cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9tn73/4
title: dataset 4

description: dataset 4, Pterostichus Melanarius (biological variable) x Corn (landscape variable)
DOI: 10.5061/dryad.9tn73/5
title: R script

description: R script of the functions used in the methods of the paper
DOI: 10.5061/dryad.9tn73/6
title: ReadMe file

description: The ReadMe file provides details about the content of the other files.
DOI: 10.5061/dryad.b2v7v/1
title: cetartiodactyla_gtr.tre
DOI: 10.5061/dryad.b2v7v/2
title: SLOUCH software 2016

description: Stochastic Linear Ornstein-Uhlenbeck Models for Comparative Hypotheses software
DOI: 10.5061/dryad.b2v7v/5
title: Supplementary Table 1. Calibrations table

description: Table with fossil calibrations used to build the phylogenetic tree of Cetartiodactyla.
DOI: 10.5061/dryad.b2v7v/6
title: Supplementary Table 2. Additional models

description: Table with results from additional models not included in the main text.
DOI: 10.5061/dryad.b2v7v/7
title: cetartiodactyla_gtr.xml
DOI: 10.5061/dryad.f4k24/3
title: S3 Dataset

description: Relative concentrations of IL1B, TNF-α, and iNOS mRNA in ileal mucosa of pigs challenged chronically with LPS and fed an olive-oil bioactive extract (OBE).
DOI: 10.5061/dryad.f4k24/4
title: S4 Dataset

description: Concentrations of permeability markers in plasma and relative concentrations of CDH1, OCLN, and ZO-1 in the ileal mucosa of pigs challenged chronically with LPS and fed an olive-oil bioactive extract (OBE).
DOI: 10.5061/dryad.f4k24/7
title: S6_2 Dataset

description: Gut microbial composition and predicted functions in pigs chronically challenged with LPS and fed an olive-oil bioactive extract (OBE).
DOI: 10.5061/dryad.f4k24/8
title: S7 Dataset

description: Cytotoxicity of the olive-oil bioactive extract (OBE) in Caco-2/TC-7 and RAW 264.7 cells.
DOI: 10.5061/dryad.f9v80/1
title: Triosephosphate Isomerase Simulations

description: The data package contains all input, topology and parameter files necessary for rerunning the simulations. It also contains coordinates, in PDB format, of all initial and equilibrated protein-substrate complexes, as well as of key stationary points along the simulation trajectories.
DOI: 10.5061/dryad.k57p6/2
title: R script for DESeq analyses and tables of read counts

description: Annotated R script for replicating DESeq analyses as described in the linked publication. Input files are tables of TagSeq read counts for host and symbionts, post-quality trimming and mapping to the Acropora millepora and Symbiodinium clade C reference transcriptomes, respectively.
DOI: 10.5061/dryad.k8bt6/1
title: ITS Sequences

description: Alignment file with ITS sequences (ITS1, 5.8S, ITS2)
DOI: 10.5061/dryad.k8bt6/2
title: Chloroplast trnG Sequences

description: Alignment file for trnG sequences
DOI: 10.5061/dryad.k8bt6/3
title: Chloroplast trnL-F Sequences

description: Alignment File for trnL-F Sequences
DOI: 10.5061/dryad.m2187/1
title: Species occurrence matrix and locality data

description: This table summarizes the 4608 observation localities and 29 species used for analyses. For each locality it gives the species occurrences ("1"), latitude, longitude, ordination value for temperature ('Temp'), and ordination value for precipitation ('Precip'). Note that temperature and precipitation data were unavailable for five observation localities. This table also designates the localities found within selected watershed regions (ark = Arkansas-White-Red; ca = California; ma = Mid Atlantic). The table, along with species information in Table 1 of the publication, can be used to reproduce all our analyses and results.
DOI: 10.5061/dryad.m7589/1
title: Gesnerioideae Bayesian Common Ancestor tree
DOI: 10.5061/dryad.mf202/1
title: Mihaljevic_etal_JAE_SM

description: Data and code for "Parasite metacommunities: Evaluating the roles of host community composition and environmental gradients in structuring symbiont communities within amphibians." A README file is included to explain each element of the .ZIP file.
DOI: 10.5061/dryad.n27r8/1
title: varfit-data

description: The data file of fruit set
DOI: 10.5061/dryad.n27r8/2
title: read me file
DOI: 10.5061/dryad.n9g60/2
title: all-contigs-by-taxon.tar.gz

description: All contigs assembled by Trinity for each taxon in the data set.  FASTA format by taxon. Contents in README.
DOI: 10.5061/dryad.n9g60/3
title: astral.tar.gz

description: Gene trees and results from coalescent-based (ASTRAL) analyses.  Contents in README.
DOI: 10.5061/dryad.n9g60/4
title: bayesian-analyses.tar.gz

description: All files (samples, parameter estimates, convergence metrics, etc.) from Bayesian analyses.  Contents in README.
DOI: 10.5061/dryad.n9g60/5
title: fish-uce-1k-probes.tar.gz

description: Probe set used for UCE enrichment.
DOI: 10.5061/dryad.n9g60/6
title: ml-analyses.tar.gz

description: All files (best trees, bootreps) from maximum likelihood analyses. Contents in README.
DOI: 10.5061/dryad.n9g60/7
title: taxon-set.txt

description: The taxon set file for use with PHYLUCE.
DOI: 10.5061/dryad.n9g60/8
title: tip-name-remappings.txt

description: A text file for PHYLUCE that we used to rename tips in each of the trees to fix taxonomy issues, incorrect spellings, etc.
DOI: 10.5061/dryad.n9g60/9
title: trees.tar.gz

description: All trees generated for this manuscript.  In newick format.  Contents in README.
DOI: 10.5061/dryad.r8ph6/1
title: Nest_Data

description: This file includes nesting data for the 2012 - 2015 northern bobwhite breeding seasons at the Packsaddle Wildlife Management Area, western Oklahoma, USA.  The file includes 16 management, life history, weather and temporal covariates for each nest that was monitored.
DOI: 10.5061/dryad.r8ph6/2
title: Weather_Data

description: This file includes weather data for the relevant northern bobwhite breeding seasons from 2012-2015 at the Packsaddle Wildlife Management Area, western Oklahoma, USA.
DOI: 10.5061/dryad.rq163/2
title: respirometry

description: Contains all raw oxygen consumption data.
DOI: 10.5061/dryad.rq163/3
title: MTT

description: Contains all MTT assay (electron flux) data
DOI: 10.5061/dryad.rq163/4
title: Heat_stress

description: Contains all raw heat stress data
DOI: 10.5061/dryad.rq163/5
title: JC1

description: Contains all JC-1 assay (mitochondrial membrane potential) data
DOI: 10.5061/dryad.t29f8/1
title: Tsykun_at_al_raw_data

description: The file has a sheet with SSR genotypes (missing data are coded as "999" allele) and SNP genotypes.
DOI: 10.5061/dryad.ts747/10
title: Supplementary Materials
DOI: 10.5061/dryad.ts747/11
title: SUPPLEMENTAL FILE S1
DOI: 10.17632/7wb6pvpbgh.1
title: TrackEtching - A Java based code for etched track profile calculations in SSNTDs

description: A java code incorporating a user friendly GUI has been developed to calculate the parameters of chemically etched track profiles of ion-irradiated solid state nuclear track detectors. Huygen’s construction of wavefronts based on secondary wavelets has been used to numerically calculate the etched track profile as a function of the etching time. Provision for normal incidence and oblique incidence on the detector surface have been incorporated. Results in typical cases are presented and compared with experimental data. Different expressions for the variation of track etch rate as a function of the ion energy have been utilized. The best set of values of the parameters in the expressions can be obtained by comparing with available experimental data. Critical angle for track development can also be calculated using the present code.
DOI: 10.5061/dryad.12546/3
title: Maximum likelihood phylogeny of 309 species

description: Maximum likelihood phylogeny generated using partitioned analysis in RAxML for 309 species, including 145 species for which data were obtained via GenBank.
DOI: 10.5061/dryad.1c32t/1
title: Data share
DOI: 10.5061/dryad.3353b/1
title: Figure S1: Victoria West cores with overshot preferential removals (a, b, c) and small sized removal (d). Note that although the size of specimen a is also small, the preferential removal is still large when compared with the overall size of the core. The yellow arrows show the preparation of the two surfaces, the red arrows show the preferential flake removal directions, and the blue arrows show scars overlapping the preferential removal. a, b , c and d correspond to the specimens CK2919, CK8091, CK4916 and CK4597 respectively (see Table S1 for raw data).
DOI: 10.5061/dryad.3353b/2
title: Figure S2: Victoria West cores with small removals (a, b, c) and non-ideal blow direction (d). The yellow arrows show the preparation of the two surfaces, and the red arrows show the preferential flake removal directions. a, b , c and d correspond to the specimens CK3708, CK8702, CK5837 and CK3936 respectively (see Table S1 for raw data).
DOI: 10.5061/dryad.3353b/3
title: Figure S3: Victoria West cores from the top of the layer containing the Victoria West core assemblage. The yellow arrows show the preparation of the two surfaces, the red arrows show the preferential flake removal directions, and the blue arrows show scars overlapping the preferential removal. a, b , c and d correspond to the specimens CK3142, CK3004, CK2225 and CK2208 respectively (see Table S1 for raw data).
DOI: 10.5061/dryad.3353b/4
title: Table S1.Raw data for the Victoria West cores excavated from the Canteen Kopje site.
DOI: 10.5061/dryad.37882/2
title: R scripts

description: The R scripts used to run the models and analysis the data.
DOI: 10.5061/dryad.4615c/1
title: FE-2016-01003_Dataset
DOI: 10.5061/dryad.74f2r.1/14.1
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.1/15.1
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.1/16.1
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.1/17.1
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.1/18.1
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.74f2r.1/20.1
title: Maximum clade credibility tree of FBDl age range

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_ageRange.xml input-file.
DOI: 10.5061/dryad.74f2r.1/21.1
title: Subsample of trees from FBDl "age range" 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_ageRange.xml file for detailed settings of the Bayesian analysis).
DOI: 10.5061/dryad.74f2r.1/22.1
title: Input file for FBDl "age range" 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, based on an "age range" dating approach (FBDl_ageRange). The file was generated in BEAUti 2.3.1.
DOI: 10.5061/dryad.74f2r.1/23.1
title: Maximum clade credibility tree of FBDs age range

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_ageRange.xml input-file.
DOI: 10.5061/dryad.7nk99/1
title: B_Data_for_cluster_analyses_Fig_2

description: Dataset 1. Matrix of quantitative interactions used to generate cluster analysis (Fig. 2)
DOI: 10.5061/dryad.7nk99/2
title: C_Data_time_to_pupation_Fig_4

description: Dataset 2. Data to generate Fig. 4. Time to pupation of rolled-leaf beetles reared on native and novel hosts.
DOI: 10.5061/dryad.7nk99/3
title: D_Data_proportion_emergence_Fig_5

description: Dataset 3. Data to generate Fig. 5. Proportion of emergence of adult rolled-leaf beetles reared on native and novel hosts.
DOI: 10.5061/dryad.80p28/11
title: Giraffe and okapi sequence file

description: Raw sequences for giraffe and okapi TLRs used in the analyses.
DOI: 10.5061/dryad.80p28/4
title: SLR raw data for TLR3

description: TLR3 raw results for site-wise likelihood analysis (Table 1).
DOI: 10.5061/dryad.80p28/5
title: SLR raw data for TLR4

description: TLR4 raw results for site-wise likelihood analysis (Table 1).
DOI: 10.5061/dryad.80p28/6
title: SLR raw data for TLR5

description: TLR5 raw results for site-wise likelihood analysis (Table 1).
DOI: 10.5061/dryad.80p28/7
title: SLR raw data for TLR7

description: TLR7 raw results for site-wise likelihood analysis (Table 1).
DOI: 10.5061/dryad.80p28/8
title: SLR raw data for TLR9

description: TLR9 raw results for site-wise likelihood analysis (Table 1).
DOI: 10.5061/dryad.80p28/9
title: SLR raw data for TLR10

description: TLR10 raw results for site-wise likelihood analysis (Table 1).
DOI: 10.5061/dryad.8217f/1
title: Appendix. Morphological characteristics of Estherites jocelynae specimens

description: Measurements of the type series.
DOI: 10.5061/dryad.8v528/1
title: Metabarcoding pipeline and scripts

description: Full metabarcoding pipeline and R scripts to produce figures and statistical analysis in the paper. Includes intermediate scripts, always use the script with the latest version number.
DOI: 10.5061/dryad.8v528/2
title: Dereplicated and preprocessed metabarcoding data

description: These are the processed reads that were used for OTU clustering. Files are 10 samples (5 for each stream) amplified with 4 primer pairs (=40). The two sequencing lanes are differentiated with L001 and L002 but were merged into one file for each of the 40 sample in the analysis (only sequencing replicates). NOTE: If you want to access the raw sequencing data without any processing, please refer to the NCBI SRA accession numbers in the manuscript.
DOI: 10.5061/dryad.8v528/3
title: FastQC and run information

description: FastQC check and metadata for all 3 lanes run on the Illumina HiSeq (1,5 rapid runs v2, 250 bp PE).
DOI: 10.5061/dryad.95s1k/1
title: RNA-Seq data of WT and Tssk6 KO spermatids

description: Spermatids were purified from three sets of adult wild type (WT) and Tssk6 knockout (KO), total RNA was isolated, RNA-Seq libraries were prepared using Illumina TruSeq Stranded mRNA sample preparation kit, and sequenced on Illumina HiSeq 2500. Quality of raw data was assessed and passed by FastQC and reads were mapped to the reference genome (Mus musculus_UCSC_mm10). Cufflinks (v2.2.1) was used to estimate transcript levels represented by FPKM (fragments per kilo bases per million mapped reads) and differential expression between samples was determined by Cuffdiff (v.2.2.1). Student’s t-test was performed to calculate the P values.
DOI: 10.5061/dryad.b12p5/1
title: Pre-dispersal capsule damage, seed germination and dormancy of Luehea seemannii in two forests in Panama

description: The dataset contains five data files of 1) number of aborted and damaged capsules, 2) number of germinants before and 3) after burial experiment, 4) number of damaged capsules from observing exposed shoots, and 5) number of seeds in damaged capsules. The data were collected both in the fields and in a growing house (germination data). There were two experimental field sites - in Gamboa (G) and in Parque Natural Metropolitano (PNM). For field experiments, five treatments were Control (no manipulation control), Exclosure (insect exclosure with net), ShamExcl (insect exclosure with cut net allowing exposure to insects), Fungicide (fungicide addition), ShamFung (water addition), and FungExcl (fungicide with insect exclosure).
DOI: 10.5061/dryad.b2v7v/10
title: BEAST input file
DOI: 10.5061/dryad.b2v7v/3
title: code
DOI: 10.5061/dryad.b2v7v/4
title: ruminants.txt

description: input file for code
DOI: 10.5061/dryad.b2v7v/8
title: SuppTable2c.txt

description: input file for code
DOI: 10.5061/dryad.b2v7v/9
title: Table2input

description: input file for code
DOI: 10.5061/dryad.dp1fh/1
title: Dayananda_Webb_Data

description: This excel file contains CTmax and CTmin data for hatchling geckos, and environmental temperatures recorded under rocks and inside crevices January 23 until 6 March 2014.
DOI: 10.5061/dryad.h7j90/1
title: Passive drift from Jamursba-Medi

description: Simulated 18-year-long trajectories of passive turtles emerging from Jamursba-Medi nesting beach (New Guinea, Indonesia) and drifting in the North Pacific. The file is in the self-described NetCDFformat
DOI: 10.5061/dryad.h7j90/2
title: Active dispersal from Jamursba-Medi

description: Simulated 18-year-long trajectories of actively swimming turtles emerging from Jamursba-Medi nesting beach (New Guinea, Indonesia) and drifting in the North Pacific. The file is in the self-described NetCDFformat
DOI: 10.5061/dryad.j8r34/1
title: Behaviour dataset for cleaner-client interactions

description: Dataset comprising the behavioural data assessed during familiarity experiments on cleanerfish under the effects of dopamine compounds (and control)
DOI: 10.5061/dryad.k57p6/1
title: Photographs of sampled corals

description: Photographs were taken at the time of collection. Image file name indicates coral colony number corresponding to raw TagSeq reads. Labels within images contain date/time/GPS information.
DOI: 10.5061/dryad.m7589/2
title: Gesneriaceae_sample_trees

description: This file contains 200 posterior trees
DOI: 10.5061/dryad.m7589/3
title: Gesnerioideae Concatenated genes

description: charset gene_ITS = 1-617
charset gene_matK = 618-1615
charset gene_rps16 = 1616-2765
charset gene_trnL = 2766-3813
DOI: 10.5061/dryad.m7589/4
title: Table S1

description: Specimen voucher information, Genbank accession numbers, and inferred pollination states
DOI: 10.5061/dryad.n9g60/10
title: uce-contigs-by-taxon.tar.gz

description: All UCE contigs identified for each taxon.  FASTA format by taxon. Contents in README.
DOI: 10.5061/dryad.n9g60/11
title: processing-steps.txt

description: Text file with step-by-step description of data processing.
DOI: 10.5061/dryad.n9g60/12
title: TableS1.xlsx

description: Supplemental Table 1: Number of reads, total number of base pairs sequenced, mean length of adapter- and quality-trimmed reads, 95 CI of trimmed read length, minimum read length, maximum read length, and median length for reads sequenced, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk).
DOI: 10.5061/dryad.n9g60/13
title: TableS2.xlsx

description: Supplemental Table 2: Number of contigs assembled, total number of base pairs sequenced, mean contig length, 95 CI of contig length, minimum contig length, maximum contig length, median contig length, and number of contigs &gt; 1 Kb in length from reads sequenced, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk).
DOI: 10.5061/dryad.n9g60/14
title: TableS3.xlsx

description: Supplemental Table 3: Number of UCE loci enriched, total number of base pairs in all UCE loci, mean length of UCE loci, 95 CI of UCE locus length, minimum UCE locus length, maximum UCE locus length, median UCE locus length, number of UCE loci having a length &gt; 1 Kb, UCE locus coverage, percentage of reads on-target, and percentage of on-target reads that were unique from reads assembled, by platform, from ostariophysan libraries enriched for UCEs (table also includes outgroup taxa, indicated with an asterisk). We collected Danio rerio UCE data from the danRer7 genome assembly.
DOI: 10.5061/dryad.n9g60/15
title: Fig_S1.pdf

description: Supplemental Figure 1: Morphology based ML and Bayesian phylogeny. Support values on every node was (BPP &gt;0.99 and bootstrap support of 100).
DOI: 10.5061/dryad.n9g60/16
title: Fig_S2.pdf

description: Supplemental Figure 2: Results from ML analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, data not partitioned but concatenated.
DOI: 10.5061/dryad.n9g60/17
title: Fig_S3.pdf

description: Supplemental Figure 3. Results from Bayesian analyses of ostariophysans using ultraconserved elements, with 50% complete data coverage, partitioned and concatenated.
DOI: 10.5061/dryad.nr654/1
title: Supplementary Appendix

description: Supplementary discussion and analyses, Figures S1-S8, and associated captions.
DOI: 10.5061/dryad.nr654/2
title: Supplementary Table 1

description: Life history data table formatted for input into the Coevol analytical software. Life history data were obtained from the AnAge senescence database Build 13 (De Magalhães, J.P. and Costa, J. 2009, Tacutu, R., Craig, T., et al. 2013). We collated the following data: (1) age at sexual maturity (days), (2) incubation time (days), (3) number of eggs laid per year, (4) mass at hatching (grams), (5) growth rate (1/days), (6), maximum recorded longevity (years), and (7) total metabolic rate (watts). Relative to the set of 198 avian taxa in (Prum, R.O., Berv, J.S., et al. 2015), when matching genera occurred in the AnAge database, we used averages at the genus level; otherwise, we used family-level averages. Body mass (grams, species average) data were collected from Dunning Jr, J.B. (1992). This yielded a data matrix with ~49% missing data overall (with no missing data for body mass).
DOI: 10.5061/dryad.nr654/3
title: Supplementary Table 2

description: Correlation coefficients and posterior probabilities from substitution rate analysis with Coevol 1.4b (partial coefficients summarized in Figure 2 colors). Raw posterior probabilities are reported as ranging from from 0.0 (100% support for a negative correlation) to 1.0 (100% support for a positive correlation). Negative correlations are reported as 1-raw in the main text.
DOI: 10.5061/dryad.nr654/4
title: Supplementary Table 3

description: Data table of estimated crown fossil masses used as body size priors to calibrate ASRs. Mean body mass estimates and associated 95% prediction intervals are derived from published predictive equations (Field, D.J., Lynner, C., et al. 2013). Unless otherwise noted, measurements for these taxa are taken from holotype specimens, and unless otherwise noted, published measurements were used from references noted in the table.
DOI: 10.5061/dryad.nr654/8
title: Data File S4

description: We provide as a zip archive the data and script files necessary to reproduce the major analyses in the present work. A detailed readme txt file is included in this zip archive which outlines the analytical procedures needed to replicate the major analyses in the present work.
DOI: 10.5061/dryad.p20n8/1
title: Community_data

description: Results of the community outcomes.
DOI: 10.5061/dryad.p20n8/2
title: Individual_data

description: Results for individual microcosms