cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.20g8r.2/6.2
title: S4-WAM & GenBank Accession Numbers

description: Lists all the GenBank accession numbers for voucher specimens.
DOI: 10.5061/dryad.33380/1
title: ELISPOT data for PloS One 24_10_15

description: ELISPOT data_Polio Study Moradabad_Plos One
DOI: 10.5061/dryad.457br/1
title: GWAS_pop_data

description: Chromosome 5 Illumina BovineHD genotypes and phenotypes for the milk fat percentage GWAS population.
DOI: 10.5061/dryad.457br/2
title: RNAseq_pop_imputed_seq_data

description: Chromsome 5 imputed sequence and gene expression data used for eQTL mapping
DOI: 10.5061/dryad.457br/3
title: RNAseq_pop_imputed_seq_data_with_gap_vars

description: Chromsome 5 imputed sequence and gene expression data used for eQTL mapping - with reference gap variants
DOI: 10.5061/dryad.457br/4
title: Large_pop_imputed_seq

description: Chromsome 5 imputed sequence and phenotype data used for milk composition association mapping
DOI: 10.5061/dryad.457br/5
title: RNAseq_pop_del_haplotype

description: Gene expression (phenotypes), pedigree, and diplotype (haplotype pair) data for analysis of the CNV-proxy haplotype
DOI: 10.5061/dryad.475g7/1
title: mosstrap-masked-coding.tar

description: RNA-Seq was conducted on Illumina Hi-Seq 2000 platform, and reads were quality trimmed using Trimmomatic. De novo transcriptome assemblies were generated using Trinity, which can produce many isoforms. We used a phylogenetic approach to decide whether to retain isoforms. Transcripts which contained a valid protein with a BLASTp hit to a known land plant proteome were clustered using mcl, and gene trees were built from sequences in each cluster. To generate the "masked" dataset, the gene trees were searched for monophyletic clades containing sequences from the same species. Only one transcript per clade was retained, and the others were pruned from further analysis. This archive contains a multi-FASTA file of coding (DNA) sequences for each of the transcriptomes generated for the study.
DOI: 10.5061/dryad.4bq4q/1
title: Egg Volumes for Experimental Lincoln's Sparrow Nests

description: These are the data used in statistical analyses presented in this manuscript.
DOI: 10.5061/dryad.51f00/25
title: Online Supplemental Material Figure S7.

description: Maximum clade credibility tree topology for unconstrained (non-clock) Bayesian analysis of nDNA in MrBayes. Circles on nodes represent the posterior probability of that node. The tree was rooted for drawing purposes only.
DOI: 10.5061/dryad.51f00/26
title: Online Supplemental Material Figure S8.

description: Maximum clade credibility tree topology for unconstrained (non-clock) Bayesian analysis of the reduced morphological dataset (369 characters) in MrBayes. Circles on nodes represent the posterior probability of that node. The tree was rooted for drawing purposes only.
DOI: 10.5061/dryad.51f00/27
title: Online Supplemental Material Figure S9.

description: The primary concordance tree topology inferred using Bayesian concordance analysis (BUCKy) of the posterior distributions of trees inferred from individual analysis of the mtDNA, nDNA and morphology. Numbers on branches indicate the concordance factor, a measure of the average number of data types that support the given branch. The tree was rooted for drawing purposes only.
DOI: 10.5061/dryad.51f00/28
title: Online Supplemental Material Figure S10.

description: Box plots of Robinson-Foulds distances (RF) from the primary concordance tree (PCT) for tree sets inferred from different data types. mtDNA = mitochondrial DNA, nDNA = nuclear DNA, TE = total evidence, Null1 and Null2 = randomized trees to generate null distributions. See main text for further details.
DOI: 10.5061/dryad.51f00/29
title: Online Supplemental Material Figure S11.

description: The tree topology with the highest likelihood found by RaxML with the bootstrap support values from 1000 pseudoreplicates indicated on branches.
DOI: 10.5061/dryad.51f00/30
title: Online Supplemental Material Figure S12.

description: 50% majority rule consensus of 55 most parsimonious tree topologies inferred from the total evidence dataset (reduced morphological dataset) using the parsimony ratchet (TNT).
DOI: 10.5061/dryad.51f00/31
title: Online Supplemental Material File S16

description: Mean clade credibility tree from FBD analysis of full morphological and full molecular dataset.
DOI: 10.5061/dryad.51f00/32
title: Online Supplemental Material File S17.

description: Mean clade credibility tree from FBD analysis of reduced morphological and full molecular dataset.
DOI: 10.5061/dryad.5nk70/1
title: Data Archive

description: Induced magnetic field over time for all experimental figures.
DOI: 10.5061/dryad.65b2g/1
title: Data and Scripts: Community rescue in experimental metacommunities

description: Data files: 1) Optical density measurements in Phase 1 2) Optical density measurements in Phase 2 3) OTU and taxonomic assignment of sequences  Scripts: Scripts for analysis in R.
DOI: 10.5061/dryad.75ph1/3
title: male choosiness
DOI: 10.5061/dryad.7qb11/1
title: Small mammal dataset

description: Presence-absence dataset of small mammals in 164 counties of the Hengduan Mountains
DOI: 10.5061/dryad.8h6k1/1
title: Perezetal_2016_Pilosocereus_SSRdata

description: SSR data from populations of Pilosocereus aurisetus and P. machrisii species (Cactaceae)
DOI: 10.5061/dryad.8h6k1/2
title: runms_Paur

description: A python script to draw values for the parameters tau, theta, ancient migration, current migration, bottleneck and population expansion. This file contains the 7 models tested in this study and outputs the ms' simulation results for both cpDNA and SSR markers in the species P. aurisetus.
DOI: 10.5061/dryad.8h6k1/3
title: runms_Pmac

description: A python script to draw values for the parameters tau, theta, ancient migration, current migration, bottleneck and population expansion. This file contains the 7 models tested in this study and outputs the ms' simulation results for both cpDNA and SSR markers in the species P. machrisii.
DOI: 10.5061/dryad.8h6k1/4
title: runPPC_Paur

description: Retrieve parameter values from the parameter estimates of the selected in the P. aurisetus dataset and use them to simulate new data to perform PPC analysis.
DOI: 10.5061/dryad.8h6k1/5
title: runPPC_Pmac

description: Retrieve parameter values from the parameter estimates of the selected in the P. machrisii dataset and use them to simulate new data to perform PPC analysis.
DOI: 10.5061/dryad.8h6k1/6
title: microsat2arp

description: A python script that converts the microsatellite data from ms' accessory program microsat to the arlequin format.
DOI: 10.5061/dryad.8sc52/2
title: CRM image scan of 6 day old biofilm, cosmic ray corrected

description: WiTec Project file of a CRM image scan of the 6 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm.
DOI: 10.5061/dryad.8sc52/3
title: CRM image scan of 9 day old biofilm, cosmic ray corrected

description: WiTec Project file of a CRM image scan of the 9 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm.
DOI: 10.5061/dryad.8sc52/4
title: CRM image scan of 35 day old biofilm, cosmic ray corrected

description: WiTec Project file of a CRM image scan of the 35 day old Shewanella oneidensis biofilm. From M&M: The measurement was performed on a WITec alpha300 confocal Raman microscope, using a 50 µm pinhole and a Zeiss LD plan-NEOFLUAR 20×/0.4 corr air objective with coverslip correction. 20× magnification was used in order to keep as many bacteria as possible in the focal plane while still resolving individual bacteria. The excitation wavelength was 532 nm, with laser power of 3 mW at the focal plane. The Raman detector was a newton EMCCD camera cooled to -60o C with a 600 g/mm grating. Integration time was 1 second and lateral resolution 2 pixel/µm.
DOI: 10.5061/dryad.c25f0/1
title: morphology data from common gardens

description: This file contains morphological maize data from four maize common gardens. Each common garden has 60 plots, 20 maize populations with three repetitions. Except one garden, which has 40 plots, 20 maize populations with two repetitions. It includes information about population and data of thirteen plant morphological traits. See detailed abbreviations in the ReadMe file.
DOI: 10.5061/dryad.c89g9/1
title: Data for statistical analyses

description: We present row data used for statistical analyses: i) the effect of the nestling age on parental activities of owls, ii) the effect of intra-seasonal variability in sunset and sunrise timing on timing of owl activities, iii) the effect of month (April-July) on light intensity at time of owl activities, iv) the effect of outdoor temperature on time spent by owl female outside the nest, and v) the effect of the night length on voltage decrease of battery.
DOI: 10.5061/dryad.f862c/1
title: Flow Cytometry Data of Sepsis Study

description: Flow cytometry data including C3d, C4d, glycocalyx (WGA), and some other data (FRAP, etc.)
DOI: 10.5061/dryad.f862c/2
title: M606 E0 + WGA

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/3
title: M606 E0

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/4
title: M606 E24 + WGA

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/5
title: M606 E24

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/6
title: M613E24-control C3d

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/7
title: M613E24-control C4d

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/8
title: M613E24-control DAF

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.gt6ks/1
title: XiaoWernberg_Temp_UV_PLoSone_raw_data

description: Raw data on growth, photosynthetic yield, Health status and absorption.
DOI: 10.5061/dryad.hp0vd/1
title: Moult scores of Carolina chickadees in forest and urban habitats

description: Adult Carolina chickadees were caught in the field in a contiguous forest, a fragmented forest, and an urban habitat in New Jersey in 2010, 2012, and 2013. We estimated the proportion of each growing feather that was newly replaced by comparing it to the lengths of neighboring, fully-grown feathers, and then assigning it a score between 0.05 and 0.95 in increments of 0.05 (e.g., 0.35 = 35% of fully grown length; only birds with at least one growing feather scored ≥0.05 were included in moult estimates). Moult score ("% moult") of each individual was calculated as the percent of each feather tract (primary [wing], secondary [wing] feathers, and rectrix [tail]). For "Number of growing flight feathers", a "." indicates that the final feather of each tract (P9,S6, and R6) is growing, and it would not be possible for those individuals to moult a greater number of feathers simultaneously. For the "Most distal growing primary", a "." means that primary moult is complete. It is possible for a moult score to be "0" (ie. new feathers are scored &lt;0.05) but for feathers to still be scored as "growing" if the old feather had just fallen out. "Pair" indicates birds that were caught in the same location on the same day.
DOI: 10.5061/dryad.kr13g/1
title: Bråthen & Ravolainen Data

description: Two sheets in a xls file with the data from both study designs: the tundra design and the tundra meadow design. Variable names are the same as those described in the text of the paper. Note the hierarchical, nested designs as depicted in Figure 3.
DOI: 10.5061/dryad.m7d12/1
title: Carnell and Keough Oikos 2016 The influence of herbivores on primary producers can vary spatially and interact with disturbance
DOI: 10.5061/dryad.q44p3/1
title: COSII makers allignments

description: Alignment of COSII markers on S. commersonii, S. tuberosum cv. Blondy, a S. phureja-S. tuberosum hybrid (clone UP88P5), S. phureja (clone IVP35).
DOI: 10.5061/dryad.0m764/1
title: Data

description: These anonymized data include 18 control subjects and 18 patients with GBM in Analyze format.
DOI: 10.5061/dryad.182dv/10
title: Combined VCF for all 29 accessions for chromosome 9
DOI: 10.5061/dryad.182dv/11
title: Combined VCF for all 29 accessions for chromosome 10
DOI: 10.5061/dryad.182dv/12
title: Combined VCF for all 29 accessions for chromosome 11
DOI: 10.5061/dryad.182dv/13
title: Combined VCF for all 29 accessions for chromosome 12
DOI: 10.5061/dryad.182dv/15
title: HQ Alignment in Multisample Variant Format
DOI: 10.5061/dryad.182dv/16
title: HD Alignment in Multisample Variant Format
DOI: 10.5061/dryad.182dv/17
title: LQ Alignment in Multisample Variant Format
DOI: 10.5061/dryad.182dv/18
title: Genome-Wide Concatenated/Coalescent/Consensus Phylogenies
DOI: 10.5061/dryad.182dv/19
title: HQ Coding Sequence Alignment in Multisample Variant Format
DOI: 10.5061/dryad.182dv/22
title: Genome-wide all sample phylogenies from gene regions, 100kb and 1Mb regions
DOI: 10.5061/dryad.1d52k/4
title: Supplementary Information

description: Associated bivalve, measurements, taxon-age data, R code, supplementary phylogeny figures.
DOI: 10.5061/dryad.30bj3/1
title: Beetle metabolic rate data

description: This dataset contains metabolic rate, respiratory quotient, body weight and ejaculate weight data from seed beetles with different mitonuclear genotypes.
DOI: 10.5061/dryad.464vm/1
title: Immunoglobulin free light chains in clinically isolated syndrome with conversion to multuiple sclerosis

description: This data file represents the concentrations of immunoglobulin free light chains in 4 groups of patients: 1) CIS-MS (clinically isolated syndrome with conversion to multiple sclerosis during 2 years) 2) CIS-nonMS (clinically isolated syndrome without conversion to multiple sclerosis during 2 years) 3) NIND - non-inflammatory neurologic disorders 4) IND - inflammatory neurologic disorders. This data was collected from clinical database and laboratory tests database for every patient. The data file was created with Microsoft Excel. Abbreviations: FLC - free light chains, CSF - cerebrospinal fluid, Q - quotient of concentration (th ratio of concentrations in CSF/serum), OCB - oligoclonal bands, abs - absent.
DOI: 10.5061/dryad.475g7/2
title: masked_orthogroup_table

description: This file contains a correspondence between assembled transcripts and the orthogroups generated by the Yang/Smith Pipeline (see manuscript for details). Each species is separated by a tab, and transcripts from the same species in the same orthogroup are separated by commas.
DOI: 10.5061/dryad.475g7/3
title: singlegene.tar

description: This archive contains single gene sequence alignments for 657 "1-to-1 orthologs" used go generate a species phylogeny for the study. Each directory contains the single-gene sequence alignment in multi-FASTA format, and the results of a maximum likelihood search in RAXML. Nucleotide sequences were aligned with MAFFT and trimmed with trimal to remove columns represented by fewer than 5 taxa. Phylogenies were reconstructed with the GTRGAMMA substitution model and nodal support was evaluated with 200 "fast bootstrap" replicates.
DOI: 10.5061/dryad.475g7/4
title: supermatrix_cds_bootstrap_ML

description: Phylogeny reconstructed from concatenated nucleotide matrix of single genes in RAXML version 8. A single GTRGAMMA partition was specified for each locus. Support values are from 200 full bootstrap replicates.
DOI: 10.5061/dryad.475g7/5
title: species_tree_astral_jackknife_cds

description: ASTRAL species tree reconstructed from nucleotide RAXML gene trees for 657 genes. Support values generated by jack-knife (sampling (without replacement) 65 gene trees 1000 times).
DOI: 10.5061/dryad.475g7/6
title: cluster_gocats

description: Gene ontology (GO) annotations for each orthogroup generated from the masked dataset. The Trinotate transcriptome annotation pipeline was used go assign GO annotations to transcripts using BLASTp searches of the UniProt database and HMM searches of the pfam protein domain database. All unique GO annotations for sequences in an orthogroup are shown.
DOI: 10.5061/dryad.475g7/7
title: sequenceID_to_speciesID

description: Correspondence between sequenceIDs used in data files and the family, genus, and species names of samples used in the analysis.
DOI: 10.5061/dryad.4cc5m/1
title: Collins and Mitchard - Above ground forest biomass estimated for 2007

description: This GeoTiff file provides estimate of per-pixel above ground biomass (AGB) for a section of Sumatra in 2007. Only those pixels with forest of height greater or equal to 20m in 2007 were included. The maximum AGB estimated per pixel is 236.5 Mg ha^-1. The minimum per pixel biomass is 0 Mg ha^-1. The projection is UTM48S. The pixel size is ~100m x 100m.
DOI: 10.5061/dryad.4cc5m/2
title: Collins and Mitchard Sumatra Deforestation 2007-10 coded -DataDryad

description: This GeoTiff map shows: *areas of forest of height greater or equal to 20m in 2007 that is stable over time (coded as 0). *Areas of forest of the above definition, but that we lost between 2007-8 (coded as 1). *Areas of forest of the above definition, but that were deforested between 2008-9 (coded as 2). *Areas of forest of the above definition, but that but that were deforested between 2009-10 (coded as 3). *Pixels which did not contain forest of height greater or equal to 20m in 2007 are excluded from the analysis (coded as 'no data').
DOI: 10.5061/dryad.51f00/33
title: Online Supplemental Material File S18.

description: Mean clade credibility tree from TD analysis of full morphological and full molecular dataset.
DOI: 10.5061/dryad.51f00/34
title: Online Supplemental Material File S19.

description: Mean clade credibility tree from TD analysis of reduced morphological and full molecular dataset.
DOI: 10.5061/dryad.51f00/35
title: Online Supplemental Material Figure S13.

description: Box plots of Robinson-Foulds distances (RF) among trees inferred from the total evidence dataset using different tree inference techniques. ML = maximum likelihood (using RaxML), parsimony = maximum parsimony (using TNT, 55 most parsimonious trees), Bayes = Bayesian inference (using MrBayes v3.2.6).
DOI: 10.5061/dryad.52t20/1
title: Zhou et al. PLOS ONE MS-data files (Tables)

description: There are six tables in this file describing the results of traits as per our research objectives. Results could be studied from our manuscript submitted to PLOS ONE journal.
DOI: 10.5061/dryad.52t20/2
title: Zhou et al. PLOS ONE MS-Figures

description: This file contains seven figures as a part of research findings in Zhou et al. manuscript submitted to PLOS ONE journal. Each figure is well defined with title and legends. Moreover, all the figures are well described in the text of our manuscript.
DOI: 10.5061/dryad.56894/1
title: Eclosion and Activity Data

description: Eclosion and flight activity data for each population (black hawthorn-, early apple-, late apple-, and ornamental hawthorn- associated flies) collected in 2013 in Vancouver, WA.
DOI: 10.5061/dryad.56894/2
title: Fruit Data

description: Softness (inverse of firmness) and diameter data for fruits from the four hosts analyzed in this study (black hawthorn, early-and late-ripening apple, and ornamental hawthorn.
DOI: 10.5061/dryad.56894/3
title: KVUO Airport Weather Data Vancouver WA_DRYAD

description: Abiotic data taken at a weather station (KVUO in Vancouver, WA) near the field site. Dates range from March to December 2013.
DOI: 10.5061/dryad.56894/4
title: Larval abundance

description: Both numbers of fruit and numbers of larvae emerging from the fruit of each host to determine larval abundance on given dates.
DOI: 10.5061/dryad.56894/5
title: Soil Temperatures

description: Soil temperatures were recorded both inside and outside eclosion tents to determine if significant alterations in temperature resulted from the shading effects of the tents themselves.
DOI: 10.5061/dryad.9jm42/1
title: 8Zone-RawData

description: Microsatellite and stable isotope data for lake and round whitefish collected at Douglas Point in 2010 and 2011.
DOI: 10.5061/dryad.c25f0/2
title: SSR data

description: This file contains SSR data of 20 populations, 10 plants per population, and data for 15 SSR. It includes some characteristics of the population, see abbreviations in ReadMe file. SSR’s are phi051, phi115, phi015, phi033, phi053, phi072, phi093, phi024, phi085, phi034, phi121, phi029, phi073, phi96342, phi109275. See publication for details. Data of each plant are in two consecutive rows. Missing data is coded as -9
DOI: 10.5061/dryad.c61n5/1
title: Microsatellite Data (GenePop file format) plus sample information

description: Microsatellite dataset used in: Edwards, T., M. Vaughn, P. C. Rosen, C. Meléndez-Torres, A. E. Karl, M. Culver, and R. W. Murphy. Shaping species with ephemeral boundaries; the distribution and genetic structure of the desert tortoise (Gopherus morafkai) in the Sonoran Desert.  Journal of Biogeography. Mocrosatellite data scored as allelic values (repeat count). File contains sample locality information and additional data from 20 captive animals genotyped from El Centro Ecológico del Estado de Sonora, summarized in; Edwards, T. (2015) A biogeographic perspective of speciation among desert tortoises in the genus Gopherus. PhD Dissertation, University of Arizona, Tucson, Arizona USA.
DOI: 10.5061/dryad.cj030/1
title: High speed video data

description: These are the data from high speed video of Agalychnis callidryas embryos hatching.
DOI: 10.5061/dryad.cj030/2
title: Embryo displacement data

description: These data are from the embryo displacement experiment. They are related to the timing of hatching events for rotation control and displaced embryos.
DOI: 10.5061/dryad.f34p5/1
title: KNP_EBP_Partial_Species_Comp

description: This data come from Kruger National Park (Kruger), Mpumalanga, South Africa near the Satara rest camp. This set from Kruger is of the partial exclosures, full exclosures, and paired plots that were established in 2007. Species composition was collect at the beginning (January) and end (March) of each growing season. Each plant species’ cover in 4 permanent 1x1m subplots inside and outside the exclosure was recorded to the nearest one percent twice a year. The maximum value of the two samplings was used, and data presented here are the mean of the 4 subplots.
DOI: 10.5061/dryad.f862c/10
title: M613E24-control RBC + WGA

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/11
title: M613E24-control RBC

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.
DOI: 10.5061/dryad.f862c/12
title: M613E24-sepsis C3d

description: Flow cytometry raw data. Flow cytometry files (.fcs) generated using a LSRII flow cytometer.