cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.f2j8s/14
title: R0 as a function of the field aspect ratio for 4 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment.

description: The file represents the basic reproductive number, R0, as a function of the field aspect ratio for 4 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment. 1st column field aspect ratio; 2nd column R0. Spatial grid 150x150 gridpoints. Plotted as points on the solid yellow curve in Fig.4(b). The data was generated by numerical solution of Eq. (6) in the manuscript.
DOI: 10.5061/dryad.f2j8s/15
title: R0 as a function of the field aspect ratio for 1 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment.

description: The file represents the basic reproductive number, R0, as a function of the field aspect ratio for 1 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment. 1st column field aspect ratio; 2nd column R0. Spatial grid 150x150 gridpoints. Plotted as points on the dashed blue curve in Fig.4(b). The data was generated by numerical solution of Eq. (6) in the manuscript.
DOI: 10.5061/dryad.f2j8s/16
title: R0, as a function of the field aspect ratio for 0.2 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment.

description: The file represents the basic reproductive number, R0, as a function of the field aspect ratio for 0.2 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment. 1st column field aspect ratio; 2nd column R0. Spatial grid 150x150 gridpoints. Plotted as points on the dash-dotted red curve in Fig.4(b). The data was generated by numerical solution of Eq. (6) in the manuscript.
DOI: 10.5061/dryad.f2j8s/7
title: R0 as a function of the field size for gaussian dispersal kernel

description: The file represents the basic reproductive number, R0, as a function of the field size for Gaussian dispersal kernel. 1st column distance [m]; 2nd column R0. Spatial grid 120x120 gridpoints. Plotted as dotted curve in Fig. 1. The data was generated by numerical solution of Eq. (6) in the manuscript.
DOI: 10.5061/dryad.f2j8s/8
title: R0, as a function of the field size for power law 2 dispersal kernel, parameters for Madras 2002 experiment

description: The file represents the basic reproductive number, R0, as a function of the field size for power law 2 dispersal kernel, parameters for Madras 2002 experiment. 1st column distance [m]; 2nd column R0. Spatial grid 120x120 gridpoints. Plotted as points on the dashed blue curve in Fig. 3. The data was generated by numerical solution of Eq. (6) in the manuscript.
DOI: 10.5061/dryad.f2j8s/9
title: R0, as a function of the field size for power law 2 dispersal kernel, parameters for Hermiston 2002 experiment.

description: The file represents the basic reproductive number, R0, as a function of the field size for power law 2 dispersal kernel, parameters for Hermiston 2002 experiment. 1st column distance [m]; 2nd column R0.  Spatial grid 120x120 gridpoints, except for last 3 points with 180x180 grid. Plotted as points on solid red curve in Fig. 3. The data was generated by numerical solution of Eq. (6) in the manuscript.
DOI: 10.5061/dryad.f9n48/4
title: Research DATA_SET

description: Tables with research results
DOI: 10.5061/dryad.fk1q6/1
title: zip archive of Kagaya_Patek_2015JEB_dataset_and_scripts

description: The zip archive contains one R image file and three R scripts. The R image file contains all R objects including data and function objects. The paper's DOI is, 10.1242/jeb.130518.
DOI: 10.5061/dryad.h6q11/10
title: MS_Ahrensetal_SupplementTable1

description: Supplementary Table 1. Sampling site data as given for the localities, collection site numbers refer to plots of Supplementary Fig. 1.
DOI: 10.5061/dryad.h6q11/11
title: MS_Ahrensetal_SupplementTable2

description: Supplementary Table 2. Genbank accession numbers for the data set including voucher number (*numbers without “DA” refer to the BMNH voucher codes used at the NHM London), shortcut, and locality information.
DOI: 10.5061/dryad.h6q11/12
title: MS_Ahrensetal_SupplementTable3

description: Supplementary Table 3. Model outputs of GMYC modeling with the empirical data: Likelihoods for null hypothesis (L0; i.e., no shift in branching rate) and GMYC (LGMYC) models, their likelihood ratio (LR) and its significance (pLRT, evaluated using a chi-square test with 3 degrees of freedom to compare GMYC and null hypothesis models), and the threshold genetic distance (T).
DOI: 10.5061/dryad.h6q11/13
title: Nexus_Files_datasets

description: Sericini data: full and subclade data sets
DOI: 10.5061/dryad.h6q11/5
title: MS_Ahrensetal_SupplementFigure5

description: Supplementary Fig. 5. Comparison of the performance of the subclade’s distance-based cluster analyses (A,C,E,G,M,Q,R) with that of the complete Sericini data set (All). X-axis: threshold divergence (%), Y-axis: number of species. Blue graph – estimated species number; pink graph – number of matching species with a priori species assignments.
DOI: 10.5061/dryad.h6q11/6
title: MS_Ahrensetal_SupplementFigure6

description: Supplementary Fig. 6. Example of the simulated trees with increased species samples distributed along with log-normal distribution of mean 5.
DOI: 10.5061/dryad.h6q11/7
title: MS_Ahrensetal_SupplementFigure7

description: Supplementary Fig. 7. Mean match ratio for the different number of sampled species under the random, clustered and clade-wise GMYC sampling simulations for simulation schemes with constant sample size and Ne (sd=0; cross), with variable sample size but constant Ne (simple line); with variable Ne but constant sample size (square), and variable Ne and sample size (triangle) assuming a median proportion of singleton species of 13% (red), 40% (green) and 52% (orange), (sd =1, 1.5, or 2, respectively).
DOI: 10.5061/dryad.h6q11/8
title: MS_Ahrensetal_SupplementFigure8

description: Supplementary Fig. 8. Lumping and oversplitting behavior of the GMYC model in simulations in relation to the sampling bias: ratio of GMYC vs true species compared for the different sampling schemes for constant Ne and constant sample size (sd=0).
DOI: 10.5061/dryad.h6q11/9
title: MS_Ahrensetal_SupplementFigure9

description: Supplementary Fig. 9. Relation of AIC confidence sets (GMYC) from simulations to the number of sampled species (above) and to the match ratio (GMYC entities vs. true species; below) in the framework of the different sampling schemes.
DOI: 10.5061/dryad.jp35r/1
title: Sexy and glow it data

description: The full data for the article. One tab includes data on female fecundity, brightness and lantern size. One tab has the data on male capture in traps.
DOI: 10.5061/dryad.kn37p/2
title: Interview Guide for Government Officials

description: Interview Guide for Government Officials
DOI: 10.5061/dryad.kn37p/3
title: Interview Guide

description: Interview Guide
DOI: 10.5061/dryad.m1n03/1
title: Data repository analyses presented in Robinson et al. 2015 PLoS Medince

description: 1) Albinama_Table1.dta: Baseline characteristics of  cohort; 2) Albinama_Table2_Po: Survival analyses of risk of P. ovale infections; 3) Albinama_Table2_Pv_clin: Survival analyses of incidence risk of P. vivax clinical episodes; 4) Albinama_Table2_Pv_LM: survival analyses of incidence risk of light-microscopically positive P. vivax infections; 5) Albinama_Table2_Pv_PCR: survival analyses of incidence risk of PCR positive P. vivax infections; 6)Albinama_Table2_Pvg: survival analyses of incidence risk of gametocyte positive P. vivax infections; 7) Albinama_Table3_0-3mo: incidence of malaria endpoints for first 3 months of follow-up; 8) Albinama_Table3_4-8mo: incidence of malaria endpoints for months 4-8 of follow-up; 9) Albinama_Table3_0-8mo: incidence of malaria endpoints for entire 8 months follow-up; 10) Albinama_Table4_Pf_clin: Survival analyses of incidence risk of P. falciparum clinical episodes; 11) Albinama_Table4_Pf_LM: survival analyses of incidence risk of light-microscopically positive P. falciparum infections; 12) Albinama_Table4_Pf_PCR: survival analyses of incidence risk of PCR positive P. falciparum infections; 13)Albinama_Table4_Pm_PCR: survival analyses of incidence risk of PCR positive P. malariae infections;
DOI: 10.5061/dryad.m96d0/1
title: LiDAR and field data for Dyke Marsh

description: LiDAR point files (Ground and All Points) collected in 2012; RTK GPS point files collected in 2012 and 2013; Field data on plant litter and surface soils; and some derived data from the LiDAR survey at the locations of plots and RTK elevations.
DOI: 10.5061/dryad.p9b0n/1
title: Pelican feather isotope data

description: Stable isotope data (C,N,H) from feathers collected at 19 pelican colonies across North America.
DOI: 10.5061/dryad.q7m07/1
title: CarabidAnalysesFinalMainTrees

description: The NEXUS file written for Mesquite which was used to test for accurate phylogenetic placement of sequences obtained from Illumina sequencing of carabid museum specimens in the context of a larger phylogeny. The file contains matricies for seven genes and the trees produced by the analyses.
DOI: 10.5061/dryad.r7g8q/1
title: gallagherWagenius2015_fieldSeedling_vigor

description: Data used to analyze first-season vigor of Andropogon gerardii, Bouteloua curtipendula and Sorghastrum nutans seedlings that were directly sown into three experimental plots located in three prairie restorations in western Minnesota. Seeds were sourced from four remnants, three restorations and three MN prairie seed nurseries. Only surviving seedlings are included in this data set.
DOI: 10.5061/dryad.r7g8q/2
title: gallagherWagenius2015_fieldSeedling_germSurvMass

description: Data used to analyze germination, first-season survival and mean seed mass of Andropogon gerardii, Bouteloua curtipendula and Sorghastrum nutans seeds that were directly sown into three experimental plots located in three prairie restorations in western Minnesota. Seeds were sourced from four remnants, three restorations and three MN prairie seed nurseries.
DOI: 10.5061/dryad.r7g8q/3
title: gallagherWagenius2015_plug_germSurv

description: Data used to analyze germination and first-season survival of Andropogon gerardii, Bouteloua curtipendula and Sorghastrum nutans plugs that were germinated in growth chambers and then transplanted into three experimental plots located in three prairie restorations in western Minnesota. Seeds were sourced from four remnants, three restorations and three MN prairie seed nurseries. Only surviving plugs that were actually planted in the field are included in this data set.
DOI: 10.5061/dryad.r7g8q/4
title: gallagherWagenius2015_plug_vigor

description: Data used to analyze first-season vigor of Andropogon gerardii, Bouteloua curtipendula and Sorghastrum nutans plugs that were germinated in growth chambers and then transplanted into three experimental plots located in three prairie restorations in western Minnesota. Seeds were sourced from four remnants, three restorations and three MN prairie seed nurseries. Only surviving plugs, with final vigor measurements, are included in this data set.
DOI: 10.5061/dryad.v30kv/1
title: Startles data
DOI: 10.5061/dryad.v30kv/2
title: Yolk sac centroid size
DOI: 10.5061/dryad.v30kv/3
title: Body length results with figure
DOI: 10.5061/dryad.v30kv/4
title: Body width-length ratio results with figure
DOI: 10.5061/dryad.v30kv/5
title: Time to catch data with figure
DOI: 10.5061/dryad.v48m0/1
title: Neophobia and dietary wariness

description: The excel file includes experimental data used to estimate object neophobia, dietary wariness and consumption, each one in a different tab.
DOI: 10.5061/dryad.0mv3q/1
title: Main data set, one paper per row

description: This is an anonymized version of the dataset used for most of the analyses in Fox et al. 2016. Manuscript ID numbers are random and the sort order within years is random. Editor ID is also randomized. Columns that could allow the dataset to be de-anonymized, such as editor seniority and editor years on the editorial board, have been deleted. The dataset includes one line per manuscript. This file allows recreation of most but not all analyses in the published manuscript. This is an anonymized version of the dataset used for the analyses in Fox et al. 2016. Manuscript ID numbers are random and the sort order within years is random.
DOI: 10.5061/dryad.17k8j/1
title: alignments_trees.tar

description: Alignments and phylogenetic trees of simulated DNA sequences and of Drosophila sequences from Larracuente A., Sackton T., Greenberg A., Wong A., Singh N., Sturgill D., Zhang Y., Oliver B., Clark A. 2008. Evolution of protein-coding genes in Drosophila. Trends in Genetics. 24:114–23.
DOI: 10.5061/dryad.17k8j/2
title: sup_fig1

description: Supplementary figure 1.
DOI: 10.5061/dryad.17k8j/3
title: sup_fig2

description: Supplementary figure 2.
DOI: 10.5061/dryad.17k8j/4
title: sup_fig3

description: Supplementary figure 3.
DOI: 10.5061/dryad.17k8j/5
title: sup_fig4

description: Supplementary figure 4.
DOI: 10.5061/dryad.17k8j/6
title: sup_fig5

description: Supplementary figure 5.
DOI: 10.5061/dryad.2r3f2/1
title: Dmelanostictus_WoganetalBioLetters

description: nexus file of 3 concatenated genes
DOI: 10.5061/dryad.2vp4v/1
title: Bombina_variegata_11loci

description: Microsatellite data in genepop format
DOI: 10.5061/dryad.31g1b/1
title: Nicotra et al MEC data archive part 1

description: Data from phenotype analyses, crossing and autogamy experiments as well as herbarium accession data.
DOI: 10.5061/dryad.31g1b/2
title: Nicotra et al MEC data archive part 2

description: Data and supporting files for DAPC, STRUCTURE, SNAPP analyses
DOI: 10.5061/dryad.33f0n/1
title: Laskowski et al_social niche disruption_DATA

description: Individual and colony data used in Laskowski et al.
DOI: 10.5061/dryad.4m897/1
title: Abundance herbivores of tropical trees, effects of diversity

description: Data is collected in the field,on the first column Species diversity with two levels monoculture and polyculture. Second column Genotypic diversity with two levels one maternal family and four maternal families. Rest of columns Ants, Sap feeders, leaf chewers (abundance) , H. grandella y P. meliacella (attacks as proxy of abundance)
DOI: 10.5061/dryad.65bd3/1
title: Data summary

description: This table show, for each nematode population, the plant status in 2013, the effective size computed with Jorde & Ryman method, the effective size computed with Wang method, The number of cyst (corrected by the proportion of heterodera schachtii cysts) for samples of 2012 and 2013, and the FIS for samples of 2012 and 2013
DOI: 10.5061/dryad.65bd3/2
title: Genetic Data

description: This zip contains our genetic data (8 microsatellites) for our nematode populations in a Fstat format. Each file correspond to one population (the name of the file),with the first lines ("1") corresponding to the sample of 2012 and the last ones ("2") corresponding to the sample of 2013.
DOI: 10.5061/dryad.75427/1
title: Alignments

description: We downloaded gene sequences of 11 of the 16 species from Ensembl release 75 (Flicek et al. 2014). After identifying orthologous loci using the EnsemblCompara pipeline (Vilella et al. 2009), we extracted the longest transcript coding sequence (CDS) of each gene. Sequences for cichlid species other than the Nile Tilapia, Oreochromis niloticus, were obtained from the deposited genome assemblies (Brawand et al. 2014; Elmer et al. 2014). Orthologous loci in cichlid genomes were identified by BLASTN searches using Nile Tilapia sequences as queries and an e-value threshold of 10 -4.The integrity of obtained sequences was double-checked by BLASTN searches against available transcriptomes to ensure correct reading frames. Multiple sequence alignments of individual genes were constructed with translatorX (Abascal et al. 2010): After translation, sequences are aligned at the amino acid level using MUSCLE (Edgar 2004), unreliable amino acid positions are removed with Gblocks (Castresana 2000) under the least stringent parameters, and the corresponding nucleotide alignments are created guided by trimmed amino acid alignments. Maximum-likelihood phylogenetic reconstruction was performed with PhyML version 3.1 (Guindon et al. 2010) after best-fit models of evolution were chosen based on AICc (Akaike information criterion with correction) scores (Hurvich and Tsai 1989) calculated in jModeltest version 2.1.5 (Posada 2008).
DOI: 10.5061/dryad.7hn84/1
title: Seed number data

description: All capsular seed number data measured by the authors and used in the analyses. The file also contains the locality and time of collection and the name of the collector.
DOI: 10.5061/dryad.7hn84/2
title: ITS alignment

description: nrITS alignment underpinning the analyses
DOI: 10.5061/dryad.7hn84/3
title: Paup*

description: Logfile created while searching for a phylogenetic hypothesis underpinning the analyses.
DOI: 10.5061/dryad.7hn84/4
title: r8s

description: Logfile created while transforming one of the MP trees to an ultrametric tree in r8s.
DOI: 10.5061/dryad.7hn84/5
title: Ultrametric tree

description: The ultrametric tree underpinning the analyses in newick format
DOI: 10.5061/dryad.7hn84/6
title: ReadMe file

description: ReadMe file describing the files, variables and abbreviations
DOI: 10.5061/dryad.8p800/1
title: Matrix in plain text

description: Matrix in plain text corresponding to publication named in submission. Please contact the corresponding author for taxonomic and nomenclatural details of accessions.
DOI: 10.5061/dryad.94j0f/1
title: NESTS
DOI: 10.5061/dryad.94j0f/2
title: YOUNG
DOI: 10.5061/dryad.94j0f/3
title: EGGS
DOI: 10.5061/dryad.b973n/6
title: Primer sequences
DOI: 10.5061/dryad.cq275/1
title: Raillietella indica parasites in Mediterranean gecko hosts

description: Within the RAIN-Gecko.zip package accompanying the above publication there are 3 files.  For any further queries please contact icabal@tamu.eduThe following files are included:1) README.txt - This file includes a description of the variables and a listing of the files used for statistical analyses.2) "RecentlyActiveGeckos.csv"This is the dataset used for the analysis of recently active geckos. 3) "RestedGeckos.csv"This is the dataset used for the analysis of rested geckos.
DOI: 10.5061/dryad.f2j8s/17
title: R0, as a function of the field aspect ratio for 0.1 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment.

description: The file represents the basic reproductive number, R0, as a function of the field aspect ratio for 0.1 ha field area, power law 2 dispersal kernel, parameters for Madras 2002 experiment. 1st column field aspect ratio; 2nd column R0. Spatial grid 150x150 gridpoints. Plotted as points on the dotted orange curve in Fig.4(b). The data was generated by numerical solution of Eq. (6) in the manuscript.
DOI: 10.5061/dryad.ff138/1
title: Fasta file of fungal unique sequences

description: Fungal unique sequences from soils of alpine grasslands dominated by Carex curvula or C. curvula sp roase and subalpine pastures dominated by Nardus stricta
DOI: 10.5061/dryad.ff138/2
title: Fasta file of bacterial unique sequences

description: Bacterial unique sequences from soils of alpine grasslands dominated by Carex curvula or C. curvula sp roase and subalpine pastures dominated by Nardus stricta
DOI: 10.5061/dryad.ff138/3
title: Fungi_unique_sequence_abundance

description: Abundance of each unique sequence in each sample
DOI: 10.5061/dryad.ff138/4
title: Bacteria_unique_sequence_abundance

description: Abundance of unique bacterial sequences in each sample
DOI: 10.5061/dryad.ff138/5
title: Experimental design

description: Correspondance between plant species, sampling site and sample
DOI: 10.5061/dryad.ff138/6
title: Soil data for multivariate analysis,

description: Solid chemical parameters by samplng site and grassland type
DOI: 10.5061/dryad.ff138/7
title: Plant communities' occurrence matrix

description: This file contains a matrix of occurrence of plant species (in columns) for each site (in rows)
DOI: 10.5061/dryad.ff138/8
title: rarefied microbial communiy matrixes

description: Excell file containing the rarefied microbial communities matrix used in this study
DOI: 10.5061/dryad.h6q11/14
title: Examples_simulated.trees

description: Examples of simulated trees for random, clustered, and clade-wise sampling
DOI: 10.5061/dryad.h6q11/15
title: Code

description: code for simulation of gene tree within species tree with sampling.requirements:R packages "ape", "apTreeshape"SIMCOAL (SIMCOAL must be in your working directory)codes:simulation.R: an example code for simulations used in the manuscriptsgene.tree.simulations.R: functions used to run SIMCOAL simulation, sample species and simulate species treessimcoal.functions.R: functions for running SIMCOAL from Rsample.lineage.R: functions for sampling species from treesusage:"gene.tree.simulations.R", "simcoal.functions.R" and "sample.lineage.R" include functions used to run simulations. "simulation.R" is a code to call these functions and run a simulation.put the four R script files and SIMCOAL in a directory. Then set your working directory to it (setwd("...")).run codes in simulation.R by source("./simulation.R") or copy and paste the codes.
DOI: 10.5061/dryad.j8227/1
title: Aggregate Annual Fluxes

description: Daily fluxes were aggregated at the plot level over a calendar year. Details of aggregation are given in the paper.
DOI: 10.5061/dryad.j8227/2
title: Gas concentrations

description: This dataset contains time series of concentrations of CO2, CH4, and N2O in static chambers. The data were used to calculate soil fluxes.
DOI: 10.5061/dryad.j8227/3
title: Daily Fluxes

description: This dataset contains single-day N2O flux measurements at the plot level and concurrent ancillary measurements of soil properties. These data were used to generate Tables 1-2 and Figures 2-4. Details of flux estimation are given in the paper.
DOI: 10.5061/dryad.m57sd/1
title: S01_EEG

description: Subject 1. Data from one session (MEG+EEG)
DOI: 10.5061/dryad.m57sd/2
title: S01_MEG

description: Subject 1. Data from one session (MEG only)
DOI: 10.5061/dryad.m57sd/3
title: S02_EEG

description: Subject 2. Data from one session (MEG+EEG).
DOI: 10.5061/dryad.q1m54/1
title: data context-dependent signalling in an insect

description: Excel file with the data of the total amount of alarm pheromone and the relative amounts of its two compounds (as explained in further detail in the Excel file); there is a separate sheet for each of the five treatments.
DOI: 10.5061/dryad.q7m07/2
title: BembidionTransversaleGroupAnalysis

description: The NEXUS file written for Mesquite we used to test for accuracy of Illumina sequences obtained from museum specimen carabids in the context of conspecific and very closely related species. The file contains matricies and phylogenetic trees for four genes.
DOI: 10.5061/dryad.q7m07/3
title: Lagriinae_AnalyzedMatrices

description: The NEXUS file written for Mesquite which was used to test for the accurate phylogenetic placement of Illumina sequences obtained from museum tenebrionid specimens in a larger phylogeny.
DOI: 10.5061/dryad.q7m07/4
title: FocalGene_QuerySet_Tribolium

description: The query sequences from the Tribolium castaneum genome which were used to identify fragments of 7 focal genes in reads from Illumina sequenced carabid and tenebrionid museum specimens.
DOI: 10.5061/dryad.q7m07/5
title: NPG_QuerySet_Tribolium

description: Query sequences from the Tribolium castaneum genome which were used to detect the presence of 67 nuclear protein coding genes in Illumina reads of tenebrionid museum specimens.
DOI: 10.5061/dryad.q7m07/6
title: Bembidion_transversale_DNA3205_67PCG

description: Query sequences from Bembidion transversale genomic reads which were used to detect the presence of 67 nuclear protein coding genes in Illumina reads of carabid museum specimens.
DOI: 10.5061/dryad.q82nn.1
title: Data from: Opposing mechanisms drive richness patterns of core and transient bird species