cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.9p7d8h2/4
title: Nexus file of coding and non-coding DNA sequences of the psbA minicircle

description: This file contains partial DNA sequences for the coding (~300 bases encoding the D1 protein of photosystem II) and non-coding region (~200-300 bases) of the chloroplast psbA minicircle (psbAncr). Two large portions (~150 and 50 bases, respectively) were removed from the Breviolum faviinorum sequences to minimize the alignment’s length. Sequences are from species of endosymbiotic dinoflagellates in the genus Breviolum (formerly Symbiodinium Clade B) obtained from host colonies in the reef coral families Mussidae (sub-family Faviinae), Meandrinidae, Merulinidae, and Astrocoeniidae. Sequences from Breviolum minutum associated with the anemone Exaiptasia were included for comparison.
DOI: 10.5061/dryad.9p7d8h2/5
title: Microsatellite locus Sym15 from Breviolum spp.

description: This nexus file contains sequence alignments of the flanking– and repeat–regions (approximately 200 bases) for the nuclear microsatellite locus Sym15, which is possessed by most species in the dinoflagellate genus Breviolum (family Symbiodiniaceae). Samples were obtained from host colonies of the reef coral families Mussidae (especially the sub-family Faviinae), Meandrinidae, Merulinidae, and Astrocoeniidae. Sequences from Breviolum minutum (common to the sea anemone Exaiptasia) and B. psygmophilum were included for comparison.
DOI: 10.5061/dryad.9p7d8h2/6
title: Multi-locus genotypes for population genetic analyses of closely related Breviolum spp.

description: This excel file contains multilocus genotypes based on 9 independently sorting microsatellite loci from four species of Breviolum obtained from Atlantic reef-building corals in the families Mussidae (subfamily Faviinae), Meandrinidae, Astrocoeniidae and Merulinidae (represented by Orbicella, formerly of the Montastraea annularis species complex).
DOI: 10.5061/dryad.d79c4cs/1
title: Collaboration in tropical ecology dataset

description: A .csv containing columns for year of publication, authors' first country of affiliation, authors' names, article title, and the journal where the article was published.
DOI: 10.5061/dryad.ng3r749/1
title: URMP Dataset

description: We introduce a dataset for facilitating audio-visual analysis of musical performances. The dataset comprises a number of simple multi-instrument musical pieces assembled from coordinated but separately recorded performances of individual tracks. For each piece, we provide the musical score in MIDI format, the high-quality individual instrument audio recordings and the videos of the assembled pieces. We anticipate that the dataset will be useful for multi-modal information retrieval techniques such as music source separation, transcription, performance analysis and also serve as ground-truth for evaluating performances.
DOI: 10.5061/dryad.pc6tp4q/1
title: Chromosomal_SNPs-InDels

description: Variant Call Format files for chromosome encoded SNPs/InDels identified for each isolate from this study.
DOI: 10.5061/dryad.pc6tp4q/2
title: Command/scripts used for SNPs/InDels identification

description: Unix command line scripts used for SNP/InDel identitcation
DOI: 10.5061/dryad.r9q3b/1
title: reads_cleaning_mapping_filtering
DOI: 10.5061/dryad.r9q3b/2
title: evaluation_cumulative_curves
DOI: 10.5061/dryad.r9q3b/3
title: consensus_phylogeny_dnds
DOI: 10.5061/dryad.r9q3b/4
title: coverage_deletion
DOI: 10.5061/dryad.r9q3b/5
title: populations_diversity_fst_dxy
DOI: 10.5061/dryad.r9q3b/6
title: Cotesia_sesamiae_Cotesia_typhae_whole_bracovirus_alignment

description: Alignment of the consensus of 98 bracovirus genes from 24 C. sesamiae, C. typhae and C. flavipes samples realized with PhyML software.
DOI: 10.5061/dryad.r9q3b/8
title: Population_genetics_statistics_and_dNdS

description: Population genetics statistics for 98 bracovirus genes of C. sesamiae populations and C. typhae including nucleotide diversity (π) for each population, relative (FST) and absolute (dxy) differentiation for each comparison and dNdS values for each population branch.
DOI: 10.5061/dryad.rf7317t/1
title: Supplementary Material

description: This Supplementary file is composed of 5 parts. In 1), 2) and 3), we provide supplementary results from our simulation analyses.  In 4) we illustrate how to compute standard errors of parameters estimates for the penalized likelihood in R, and in 5) we discuss how to efficiently account for within-species variation and measurement error.
DOI: 10.5061/dryad.rf7317t/4
title: Supplementary R codes

description: R codes providing the simulations procedures and miscellaneous functions (warps reconstructed changes, ...).
DOI: 10.5061/dryad.tg8fq3c/1
title: CB_600m

description: Fasta file of MOTU from plants at 600m
DOI: 10.5061/dryad.tg8fq3c/2
title: FR_800m

description: Fasta file of MOTU from plants at 800m
DOI: 10.5061/dryad.tg8fq3c/3
title: LE_1000m

description: Fasta file of MOTU from plants at 1000m
DOI: 10.5061/dryad.tg8fq3c/4
title: LT_1200m

description: Fasta file of MOTU from plants at 1200m
DOI: 10.5061/dryad.tg8fq3c/5
title: LM_1450m

description: Fasta file of MOTU from plants at 1450m
DOI: 10.17632/fjv7yxfcbx.1
title: Data for: Topological support and data quality can only be assessed through multiple analytics in reviewing Blattodea phylogeny

description: Alignment of 12s, 16s, 18s, 28s, COI and COII for 500+ insects, mostly in the order Blattodea
DOI: 10.5061/dryad.10j18k2/1
title: De Jager et al. 2018 Field experiment data

description: This file contains the raw data of our field experiments described in De Jager et al. 2018.
DOI: 10.5061/dryad.1nd7372/1
title: Psychiatric disorders in C9orf72 carriers and non-carriers - age of onset and survival

description: Supplementary Table 1: Age of onset (in years) of psychiatric disorders in C9orf72 carrier and non-carrier kindreds. Cox regression analysis hazard ratio (HR) with 95% confidence intervals (CI) shows effect of genetic status on survival in family members with psychiatric disorders.
DOI: 10.5061/dryad.212777q/1
title: Total.lsm

description: This is a xyzt confocal image set in the Zeiss lsm format. It is the raw data used in Figure 3C.
DOI: 10.5061/dryad.387c58v/53
title: MrBayes, partitioned, exon-only data, 25% occupancy

description: Nexus file for the MrBayes, partitioned, exon-only data, 25% occupancy analysis.
DOI: 10.5061/dryad.387c58v/54
title: MrBayes, partitioned, exon-only data, 25% occupancy

description: Resulting phylogeny from the MrBayes, partitioned, exon-only data, 25% occupancy analysis.
DOI: 10.5061/dryad.387c58v/55
title: Table 1 from manuscript

description: Use this table to relate tip labels to genus and species names in the phylogeny files that were uploaded to Dryad. In all uploaded phylogeny files the tree needs to be rooted with the clade containing the Hypochilidae, Filistatidae, and Synspermiata specimens.
DOI: 10.5061/dryad.387c58v/56
title: ASTRAL results, combined data, 70% occupancy

description: ASTRAL results, combined data, 70% occupancy
DOI: 10.5061/dryad.387c58v/57
title: ASTRAL results, combined data, 50% occupancy

description: ASTRAL results, combined data, 50% occupancy
DOI: 10.5061/dryad.387c58v/58
title: ASTRAL results, combined data, 25% occupancy

description: ASTRAL results, combined data, 25% occupancy
DOI: 10.5061/dryad.387c58v/59
title: ASTRAL results, UCE-only data, 70% occupancy

description: ASTRAL results, UCE-only data, 70% occupancy
DOI: 10.5061/dryad.387c58v/60
title: ASTRAL results, UCE-only data, 50% occupancy

description: ASTRAL results, UCE-only data, 50% occupancy
DOI: 10.5061/dryad.387c58v/61
title: ASTRAL results, UCE-only data, 25% occupancy

description: ASTRAL results, UCE-only data, 25% occupancy
DOI: 10.5061/dryad.40877s4/6
title: File 6

description: File 6 of 9.  All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)
DOI: 10.5061/dryad.40877s4/7
title: File 7

description: File 7 of 9.  All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)
DOI: 10.5061/dryad.40877s4/8
title: File 8

description: File 8 of 9.  All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)
DOI: 10.5061/dryad.40877s4/9
title: File 9

description: File 9 of 9.  All of the files need to be downloaded, then the data can be extracted via: cat uldb.tar.gza* | (tar -xz)
DOI: 10.5061/dryad.4bk56qr/2
title: Worker Ant CTmax

description: CTmax = critical thermal maximum in degrees Celsius; ColonyID = identity of the colony from which the individual worker ants were tested; habitat.designation = whether the habitat is "urban" or "rural"; longitude = the decimal degrees longitude of the collection site of the colony; latitude = the decimal degrees latitude of the collection site of the colony; treatment = the temperature treatment under which the colonies were reared in the laboratory, including 21, 23, 25, 27, or 29 degrees Celsius; city = the urbanization cline from which the colonies were obtained, including "Knx" (Knoxville, TN), "Cin" (Cincinnati, OH), "Cle" (Cleveland, OH)
DOI: 10.5061/dryad.4bk56qr/3
title: Queen Ant CTmin

description: CTmin = critical thermal minimum in degrees Celsius; ColonyID = identity of the colony from which the individual queen ants were tested; habitat.designation = whether the habitat is "urban" or "rural"; longitude = the decimal degrees longitude of the collection site of the colony; latitude = the decimal degrees latitude of the collection site of the colony; treatment = the temperature treatment under which the colonies were reared in the laboratory, including 21, 23, 25, 27, or 29 degrees Celsius; city = the urbanization cline from which the colonies were obtained, including "Knx" (Knoxville, TN), "Cin" (Cincinnati, OH), "Cle" (Cleveland, OH)
DOI: 10.5061/dryad.4bk56qr/4
title: Queen Ant CTmax

description: CTmax = critical thermal maximum in degrees Celsius; ColonyID = identity of the colony from which the individual queen ants were tested; habitat.designation = whether the habitat is "urban" or "rural"; longitude = the decimal degrees longitude of the collection site of the colony; latitude = the decimal degrees latitude of the collection site of the colony; treatment = the temperature treatment under which the colonies were reared in the laboratory, including 21, 23, 25, 27, or 29 degrees Celsius; city = the urbanization cline from which the colonies were obtained, including "Knx" (Knoxville, TN), "Cin" (Cincinnati, OH), "Cle" (Cleveland, OH)
DOI: 10.5061/dryad.4bk56qr/5
title: Alate production

description: alates = number of alates (reproductive ants) produced over the course of the experiment; ColonyID = identity of the colony from which the number of alates produced was assessed; habitat.designation = whether the habitat is "urban" or "rural"; treatment = the temperature treatment under which the colonies were reared in the laboratory, including 21, 23, 25, 27, or 29 degrees Celsius; city = the urbanization cline from which the colonies were obtained, including "Knx" (Knoxville, TN), "Cin" (Cincinnati, OH), "Cle" (Cleveland, OH)
DOI: 10.5061/dryad.4tc6292/1
title: NFPSF_JEcol_data_soil_chem

description: Soil chemical data. Soils were field-collected along the Jurien Bay dune chronosequence in Western Australia in 2014. A subset of soils were subjected to gamma irradiation (50 kGy). Soil data in this file include: pH, total phosphorus (P), resin P,  total carbon, total nitrogen, nitrate, ammonium, exchangeable potassium and exchangeable sodium concentrations, and exchangeable cation-exchange capacity. This NFPSF_JEcol_data_soil_chem.csv file was created using Microsoft Excel 2013. See 'README' file for descriptions of (abbreviated) column headings.
DOI: 10.5061/dryad.4tc6292/2
title: NFPSF_JEcol_data_biomass_PSF

description: Plant biomass and plant-soil feedback data. Common nitrogen (N)-fixing and non-N-fixing plants grown in field, biotic and abiotic soil treatments established from field-collected soils along the Jurien Bay dune chronosequence in Western Australia in 2014. Plants were grown within a glasshouse at the University of Western Australia for six months and harvested in 2015. Data in this file include: total, above- and below-ground plant biomass (fresh and dry), and plant-soil feedback values of a given plant when grown in soils conditioned by either all co-occurring heterospecific plants, or co-occurring heterospecific N-fixing plants, or co-occurring heterospecific non-N-fixing plants (compared with growth in conspecific soil). This NFPSF_JEcol_data_biomass_PSF.csv file was created using Microsoft Excel 2013. See 'README' file for descriptions of (abbreviated) column headings.
DOI: 10.5061/dryad.64q763h/1
title: Szipl_et_al_data_main

description: Full data set and genotypes
DOI: 10.5061/dryad.7b150n7/1
title: Mangrove and salt marsh artificial warming study

description: This data file includes data for the growth of mangroves and salt marsh and soil elevation change for an in field warming study conducted at Merritt Island, FL.
DOI: 10.5061/dryad.7f9j57n/1
title: Camera Trap Detections of Carnivore Species for Co-occurrence Model

description: Raw camera trap detections of paired mammalian carnivore species in each of the 13 study areas. Detections of the paired species (Spp1Det and Spp2Det) reflect the number of 24-hr. time periods that species 1 (SppCode1) and species 2 (SppCode2) were detected. Species codes (SppCode1 and SppCode2) were derived from the first two letters of the genus and species name (e.g., EIBA = Eira barbara). Num.nights reflects the number of 24-hr. periods during which the camera trap was active at a particular site. This file can be used to estimate the species interaction factor (SIF) within the species co-occurrence model.
DOI: 10.5061/dryad.7f9j57n/2
title: Species Trait Data for Regression Analysis

description: Species trait data for each of the 768 paired carnivores in all 13 study areas. Species codes (Spp1 and Spp2) were derived from the first two letters of the genus and species name (e.g., EIBA = Eira barbara). Appendix S2 contains the full list of species examined in this study. We summarized the categorical variables of diet, temporal activity pattern, social structure, body size and taxonomic similarity in two ways. For the first coarse comparison method (e.g., DietCovSimple), we compared species with differing trait values (e.g., when species A | B are strict carnivore | omnivore) to those where pairs shared the trait value (e.g., strict carnivore | strict carnivore). In other words, species pairs were either labeled the ‘same’ or ‘different’ for all categorical variables of interest. For the fine-scale trait comparison (e.g., DietCov), species pairs were categorically valued for all combinations of a trait (e.g., strict carnivore | strict carnivore = 1, strict carnivore | omnivore = 2, strict carnivore | insectivore = 3, etc.). We also characterized the mean weight ratio (heavier:lighter species, MeanBodySize) between two species, including it as a log-transformed continuous variable (logMeanBodySize). We also include the observed number of carnivore species in each study area (NumSpecies) and the study area’s climate as determined by the Köppen-Geiger climate classification system (Climate). Finally, this file also includes the estimated Species Interaction Factor (SIF), the standard deviation of SIF (sd), and the log-transformed SIF values (logSIF).
DOI: 10.5061/dryad.83576bv/1
title: NCT02724046 Main trial database

description: Data from NCT02724046
DOI: 10.5061/dryad.8403km4/1
title: Beast header file for Inga species tree analysis

description: Beast header file for Inga species tree analysis that includes specific sample names
DOI: 10.5061/dryad.8403km4/2
title: locus5 nexus alignment

description: Nexus format alignment for locus 5, Aminocyclopropanecarboxylate oxidase (see Table S3)
DOI: 10.5061/dryad.8403km4/3
title: locus7 nexus alignment

description: Nexus format alignment for locus 7, Trans-cinnamate 4-monooxygenase. See Table S3
DOI: 10.5061/dryad.bh78sn5/1
title: Readme

description: General description of the content of the .zip files and how to interact with them.
DOI: 10.5061/dryad.bh78sn5/2
title: Mouse 1

description: Image stack and blender files with the 3D mesh data reconstructed from a 4 months old layer I somatosensory cortex neuropil
DOI: 10.5061/dryad.bh78sn5/3
title: Mouse 2

description: Image stack and blender files with the 3D mesh data reconstructed from a 24 months old layer I somatosensory cortex neuropil
DOI: 10.5061/dryad.bh78sn5/4
title: Mouse 4

description: Image stack and blender files with the 3D mesh data reconstructed from a 24 months old layer I somatosensory cortex neuropil
DOI: 10.5061/dryad.j68v33v/1
title: Data matrices and trees
DOI: 10.5061/dryad.j68v33v/2
title: Files associated with trait evolution and diversification analyses
DOI: 10.5061/dryad.j68v33v/3
title: Trinity assembled contig files used for phylogenetic analyses
DOI: 10.5061/dryad.kh16d4k/1
title: Data from exaggerated male legs P waitomoensis

description: Excel spreadsheet with data for each test on a different tab. Units and methods are described in the manuscript
DOI: 10.5061/dryad.nd4169j/1
title: Data for ANOVAs of nest characteristics across study plots

description: Data table for analyses of variance (ANOVAs) examining stem density and nest wall thickness across study plots (Figure 1 of published article).  Column headings: Year: year of nest construction; Plot: low, mid, or high elevation study plot; Nest: unique nest identifier; Density: number of woody stems per square m within 1-m radius of nest; Thickness: nest wall thickness in cm.  Missing data are indicated by “NA.”

Data were collected from a breeding population of the migratory Black-throated Blue Warbler at the Hubbard Brook Experimental Forest (HBEF), Woodstock, New Hampshire, USA (43.93N, 71.75W), from 2010-2013.
DOI: 10.5061/dryad.nd4169j/2
title: Data for ANOVAs of brooding patterns across study plots

description: Data table for analyses of variance (ANOVAs) examining brooding patterns across study plots (Figure 1 of published article).  Column headings: Year: year of nest construction; Plot: low, mid, or high elevation study plot; Nest: unique nest identifier; DayOffboutDuration: mean brooding off-bout duration in s over days 3-5 of the nestling stage; DayOffboutFrequency: brooding off-bout frequency per h over days 3-5 of the nestling stage; DayPercentTimeOff: proportion of time female was off the nest over days 3-5 of the nestling stage.

Data were collected from a breeding population of the migratory Black-throated Blue Warbler at the Hubbard Brook Experimental Forest (HBEF), Woodstock, New Hampshire, USA (43.93N, 71.75W), from 2010-2013.
DOI: 10.5061/dryad.nt2g6/1
title: xiphophorus_genetree_pairwiseDistances

description: Pairwise distances obtained from RAxML gene trees, averaged across genes after normalization to a median branch length of 1 within each tree.
DOI: 10.5061/dryad.p564p61/1
title: All input ascis

description: Resistance models of all environmental factors of all cities used for landscape genetic optimization (ASCI-format).
DOI: 10.5061/dryad.p564p61/2
title: Microsatellites_all_citites

description: Microsatellites of all individuals genotyped in this study.
DOI: 10.5061/dryad.p7n02t0/1
title: Supplemental data

description: Tables e-1-5.
DOI: 10.5061/dryad.qm01v75/1
title: PerronIJ_PLOS_RawData

description: Zip file containing 6 files and 2 folders (with 4 files and 9 files).
DOI: 10.5061/dryad.qp745/4
title: RQUA tree datasets

description: File - Description

## Within MLanalysis ##

	*iqtree.log					
			logfile from IQTREE analysis
	*IQtreefile.nex 			
			IQTREE output tree
	*seqs.fasta 				
			sequences unaligned
	*mafft.fasta				
			sequences aligned with mafft
	*mafft.bmge_masked.fasta	
			BMGE masked alignment

## Within TopologyTests ##

	*.log
			IQTREE logfile from site likelihood inference
	*.sitelh
			site likelihood file from IQTREE
	*_ContrainTrees_BootstrapTrees.tre	
			ML cosntrain trees
	*_consel.catpv
			output from CONSEL
		
## FILES ##

RQUA_full_datasets/MLanalysis

	rqua.iqtree.log
	rqua.IQtreefile.nex
	rqua.mafft.bmge_masked.fasta
	rqua.mafft.fasta
	rqua.seqs.fasta

RQUA_full_datasets/TopologyTests

	RQUA_fulldataset_consel.catpv
	RQUA_fulldataset_ContrainTress_BootstrapTrees.tre
	RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.log
	RQUA_fulldataset_SiteLikelihoodGeneration.IQTREE.sitelh
	
	
RQUA_GroupA_datasets/MLanalysis

	rqua.GroupA.IQtree.log
	rqua.GroupA.IQtree.treefile
	rqua.GroupA.mafft.bmge_masked.fasta
	rqua.GroupA.mafft.fasta
	rqua.GroupA.seqs.fasta
	
RQUA_GroupA_datasets/TopologyTests

	RQUA_GroupA_consel.catpv
	RQUA_GroupA_ConstrainTrees.tre
	RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.log
	RQUA_GroupA_SiteLikelihoodGeneration.IQTREE.sitelh
	
	
RQUA_GroupB_datasets/MLanalysis

	rqua.GroupB.IQtree.log
	rqua.GroupB.IQtree.treefile
	rqua.GroupB.mafft.bmge_masked.fasta
	rqua.GroupB.mafft.fasta
	rqua.GroupB.seqs.fasta


RQUA_GroupB_datasets/TopologyTests

	RQUA_GroupB_consel.catpv
	RQUA_GroupB_ConstrainTrees.tre
	RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.log
	RQUA_GroupB_SiteLikelihoodGeneration.IQTREE.sitelh
DOI: 10.5061/dryad.qp745/5
title: alphaprotebacteria_datasets

description: Alignment file and raw tree file for alphaproteobacteria phylogeny.  See Figure 2 - figure supplement 2.
DOI: 10.5061/dryad.s24121t/1
title: Data and code

description: This file contains data and R code associated with "The lingering impact of stress: brief acute glucocorticoid exposure has sustained, dose-dependent effects on reproduction."
DOI: 10.5061/dryad.tg8fq3c/6
title: all_motu

description: Binary datasheet of denovo MOTU by plant. This was used as the input datasheet for the mantel test and linear model in the manuscript.
DOI: 10.5061/dryad.1fm52vv/1
title: Supplementary Figure 1 (Neognathodus plate)

description: Figure 1. Images of type specimens for synonymized Neognathodus species N. medadultimus/N. medexultimus and N. dilatus/N. metanodosus. Pairs are synonymized here to N. medadultimus and N. dilatus, respectively. All images are re-illustrated from previous studies. Scale bar represents one mm. Conodont element identification is fol¬lowed by repository number (if available) and photo reference, stratigraphic unit and the county and state location. See README file for more specific details.
DOI: 10.5061/dryad.1fm52vv/2
title: Supplementary Table 1 (Specimen collection numbers)

description: Supplementary Table 1. Table showing the stratigraphic distribution of Neognathodus specimens selected to test morphotype group affinities. Specimens were chosen between multiple stratigraphic boundaries. For example, to select the 30-specimen sample of N. bassleri, 27 N. bassleri specimens were chosen from the Perth Limestone Member, two were chosen from the Mecca Quarry Shale and Velpen Limestone members, and one was chosen from the Alum Cave Limestone Member. LS = limestone, SH = shale and Mbr = member. The number of specimens chosen from each unit is proportional to the total number of morphotype group occurrences in that unit.
DOI: 10.5061/dryad.1nd7372/2
title: Risk for psychiatric disorders in C9orf72 FTD and ALS kindreds

description: Rates (first 2 columns) of psychiatric disorders in C9orf72 FTD and ALS kindreds, and risk for psychiatric disorders between kindreds of probands with C9orf72 FTD vs ALS. Hazard ratios (HR) represent the risk to relatives of developing psychiatric disorders with upper and lower confidence intervals (CI) displayed. Significant values are highlighted in bold.
DOI: 10.5061/dryad.387c58v/62
title: ASTRAL results, exon-only data, 70% occupancy

description: ASTRAL results, exon-only data, 70% occupancy
DOI: 10.5061/dryad.387c58v/63
title: ASTRAL results, exon-only data, 50% occupancy

description: ASTRAL results, exon-only data, 50% occupancy
DOI: 10.5061/dryad.387c58v/64
title: ASTRAL results, exon-only data, 25% occupancy

description: ASTRAL results, exon-only data, 25% occupancy