cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m6n2t/4
title: GenBank Pipeline Subscripts

description: This zip file contains multiple Python scripts called by the scripts in the GenBank Main Scripts file. These execute the specific functions to download sequences from GenBank and convert them into an aligned supermatrix of genes for use in phylogenetics. For details on individual scripts, see README.txt.
DOI: 10.5061/dryad.m6n2t/5
title: Subset_XX_Genes_100bp.fasta Alignment Files

description: This zip file contains 15 fasta-formatted alignment files. These are supermatrices produced from GenBank sequence data. They are subsets of the main supermatrix (a.k.a. Subset_01) where each subset requires that all individual species retained in the supermatrix have at least XX genes, with XX ranging from 01 to 15.
DOI: 10.5061/dryad.m6n2t/6
title: RunPartitionFinder_Subset_XX_Genes_rclusterf.cfg Config Files

description: This zip file contains config files for the program PartitionFinder2. They are associated with the gene subsets found in "Subset_XX_Genes_100bp.fasta Alignment Files.zip".
DOI: 10.5061/dryad.m6n2t/7
title: best_scheme_Subset_XX_Genes_rcluserf.part Partition files

description: This zip file contains our results from PartitionFinder2. It gives the nucleotide partitions for use in later phylogenetic analyses such as RAxML. Each file is associated with one of the gene subsets from "Subset_XX_Genes_100bp.fasta Alignment Files.zip".
DOI: 10.5061/dryad.m6n2t/8
title: COMBINED_Parrots_XXXX.asc ASCII raster files

description: This zip file contains multiple raster files in ASCII format. They are worldwide summaries of parrot species diversity, IUCN status, within-species sampling, GenBank sampling, and combinations of the above. Four of these files were used to make Figure 4 in the main manuscript, while the remainder were not used.
DOI: 10.5061/dryad.m6n2t/9
title: Intraspecific_Genetic_Sampling_Citations

description: This CSV file represents our dataset used to determine whether parrot species had intraspecific within-species genetic sampling done. If within-species sampling was found, we cite the reference. We also note situations in which we are aware of ongoing but unpublished work on this subject. In some cases due to taxonomic uncertainty, whether a species has been sampled is unclear, indicated by a "?".
DOI: 10.5061/dryad.n82g9/12
title: Z12 (Snowbed-Salix-Plot 1)
DOI: 10.5061/dryad.n82g9/13
title: Z13 (Snowbed-Bare ground-Plot 3)
DOI: 10.5061/dryad.n82g9/14
title: Z14 (Snowbed-Salix-Plot 3)
DOI: 10.5061/dryad.n82g9/15
title: Z15 (Snowbed-Dryas-Plot 3)
DOI: 10.5061/dryad.n82g9/16
title: Z16 (Snowbed-Bare ground-Plot 2)
DOI: 10.5061/dryad.n82g9/17
title: Z17 (Snowbed-Salix-Plot 2)
DOI: 10.5061/dryad.n82g9/18
title: Z18 (Snowbed-Dryas-Plot 2)
DOI: 10.5061/dryad.n82g9/19
title: Z19 (Snowbed-Dryas-Plot 1)
DOI: 10.5061/dryad.n82g9/20
title: Z20 (Heath-Dryas-Plot 2)
DOI: 10.5061/dryad.qc1bc/1
title: Genotype data

description: The TalentiEtAl_2017.ped file contains the unphased genotype data for all the 929 animals described in the paper: "Genomic analysis suggests KITLG is responsible for a roan pattern in two Pakistani goat breeds".
In this file, data are coded as following:
- FID contains the breed of every individual coded as a number, with the exception of the Beetal Muki Cheni and Barri animals coded BeetalMukiCheni and Barri, respectively
- IID column contains the id code of every individual
- the phenotype column contain the information of the country, with 1 that indicates breeds from Italy and 2 indicates breeds from Pakistan
The TalentiEtAl_2017.map file contain the data of all 53K markers.
DOI: 10.5061/dryad.s2b68/1
title: Traits of Zostera marina (eelgrass)

description: Each row contains the measurements for one eelgrass shoot, identified by its site of collection and the experimental treatment (plot)
DOI: 10.5061/dryad.sf211/1
title: Spreadsheet: Tracking data of tadpole group frogs

description: Tracking points spreadsheet of tadpole group frogs
DOI: 10.5061/dryad.sf211/2
title: Spreadsheet: Tracking data of jelly group frogs

description: Tracking points spreadsheet of tadpole group frogs
DOI: 10.5061/dryad.sf211/3
title: Spreadsheet: deposition site locations

description: Deposition sites locations in the study area
DOI: 10.5061/dryad.sf211/4
title: GIS shapefile: tadpole group points

description: GIS shapefile of tadpole group frog points
DOI: 10.5061/dryad.sf211/5
title: GIS shapefile: tadpole group lines

description: GIS shapefile of tadpole group frog trajectory lines
DOI: 10.5061/dryad.sf211/6
title: GIS shapefile: jelly group points

description: GIS shapefile of jelly group frog points
DOI: 10.5061/dryad.t130r/1
title: Genetic data Tursiops Southwest Atlantic

description: 33 identified sequences from the analysis of 458bp of D-loop control region (mtDNA) and genotyping data from 11 microsateliltes used to investigate pop. structure and diversity in bottlenose dolphins sampled along the Southwest Atlantic Ocean.
DOI: 10.5061/dryad.03n60/10
title: DS3: Median, upper quartile, and lower quartile GR metrics per perturbagen

description: DS3 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol and reagent metadata tables; and a ReadMe file.
DOI: 10.5061/dryad.03n60/11
title: DS4: Median, upper quartile, and lower quartile GR metrics per perturbagen class

description: DS4 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol; and a ReadMe file.
DOI: 10.5061/dryad.03n60/8
title: DS1: Relative cell counts and normalized growth rate inhibition values across technical replicates

description: DS1 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol and reagent metadata tables; and a ReadMe file.
DOI: 10.5061/dryad.03n60/9
title: DS2: Calculated dose response metrics

description: DS2 consists of a downloadable zip file containing a data file; data file metadata in the form of a data column LUT; experimental metadata including a detailed protocol and reagent metadata tables; and a ReadMe file.
DOI: 10.5061/dryad.0rp52/1
title: Phylogenies

description: Phylogenies used for each analysis
DOI: 10.5061/dryad.0rp52/2
title: DataZr_Dry

description: List of studies with Effect Sizes
DOI: 10.5061/dryad.1sg4j/1
title: traits and interactions dataset

description: Consumer and resource traits and taxonomy with their respective interactions.
DOI: 10.5061/dryad.247st/1
title: Summary phylogenetic tree avian influenza HA segment

description: Summary time-rooted Maximum clade credibility phylogenetic tree of the hemagglutinin segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was &gt; 0.5.  NEXUS file
DOI: 10.5061/dryad.247st/2
title: Summary phylogenetic tree avian influenza PB2 segment

description: Time-rooted Maximum clade credibility phylogenetic tree of the polymerase subunit (PB2) segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was &gt; 0.5.  NEXUS file
DOI: 10.5061/dryad.247st/3
title: Summary phylogenetic tree avian influenza M segment

description: Summary time-rooted Maximum clade credibility phylogenetic tree of the matrix gene (M) segment of highly pathogenic avian influenza viruses isolated from wild birds and poultry during the 2014-2015 outbreak in North America. Nodes dates are the mean posterior estimate and are annotated with phylodynamic estimates of uncertainty if posterior probability was &gt; 0.5.  NEXUS file
DOI: 10.5061/dryad.2vn0d/1
title: Body height and immune efficacy-testing body stature as a signal of biological quality - database
DOI: 10.5061/dryad.3f5q5/1
title: DATA SET USED IN THE PAPER

description: DATA SET FOR 

Knowledge based prediction of protein backbone conformation using a structural alphabet

Authors : Iyanar Vetrivel, Swapnil Mahajan, Manoj Tyagi, Lionel Hoffmann, Yves-Henri Sanejouand, Narayanaswamy Srinivasan, Alexandre G. de Brevern, Frédéric Cadet, Bernard Offmann

Corresponding author : bernard.offmann@univ-nantes.fr


FILES DESCRIPTIONS :

1) PDB30_aaseq.txt. This file contains the amino acid sequence of the PDB chains from PDB30 dataset described in the manuscript.

2) PDB30_assigned_pb.txt. This file contains the PB sequence assignment of the PDB chains from the same PDB30 dataset. PB assignment is performed according to reference [29] in the manuscript.

3) PDB30_predited_pb.txt. This file contains the predicted PB sequences of the PDB chains from the PDB30 dataset as per the hybrid method described in the manuscript.
DOI: 10.5061/dryad.4g55s/1
title: Treated Female Data

description: This data set includes date of treatment (KLH or saline), date of the first egg laid (when known), female morphometrics, female VLDL levels, and nest information.
DOI: 10.5061/dryad.4g55s/2
title: Nest Success Data

description: This file includes nestling mass and tarsus length for each individual nestling across the different sampling dates.
DOI: 10.5061/dryad.4vn11/1
title: Heart rate, stroke frequency, and energetic costs of diving narwhals

description: This file contains three pages of data related to the physiology of adult narwhals during escape and post-escape dive periods. Page 1 compares heart rate/stroke frequency relationships for dives associated with different handling periods. Page 2 includes data for minimum heart rate in relation to maximum dive depth.  Page 3 provides data for the energetic cost of escape dives, post-escape dives, and transit swimming. Further details are provided in the manuscript text.
DOI: 10.5061/dryad.58k34/2
title: BF CxG hybrids - adults

description: Data on numbers of adult Anopheles gambiae s.s., An. coluzzii, An. arabiensis and relative hybrids collected during surveys in Burkina Faso.
DOI: 10.5061/dryad.58k34/3
title: CM CxG hybrids - larvae

description: Data on numbers of larvae Anopheles gambiae, An. coluzzii, An. arabiensis collected during surveys in Cameroon.
DOI: 10.5061/dryad.58k34/4
title: systematic review

description: Data retrieved from systematic review of relative presence of Anopheles coluzzii, An. gambiae s.s., An. arabiensis and their relative hybrids in continental Africa
DOI: 10.5061/dryad.666sn/1
title: SSR Data of  Bactocera dorsalis

description: All samples were collected from six island of South China, genotyped 120 individuals using 8 microsatellite loci.
DOI: 10.5061/dryad.666sn/2
title: COI sequences of six island populations of Bactocera dorsalis

description: Identified 120 COI sequences in six islands using mitochondria DNA.
DOI: 10.5061/dryad.6d5m2/6
title: Table S2. Model comparison results from the BioGeoBEARS analysis.
DOI: 10.5061/dryad.789pv/1
title: Ameivula ocellifera Ribossomal 12S DNA

description: Complete 12S alignment of Ameivula ocellifera before bGMYC analysis. This data was first published by Oliveira et al. (2015), Mol Ecol 24, 5957–5975. Information on the 2 lineages used in this study can be found in the Excel file bellow. The complete information of GPS coordinates, locality and GenBank accession numbers for the entire alignment can be found in Table S1 of Oliveira et al. (2015).
DOI: 10.5061/dryad.789pv/2
title: Dermatonotus muelleri NADH dehydrogenase 2

description: Complete ND2 alignment of Dermatonotus muelleri before bGMYC analysis. Information on the 2 lineages used in this study can be found in the Excel file bellow.
DOI: 10.5061/dryad.789pv/3
title: Lygodactylus klugei NADH dehydrogenase 4

description: Complete ND4 alignment of Lygodactylus klugei before bGMYC analysis. Information on the lineage used in this study can be found in the Excel file bellow.
DOI: 10.5061/dryad.789pv/4
title: Micrablepharus maximiliani concatenated mtDNA

description: Complete concatenated cyb+ND4 alignment of Micrablepharus maximiliani before bGMYC analysis. Information on the  lineage used in this study can be found in the Excel file bellow.
DOI: 10.5061/dryad.789pv/5
title: Polychrus acutirostris Cytochrome-b

description: Complete Cyb alignment of Polychrus acutirostris before bGMYC analysis. Information on the lineages used in this study can be found in the Excel file bellow.
DOI: 10.5061/dryad.789pv/6
title: Pleurodema diplolister Cytochrome oxydase 1

description: Complete COI alignment of Pleurodema diplolister before bGMYC analysis. Data first published by Thomé et al 2016, Jbiogeo, 43, 5, 1045–1056. Information on the lineage used in this study can be found in the Excel file. Complete information for the alignment can be found in Thomé et al 2016.
DOI: 10.5061/dryad.84b09/1
title: Gunter2017_linearmorphometrics

description: Linear, meristic and mass measurements of the lower pharyngeal jaws of various cichlid species, which are specified in column A. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD), specified in column B. Standard length of each fish is recorded in mm in column E. Linear measurements are in mm, area is in mm squared and mass is in mg.
DOI: 10.5061/dryad.84b09/2
title: Gunter2017_landmarks

description: Landmarks of geometric morphometric measurements of the lower pharyngeal jaws of various cichlid species, as specified in tpsDig. Individuals were fed one of of two experimental diets, either a soft diet (SD) or hard diet (HD).
DOI: 10.5061/dryad.bh6k6/1
title: Details of all fungal isolates in this study, including GenBank sequence accessions, classification into ITS-based haplotypes, and data on their location of origin.
DOI: 10.5061/dryad.bh6k6/3
title: Matrices with binary AFLP data generated in this study
DOI: 10.5061/dryad.fg700/26
title: Figure S10
DOI: 10.5061/dryad.fg700/29
title: Figure S13
DOI: 10.5061/dryad.fg700/30
title: Figure S14
DOI: 10.5061/dryad.fg700/31
title: Figure S15
DOI: 10.5061/dryad.fg700/32
title: Figure S16
DOI: 10.5061/dryad.fg700/33
title: Figure S17
DOI: 10.5061/dryad.fg700/34
title: Figure S18
DOI: 10.5061/dryad.fg700/35
title: Figure S19
DOI: 10.5061/dryad.fg700/36
title: Figure S20
DOI: 10.5061/dryad.fg700/37
title: Figure S21
DOI: 10.5061/dryad.g14k2/22
title: Zeale PCR replicate 2 - PE1

description: Compressed raw sequence output file. Contains the following data: Zeale primer set, 2nd PCR replicate, forward read.
DOI: 10.5061/dryad.g14k2/23
title: Zeale PCR replicate 1 - PE2

description: Compressed raw sequence output file. Contains the following data: Zeale primer set, 1st PCR replicate, reverse read.
DOI: 10.5061/dryad.g14k2/24
title: Zeale PCR replicate 1 - PE1

description: Compressed raw sequence output file. Contains the following data: Zeale primer set, 1st PCR replicate, forward read.
DOI: 10.5061/dryad.gv1q5/1
title: Supplementary Materials: main file
DOI: 10.5061/dryad.gv1q5/10
title: Supplementary Materials: file 2
DOI: 10.5061/dryad.gv1q5/3
title: simuLBA.C60F.fourtaxa.tar: 4 taxa 20K sites

description: The sequence data (20K sites) were simulated under LG+C60+F+G for four-taxon trees under the LBA-inducing conditions. The tree files are also included.
DOI: 10.5061/dryad.gv1q5/4
title: simuLBR.C20F.fourtaxa.tar: 4 taxa 20K sites

description: The sequence data were simulated under LG+C20+F+G for four-taxon trees under the LBR-inducing conditions. The tree files are also included.
DOI: 10.5061/dryad.gv1q5/5
title: simuLBR.C60F.fourtaxa.tar: 4 taxa 20K sites

description: The sequence data were simulated under LG+C60+F+G for four-taxon trees under the LBR-inducing conditions. The tree files are also included.
DOI: 10.5061/dryad.gv1q5/6
title: simuLBR.8taxa.tre.seq

description: The sequence data were simulated under LG+C20+F+G for an 8-taxon tree under an LBR-inducing condition. The tree file is also included.
DOI: 10.5061/dryad.gv1q5/7
title: simuLBR.12taxa.tre.seq

description: The sequence data were simulated under LG+C20+F+G for a 12-taxon tree under an LBR-inducing condition. The tree file is also included.
DOI: 10.5061/dryad.gv1q5/8
title: simuLBR.16taxa.tre.seq

description: The sequence data were simulated under LG+C20+F+G for a 16-taxon tree under an LBR-inducing condition. The tree file is also included.
DOI: 10.5061/dryad.gv1q5/9
title: simuLBR.20taxa.tre.seq

description: The sequence data were simulated under LG+C20+F+G for a 20-taxon tree under an LBR-inducing condition. The tree file is also included.
DOI: 10.5061/dryad.k0gq6/107
title: E_rare_heterotrichum_241.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/108
title: E_rare_kelleyi_246.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/109
title: E_rare_lanceifolium_43.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/110
title: E_rare_lanceifolium_327.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/111
title: E_rare_lechlerianum_815.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/112
title: E_rare_marginatum_151.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/113
title: E_rare_marginatum_187.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.k0gq6/114
title: E_rare_marsupiiferum_418.fastq

description: Individual fastq file from the genotyping by sequencing dataset.
DOI: 10.5061/dryad.kg008/1
title: Data from Webster & Laland 2017

description: Data from Webster & Laland (2017) Social information use and social learning in non-grouping fishes. Behavioural Ecology
DOI: 10.5061/dryad.m6n2t/11
title: getUniqueGbAccession

description: This Python script is used to extract the unique GenBank accession numbers from Fasta-formatted alignment files produced by our GenBank pipeline.
DOI: 10.5061/dryad.m6n2t/12
title: extractReferencesFromGenbank

description: This Python script is used to extract all of the reference information from a large GenBank-formatted (.gb) file and place it into a CSV for ease of access later on. This was used to create Supplementary Table 1.
DOI: 10.5061/dryad.m6n2t/13
title: RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_Partitioned

description: This newick-formatted file contains 15 maximum-likelihood phylogenies produced in RAxML, one for each of the 15 gene subsets. These contain bootstrap values as well. This file incorporates nucleotide partitioning into the RAxML runs, and forms the basis for all of the trees in the manuscript.
DOI: 10.5061/dryad.m6n2t/14
title: RAxML_AllSubsets_BestTrees_WithBootstraps_100bp_NotParitioned

description: This newick-formatted file contains 15 maximum-likelihood phylogenies produced in RAxML, one for each of the 15 gene subsets. These contain bootstrap values as well. This file does not use any nucleotide partitioning. None of the trees were used in the main manuscript, but are provided for comparison with the partitioned trees.
DOI: 10.5061/dryad.n82g9/21
title: Z21 (Heath-Salix-Plot 2)
DOI: 10.5061/dryad.n82g9/22
title: Z22 (Heath-Bare ground-Plot 1)
DOI: 10.5061/dryad.n82g9/23
title: Z23 (Heath-Dryas-Plot 1)
DOI: 10.5061/dryad.n82g9/24
title: Z24 (Heath-Salix-Plot 1)
DOI: 10.5061/dryad.n82g9/25
title: Z25 (Heath-Bare ground-Plot 3)
DOI: 10.5061/dryad.n82g9/26
title: Z26 (Heath-Salix-Plot 3)
DOI: 10.5061/dryad.n82g9/27
title: Z27 (Heath-Dryas-Plot 3)
DOI: 10.5061/dryad.p148m/1
title: raw_data

description: Raw qPCR data for all analyzed genes (Detectors) for all individuals (Samples). Values are cycle relative threshold (Cq) output by QuantStudio 12K Flex instrument including technical replicates for each gene.
DOI: 10.5061/dryad.p148m/2
title: sample_annotation

description: Data file containing family, rearing environment, stress treatment and tank associations for each individual.
DOI: 10.5061/dryad.p148m/3
title: pcr_efficiencies

description: PCR efficiencies calculated for each gene using LinRegPCR
DOI: 10.5061/dryad.q8rp3/1
title: Deeming JAB data

description: Data on female body mass, egg and egg component mass plus PC values derived from geometric morphometric analysis
DOI: 10.5061/dryad.sf211/10
title: Photograph of A. femoralis tadpoles inside egg-jelly

description: Photograph showing A. femoralis tadpoles hatched inside egg-jelly before the tadpole adding procedure.
DOI: 10.5061/dryad.sf211/11
title: Supplementary movie 1: natural transport

description: Movie showing the cascade of behaviors involved in natural tadpole transport.
DOI: 10.5061/dryad.sf211/12
title: Supplementary movie 2: induced transport

description: Movie showing the induced tadpole transport.
DOI: 10.5061/dryad.sf211/7
title: GIS shapefile: jelly group lines

description: GIS shapefile of jelly group frog trajectory lines
DOI: 10.5061/dryad.sf211/8
title: GIS shapefile: deposition sites

description: GIS shapefile of tadpole deposition sites in the study area
DOI: 10.5061/dryad.sf211/9
title: Supplementary Table 1: induced transport per individual

description: Spatio-temporal variables of induced tadpole transport per individual.
DOI: 10.5061/dryad.tb536/1
title: Drought_Plasticity_Dataset

description: The dataset “Drought_Plasticity_Dataset” by Puglielli et al. reports data on the drought response of three Cistus species (C. salvifolius, C. creticus subsp. eriocephalus and C. monspeliensis). The plants were grown from seeds of different provenances under common garden conditions (provenances are reported in the second column of the dataset). 
The dataset includes data for Control (C) and stress (S) treatment with five replicates per each provenance. 
The parameters are explicitly labeled within the dataset along with the abbreviations used in the paper and their units. 
The values of the Phenotypic Plasticity Index sensu Valladares et al. (New Phytologist 148, 79–91) for the drought (PIstress) and recovery (PIrecovery) responses are reported in columns 17 and 18. Each values is associated to the specific parameter and provenance.
DOI: 10.5061/dryad.vg7r3/1
title: TableS1

description: Raw genotype data, individual scores for discriminant factors and cluster assignments. Y and X-specific haplotypes are highlighted (the latter in pale yellow).
DOI: 10.5061/dryad.0g210/1
title: Mating data Callosobruchus subinnotatus

description: Excel file with mating data of 163 mating observations of Callosobruchus subinnotatus. There is one treatment group: AJ (ablated jaws), and three control groups: APy (ablated pygidium), APa (ablated paramere), and Non (no treatment). Every row is an observation of one couple mating twice. The female lays eggs in between (Total Eggs Between) and after the second mating (Total Eggs after Second). 'Scars old' and 'Scars new' refer to scar data gained by two different methods. 'Scars old' is count data of the number of scars, 'Scars new' is the surface area in pixels that is occupied by scars.
DOI: 10.5061/dryad.1sm54/1
title: List of species with obligate parthenogenesis.

description: This list contains the species (with populations) that reproduce via obligate parthenogenesis (thelytoky).
DOI: 10.5061/dryad.1sm54/2
title: List of species with tychoparthenogenesis.

description: This list contains the species for which asexual reproduction is likely tychoparthenogenesis.
DOI: 10.5061/dryad.1sm54/3
title: List of species with facultative parthenogenesis

description: This is the list with species that are characterised by facultative parthenogenesis.