
DOI: 10.5061/dryad.c44h0/1
title: Data from: Testing the hierarchical model of litter decomposition

description: All litter decomposition data, data on measured controlling variables, and treatment identifiers. The ReadMe text file describes the variables for all 52 columns of data.
DOI: 10.5061/dryad.c44h0/2
title: Statistical code used to analyze the data from: Testing the hierarchical model of litter decomposition

description: All R code used to analyze the data presented in the Bradford, Veen et al. manuscript titled, "Testing the hierarchical model of litter decomposition". Please also see the ReadMe file associated with the data for descriptions of the full data and code package.
DOI: 10.5061/dryad.c8mh3/1
title: Braga Goncalves et al. data for dryad

description: Entelurus aequoreus specimens and voucher specimens used for DNA sequencing. Location, collection, habitat, collection date (m/d/yr), latitude, longitude, responsible persons for making collections (collected by), sex of individual (in most cases by visual inspection and not verified by gonad inspection), total length (TL) in mm, total wet weight (WT) in grams, reproductive status of males, notes, and gene bank assession #s for cytochrome b and control region sequences are listed for each individual. na = not applicable. ? = unknown
DOI: 10.5061/dryad.ck5vv/1
title: Crocodile capture data 1978-2014

description: Crocodile capture data 1978-2014 at Turkey Point/South Florida, USA
DOI: 10.5061/dryad.dh1sd/1
title: Mammals roadkills for the year 2006
DOI: 10.5061/dryad.dh1sd/2
title: Mammals roadkills for the year 2007
DOI: 10.5061/dryad.dh1sd/3
title: Mammals roadkills for the year 2008
DOI: 10.5061/dryad.dh1sd/4
title: Mammals roadkills for the year 2009
DOI: 10.5061/dryad.fg700/38
title: Figure S22
DOI: 10.5061/dryad.fg700/39
title: Figure S23
DOI: 10.5061/dryad.fg700/40
title: Figure S24
DOI: 10.5061/dryad.g4623/1
title: Hummingbird community, local site characteristics, and landscape metrics

description: Data on hummingbirds captures at each sampling site and local and landscape covariates used in the analysis. First tab/sheet (DATA) contains the data, the second tab/sheet (COLUMN NAMES) contains the column descriptions.
DOI: 10.5061/dryad.gv1q5/11
title: simuLBA.LGFG.tar

description: Simulation under LG+F+G for 4 taxa 1000 sites under LBA setting.
DOI: 10.5061/dryad.gv1q5/12
title: simuLBR.LGFG.tar

description: Simulation under LG+F+G for 4 taxa 1000 sites under LBR setting.
DOI: 10.5061/dryad.gv1q5/13
title: simuLBR.EXEHO.tar

description: Simulation under EX_EHO for 4 taxa 6000 sites under LBR setting.
DOI: 10.5061/dryad.gv1q5/14
title: simuLBA.EXEHO.tar

description: Simulation under EX_EHO for 4 taxa 6000 sites under LBA setting.
DOI: 10.5061/dryad.gv1q5/15
title: simu.amborella.JTT.tar

description: Simulate under JTT+F+G based on an Amborella/Angiosperm tree for 12549 sites; used for Fig. S25.
DOI: 10.5061/dryad.gv1q5/16
title: simu.Ord0245.tar

description: Bootstrap alignment files for fitting PMSF based on the ML tree estimated from Ord0245, one of the 300 proteins in the HSSP test datasets. These data were used for producing Fig. S1.
DOI: 10.5061/dryad.gv1q5/17
title: simuLBA.C20F.1050sites.tar

description: Simulation under LG+C20+F+G for 4 taxa 1050 sites under LBA setting.
DOI: 10.5061/dryad.k0gq6/115
title: E_rare_marsupiiferum_419.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/116
title: E_rare_musteum_51.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/117
title: E_rare_napo-pastazanum_404.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/118
title: E_rare_napo-pastazanum_406.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/119
title: E_rare_obliquum_complex_138.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/120
title: E_rare_obtusifolium_41.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/121
title: E_rare_prismaticum_843.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/122
title: E_rare_schiedeanum_841.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k16gv/1
title: Sams_Mayfield_Rf1_All

description: This file contains all of the data used in this paper.  The file contains nine Excel sheets.  The first is a summary of what is contained in each sheet and the remaining eight are pairs of metadata and raw data files.  Each metadata sheet matches the name of the relevant datasheet.  Data in this file include trait, climate, abundance and landscape data.
DOI: 10.5061/dryad.k36n4/1
title: DominanceStatus

description: Dominance status for each male over both experimental rounds.
DOI: 10.5061/dryad.k36n4/2
title: MalePCs

description: Data from PCAs to combine behavioural parameters
DOI: 10.5061/dryad.k36n4/3
title: OffspringActivity

description: Raw data on offspring activity from video recordings
DOI: 10.5061/dryad.k36n4/4
title: ReadMe Zajitschek etal BMCEvolBiol 2017

description: Information in data filters applied
DOI: 10.5061/dryad.k36n4/5
title: SpermLongevity

description: Data on sperm longevity for each male
DOI: 10.5061/dryad.np4pm/1
title: Time series prevalence data
DOI: 10.5061/dryad.np4pm/2
title: Code to estimate CCS for a single strain
DOI: 10.5061/dryad.np4pm/3
title: Code to estimate CCS for the co-infected strain
DOI: 10.5061/dryad.p148m/4
title: R_code

description: R code to perform analyses described in the paper.
DOI: 10.5061/dryad.q9533/1
title: Data sets Mahen In situ 14SEP2017

description: It includes data on (a) actual and estimated subject-distance for all the 29 images of cardboard model fish in the first worksheet. (b) EXIF information for all the 29 images in the second worksheet.
DOI: 10.5061/dryad.qs1k6/1
title: Site Data for statistical biodiversity models
DOI: 10.5061/dryad.t4313/1
title: Converted-qPCR-Data_nematodes_bacteria_fungi

description: In this data file you can find the data we used to execute our statistical tests. Converted Ct values are shown and the transformed data is shown in purple. (Making use of linear relationship between primary qPCR output, Ct values, and the number of individuals, nematode concentrations expressed as individuals per 100 g of soil were calculated. As both the resulting nematode densities and the concentrations of bacterial and fungal DNA (ng per 0.25 g soil) didn’t show a normal distribution, data were transformed. Primary counts were log transformed (ln(y+0.1)). A constant (0.1) was added to push data away from the lower bound zero.) A legend is added to explain the meaning of the first six rows.
DOI: 10.5061/dryad.td223/1
title: Stern2017recordings.tar
DOI: 10.5061/dryad.td223/2
title: Stern2017segmentations

description: Songs segmented using FlySongSegmenter from Stern 2017.
DOI: 10.17632/63g8xc9ky2.1
title: Data for: Excimer Formation from Particially Overlapped Anthracene Dimer Based on Saddle-shaped Cyclooctatetrathiophene as Spacer

description: The supporting information of the article, including the NMR spectra and crystal data are provided.
DOI: 10.5061/dryad.02bf1/1
title: 2b-RAD raw data of Rhodnius ecuadoriensis

description: Sequencing
A) Clustering was done by ‘onboard clustering’ and samples were sequenced on MiSeq (MSC 2.5.0.5/RTA
1.18.54) with a 1x51 setup using ‘Version2’ chemistry. The Bcl to FastQ conversion was performed using
bcl2fastq-1.8.4 from the CASAVA software suite. The quality scale used is Sanger / phred33 / Illumina
1.8+.
DOI: 10.5061/dryad.12751/1
title: Figure 1 (all responses to stimuli)

description: Origin (OriginLab software) file that contains the data in Figure 1
DOI: 10.5061/dryad.12751/2
title: Figure 1-Fig Supl 1 (data from all cells)

description: Origin (OriginLab software) file that contains the data in Figure 1-Figure Supplement 1
DOI: 10.5061/dryad.12751/3
title: Figure 2 (SNR, infromation and efficiency)

description: Origin (OriginLab software) file that contains the data in Figure 2
DOI: 10.5061/dryad.12751/4
title: Figure 2-Fig Supl 1

description: Origin (OriginLab software) file that contains the data in Figure 2-Figure Supplement 1
DOI: 10.5061/dryad.12751/5
title: Figure 2-Fig Supl 2 (eye-movement noise)

description: Origin (OriginLab software) file that contains the data in Figure 2-Figure Supplement 2
DOI: 10.5061/dryad.217fn/1
title: Geographic locations of sampling sites

description: Geographic coordinates in decimal degrees of the sampling locations.
DOI: 10.5061/dryad.217fn/2
title: Genetic RDAs-data

description: Data used to test associations of genetic variation with geography and climate by means of RDA and pRDA.
DOI: 10.5061/dryad.217fn/3
title: Phenotypic RDAs-data

description: Data used to test associations of phenotypic variation with geography and climate by means of RDA and pRDA.
DOI: 10.5061/dryad.2np3s/1
title: Phenology of the common lizard on five study sites

description: This file includes data collected on the phenology of the common lizard on five sites (variable SITE) of the Mont-Lozère. TEMPERATURE is the mean of daily maximum air temperature in June (°C). Parturition dates are described by the mean of the time interval since July 1 (MEAN in days) and its standard deviation (SD). The file also reports the sample size N (number of litters per site and year), the coefficient of variation CV (SD divided by the mean date), the SKEWNESS and KURTOSIS of the frequency distributions of parturition dates.
DOI: 10.5061/dryad.2np3s/2
title: Experimental test

description: This file includes data on the experiment performed in 2005. This experiment tested the influence of temperature during gestation on the parturition date of the common lizard. The variable DATE is the number of days since July 1, IDENTITY is the female identity, and TEMPERATURE reports the three experimental groups:  A = warm group, B = intermediate-heat group, C = cold group.
DOI: 10.5061/dryad.30tg8/5
title: Proportion of MA versus PAH

description: data of Table 3 and Table 4
DOI: 10.5061/dryad.44m2h/2
title: data for niche width

description: Heritability, CVa and Heterozygosity for wild bird populations assiciated with niche width.
DOI: 10.5061/dryad.5gr8r/1
title: All_control_t_posterior_G

description: Complete set of posterior distribution of 1000 variance and covariance G-matrices from the BSFG model for control t line in .csv format.
DOI: 10.5061/dryad.5gr8r/10
title: All_upwards_h'_posterior_P

description: Complete set of posterior distribution of 1000 variance and covariance P-matrices from the BSFG model for upwards h' line in .csv format.
DOI: 10.5061/dryad.5gr8r/2
title: All_downwards_s_posterior_G

description: Complete set of posterior distribution of 1000 variance and covariance G-matrices from the BSFG model for downwards s line in .csv format.
DOI: 10.5061/dryad.5gr8r/3
title: All_downwards_h_posterior_G

description: Complete set of posterior distribution of 1000 variance and covariance G-matrices from the BSFG model for downwards h line in .csv format.
DOI: 10.5061/dryad.5gr8r/4
title: All_upwards_s'_posterior_G

description: Complete set of posterior distribution of 1000 variance and covariance G-matrices from the BSFG model for upwards s' line in .csv format.
DOI: 10.5061/dryad.5gr8r/5
title: All_upwards_h'_posterior_G

description: Complete set of posterior distribution of 1000 variance and covariance G-matrices from the BSFG model for upwards h' line in .csv format.
DOI: 10.5061/dryad.5gr8r/6
title: All_control_t_posterior_P

description: Complete set of posterior distribution of 1000 variance and covariance P-matrices from the BSFG model for control t line in .csv format.
DOI: 10.5061/dryad.5gr8r/7
title: All_downwards_s_posterior_P

description: Complete set of posterior distribution of 1000 variance and covariance P-matrices from the BSFG model for downwards s line in .csv format.
DOI: 10.5061/dryad.5gr8r/8
title: All_downwards_h_posterior_P

description: Complete set of posterior distribution of 1000 variance and covariance P-matrices from the BSFG model for downwards h line in .csv format.