cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q0032/3
title: common_garden

description: This file contains the data for family-level analyses of the common garden experiment.
DOI: 10.5061/dryad.q0032/4
title: no_choice_experiment

description: This file contains the data for the no choice experiment
DOI: 10.5061/dryad.q0032/5
title: choice_experiment

description: This file contains the data for the choice experiment.
DOI: 10.5061/dryad.q0032/6
title: greenhouse_experiment

description: This file contains data from the greenhouse experiment.
DOI: 10.5061/dryad.q5qm1/5
title: LAX-Ground-Summary_TP_20140518_R01_thru20140525

description: Assimilated aircraft engine test point data containing aircraft and engine specifications, measured particle emissions indices, and engine certification data. Each test point corresponds to an aircraft take-off event on either 18 or 25 May 2014.
DOI: 10.5061/dryad.t1p7c/10
title: Dataset 6.1 Liver transcriptome functionally annotated

description: Dataset 6 consists of functional annotation data (from the Gene Ontology [GO] consortium, Enzyme Code and Inter Pro databases) for each gene assembled, across the three tissue types (skin, liver and spleen). These data are contained in Dataset 6, as three individual comma-separated files (.csv format) [Data Citation 1]. Full descriptions of the column headers are contained in the associated readme file.
DOI: 10.5061/dryad.t1p7c/11
title: Dataset 6.2 Skin transcriptome functionally annotated

description: Dataset 6 consists of functional annotation data (from the Gene Ontology [GO] consortium, Enzyme Code and Inter Pro databases) for each gene assembled, across the three tissue types (skin, liver and spleen). These data are contained in Dataset 6, as three individual comma-separated files (.csv format) [Data Citation 1]. Full descriptions of the column headers are contained in the associated readme file.
DOI: 10.5061/dryad.t1p7c/12
title: Dataset 6.3 Spleen transcriptome functionally annotated

description: Dataset 6 consists of functional annotation data (from the Gene Ontology [GO] consortium, Enzyme Code and Inter Pro databases) for each gene assembled, across the three tissue types (skin, liver and spleen). These data are contained in Dataset 6, as three individual comma-separated files (.csv format) [Data Citation 1]. Full descriptions of the column headers are contained in the associated readme file.
DOI: 10.5061/dryad.t1p7c/13
title: Dataset 7.1 Liver matrix.isoforms.counts

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
DOI: 10.5061/dryad.t1p7c/5
title: Dataset 5.2 Liver-filtered-condensed-transdecoder

description: Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
DOI: 10.5061/dryad.t1p7c/6
title: Dataset 5.3 Skin-filtered-condensed

description: Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
DOI: 10.5061/dryad.t1p7c/7
title: Dataset 5.4 Skin-filtered-condensed-transdecoder

description: Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
DOI: 10.5061/dryad.t1p7c/8
title: Dataset 5.5 Spleen-filtered-condensed

description: Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
DOI: 10.5061/dryad.t1p7c/9
title: Dataset 5.6 Spleen-filtered-condensed-transdecoder

description: Dataset 5 consists of de novo assembled transcriptomes for each tissue type from frogs in Experiment B (n = 61). These data are contained in Dataset 5, as six individual .fasta text files, including both nucleotide sequence assembly files and amino acid sequence assembly files (translated using TransDecoder) for each of the three tissue types (skin, liver and spleen) [Data Citation 1]. Descriptions of the sequence identifier lines are contained in the associated readme file.
DOI: 10.17632/z7ftvpdvpd.1
title: Data for: First-principles investigation of Cr-doped Fe2B: structural, mechanical, electronic and magnetic properties

description: Detailed simulated diffraction data of Fe8-xCrxB4 (x=0, 0.25, 0.5, 1, 2, 3, 4,5, 6, 7 and 8)
DOI: 10.5061/dryad.1qt0k/2
title: Mitochondrial Datasets and Results

description: Mitochondrial alignments and RAxML results.  Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala
DOI: 10.5061/dryad.1qt0k/3
title: RAxML Concatenated Alignments and Results

description: RAxML Concatenated Alignments and Results.  Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala
DOI: 10.5061/dryad.1qt0k/4
title: RAxML GeneTree 1allele Alignments

description: RAxML 1-allele Alignments.  Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala
DOI: 10.5061/dryad.1qt0k/5
title: RAxML GeneTree 2alleles Alignments and Results

description: RAxML GeneTree 2alleles Alignments and Results.  Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala
DOI: 10.5061/dryad.1qt0k/6
title: Python scripts

description: Python scripts for extracting SNPs from 1-allele RAxML (phylip) files; and script for summarizing bootstrap values from RAxML 2-allele results.  Additional details are commented in each script.
DOI: 10.5061/dryad.1qt0k/7
title: SNP datasets

description: SNP datasets for each species and summary table of SNP information.  Note that Lithobates sphenocephalus (Lsp) = Rana sphenocephala.
DOI: 10.5061/dryad.286gn/1
title: Panicinae_ndhF_alignment

description: ndhF alignment for subfamily Panicoideae (Poaceae) including members of subtribe Panicinae
DOI: 10.5061/dryad.286gn/2
title: Panicinae(RAxML)_bestTree

description: Maximum likelihood tree for subtribe Panicinae generated with RAxML 8.2.4 using the ndhF alignment under the GTRCAT model across codon positions.
DOI: 10.5061/dryad.286gn/3
title: Panicinae(BEAST)CAL1

description: xml file for phylogenetic analyses and divergence time estimation in BEAST 1.8.4 using the nucleotide substitution models unlinked across codon position,  a birth-death model with incomplete sampling as tree prior, an uncorrelated lognormal clock model for the rate variation among tree branches, and a calibration based only on external angiosperm fossils (eudicots and non-grass monocots) (calibration scheme 1). We used secondary calibrations in normal prior distributions for the following six crown nodes: subfamily Panicoideae (scheme 1: mean= 38.18 Mya, SD= 3.86), most recent common ancestor (MRCA) of supertribes Andropogonodae –Panicodae (mean= 30.31 Mya, SD= 3.27), supertribe Andropogonodae (mean= 28.5  Mya, SD= 3.33), tribe Andropogoneae (mean= 11.79 Mya, SD= 2.95), tribe Paspaleae (mean=  22.6 Mya, SD= 3.13), and supertribe Panicodae (mean= 25.46 Mya, SD= 7.76). Analyses were conducted using  three independent runs of 100 million generations, sampling every 50,000, and discarding the first 25% of each run as burn-in.
DOI: 10.5061/dryad.286gn/4
title: Panicinae(BEAST)CAL2

description: xml file for phylogenetic analyses and divergence time estimation in BEAST 1.8.4 using the nucleotide substitution models unlinked across codon position,  a birth-death model with incomplete sampling as tree prior, an uncorrelated lognormal clock model for the rate variation among tree branches, and a calibration based on external angiosperm fossils (eudicots and non-grass monocots) together with the controversial phytolith microfossils of Poaceae (calibration scheme 2). We used secondary calibrations in normal prior distributions for the following six crown nodes: subfamily Panicoideae (mean= 48.09.18 Mya, SD= 4.94), most recent common ancestor (MRCA) of supertribes Andropogonodae –Panicodae (mean= 36.65 Mya, SD= 3.64), supertribe Andropogonodae (mean= 34.29 Mya, SD= 3.73), tribe Andropogoneae (mean= 14.45 Mya, SD= 2.71), tribe Paspaleae (mean=  26.25 Mya, SD= 3.61), and supertribe (mean= 30.74 Mya, SD= 2.97). Analyses were conducted using three independent runs of 100 million generations, sampling every 50,000, and discarding the first 25% of each run as burn-in.
DOI: 10.5061/dryad.286gn/5
title: Panicinae_CAL1_MCCT_BEAST

description: Maximum clade credibility (MCC) tree of Panicoideae obtained from BEAST analyses with the ndhF sequences, using the uncorrelated lognormal relaxed clock model and secondary calibrations based only on external angiosperm fossils (calibration scheme 1).
DOI: 10.5061/dryad.286gn/6
title: Panicinae_CAL2_MCCT_BEAST

description: Maximum clade credibility (MCC) tree of Panicoideae obtained from BEAST analyses with ndhF sequences using the uncorrelated lognormal relaxed clock model and secondary calibrations based on external angiosperm fossils together with the phytolith microfossils of Poaceae (calibration scheme 2).
DOI: 10.5061/dryad.32bp4/12
title: Appendix 20 - CoMET analyses

description: Rate-through-time plot as inferred with CoMET for Parnassiinae. The analyses detected one possible mass extinction around 15 Ma and one speciation rate shift around 3.5 Ma, in agreement with two TreePar analyses allowing or not the mass extinction.
DOI: 10.5061/dryad.32bp4/19
title: Appendix 19 - BAMM-like RevBayes analyses

description: Rate-through-time plot as inferred with RevBayes for Parnassiinae. Net diversification rates significantly changed and increased along the stem of the genus Parnassius, in agreement with the rates as estimated with BAMM.
DOI: 10.5061/dryad.32bp4/20
title: Appendix 21 - Correlation parameters for Bayesian models

description: Credibility intervals of the correlation parameters for the Bayesian (RevBayes) environment-dependent diversification models.
DOI: 10.5061/dryad.32bp4/21
title: Appendix 22 - Relation butterfly diversification and host-plant diversity

description: Correlation (linear regression) between speciation rates as inferred with MuSSE (a) and BAMM (b) and the species richness of host plants on which each parnassiine clade is feeding. In both cases, a strong and positive correlation is found.
DOI: 10.5061/dryad.32bp4/23
title: Scripts and R codes for diversification analyses
DOI: 10.5061/dryad.4m518/1
title: Simulation of trial and error learning

description: An example Matlab code for simulating a trial and error learning process.
DOI: 10.5061/dryad.64149/1
title: Trebouxia.sp_raw.seqs.ITS

description: Raw sequence data, ITS, Trebouxia sp. photobionts, headers correspond to columns: DNA.ID and Pop.ID in raw data table
DOI: 10.5061/dryad.64149/2
title: Lasallia.pustulata_raw.seqs.MCM7

description: Raw sequence data, MCM7, Lasallia pustulata mycobionts, headers correspond to columns: DNA.ID and Pop.ID in raw data table
DOI: 10.5061/dryad.6b058n7/25
title: Schuermann_Figure_7

description: Schuermann_Figure_7 - shows severe dominant phenotypes (including lethality, see excel-table) of N-terminally HA-tagged Hh variants. Two different en-drivers were used (en&gt; and en(2)) and two independent HAHh lines that integrated at different chromosomal locations. ptc&gt; expression results are also shown, demonstrating severe dominant activities only if expressed in the posterior (Hh-producing) but not anterior (pic-expressing, Hh receiving) compartment. Experiments conducted at different temperatures are shown, because UAS-transgenes are expressed in temperature-dependent manner.
DOI: 10.5061/dryad.6b058n7/26
title: Schuermann_Figure_9

description: Schuermann_Figure_9 - contains data obtained from the en&gt; or 34B&gt; controlled co-expression of Hh from chromosome two and HA-tagged transgenes, HhC85S and HAHhC85S from chromosome 3. HAHh also suppresses co-expressed Hh activity in these settings, confirming dominant-negative HAHh function in vivo.
DOI: 10.5061/dryad.6d831/1
title: Environmental data

description: Environmental data used in models associating climate with fine-scale genetic structure (FSGS).
DOI: 10.5061/dryad.6tc61/1
title: Szucs and Vahsen_data_PNAS

description: The first tab of the excel file contains description of the data.
DOI: 10.5061/dryad.745t0/1
title: Family information, MHC genotypes and MHC haplotypes

description: The file includes three sheets: (i) family information for 140 families (columns: ID_family, Status, ID_individual, Sex); (ii) MHC genotypes (columns: ID_individual and genotypes for each locus); (iii) MHC haplotypes (columns: ID_family, ID_parent, Sex, Haplotype)
DOI: 10.5061/dryad.9tr75/1
title: Vibration Signal

description: The following file “Yung_et_al_PlosOne_Vibration.prn” is the vibration code that was imported into a 6 degree of freedom hexapod platform (Mikrolar R3000 Rotopod) to simulate all-terrain vehicle (ATV) operation. The resulting vibration simulation code was programmed and is designed to be operated with MRLHPOD v.8.2 software and R3000 rotopod.
DOI: 10.5061/dryad.gb786/1
title: ConsNS_data

description: Data used to estimate annual consumption of zooplankton by small pelagic fish in the Northeast Atlantic. Bioenergetics modeling has been used to make such estimations. Therefore diet composition data, fish length & growth data (length distribution), ambient temperatura data, energy density data, stock biomass information, etc. are included.
DOI: 10.5061/dryad.h103j/1
title: LambertzEtAl_BiolLett_Bone-Histological-Correlates-AirSacs_ESM2

description: Interactive three-dimensional model of the Europasaurus holgeri vertebral neural arch.
DOI: 10.5061/dryad.hr744/1
title: Data_RosnerVoigt

description: Metabolic rate, APE values and TOR for pre-hibernating common noctule bats (Fig. 1), body temperature, metabolci rate and APE values for hibernating noctule bats (early Fig. 2, late Fig. 3)
DOI: 10.5061/dryad.hv631/1
title: Nocturnal location data for birds on Saipan

description: Each row represents a single location for a bird. X and Y columns correspond to the estimated X and Y location, in UTMs, for a given bird on Saipan. Individual Bird IDs are in the Bird_ID column and a species identifier is given in the Sp column.
DOI: 10.5061/dryad.hv631/2
title: Estimated diurnal location data for birds on Saipan

description: Each row represents a single location for a bird. X and Y columns correspond to the estimated X and Y location, in UTMs, for a given bird on Saipan. Individual Bird IDs are in the Bird_ID column and a species identifier is given in the Sp column. Rows with NA mean that the bird was not located during that movement interval
DOI: 10.5061/dryad.k50s6/1
title: Data for LowParasitemia_AerobicPerformance In MigratoyBirds

description: The file contains all data for displaying the figures (incl. supplement). For raw data on respirometry, please contact: steffen.hahn@vogelwarte.ch
DOI: 10.5061/dryad.kq7h7/1
title: Daily Soil GHG fluxes

description: Daily measurements of soil GHG fluxes used to describe soil functional types in Petrakis et al. Fluxes are calculated as daily means and curated for QA/QC as described in the journal article. Measurement dates comprise from September 2014 to September 2015. Values as -9999 represent missing values due to QA/QC or instrument failure.
DOI: 10.5061/dryad.m8t72.1
title: Data from: Female dietary bias towards large migratory moths in the European free-tailed bat (Tadarida teniotis)
DOI: 10.5061/dryad.m8t72.1/1.1
title: Sequence Raw Data - Part 1

description: First part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.
DOI: 10.5061/dryad.m8t72.1/2.1
title: Sequence Raw Data - Part 2

description: Second part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.
DOI: 10.5061/dryad.m8t72.1/4.1
title: Sequence Raw Data - Part 4

description: Fourth part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.
DOI: 10.5061/dryad.m8t72.2/3.2
title: Sequence Raw Data - Part 3

description: Third part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.
DOI: 10.5061/dryad.m8t72.2/4.2
title: Sequence Raw Data - Part 4

description: Fourth part of a file containing the raw illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.
DOI: 10.5061/dryad.m8t72.2/5.2
title: Sample Sheet

description: Sample sheet of the illumina sequencing data regarding Tadarida teniotis diet described in Mata et al.
DOI: 10.5061/dryad.m8t72.2/6.2
title: Diet analysis dataset

description: Data used for analysis. Contains all the prey identified in the diet per sample, as well as the characteristics of the prey and the samples.
DOI: 10.5061/dryad.q5qm1/6
title: LAX-Ground-Summary_TS_20140518_R01_thru20140525

description: Time series data collected on 18 May 2014 and 25 May 2014. Includes environmental data and particle and carbon dioxide concentrations.
DOI: 10.5061/dryad.q5qm1/7
title: LAX-Ground-ProcessingCode_R01

description: Data analysis code written in 'R' to generate the summary statistics and figures associated with the Data Descriptor for this data set.
DOI: 10.5061/dryad.t1p7c/14
title: Dataset 7.2 Liver matrix.isoforms.TMM.EXPR

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
DOI: 10.5061/dryad.t1p7c/15
title: Dataset 7.3 Liver matrix.isoforms.TPM.not_cross_norm

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
DOI: 10.5061/dryad.t1p7c/16
title: Dataset 7.4 Liver matrix.isoforms.TPM.not_cross_norm.TMM_info

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
DOI: 10.5061/dryad.t1p7c/17
title: Dataset 7.5 skin matrix.isoforms.counts

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
DOI: 10.5061/dryad.t1p7c/18
title: Dataset 7.6 Skin matrix.isoforms.TMM.EXPR

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
DOI: 10.5061/dryad.t1p7c/19
title: Dataset 7.7 Skin matrix.isoforms.TPM.not_cross_norm

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.
DOI: 10.5061/dryad.t1p7c/20
title: Dataset 7.8 Skin matrix.isoforms.TPM.not_cross_norm.TMM_info

description: Dataset 7 contains the raw gene/transcript counts data for each frog tissue sample (Experiment B, n = 61) resulting from allocation of sequence reads to genes from the transcriptome assemblies. These data are contained in Dataset 7, as 12 individual tab-separated text files (.txt) [Data Citation 1]. The four files for each tissue type (skin, liver and spleen) represent raw (1) counts, (2) TMM.EXPR files, (3) TPM.not_cross_norm files, and (4) normalisation information (as per the standard output from RSEM). The first row of these files (1-3 above) represents frog ID, and the first element of all subsequent rows represents transcript/isoform ID.