cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.g6bq21b/7
title: Nucleotide sequences for Xenopus TRPA1

description: Aligned nucleotide sequences for TRPA1 from Xenopus species.
DOI: 10.5061/dryad.gv0p9n4/23
title: MLTET_OH64
DOI: 10.5061/dryad.gv0p9n4/24
title: MLTET_OH119
DOI: 10.5061/dryad.gv0p9n4/25
title: MLTET_OK61
DOI: 10.5061/dryad.gv0p9n4/26
title: MLTET_PA27
DOI: 10.5061/dryad.gv0p9n4/27
title: MLTET_TN19
DOI: 10.5061/dryad.gv0p9n4/28
title: MLTET_WI128
DOI: 10.5061/dryad.gv0p9n4/29
title: README_final
DOI: 10.5061/dryad.h8f22dh/1
title: DRYAD_2019-06-13

description: Raw interaction data between plants and AM fungi
DOI: 10.5061/dryad.hm3v1dm/1
title: Gillet_otus

description: Fasta file of the OTUs built from mini-COI sequences amplified from bat faeces with Gillet primers
DOI: 10.5061/dryad.hm3v1dm/2
title: Zeale_otus

description: Fasta file of the OTUs built from mini-COI sequences got from bat faeces with Zeale primers
DOI: 10.5061/dryad.nc0f501/12
title: snapshots_10_2

description: Contains the Matlab (.mat) file output for each simulation run for rho=10 and transmission type=2
DOI: 10.5061/dryad.pp5qk07/1
title: N. vectensis light removal experiment, raw all counts table

description: Raw tag-based sequencing data used as input file for DESeq2 meta-analysis. This data set was collected in the Reitzel Lab at the University of North Carolina at Charlotte in December, 2017. A description of the sampling protocol is given in the materials and methods section of the manuscript. Briefly, sea anemones were sampled at 4-hour intervals over a ~ 3 day period, pre- and post- light cue removal and during constant conditions for a total of 136 samples. Columns correspond to single genes mapped to the Vienna Nematostella transcriptome, and each row corresponds to 1 individual (4 reps per time point, 17 time points, 2 light treatments).
DOI: 10.5061/dryad.pp5qk07/2
title: Data1

description: Data1 contains all raw Illumina sequencing files associated with diel-entrained subjects. File names contain information regarding treatment (LD), timepjoint (T#), and biological replicate (A-D).
DOI: 10.5061/dryad.pp5qk07/3
title: Data2

description: Data2 contains all Illumina raw sequencing files associated with long-term constant darkness-entrained subjects. File names contain information regarding treatment (DD), timepjoint (T#), and biological replicate (A-D).
DOI: 10.5061/dryad.sg77240/1
title: SNP data, Table S1

description: The genotype data used for this study in PLINK map/ped format and Table S1
DOI: 10.5061/dryad.tq20c08/1
title: Olsen et al 2019_JAB - bill data

description: This file includes body measurements and relevant ecological setting (i.e., whether the site was within a hybrid zone, an index of species density within a tenth of a degree of latitude) for bill measurements of two sparrow species.
DOI: 10.5061/dryad.tr6d8q2/1
title: Evolution of the Rhodelphis heme biosynthetic pathway.

description: Maximum likelihood phylogenetic trees were generated for all Rhodelphis heme biosynthetic proteins including: aminolevulinate synthase (ALAS), delta aminolevulinic acid dehydratase (HemB), porphobilinogen deaminase (HemC), uroporphyrinogen-III synthase (HemD), uroporphyrinogen-III decarboxylase (HemE), coproporphyrinogen-III oxidase (HemF), protoporphyrinogen-IX oxidase (HemY), ferrochelatase (HemH). Only the first step in heme synthesis, catalyzed by ALAS, is most similar to mitochondrial homologs, and is predicted to be mitochondrial. All others, with the exception of HemH, are plastid-type proteins. The atypical HemH protein is found in some, but not all red algae, and is closely related to HemH from myxobacteria. Untrimmed and trimmed alignments used to generate the trees are also included.
DOI: 10.5061/dryad.tr6d8q2/2
title: Evolution of the Rhodelphis plastid FeS cluster biosynthesis pathway.

description: Maximum likelihood phylogenetic trees were generated for all Rhodelphis plastid iron-sulfur biosynthetic proteins including: SufB, SufC, SufD, SufE, SufS, ferredoxin, ferredoxin reductase, and NiFU. Untrimmed and trimmed alignments used to generate the trees are also included.
DOI: 10.5061/dryad.tr6d8q2/3
title: Rhodelphis retain relic plastids including subunits of conserved plastid protein import complexes.

description: Maximum likelihood phylogenetic trees were generated for Rhodelphis plastid Cpn60, along with conserved subunits of plastid protein import complexes. The presence of plastid import complexes is strong evidence for the retention of plastids in Rhodelphis cells. Untrimmed and trimmed alignments used to generate the trees are also included.
DOI: 10.5061/dryad.tr6d8q2/4
title: Unaltered microscopic photographs of Rhodelphis cells.

description: Raw photographs of Rhodelphis limneticus and R. marinus that correspond to photographs in Figure 1, along with Extended Data Figures 1 and 2 are presented.
DOI: 10.5061/dryad.tr6d8q2/5
title: Individual and concatenated protein alignments for 151/253 dataset

description: This folder contains trimmed individual protein alignments that were used to construct the 151/253 concatenated supermatrix using SCaFoS. The resulting concatenated alignment - also included - was used to generate Figure 2a-b, along with Extended Data Figure 4.
DOI: 10.5061/dryad.tr6d8q2/6
title: Individual and concatenated protein alignments for 153/253 dataset

description: This folder contains trimmed individual protein alignments tthat were used to construct the 153/253 concatenated supermatrix using SCaFoS. The resulting concatenated alignment - also included - was used to generate Extended Data Figure 3.
DOI: 10.5061/dryad.tr6d8q2/7
title: Coalescence recovers Rhodelphis as sister to red algae based on individual gene trees

description: Individual bootstrapped gene trees were generated with RAxML v8.1.6 and used to generate a species tree with ASTRAL-III under default parameters and 100 bootstrap replicates. Species trees were made from either all 253 single-gene trees from the 151/253 dataset, or b, the 50 trees with the highest relative tree certainty. The sister relationship of Rhodelphis and red algae is recovered with both datasets, and is in agreement with concatenated phylogenomic analyses. The resulting coalescent trees for each dataset, along with the gene trees used to generate the species tree, are included.
DOI: 10.5061/dryad.tr6d8q2/8
title: Concatenation of alignments from the 50 single-gene datasets with highest relative tree certainty scores recovers Rhodelphis as sister to red algae.

description: A maximum likelihood phylogenetic tree was generated with IQ-TREE based on a concatenated alignment of the 50 single gene trees with the highest relative tree certainty (151 taxa, 21,886 sites). The sister relationship of Rhodelphis and red algae still receives full statistical support with a highly reduced, phylogenetically well-supported dataset. This dataset represents Extended Data Figure 6.
DOI: 10.17632/f7hbp4ykpb.1
title: Data for: Experimental Investigation of Surface Adhesion of Titan Analog Materials: Mitigation by Dust-Repellent Coatings

description: Raw data for particle accumulation on transparent windows with different dust-repellant coatings.
DOI: 10.17632/m8s89d68sn.1
title: Data for: Chinese Medicine JQ Granule Combined with Half-dose Omeprazole for Non-erosive Reflux Disease: A Multicenter, Randomized, Double-blind, Placebo-controlled Trial Study Protocol
DOI: 10.17632/s96znr3t36.1
title: Data for: The enrichment and purification of hexabromocyclododecanes in zebrafish and its effects on thyroid

description: data
DOI: 10.5061/dryad.30bf364/1
title: Suppl Tables and Figures

description: Supplemental tables 1-3 and supporting Figures 1 and 2 with legend.
DOI: 10.5061/dryad.3pn57h0/1
title: Supporting_Information_Data_S1_Thamnophiini_Final_Morph_Data

description: Morphological Data Raw
DOI: 10.5061/dryad.3pn57h0/2
title: Supporting_Information_Data_S2_Thamnophiini_Tree_Total

description: Phylogeny of Thamnophiini from McVay et al. 2015
DOI: 10.5061/dryad.3pn57h0/3
title: Supporting_Information_Data_S3_Morph_data_total

description: All morphological data summarized with references
DOI: 10.5061/dryad.3pn57h0/4
title: Supporting_Information_Data_S4_Morph_data_for_R

description: Data for importation and processing in R.
DOI: 10.5061/dryad.3pn57h0/5
title: Supporting_Information_Table_S1_SMA_Statistics

description: SMA and OLS regression stats.
DOI: 10.5061/dryad.3pn57h0/6
title: Supporting_Information_Table_S2_Trait_Model_Evolution

description: Table of trait model AICc and weighted AICc values.
DOI: 10.5061/dryad.3pn57h0/7
title: Supporting_Information_Table_S3 Model Adequacy Tests

description: Table of model adequacy tests using Arbutus (R package).
DOI: 10.5061/dryad.3qc6328/1
title: Data from: Patterns, dynamics and consequences of microplastic ingestion by the temperate coral, Astrangia poculata

description: This is an excel file with annotated raw data. Each sheet (tab) is associated with a figure, and is named as such.
DOI: 10.5061/dryad.3tv1523/18
title: Raw: Blank 400/200/4 Inject 3

description: Raw MS data file for Blank Negative Control Sample, 400/200/4 Fraction, Injection 3
DOI: 10.5061/dryad.3tv1523/19
title: Complete Scaffold Data File

description: Scaffold project data file containing completed database search data
DOI: 10.5061/dryad.3tv1523/20
title: Scaffold Output Files

description: Scaffold data output files in excel format
DOI: 10.5061/dryad.3tv1523/21
title: README
DOI: 10.5061/dryad.43sd180/1
title: Data_nestlings_means

description: Phenotypic measures of all nestling traits (body mass on d16, wing length on d16, PHA response on d13, brightness, hue and UV chroma of 1 tail feather on d16).Color traits are averaged for each individual. Nestlings were cross-fostered between 2005 and 2009 and thus RearID is their nest of rearing while GeneticID is their nest of origin. Sex is 1 for female, 2 for male and 0 when unknown. Vane tarsus, and wing length are measured in mm and weight_d16 is measured in g. machine refers to the spectrophotometer that was used for measuring tail feathers (1 for 2005-2006, 2 for the other years).
DOI: 10.5061/dryad.4h75q1p/1
title: Use Values & Plant Parts used for main forest tree species of the Guiana Shield

description: A binary table describing for each species (in rows), its use values (construction, firewood, human food, medicinal, arts and crafts) the used tree parts (bark, wood, fruits, leaves or flowers, exudates, underground organs). This dataset compile information from many databases of the region. Details in the published paper.
DOI: 10.5061/dryad.5tq5dn6/1
title: Julian date of emergence of Osmia cornuta, Osmia bicornis and flowering of Pulsatilla vulgaris

description: Julian date of first, abundance-weighted mean and last emergence of O. cornuta and O. bicornis males and females and of first, abundance-weighted mean and last flowering of P. vulgaris. Number of emerged O. cornuta and O. bicornis males and females, maximum number of P. vulgaris flowers on transect, Julian date of first other than P. vulgaris flowering plant and site temperature.
DOI: 10.5061/dryad.600vs50/2
title: Data and R code for logistic regression analyses

description: Zip folder containing data and R code for running the logistic regression analyses. The 'LogisticRegression_FinalScript.R' script contains R code for the General Additive Models (GAMs) and the Generalized Linear Mixed Models that were used to analyse the Incidence Function Model (IFM) simulation results. The summarised IFM simulation outputs used in the statistical analyses are contained within the 'SuccessGLMDataNew.csv' file. Definitions of column headings within this file are provided in the R script.
DOI: 10.5061/dryad.600vs50/3
title: HCVA and NPP plantation summary data

description: Zip folder containing three Excel spreadsheets with summary information for the 70 New Planting Procedure (NPP) plantations and associated High Conservation Value Areas (HCVAs) used in our study. The 'SummaryData_ForHistograms.xlsx' file contains the data used for Fig. 3 in the main text, and includes the area and forest cover of HCVAs within each NPP plantation. It also includes the size of each NPP plantation estate and the area of non-HCVA forest cover within each NPP plantation. The 'SummaryData_HCVAPatchSize.xlsx' file contains the size of all spatially discrete HCVA patches within each NPP plantation and the 'SummaryData_HCVAType.xlsx' contains the size and forest cover of all spatially discrete HCVA patches within each NPP plantation that could be identified to Type (e.g., HCV 1-6). Descriptions of column headings are provided in the Excel files.
DOI: 10.5061/dryad.6h661t9/1
title: rummel_etal_2019
DOI: 10.5061/dryad.87f53d7/1
title: Dunlin sample information
DOI: 10.5061/dryad.8k3d81r/1
title: Mysuru City Bird Atlas (2014-2016) raw data

description: Raw data from the Mysuru City Bird Atlas (2014-2016). Full description in the accompanying article in Indian Birds journal.
DOI: 10.5061/dryad.bd4486s/3
title: Turbidity data

description: Raw data and the script to determine how similar the UV threat will be across the three selected blue holes.
DOI: 10.5061/dryad.c806hk2/1
title: Krause et al, raw data for all graphs

description: This file contains all data points for all the displayed graphs in the article Krause et al.
DOI: 10.5061/dryad.cb0d8ft/1
title: Data 1-tarsi

description: Data 1-tarsi: Tarsi length, distance from the back of inter-tarsal joint to the point where the toes bending an angle of 90 degree to the tarsus and was measured in the field to the nearest 0.1 mm using slide callipers.
DOI: 10.5061/dryad.cb0d8ft/2
title: Data 2-Rectrice

description: Dtata 2-Rectrice: The rectrices measured with a calliper and weighted twice using an analytical balance to the nearest 0.1 mg.
DOI: 10.5061/dryad.cb0d8ft/3
title: Data 3-Growth bars

description: Growth bar widths and total feather lengths measured to the nearest 0.01 mm with a digital calliper
DOI: 10.5061/dryad.d5dt7d0/1
title: R and Stan code for analysis

description: Contains R and Stan code for cleaning, processing, analyzing, and visualizing data on vertebrate abundance and richness at the Missouri Ozark Forest Ecosystem Project.
DOI: 10.5061/dryad.f83t155/1
title: adiv_Cecropia_Readinfile_Bact_OTUS_even1344

description: alpha diversity values for 16S Bacterial dataset
DOI: 10.5061/dryad.g893nb0/1
title: SPDT_NET

description: This is the constructed SPDT contact network among 364K nodes over 32 days using GPS locations of Momo users. This network has both direct and indirect links. In this network, the links have the following format: Host-ID, Neighbor-ID, Host-Arrival-Time, Host-Depart-Time, Neb-Arrival-Time, Neb-Depart-Time. Each link has been created for visiting a common location within 3 hours of host node departure. The node ID is anonymised and spatial location information is also removed. This is only the links over time.
DOI: 10.5061/dryad.g8k7261/1
title: Full Data Archive - Stam et al 2019 - Community Legacy - Journal of Ecology

description: The file contains folders with all data used in the study. The first folder includes a readme with explanation of all content. The data has been collected on the field site Droevendaal of Wageningen University, Wageningen, the Netherlands in 2012 and 2013.
DOI: 10.5061/dryad.mm4qb48/1
title: Appendix 1

description: Altitudinal distribution and main black color of plumage in males of 60 species and subspecies of thrushes used in the plumage reconstruction analysis. It is include the continent where each species inhabit and if have latitudinal migration (partial migration mean that all individuals from one species migrate to non-reproductive areas, but reproductive and non-reproductive areas overlap geographically). Information was obtained from Clement and Hathway (2000) and Collar (2005) reviews of the Turdidae family.
DOI: 10.5061/dryad.n50st0n/1
title: S1. Video of segmented adult T. radix skull

description: This supplementary video depicts the skull of an adult T. radix individual (see figure captions in main text for labelling of bones). This specimen is housed in the University of Alberta Museum of Zoology (UAMZ R636), and was scanned using a Bruker-SkyScan 1076 micro-CT scanner (see article text for details regarding methods). The micro-CT scans were visualized and segmented in Dragonfly 1.0, and the video was created using Dragonfly 3.0.
DOI: 10.5061/dryad.n50st0n/2
title: S2. Video of segmented juvenile T. radix skull

description: This supplementary video depicts the skull of a juvenile T. radix individual (see figure captions in main text for labelling of bones). This specimen is housed in the University of Alberta Museum of Zoology (UAMZ R950), and was scanned using a Bruker-SkyScan 1076 micro-CT scanner (see article text for details regarding methods). The micro-CT scans were visualized and segmented in Dragonfly 1.0, and the video was created using Dragonfly 3.0.
DOI: 10.5061/dryad.n50st0n/3
title: S3. Video of segmented embryonic T. radix skull

description: This supplementary video depicts the skull of an embryonic T. radix individual (see figure captions in main text for labelling of bones). This specimen is housed in the University of Alberta Museum of Zoology (UAMZ R620), and was scanned using a Bruker-SkyScan 1076 micro-CT scanner (see article text for details regarding methods). The micro-CT scans were visualized and segmented in Dragonfly 1.0, and the video was created using Dragonfly 3.0.
DOI: 10.5061/dryad.n50st0n/4
title: S4. 3D mesh files of all segmented skull bones of adult T. radix

description: This folder contains 3D mesh (.stl) files of all skull bones of an adult T. radix individual. This specimen is housed in the University of Alberta Museum of Zoology (UAMZ R636), and was scanned using a Bruker-SkyScan 1076 micro-CT scanner (see article text for details regarding methods). The micro-CT scans were visualized and segmented in Dragonfly 1.0. The mesh (.stl) files can be viewed in many 3D visualization programs (e.g., Avizo, Adobe Photoshop, etc).
DOI: 10.5061/dryad.n50st0n/5
title: S5. 3D mesh files of all segmented skull bones of juvenile T. radix

description: This folder contains 3D mesh (.stl) files of all skull bones of a juvenile T. radix individual. This specimen is housed in the University of Alberta Museum of Zoology (UAMZ R950), and was scanned using a Bruker-SkyScan 1076 micro-CT scanner (see article text for details regarding methods). The micro-CT scans were visualized and segmented in Dragonfly 1.0. The mesh (.stl) files can be viewed in many 3D visualization programs (e.g., Avizo, Adobe Photoshop, etc).
DOI: 10.5061/dryad.q2j3161/1
title: Field experiment

description: Results of the common garden field experiment conducted during two consecutive years (2013/2014) at Cape Race (NL, Canada). Adult L. minutus survival to acidity was measured as [Log10 (Nﬁnal + 1) - Log10 (Ninitial + 1)].
DOI: 10.5061/dryad.q2j3161/2
title: Pond pH throughout years

description: pH regime shifts of 108 ponds between three consecutive years (2013, 2014, 2015) at Cape Race (NL, Canada).
DOI: 10.5061/dryad.tr6d8q2/10
title: Bayesian phylogenomic analyses of concatenated protein datasets recover Rhodelphis as sister to red algae

description: Bayesian phylogenomic analyses were carried out for two very similar datasets: 153/253 (153 taxa, 253 proteins, 56,312 sites) and 151/253 (151 taxa, 253 proteins, 56,530 sites) using PhyloBayes under the CAT+GTR+G4 framework. In each case, Rhodelphis were shown to be sister to red algae; in the 153/253 dataset, picozoa were shown to be sister to Rhodelphis + red algae. Unlike maximum likelihood analyses, Bayesian analyses recovered the monophyly of Archaeplastida.
DOI: 10.5061/dryad.tr6d8q2/11
title: Rhodelphis limneticus genome assemblies and predicted protein sequenecs

description: This folder contains R. limneticus genomic scaffolds from mixed culture (including the prey kinetoplastid Parabodo caudatus and bacteria) and manually isolated cells amplified by whole genome amplification (WGA). In each case, the assembly is based on a combination of Illumina HiSeq X and Oxford Nanopore minION reads that were assembled using SPAdes. Contaminant contigs were identified and removed using a combination of megablast and Autometa. For the WGA dataset, proteins were predicted using braker2; protein sequences are provided with soft repeat masking and no repeat masking.
DOI: 10.5061/dryad.tr6d8q2/12
title: Rhodelphis limneticus filtered transcriptome assemblies and protein sequences

description: RNA-seq was performed on R. limneticus from mixed culture (including the prey kinetoplastid, Parabodo caudatus and bacteria) and from manually isolated single cells after amplification using the Smart-seq2 protocol. Paired-end reads were generated with the Illumina MiSeq platform and assembled with Trinity. In each case, contamination from prey organisms was subtracted using prey-only transcriptomes. Trinity contigs and Transdecoder protein sequences collapsed at 95% sequence identity with CD-HIT are included.
DOI: 10.5061/dryad.tr6d8q2/13
title: Rhodelphis marinus filtered transcriptome assembly and predicted proteins

description: RNA-seq was performed on R. marinus from mixed culture (including the prey kinetoplastid, Procryptobia sorokini and bacteria). Strand-specific paired-end reads were generated with the Illumina HiSeq 2500 platform and assembled with Trinity. In each case, contamination from prey organisms was subtracted using prey-only transcriptomes. Transdecoder protein sequences collapsed at 95% sequence identity with CD-HIT are included, along with Transdecoded mRNA sequences corresponding to the protein predictions.
DOI: 10.5061/dryad.tr6d8q2/14
title: Fast site removal analyses demonstrate the robustness of the sister relationship of Rhodelphis and red algae

description: The fastest evolving sites in the 151/253 and 153/253 concatenated datasets were estimated with AgentSmith and removed progressively in blocks of 3,000 amino acids. Maximum likelihood phylogenies were generated under the PROT+CAT+LG+F model with 100 rapid bootstrap replicates in RAxML 8.1.6. Here we include the individual phylogenies and alignments generated by AgentSmith. The support for various relationships is depicted in Figure 2c and Extended Data Figure 3c.
DOI: 10.5061/dryad.tr6d8q2/9
title: Maximum likelihood phylogenomic analyses of concatenated datasets demonstrate that Rhodelphis are sister to red algae

description: Maximum likelihood phylogenomic analyses were carried out for two very similar datasets: 153/253 (153 taxa, 253 proteins, 56,312 sites) and 151/253 (151 taxa, 253 proteins, 56,530 sites) using IQ-TREE under the LG+C60+F+G4 model. In each case, Rhodelphis were shown to be sister to red algae; in the 153/253 dataset, picozoa were shown to be sister to Rhodelphis + red algae. Unlike Bayesian analyses, maximum likelihood did not recover the monophyly of Archaeplastida, instead grouping Cryptista with green algae/plants and glaucophytes, though with only modest statistical support. The 153/253 tree corresponds to Extended Data Figure 3b, and the 151/253 tree corresponds to Extended Data Figure 4b.
DOI: 10.15159/phytop.20
title: Lake Peipsi 1995 (Phytoplankton samples)

description: Methods: Samples were in most cases concentrated by precipitation up to 15 ml. Count was made on striped microscope slides within volume 0,1 ml. Microscopes: MBI-3 (magnification 15x20 and 15x40) and Jenaval (7x40). Macroscopic colonies of Gloeotrichia echinulata were counted visually in 500 ml measuring cylinder.