cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q9m45/4
title: Data for Figure 4A-D

description: This file contains 4 datasheets providing the individual numeric values plotted in Figure 4A-D.
DOI: 10.5061/dryad.q9m45/5
title: Data for Figure 5

description: This file provides the cell values (species richness and coexistence) and realm assignments used in Figure 5.
DOI: 10.5061/dryad.q9m45/6
title: Data for Figure S2A-B

description: This file contains the cell values (species richness, sister species richness and coexisting richness) used in Figure S2A-B.
DOI: 10.5061/dryad.q9m45/7
title: Data for Figure S4

description: This file contains the observed and estimated vales of σ and ε for different sister species age distributions plotted in Figure S2.
DOI: 10.5061/dryad.r47tm/1
title: data_Derroire_et_al_2016_Oikos

description: The provided data give the values of diversity and similarity indices for trees and shrubs, the successional age of the plot and values for environmental factors for 829 plots of 13 chronosequences in successional tropical dry forests used in the meta-analyses presented in the paper.
DOI: 10.5061/dryad.sf937.2
title: Data from: Symbiont-mediated RNA interference in insects
DOI: 10.5061/dryad.sf937.2/1.2
title: Thrips QRTPCR

description: Raw cq values for thrips QRTPCR
DOI: 10.5061/dryad.v67g3/1
title: Reproductive characteristics of hylid and leptodactylid frogs (Amphibia, Anura)

description: Data for 330 hylid and leptodactylid species included in Zamudio et al. 2016 (The American Naturalist) with references. Species in bold were used for non-phylogenetic analyses only. Blank cells represent missing data. Complete references in alphabetical order are given on the second sheet.
DOI: 10.5061/dryad.vb654/1
title: Flies' positions

description: This .zip file contains 10 positions per second for each fly collected during 62 experiments lasting 4 hours each one.
DOI: 10.5061/dryad.1j6sk/2
title: Landscape_Temperature_2013_2014_PSWMA_

description: Black bulb temperatures recorded at random landscape sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).
DOI: 10.5061/dryad.1j6sk/3
title: Nest_Landscape_Temperature_MEANS_

description: Hourly means of black bulb temperatures recorded at nest and random landscape sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).
DOI: 10.5061/dryad.1j6sk/4
title: Successful_Unsuccessful_Nests

description: Black bulb temperatures recorded at successful and unsuccessful nest at the Packsaddle WMA, Oklahoma, USA (2013-2014).
DOI: 10.5061/dryad.1j6sk/5
title: Vegetation

description: Vegetation variables recorded nest and random landscape sites at the Packsaddle WMA, Oklahoma, USA (2013-2014).
DOI: 10.5061/dryad.3126v/4
title: sce1
DOI: 10.5061/dryad.3126v/5
title: sce2
DOI: 10.5061/dryad.635ds/3
title: Supplemental File 5

description: Genetic map file of consensus genotypes for each contig.
DOI: 10.5061/dryad.635ds/4
title: Supplemental File 6

description: Raw Data file of genotypes for each SNP.
DOI: 10.5061/dryad.762b8/10
title: SM2_BD_OK

description: Core SM2: Bulk density data
DOI: 10.5061/dryad.762b8/3
title: SM1_BD_OK

description: Core SM1: Bulk density data
DOI: 10.5061/dryad.762b8/4
title: SM1_geochem_OK

description: Core SM1: Geochemical data
DOI: 10.5061/dryad.762b8/5
title: SM1_LOI_OK

description: Core SM1: Loss-on-ignition data
DOI: 10.5061/dryad.762b8/6
title: SM1_macrofossils_OK

description: Core SM1: % Plant macrofossil data
DOI: 10.5061/dryad.762b8/7
title: SM1_pollen_OK

description: Core SM1: Pollen count data
DOI: 10.5061/dryad.762b8/8
title: SM1_SCP_OK

description: Core SM1: Spheroidal carbonaceous particle data
DOI: 10.5061/dryad.762b8/9
title: SM1_testateamoebae_OK

description: Core SM1: % Testate amoeba data and water table reconstruction
DOI: 10.5061/dryad.782m8/1
title: Assortative mating data from "Klingavälsåns Naturreservat"

description: Male and female mating couples and morphological data in mating pairs from "Klingavälsåns Naturreservat". Male and female ID:s and date of capture are given (male above the female he was mating with), and value for each of the eight measured morphological traits that we measured. These trait values were used to estimate the strength of assortative mating.
DOI: 10.5061/dryad.782m8/2
title: Assortative mating data from "Sövdemölla"

description: Male and female mating couples and morphological data in mating pairs from "Sövdemölla". Male and female ID:s and date of capture are given (male above the female he was mating with), and value for each of the eight measured morphological traits that we measured. These trait values were used to estimate the strength of assortative mating.
DOI: 10.5061/dryad.782m8/3
title: Combined assortative mating data from both localities (trait values centred by mean)

description: Male and female mating couples and morphological data in mating pairs from "Klingavälsåns Naturreservat" and "Sövdemölla" (both populations combined, morphological trait data centred to mean zero). Male and female ID:s and date of capture are given (male above the female he was mating with), and value for each of the eight measured morphological traits that we measured. These trait values were used to estimate the strength of assortative mating.
DOI: 10.5061/dryad.782m8/4
title: Combined assortative mating data from both localities (trait values scaled to mean zero and unit variance))

description: Assortative mating data (male and female trait values; scaled to mean zero and unit variance) from "Klingavälsåns Naturreservat" and "Sövdemölla" (combined). Eight morphological traits were measured in both males and females, and each male that was found copulating with his female is given (male above, female below).
DOI: 10.5061/dryad.782m8/5
title: Male mate preferences for con- and heterospecific females (Fig. 4)

description: Dataset behind Fig. 4, showing Calopteryx male mate preferences for con- and heterospecific females in field presentation experiments."Score" shows male mating response. Female ID, year and population are also given.
DOI: 10.5061/dryad.8fv83/1
title: Scorpaena_porcus_175sequences

description: alignment of the 175 cytochrome b sequences of Scorpaena porcus used in the analyses
DOI: 10.5061/dryad.8fv83/2
title: Scorpaena_porcus_670_genotypes

description: Multilocus genotypes for the 670 specimens of Scorpaena porcus analysed at 11 loci.
DOI: 10.5061/dryad.8t3v5/10
title: Fig 4b Temperature data_experimental data-set for validation

description: Temperature data used in the three models to calculate predictions on timing of egg-hatching
DOI: 10.5061/dryad.8t3v5/11
title: Fig 4c Temperature data_field data-set for validation

description: Temperature data used in the three models to calculate predictions on timing of egg-hatching
DOI: 10.5061/dryad.8t3v5/2
title: Fig 2a developmental rate at different developmental stages

description: Data used in Figure 2a
DOI: 10.5061/dryad.8t3v5/3
title: Fig 2b development versus time

description: Data used in Figure 2b
DOI: 10.5061/dryad.8t3v5/4
title: Fig 3 development against time

description: Data used in Figure 3
DOI: 10.5061/dryad.8t3v5/5
title: Fig 4a Model results_ model-fit

description: Data used in Figure 4a
DOI: 10.5061/dryad.8t3v5/6
title: Fig 4b Model results_ validation_ experiments 20052007

description: Data used in Figure 4b
DOI: 10.5061/dryad.8t3v5/7
title: Fig 4c Model results_ validation experimental data

description: Data used in Figure 4c
DOI: 10.5061/dryad.8t3v5/8
title: Fig 4a Temperature data_experimental data-set for parameterization

description: Temperature data used in the three models to estimate optimal parameters values
DOI: 10.5061/dryad.8t3v5/9
title: Fig 4a Egg-hatching data_experimental data-set for parameterization

description: Egg-hatching data used in the three models to estimate optimal parameters values
DOI: 10.5061/dryad.br0h8/1
title: Genome assemblies

description: Assembled genomes used in this study to identify rMLST, virulence and biofilm-associated gene sequences.
DOI: 10.5061/dryad.br0h8/2
title: Isolate List
DOI: 10.5061/dryad.dm293/1
title: Supplemental information to accompany the manuscript “Interactions between plants and primates shape community diversity in a rainforest in Madagascar” by James P. Herrera

description: This file contains the following supporting information: Appendix S1: Supplementary Information on lemur field surveys, Appendix S2 Supplemental Information on habitat sampling, List of tree species on study transects used for food by lemurs, Appendix S3 Supplemental Information on the functional traits of species in the study communities and raw data on lemur functional traits with references from the literature, Appendix S4 Supplementary Information on data processing especially estimating population density using program DISTANCE, the phylogeny of study species, computer code for the statistical environment R to replicate analyses, Appendix S5 Supplementary results including population density estimates for each study species on each transect, the results of significance tests of phylogenetic and functional structure on each transect, full results of linear mixed model analyses, Appendix S6 Supplementary Information on simulation experiments detailing the design of simulations to evaluate the statistical power of tests for phylogenetic community structure, giving the computer code to replicate the simulations in R, and detailing the results.
DOI: 10.5061/dryad.dm293/2
title: Supplemental Information Table S10

description: Table S10. Full results of the phylogenetic generalized linear mixed models testing the effects of environmental, phylogenetic, and trait variables on the abundance of species in the communities.
DOI: 10.5061/dryad.k3479/5
title: Model_Selection_Landscape_10kmradius
DOI: 10.5061/dryad.k3479/6
title: Model_Selection_Landscape_100kmradius
DOI: 10.5061/dryad.k3479/7
title: References
DOI: 10.5061/dryad.k3mr1/1
title: Supplementary figure 1

description: ROC (i.e. receiver operating characteristic) curve (thick continuous line) from the leave-one-family-out cross-validation analysis. Area under the ROC curve is 0.988, which can be interpreted as the probability that the model under investigation will score a randomly sampled positive (non-monophyletic) sample higher than a randomly drawn negative (monophyletic) sample. The dashed line is a reference that would be expected if the model classifies cases randomly.
DOI: 10.5061/dryad.k3mr1/2
title: Supplementary Table 1

description: Species found non-monophyletic in ML trees, with information of type of non-monophyly, entangled species, K2P intraspecific variation, geographic relationship to the entangled species, possible oversplitting of species, presence of cryptic species and identification difficulties. Other remarks are shown in the last column.
DOI: 10.5061/dryad.k3mr1/3
title: ML trees

description: Maximum Likelihood trees used in the study (Newick format).
DOI: 10.5061/dryad.k3mr1/4
title: NJ trees

description: Neighbor-Joining trees in in the study (Newick format).
DOI: 10.5061/dryad.mc2p8/1
title: Data for baseline Leslie matrices for the Luangwa valley lion population

description: Data and description for baseline Leslie matrices for male and female lions.
DOI: 10.5061/dryad.mr2mh/1
title: carabids

description: carabid data with raw landmark coordinates of the entire configuration
DOI: 10.5061/dryad.mr2mh/2
title: humans

description: human  data with raw landmark coordinates of the entire configuration
DOI: 10.5061/dryad.r6dv6/1
title: Overview experiments

description: List of experiments that were used per analysis
DOI: 10.5061/dryad.r6dv6/10
title: CTRL (2)

description: control recordings during normoxia.
DOI: 10.5061/dryad.r6dv6/12
title: ReadXDat

description: Script to read .xdat files in MATLAB
DOI: 10.5061/dryad.r6dv6/5
title: CTRL experiments (1)

description: Neural activity recordings during normoxia.
DOI: 10.5061/dryad.sf937.1
title: Data from: Symbiont-mediated RNA interference in insects
DOI: 10.5061/dryad.sf937.2/2.2
title: PRS raw data 23Feb
DOI: 10.5061/dryad.18df7/1
title: Sphingolipid composition in 4 species of bats

description: TRi is torpor index calculated for each bat; ssCEWL is surface area specific cutaneous water loss
DOI: 10.5061/dryad.2v0m8/1
title: Genotype data of populations selected for virus resistance

description: Columns indicate the generation during selection, the Wolbachia infection status, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).
DOI: 10.5061/dryad.2v0m8/2
title: Genotype data of control populations not exposed to the virus

description: Columns indicate the generation during selection, the Wolbachia infection status, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).
DOI: 10.5061/dryad.2v0m8/3
title: Genotype data of populations tested for DCV resistance after selection

description: Columns indicate the generation during selection, the Wolbachia infection status, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).
DOI: 10.5061/dryad.2v0m8/4
title: Phenotypic data on DCV resistance of populations after selection

description: Columns indicate the selection treatment, the Wolbachia infection status, the tetracycline treatment after selection, the infection treatment (stabbing with Ringer's solution or DCV), the replicate population, the replicate vial, the number of infected flies in a vial (N_flies) and the cumulative number of dead flies post-infection on a given day.
DOI: 10.5061/dryad.2v0m8/5
title: Phenotypic data on effect of infection procedure in control populations

description: Columns indicate the selection treatment, the Wolbachia infection status, the infection treatment (no stabbing, stabbing with Ringer's solution or DCV), the population, the replicate vial, the number of infected flies in a vial (N_flies) and the cumulative number of dead flies post-infection on a given day.
DOI: 10.5061/dryad.3126v/6
title: sce3
DOI: 10.5061/dryad.3126v/7
title: sce4
DOI: 10.5061/dryad.3126v/8
title: sce5
DOI: 10.5061/dryad.3126v/9
title: sce6
DOI: 10.5061/dryad.3s4d3/1
title: COI alignment

description: COI alignment file in Nexus format. NCBI block included after data block, which gives organism and isolation information for each sequence (as submitted to GenBank).
DOI: 10.5061/dryad.762b8/11
title: SM2_geochem_OK

description: Core SM2: Geochemical data
DOI: 10.5061/dryad.762b8/12
title: SM2_LOI_OK

description: Core SM2: Loss-on-ignition data
DOI: 10.5061/dryad.762b8/13
title: SM2_macrofossils_OK

description: Core SM2: % Plant macrofossil data
DOI: 10.5061/dryad.762b8/14
title: SM2_pollen_OK

description: Core SM2: Pollen count data
DOI: 10.5061/dryad.762b8/15
title: SM2_SCP_OK

description: Core SM2: Spheroidal carbonaceous particle data
DOI: 10.5061/dryad.762b8/16
title: SM2_testateamoebae_OK

description: Core SM2: % Testate amoeba data and water table reconstruction
DOI: 10.5061/dryad.762b8/17
title: SM3_BD_OK

description: Core SM3: Bulk density data
DOI: 10.5061/dryad.762b8/18
title: SM3_geochem_OK

description: Core SM3: Geochemical data
DOI: 10.5061/dryad.762b8/19
title: SM3_LOI_OK

description: Core SM3: Loss-on-ignition data
DOI: 10.5061/dryad.782m8/10
title: R-script behind Table S3 (calculating individual scores)

description: R-script behind the calculations of individual scores in Table S3.
DOI: 10.5061/dryad.782m8/11
title: R-script behind Table S4 (CCA:s for each species separately)

description: R-script behind the Canonical Correlation Analyses (CCA:s) for Calopteryx splendens and C. virgo (Table S4).
DOI: 10.5061/dryad.782m8/12
title: R-script (Table S5) and data on female mating preferences

description: R-script and dataset (N=30 males) behind analyses in Table S5 on female mating preferences in relation to male body size and male wing patch characteristics.
DOI: 10.5061/dryad.782m8/13
title: RScript behind Table S6 (four separate Principal Component Analyses)

description: R-script for Principal Component Analyses (PCA:s) of the eight morphological traits of all four phenotypes (C. splendens males and females and C. virgo males and females). Results are given i Table S6.
DOI: 10.5061/dryad.782m8/6
title: R-script for analyzing male mate preferences (Fig. 4)

description: R-script to analyze male mate preferences (binomial variable) using a Generalized Linear Model (GLZ). Results are presented in Fig. 4, and the dataset is provided as another file in DRYAD associated with this paper.
DOI: 10.5061/dryad.782m8/7
title: R-script for CCA-analyses (Table 2 and Table S6)

description: R-script behind the Canonical Correlation Analyses (CCA) presented in Table 2 and Table S6.
DOI: 10.5061/dryad.782m8/8
title: R-script for Table S1

description: R-script behind the analyses for Table S1.
DOI: 10.5061/dryad.782m8/9
title: R-script for Table S2 (factor loadings)

description: R-script behind the analyses in Table S2 (factor loadings).
DOI: 10.5061/dryad.8t3v5/12
title: Fig 4b Egg-hatching data_experimental data-set for validation

description: Data on timing of egg-hatching for the experimental data-set used for the validation shown in Fig 4b
DOI: 10.5061/dryad.8t3v5/13
title: Fig 4c Egg-hatching data_field data-set for validation

description: Data on timing of egg-hatching for the experimental data-set used for the validation shown in Fig 4c
DOI: 10.5061/dryad.8t3v5/14
title: Fig A1 Sensitivity analysis

description: Data used in Fig A1 (supplementary material)
DOI: 10.5061/dryad.8t3v5/15
title: Fig A2 MeanDD vs frostdays

description: Data used in Fig A2
DOI: 10.5061/dryad.c5t22/1
title: The source code of the model

description: This file contains the source of the model described in the paper.
DOI: 10.5061/dryad.c6344/1
title: Dataset
DOI: 10.5061/dryad.dc440/1
title: Flight performance and metabolism of Maniola jurtina

description: This data is associated to the manuscript entitled "Nectar resource limitation affects butterfly flight performance and metabolism differently in intensive and extensive agricultural landscapes"
DOI: 10.5061/dryad.g58k0/1
title: Case study files for ST-Sim software

description: As outlined in Appendix S2, this file contains all of the files required to run and view the results of the paper's simulations using the ST-Sim software
DOI: 10.5061/dryad.jf763/1
title: Caryophyllales-wide matK and rbcL

description: This is the sequence alignment (produced by Muscle v. 3.5) and the maximum likelihood tree (produced by RAxML-HPC2 v. 8.1.11) of the chloroplast matK and rbcL sequences in the Caryophyllales-wide dataset.
DOI: 10.5061/dryad.jf763/2
title: Portullugo matK and ITS dataset

description: This is the sequence alignment (produced by Muscle v. 3.5) and the maximum likelihood tree (produced by RAxML-HPC2 v. 8.1.11) of the chloroplast matK and nuclear ribosomal ITS sequences in the Portullugo dataset.
DOI: 10.5061/dryad.jf763/3
title: voucher information

description: This is a tab-delimitted text file containing the columns described in the ReadMe file.
DOI: 10.5061/dryad.k3mr1/5
title: NJ_p_trees

description: Neighbor-Joining trees calculated under p-distance model of nucleotide substitution.
DOI: 10.5061/dryad.k3mr1/6
title: Data from: Species-level para- and polyphyly in DNA barcode gene trees: strong operational bias in European Lepidoptera

description: Collection localities in .klm format (viewable with Google Earth).
DOI: 10.5061/dryad.r6dv6/11
title: LifeDeath Staining

description: fluorescent images of combined PI (red) and DAPI (blue)staining
DOI: 10.5061/dryad.r6dv6/2
title: 12 hours hypoxia

description: Raw datafiles of 12 hours hypoxia at 10% of normoxia
DOI: 10.5061/dryad.r6dv6/3
title: 6 hours hypoxia

description: Neural activity before, during, and after 6 hours of hypoxia at pO2=20mmHg.
DOI: 10.5061/dryad.r6dv6/4
title: 24 hours hypoxia (1)

description: Neural activity recorded before, during and after 24 hours of hypoxia at pO2=20mmHg.
DOI: 10.5061/dryad.r6dv6/6
title: 24 hours hypoxia(2)

description: Activity recording before, during and after 24 hours of hypoxia at pO2=20mmHg.
DOI: 10.5061/dryad.r6dv6/7
title: 48 hours hypoxia pO2=20mmHg

description: Activity recording before, during and after 48 hours of hypoxia at pO2=20mmHg
DOI: 10.5061/dryad.r6dv6/8
title: 48 hours hypoxia at pO2=80mmHg(1)

description: Activity recording before, during and after 24 hours of hypoxia at pO2=80mmHg.
DOI: 10.5061/dryad.r6dv6/9
title: 48 hours hypoxia at pO2=80mmHg(2)

description: Activity recording before, during and after 24 hours of hypoxia at pO2=80mmHg.
DOI: 10.5061/dryad.vp6fs/1
title: Genotype and Phenotype of 96 Recombinant Inbred Lines

description: The data files contain the genotypic and phenotypic information of a recombinant inbred (RI) population. This population was obtained by crossing the cultivated Glycine max (C08) with the wild type Glycine soja (W05) was adopted from a previous study (Qi et al., 2014). In our previous research (Qi et al., 2014), a core panel of 96 RI lines was re-sequenced at ~1 X depth to generate high-quality single nucleotide polymorphism (SNP) information. An array of high-quality SNPs were grouped into 2,757 bin markers distributed on the 20 chromosomes. A bin map of 2,992.0 cM in the Kosambi mapping function was generated using the bin markers. Biological nitrogen fixation related phenotypes of the RILs were collected in controlled environment as mentioned in materials and methods.
DOI: 10.5061/dryad.17n4d/1
title: 16S rRNA gene OTU table

description: 16S rRNA gene OTUs
DOI: 10.5061/dryad.17n4d/2
title: M5NR taxonomic profile at class level

description: M5NR taxonomic profile at class level
DOI: 10.5061/dryad.17n4d/3
title: SEED functional profile at subsystem level 3

description: Functional gene categories at subsystem level 3 (SEED database)
DOI: 10.5061/dryad.17n4d/4
title: Soil chemical variables

description: Values of soil chemical variables in different land uses
DOI: 10.5061/dryad.2v0m8/6
title: Genotype data of surviving flies 15 days post-infection in control populations (test of the infection procedure)

description: Columns indicate the infection treatment, the Wolbachia infection status, the population, the number of females with a given genotype (N_CC, N_CT, N_TT), the frequency of pastrel resistant allele (freq_C), the frequency of each genotype (freq_CC, freq_CT, freq_TT) and the number of individuals genotyped (N_individuals).
DOI: 10.5061/dryad.3c7jb/1
title: OH-reply-code

description: Main code file for Hamm and Fordyce 2016
DOI: 10.5061/dryad.3c7jb/2
title: OH-reply-data

description: Main data file for Hamm and Fordyce 2016
DOI: 10.5061/dryad.3c7jb/3
title: event_data

description: Event data from the BAMM analysis used in Hamm and Fordyce 2015 and used for Hamm and Fordyce 2016.
DOI: 10.5061/dryad.3c7jb/4
title: Janz_Data

description: The code and data file provided to us by Janz et al. (2016) and used for their response. Note, that one will need to adjust the sampling frequencies to reflect accurate proportions of specialists and herbivores.
DOI: 10.5061/dryad.3pt7b/1
title: Etheostoma simoterum_meristic_data

description: Meristic data from specimens of Etheostoma simoterum
DOI: 10.5061/dryad.3pt7b/2
title: E_simoterum_localities

description: Locality data of specimens included in the morphological analyses.
DOI: 10.5061/dryad.3s4d3/2
title: COI alignment MEGA format

description: COI alignment formatted for analysis in MEGA. Missing data coded as '?'
DOI: 10.5061/dryad.3s4d3/3
title: COI Neighbor-joining Tree

description: Newick format tree file from neighbor-joining analysis in MEGA (Kimura 2-Parameter model, pairwise deletion of gaps/missing data).
DOI: 10.5061/dryad.3s4d3/4
title: COI Neighbor-joining Tree with Species Labels

description: PDF file of tree from neighbor-joining analysis with species (or aff) designations labeled.