cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6g2c7/1
title: BiChroM Raw R Files

description: 1. Dataset and tree
2. Raw R files for optimizations
3. Full model optimizations
4. Reduced model optimizations
5. Profile rhoH and Profile rhoW
6. Bivariate profile rhoqH and Bivariate profile rhoqW
7. Raw R files for simulations
8. Simulations number of taxa
9. Simulations for tree height
DOI: 10.5061/dryad.74f2r.2/1.2
title: Maximum clade credibility tree of FBDl

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 21 fossils, resulting from the beast2 analysis using the FBDl.xml input-file.
DOI: 10.5061/dryad.74f2r.2/10.2
title: Subsample of trees from NDbs analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with broad calibration densities) using 12 fossils (see NDbs.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/2.2
title: Subsample of trees from FBDl analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 21 fossils (see FBDl.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/3.2
title: Input file for FBDl analysis

description: This is the XML file which configures all parameters for the beast2 program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 21 fossils (FBDl). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.2/4.2
title: Maximum clade credibility tree of FBDs

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the fossilized birth-death analysis using 14 fossils, resulting from the beast2 analysis using the FBDs.xml input-file
DOI: 10.5061/dryad.74f2r.2/5.2
title: Subsample of trees from FBDs analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the fossilized birth-death analysis using 14 fossils (see FBDs.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/6.2
title: Input file for FBDs analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the fossilized birth-death dating approach including 14 fossils (FBDs). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.2/7.2
title: Maximum clade credibility tree of NDbl

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with broad calibration densities), using 15 fossils; resulting from the beast2 analysis using the NDbl.xml input-file.
DOI: 10.5061/dryad.74f2r.2/8.2
title: Subsample of trees from NDbl analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with broad calibration densities) using 15 fossils (see NDbl.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/9.2
title: Input file NDbl analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with broad prior calibration densities. This approach included 15 calibration constraints based on fossil information (NDbl). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.78j8g/1
title: Data_files_-_ECOG03137_Pinkert_et_al_2017

description: Here we provide the environmental, distributional and trait data used in Pinkert et al. 2017 (ECOG-03137), at both the species-level (for habitat preferences, i.e. lentic/lotic) and aggregated at the assemblage-level. We also provide the breakpoints from segmented regressions of the relationship between latitude and four different measures of the diversity of European dragonfly assemblages (species richness, corrected weighted endemism, the residuals of total taxonomic distinctiveness against species richness and standardized effect sizes of mean pairwise distances). For further information and a more detailed description see the manuscript or contact the first author via email (StefanPinkert@posteo.de).
DOI: 10.5061/dryad.846nj.2/2.2
title: G.ac_2006_corrected_v2

description: See also: Corrigendum, Molecular Ecology 22(20): 5270. doi:10.1111/mec.12532
DOI: 10.5061/dryad.846nj.3/3.3
title: G.ac_2006_corrected_v2

description: Version 3. See also: Corrigendum, Molecular Ecology 22(20): 5270. doi:10.1111/mec.12532
DOI: 10.5061/dryad.94kq1/1
title: Dryad_Eldridge_Ecology

description: This file contains environmental data (soils, vegetation cover, aridity), information on grazing by different herbivores, soil enzyme concentrations, and richness and abundance of bacteria and fungi. These data are used in the Structural Equation Modelling in the manuscript. A metadata tab in the file describes the data columns in the data file.
DOI: 10.5061/dryad.bp79f/3
title: JPEdawsonSA1

description: Appendix 1: Details on field history and flooding frequency at each site in the paper: 
 'Plant traits in propagule banks and standing vegetation reveal flooding alleviates impacts of agriculture on wetland restoration'

Ethics: data acquisition, archiving and use do so in an ethicial manner, in particular, we believe that those individuals 
whose time, efforts and intellect designed and created the studies are acknowledged appropriately.
As a condition for use of the dataset we request that users agree: 
1. to notify the database custodians (Samantha Dawson) if the dataset is used in any publication,
2. To provide database custodians with formal recognition, that at their discreation,  
may include co-authorship or acknowledgements on publications
DOI: 10.5061/dryad.d5s4g/1
title: Arantes et al 2017 data

description: Excel file containing 450 × 60 site-by-species matrix and geographic coordinates, land cover and environmental data for the same sites (see Arantes et al. JAE for  details).
DOI: 10.5061/dryad.h1157/1
title: Figures

description: Scripts for generating figures and the final figures
DOI: 10.5061/dryad.h1157/2
title: figure_environment

description: Python software environment for figure creation
DOI: 10.5061/dryad.h1157/3
title: Figure 1 and S2 and S6

description: Data for figures 1, S2, and S6
DOI: 10.5061/dryad.k029v/1
title: Weekly location data deer fidelity analysis

description: File contains individual deer ID as well as date, latitude, longitude and allocated season of GPS locations used to determine site fidelity of black-tailed deer in the Mendocino National Forest, California, USA.
DOI: 10.5061/dryad.k029v/2
title: Fidelity_deer_summary

description: File contains information on deer ID, age, area and period of time a deer was colalred, number of seasons (summer and winter) a deer was monitored, info on weather a deer was non-migratory (column N0 = 1) and status at the end of the monitoring period to estimate cox proportional hazards.
DOI: 10.5061/dryad.k98k0/1
title: Raw historic equid tail hair isotope data

description: The data file contains raw stable isotope data (CNH) of historic (museum) tail hair samples of two sympatric equid species, namely the Przewalski´s horse and the Asiatic wild ass (khulan) from the Dzungarian Gobi (Mongolia, China). Data were originally used to draw inferences about multi-year diet seasonality and isotopic dietary niche characteristics of historic (pre-extinction) Przewalski´s horses and historic Asiatic wild asses, as well as for comparison with their extant conspecifics (previously published in Burnik Šturm et al, J. Appl. Ecol., doi:10.1111/1365-2664.12825; 2016).
DOI: 10.5061/dryad.mb7qk/1
title: data_JAPPL201601169

description: Species counts were collected using ecological transects (Traditional Sampling, TS =1) and citizen scientists on game drives (Safari Science, SS =1) from June - August 2013. Dist_Livestock was created using points from livestock locations collected during the TS fieldwork, and distance to those points was calculated in ArcGIS. TWI was calculated in ArcGIS using slope and elevation from a 30m DEM. Dist_river was calculated using stream data produced from the same DEM. The wildlife location data were separated into groups ("Groups" column) spanning 16 days, which were centered on each of the Landsat scenes, and the NDVI values were extracted to those locations.
DOI: 10.5061/dryad.n0s75/1
title: Liver Biopsy Microarray

description: This data represents gene expression from genotype 1 HCV infected liver biopsies using an Illumina microarray. All data has been normalized.
DOI: 10.5061/dryad.n276d/1
title: raw SNP file

description: This is the raw SNP file used for all analyses. It was produced using GATK and pre-filtered using vcftools (i.e. minimal genotyping rate of 0.45 and a maximal normalized coverage of 2). This includes SNPs which are not within 90bp of cut sites (hence SNPs located on R2 reads are included here).
For analyses presented in the manuscript, further filters were applied. See methods part in the manuscript.
DOI: 10.5061/dryad.nj698/1
title: Combined four-marker DNA dataset of Malvoideae

description: This file contains the concatenated four marker (matK/trnK, ndhF, rpl16 and ITS) dataset in nexus format.
DOI: 10.5061/dryad.ns315/2
title: Genes_More_Highly_Expressed_in_Skin

description: List of genes more highly expressed in at least one skin colour (blue, grey, yellow, orange) than in non-skin samples. Data are transcripts per million reads (TPM) estimated using RSEM.
DOI: 10.5061/dryad.ns315/3
title: RSEM_Reference

description: Ctenophorus decresii specific reference for downstream mapping (for estimating gene expression) consisting of 19,407 protein coding regions annotated for Pogona vitticeps (the closest con-familial species for which a fully annotated genome is available).
DOI: 10.5061/dryad.ns315/4
title: EdgeR_Matrix

description: Gene count matrix for differential expression analysis.
DOI: 10.5061/dryad.ns315/5
title: EdgeR_Script

description: R script for differential expression analysis using EdgeR.
DOI: 10.5061/dryad.ns315/8
title: Assemblies

description: Trinity assemblies for each transcriptome used in this study.
DOI: 10.5061/dryad.p4q26/1
title: Florida Panhandle Cactus Survey Data

description: Survey data of cactus plants located in the Florida Panhandle. Each row describes a unique survey of a plant, and provides the date and location of the survey, information about the plant's size, number of fruit observed, the presence/absence of insects, and whether the plant was observed to be alive or dead.
DOI: 10.5061/dryad.p4q26/2
title: Florida Panhandle Location Data

description: Information about the six locations in the Florida Panhandle at which cactus plants were surveyed. Information provided include the abbreviations of the locations (which corresponds to the "Location" column in the Florida Panhandle Cactus Survey Data) as well as each location's latitude and longitude.
DOI: 10.5061/dryad.p4q26/3
title: Metadata for the Florida Panhandle Cactus Survey Data

description: Metadata defining column names in the Florida Panhandle Cactus Survey Data.
DOI: 10.5061/dryad.q3567/1
title: DATA
DOI: 10.5061/dryad.q771r.3/4.3
title: Batch-catalogs for American lobster
DOI: 10.5061/dryad.qh47m/2
title: Multivariate_analyses

description: This file contains data used in the analyses of correlated ecological variables in Lake Mendota (ME) and Lake Monona (MO). We analyzed 10 variables in total, including Daphnia pulicaria body length. The time period is either before (Pre-invasion) or after (Post-invasion) invasions. The year is also specified. Sampling was performed by the North Temperate Lakes LTER. All data are available at: https://lter.limnology.wisc.edu/.
DOI: 10.5061/dryad.qh47m/3
title: Phenotypic_size_trends_final

description: This file corresponds to the analyses of long-term phenotypic trends in Daphnia pulicaria. Status specifies whether Bythotrephes is present (Invaded) or absent (Uninvaded) from a lake. The time period is either before (Pre-invasion) or after (Post-invasion) invasions. The lake and year in which sampling was performed are also specified. AL = Allequash, BM = Big Muskellunge, CB = Crystal Bog, FI = Fish, ME = Mendota, MO = Monona, TB = Trout Bog. Sampling was performed by the North Temperate Lakes LTER. All data are available at: https://lter.limnology.wisc.edu/.
DOI: 10.5061/dryad.qh47m/4
title: Pulicaria_age_clutch_size

description: This file contains data for the age at maturation (in days) and reproduction (clutches 1-4) of Daphnia pulicaria assessed in the common garden experiments. Each observation is specified by the generation (either 1 or 2), lake (of origin), status of the lake (Invaded or Not-invaded), experimental treatment (no predator-NP or predator-P), and the clone.
DOI: 10.5061/dryad.qh47m/5
title: Pulicaria_size_at_maturation

description: This file contains data for the size at maturation (in millimeters) of Daphnia pulicaria from the common garden experiment. Each observation is specified by the generation, (either 1 or 2), lake (of origin), status of the lake (Invaded or Non-invaded), experimental treatment (no predator-NP or predator-P), and the clone.
DOI: 10.5061/dryad.qs65q/1
title: Data_JRSOS_Supplementary_Oriola

description: Data_JRSOS_Supplementary_video_1 (MATLAB data files):

-t_SV1.mat:    Time series. Total time 2000 ms. Time step: 0.5 ms.
-X_SV1.mat:   X-coordinate of every point along the flagellum at every time step (um).
-Y_SV1.mat:   Y-coordinate of every point along the flagellum at every time step (um).
-dn_SV1.mat:  dn value at every point along the flagellum at every time step.

Data_JRSOS_Supplementary_video_2 (MATLAB data files):

-t_SV2.mat:    Time series. Total time 1500 ms. Time step: 0.5 ms.
-X_SV2.mat:   X-coordinate of every point along the flagellum at every time step (um).
-Y_SV2.mat:   Y-coordinate of every point along the flagellum at every time step (um).
-dn_SV2.mat:  dn value at every point along the flagellum at every time step.

Data_JRSOS_Supplementary_video_3 (MATLAB data files):

-t_SV3.mat:    Time series. Total time 1000 ms. Time step: 0.5 ms.
-X_SV3.mat:   X-coordinate of every point along the flagellum at every time step (um).
-Y_SV3.mat:   Y-coordinate of every point along the flagellum at every time step (um).
-dn_SV3.mat:  dn value at every point along the flagellum at every time step.
DOI: 10.5061/dryad.s0b80/1
title: Open Tag data for Hawaiian monk seals

description: Accelerometer data collected from Open Tags (Loggerhead Instruments) in the main Hawaiian Islands. Seals were instrumented on the islands of Molokai, Kauai, and Oahu.
DOI: 10.5061/dryad.s0b80/2
title: Movement and Corresponding Environmental Data for monk seal dives

description: Accelerometer data, per dive, collected for Hawaiian monk seals in the main Hawaiian Islands. A GPS location for each dive was used to extract environmental data.
DOI: 10.5061/dryad.s0b80/3
title: Animation of the pitch metric to identify search events for Hawaiian monk seals in the main Hawaiian Islands

description: This is an animation of the Pitch Metric that was used to identify search events for Hawaiian monk seals. The animation shows pitch (bottom figure) for one complete dive with concurrent dive depth (middle) and video footage (top). Video footage shows seal RW02 foraging off the coast of Kauai. The orange line across the pitch figure is our threshold for identifying search events (70 degrees). Time is along the X axis in both figures with depth and pitch on the Y axes, respectively.
DOI: 10.5061/dryad.tf45v/1
title: Penn et al_ELE_FinalData

description: All arthropod information gathered in the field. Landscape data collected from USDA NASS Crop Data Layer. Definitions included in excel spreadsheet.
DOI: 10.5061/dryad.vn269/1
title: FLEX_row_data_anonym_english

description: Every patient got an ID number, all dates were reduced to years, ages were aggregated and we removed data which are not necessary for analysis.
DOI: 10.5061/dryad.053jh/1
title: coral interaction data, model output, code

description: (a) pairwise interspecific coral interactions with outcomes, for training and test sets, and references from which interactions are drawn, (b) coral traits and references, (c) model output, (d) R code
DOI: 10.5061/dryad.178vs/1
title: Mobbing

description: Patients with and without workplace mobbing experience treated in German general practitioner practices
DOI: 10.5061/dryad.31048.2/1.2
title: Appendix_1_05-11-17

description: List of 66 morphological characters used, revised from Schreiber et al. (2013).
DOI: 10.5061/dryad.31048.2/12.2
title: SuppTable1_contraTable

description: Supplemental Table 1 as a PDF, reporting pair-wise CDs between considered summary topologies.
DOI: 10.5061/dryad.31048.2/13.2
title: SuppMat_allTreesPlotted_suppFigures

description: PDF Supplementary Material containing plots of all summary trees considered in this paper, with associated support values.
DOI: 10.5061/dryad.31048.2/15.2
title: test_which_parsimony_informative_01-16-17

description: Revised script for testing whether characters are parsimony informative.
DOI: 10.5061/dryad.31048.2/17.2
title: write_simple_sumt_01-16-17

description: Revised script for obtaining the simple summary tree files from MrBayes
DOI: 10.5061/dryad.31048.2/18.2
title: runFiles.zip

description: Zipped directory containing output from phylogenetic analyses, necessary for use with analyses in Rmd file. All tree files are contained in this zipped directory.
DOI: 10.5061/dryad.31048.2/19.2
title: run_coding_12-15-16a.pdf

description: PDF table explaining how the identifiers, labels and conditions of the different phylogenetic analyses as given in the main text and in the supplemental data materials relate.
DOI: 10.5061/dryad.31048.2/2.2
title: Appendix_2_05-11-17

description: Morphological character matrix used for parsimony analyses, revised from Schreiber et al. (2013), for 25 genera and 66 characters (the codings for the two Basiliola species are not repeated).
DOI: 10.5061/dryad.31048.2/21.2
title: raw_morphMat_MrBayes_04-21-17.nex

description: The raw morphological matrix, as used in the Bayesian analyses, as a Nexus-formatted text file.
DOI: 10.5061/dryad.3jq14/2
title: Pérez-Crespo et al_ITS

description: ITS_File: Psittacanthus calyculatus sequences of the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA (nrDNA) sequences.
DOI: 10.5061/dryad.3jq14/3
title: Pérez-Crespo et al_trnL-F

description: trnL-F_File: Psittacanthus calyculatus sequences of the trnL-F intergenic spacer region from the chloroplast genome (cpDNA).
DOI: 10.5061/dryad.3q471/1
title: README_Astrotoma

description: README file describing the details of all uploaded data
DOI: 10.5061/dryad.3q471/2
title: astrotoma_94_955

description: This is the main data matrix file, ready for downstream analyses.
DOI: 10.5061/dryad.3q471/3
title: Astrotoma_cleaned_fasta

description: This file contains all sample files.  All files have be checked for quality, size, and the presence of the restriction enzyme AlfI.  Samples are ready for further processing through custom pipelines or through programs such as STACKS.
DOI: 10.5061/dryad.57917/1
title: Bacterial growth data

description: Bacterial densities as colony forming units per milliliter of a high-virulence strain B067 (A) and a low-virulence strain B398 (B) of Flavobacterium columnare at different levels of nutrient enrichment in sterile tap water. The volumes of nutrient medium at each nutrient level (baseline, low and high) are expressed .
DOI: 10.5061/dryad.5k0s6/1
title: Data for Dungan & Chang 2017, Proceedings B

description: The .zip archive contains two files: 1) A fasta alignment of the rhodopsin coding sequences used for ancestral sequence reconstruction and 2) an excel file with fluorescence and absorbance data series
DOI: 10.5061/dryad.68fn0/1
title: AK1_I5_File

description: AK1_I5_File: Bee hummingbirds sequences of the adenylate kinase 1 intron 5 (nuDNA).
DOI: 10.5061/dryad.68fn0/2
title: FBG_I7_File

description: FBG_I7_File: Bee hummingbirds sequences of the fibrinogen beta chain intron (nuDNA).
DOI: 10.5061/dryad.68fn0/3
title: ODC_1_File

description: ODC_1_File: Bee hummingbirds sequences of the ornithine decarboxylase 1 introns 6 and 7 intervening exon (nuDNA).
DOI: 10.5061/dryad.68fn0/4
title: MUSK_I3_File

description: MUSK_I3_File: Bee hummingbirds sequences of the Z-linked muscle, skeletal, receptor tyrosine kinase intron 3 (nuDNA).
DOI: 10.5061/dryad.74f2r.2/11.2
title: Maximum clade credibility tree of NDbs

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with broad calibration densities) using 12 fossils, resulting from the beast2 analysis using the NDbs.xml input-file.
DOI: 10.5061/dryad.74f2r.2/12.2
title: Input file NDbs analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with broad prior calibration densities. This approach included 12 calibration constraints based on fossil information (NDbs). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.2/13.2
title: Subsample of trees from NDnl analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with narrow calibration densities) using 15 fossils (see NDnl.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/14.2
title: Maximum clade credibility tree of NDnl

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with narrow calibration densities), using 15 fossils; resulting from the beast2 analysis using the NDnl.xml input-file.
DOI: 10.5061/dryad.74f2r.2/15.2
title: Input file NDnl analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with narrow prior calibration densities. This approach included 15 calibration constraints based on fossil information (NDnl). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.2/16.2
title: Subsample of trees from NDns analysis

description: This is a set of 1401 subsampled random trees from the posterior distribution of the node dating analysis (with narrow calibration densities) using 12 fossils (see NDns.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.2/17.2
title: Maximum clade credibility tree of NDns

description: This is the inferred maximum clade credibility tree based on common ancestor tree heights. The tree summarizes the 1401 randomly subsampled trees of the node dating analysis (with narrow calibration densities), using 12 fossils; resulting from the beast2 analysis using the NDns.xml input-file.
DOI: 10.5061/dryad.74f2r.2/18.2
title: Input file NDns analysis

description: This is the XML file which configures all parameters for the BEAST program for the Bayesian MCMC analysis using the node dating approach with narrow prior calibration densities. This approach included 12 calibration constraints based on fossil information (NDns). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.9rs5d/1
title: Protonibea diacanthus microsatellite genotypes

description: This file contains the individual genotypes used for the paper entitled "Strong population structure deduced from genetics, otolith chemistry and parasite abundances explains vulnerability to localised fishery collapse in a large Sciaenid fish, Protonibea diacanthus".