cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh1259744.08fu
title: SH1259744.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.25549/one-c4-15106
title: ONE, Inc. meeting minutes (1974)

description: Minutes for the annual, trustees, board of directors meetings (1974)
DOI: 10.15156/bio/sh1259745.08fu
title: SH1259745.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1259746.08fu
title: SH1259746.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1259747.08fu
title: SH1259747.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.15156/bio/sh1259748.08fu
title: SH1259748.08FU

description: UNITE provides a unified way for delimiting, identifying, communicating, and working with DNA-based Species Hypotheses (SH). All fungal ITS sequences in the international nucleotide sequence databases are clustered to approximately the species level by applying a set of dynamic distance values (<0.5 - 3.0%). All species hypotheses are given a unique, stable name in the form of a DOI, and their taxonomic and ecological annotations are verified through distributed, web-based third-party annotation efforts. SHs are connected to a taxon name and its classification as far as possible (phylum, class, order, etc.) by taking into account identifications for all sequences in the SH. An automatically or manually designated sequence is chosen to represent each such SH. These sequences are released (https://unite.ut.ee/repository.php) for use by the scientific community in, for example, local sequence similarity searches and next-generation sequencing analysis pipelines. The system and the data are updated automatically as the number of public fungal ITS sequences grows.
DOI: 10.5061/dryad.1c9g5mm.2/33.2
title: MacGuigan&Near_appendix

description: Online appendix for "Phylogenomic signatures of ancient introgression in a rogue lineage of darters (Teleostei: Percidae)" by Daniel J. MacGuigan and Thomas J. Near. Table A1, A2, and A3 are included in this file.
DOI: 10.5061/dryad.43d0509/1
title: Data_Figure_3

description: Data of the first experiment.
DOI: 10.5061/dryad.43d0509/2
title: Data_Figure_4

description: Data of the second experiment.
DOI: 10.5061/dryad.47174j0/1
title: Empirical_RCode

description: The attached code goes through the differing methods to model functional responses using the lynx example dataset ("LynxExample.csv").  The final figure combines all of the different approaches to easily visualize the similarities and differences.
DOI: 10.5061/dryad.47174j0/2
title: LynxExample
DOI: 10.5061/dryad.47174j0/3
title: Simulation_RCode

description: The attached provides the simulation code used to develop the different functional response scenarios and implement the different modeling approaches.
DOI: 10.5061/dryad.4b14m4r/1
title: Growth-, resistance-, and chemical-related trait measurement of C. pratensis and P major plant

description: The data file consists into an excel document divided in three worksheets; the first two named "C_pratensis" and P_major" contain data about the treatments, measurements of plant growth and plant secondary metabolites and the herbivore performance (one file for each species used in the study); the third worksheet called "Unit and Info About Variables" contains info and measuring units about treatments and dependent variables used in the study.
DOI: 10.5061/dryad.548c1p1/5
title: Measurements for new species of Aegiria

description: Measurements (in mm) for complete specimens of Aegiria apta sp. nov. Abbreviations L. Mus. and W. Mus. represent length and width of ventral muscle fields respectively.
DOI: 10.5061/dryad.548c1p1/6
title: Measurements for new species of Cathaysiorthis

description: Measurements (in mm) for complete specimens of Cathaysiorthis xichuanensis sp. nov. Abbreviations L. Mus. and W. Mus., L. Car. and W. Car. represent length and width of ventral muscle field and cardinalia respectively.
DOI: 10.5061/dryad.66jr2/1
title: Laodelphax striatellus microsatellite data

description: microsatellite genotype of 26 Laodelphax striatellus populations sampled in China
DOI: 10.5061/dryad.66jr2/2
title: Data matrix of concatenated partial COI and COII sequences from  1323 individuals

description: Concatenated partial COI and COII sequences of 26 laodelphax striatellus populations sampled in China.
DOI: 10.5061/dryad.66jr2/3
title: 107 haplotype sequences of concatenated partial COI and COII sequences from 1323 individuals
DOI: 10.5061/dryad.66jr2/4
title: GPS values

description: GPS values of the sampling locations
DOI: 10.5061/dryad.6cp0f00/1
title: Landmark data for pectoral fin integration and modularity

description: R data file containing list of unaligned landmarks of teleost pectoral fin skeleton, definition of sliding semi-landmarks, partition assignment, and taxonomic information.
DOI: 10.5061/dryad.6cp0f00/2
title: R code for pectoral fin integration and modularity

description: R script for running disparity, integration, modularity, evolutionary rate, and evolutionary trajectory comparison between non-acanthomorph and acanthomorph teleosts.
DOI: 10.5061/dryad.8k1c2p1/1
title: Genotypic data used for GAPIT analysis

description: This file contains the genotypic data used for the GAPIT genome wide association analysis.
DOI: 10.5061/dryad.8k1c2p1/2
title: GAPIT trait score for the core 120 Japonica MAGIC lines

description: For each or the Japonica MAGIC lines in the core set of 120 lines, these are the reactions to BB inoculation
DOI: 10.5061/dryad.8k1c2p1/3
title: Genotypic data for the F2 mapping population

description: These are the genotypic data for the F2 mapping population
DOI: 10.5061/dryad.8k1c2p1/4
title: Phenotypic data for the F2 population

description: This file contains the phenotypic data (lesion length after inoculation) of the F2 populations used for Composite Interval Mapping analysis
DOI: 10.5061/dryad.966ff04/1
title: all_MG_food_data

description: C & N stable isotope data of squirrel diet items, Mount Graham, AZ
DOI: 10.5061/dryad.966ff04/2
title: nonMG_redsquirrel_data

description: C & N stable isotope data of red squirrel, San Francisco Peaks and White Mountains, AZ
DOI: 10.5061/dryad.966ff04/3
title: nonMG_Abert_data

description: C & N stable isotope data of Abert's squirrels, San Francisco Peaks and White Mountains, AZ
DOI: 10.5061/dryad.966ff04/4
title: MG_Aberts_data

description: C & N stable isotope data of Abert's squirrels, Mount Graham, AZ
DOI: 10.5061/dryad.966ff04/5
title: MGRS_data

description: C & N stable isotope data of Mount Graham red squirrels, Mount Graham, AZ
DOI: 10.5061/dryad.9pc7458/1
title: Single molecule tracking data and code of Raccaud et. al

description: The file contains single molecule tracks and Hoechst areas of nine transcription factors and the code to analyse lifetimes and pseudo-on-rates.
DOI: 10.5061/dryad.9sv4q00/5
title: Raw data used to produce 5p logistic curve for 1996
DOI: 10.5061/dryad.9sv4q00/6
title: Raw data used to produce 5p logistic curve for 2001
DOI: 10.5061/dryad.9sv4q00/7
title: Raw data used to produce 5p logistic curve for 2016
DOI: 10.5061/dryad.dv15kp5.1
title: Data from: Phylogenetic analysis of the genus Retrotapes del Río, 1997 (Bivalvia: Veneridae) and systematic analysis of its taxa from Chile
DOI: 10.5061/dryad.dv15kp5.1/1.1
title: Supplementary Data Set 1

description: List of the reviewed materials.
DOI: 10.5061/dryad.dv15kp5.1/2.1
title: Supplementary Data Set 2

description: List of several taxa used for comparison and performed the phylogenetic analysis.
DOI: 10.5061/dryad.gc06qt7/1
title: playback_data_summaryCSV_clean

description: behavioral data associated with playback trials.
DOI: 10.5061/dryad.gc2k9r9/5
title: Input files and the results of the phylogenomic analysis

description: Following the all-versus-all blast using mpiBLAST 1.6.0 with default parameters, we identified gene families using the Markov clustering algorithm MCL 14-137 with an inflation parameter of 2.0. We performed multiple sequence alignment using PRANK 140603. Ambiguously aligned regions were removed from the alignments using Gblocks 091b with the settings -p=yes -b2=26 -b3=10 -b4=5 -b5=h -t=p -e=.gbl. we screened for gene families that contains a single representative gene of each species, or ones that contained inparalogs but no deep paralogs. Deep paralogs were identified following Nagy et al. Gene trees were inferred using the PTHREADS version of RAxML 8.1.2 using the PROTGAMMAWAG model and the standard algorithm. A single inparalog, closest to the root based on root-to-tip patristic distances was retained for each species. Gene families in which &gt;=75% of the species were represented were concatenated into a supermatrix. We used RAxML 8.1.2 to perform ML analysis and bootstrapping on the concatenated dataset, under a WAG model with gamma-distributed rate heterogeneity partitioned by input gene. We ran 100 bootstrap replicates using the rapid hill climbing algorithm. The robustness of the dataset was tested by eliminating incrementally higher numbers of fast-evolving sites using six levels of stringency in Gblocks 091b. Using these parameters, we eliminated 8.5% (-b1=78 -b2=78 -b3=10 -b4=10), 24.3% (-b1=78 -b2=78 -b3=8 -b4=15), 36.7% (-b1=88 -b2=88 -b3=8 -b4=15), 46.4% (-b1=95 -b2=95 -b3=8 -b4=15), 50.1% (-b1=100 -b2=100 -b3=8 -b4=15) and 55.2% (-b2=104 -b3=5 -b4=20) of the least reliably aligned regions of the alignments, resulting in trimmed concatenated datasets with 129.886, 107.496, 89.732, 76.153, 70.862 and 63.309 amino acid sites, respectively. We performed ML phylogenetic inference for each of the reduced datasets in RAxML as described above.
The following files were included. RAxML_Genomic_Backbone_Alignment.phy: input alignment for the ML analysis. RAxML_Genomic_Backbone_Phylogeny.tre: ML tree with bootstrap values. MultipleAlignment_GenomeTree_sensitivity_gbl_*_bip_SupplFig2_A-F.phy: six alignment for the sensitivity test. RAxML_GenomeTree_sensitivity_gbl_*_bip_SupplFig2_A-F.tre: six phylogeny, the results of the sensitivity test. These trees were depicted in the Supplement Figure 2 of the article.
DOI: 10.5061/dryad.gc2k9r9/6
title: Species names to track names across analysis

description: A three columned data matrix. Species_names_final column contains names occurring in the article. Alignment_names column contains species names found in in the alignment of 5284 taxa dataset. BayesTrait_names column contains species names used in BayesTraits analysis and BAMM analysis.
DOI: 10.5061/dryad.k3583p1/1
title: Gape-limitation

description: Data on relationships between total length (mm)/body depth (mm) and total length (mm)/gape size (mm) for both juvenile pike and adult sticklebacks.
DOI: 10.5061/dryad.k3583p1/2
title: Spatial variation in abundances

description: Data on the number of captured pike juveniles with (predation site) and without (no predation site) sticklebacks present. Data were sampled in 2014 and represent four populations of anadromous pike.
DOI: 10.5061/dryad.k3583p1/3
title: Spatial variation in size distribution

description: Data on the size distribution (total length mm) of captured pike juveniles with (predation site) and without (no predation site) sticklebacks present. Data sampled in 2014 and represent 4 populations.
DOI: 10.5061/dryad.k3583p1/4
title: Temporal variation in abundances

description: Data on the number of captured pike juveniles with (predation site) and without (no predation site) sticklebacks present. Data sampled in one popualtion (pop O) across 5 years (2007-2009, 2013-2014)
DOI: 10.5061/dryad.m04r4b5/1
title: Microsatellite data for 24 Ephippiger diurnus populations
DOI: 10.5061/dryad.nm1189t.2
title: Data from: Mapping a systematic ribozyme fitness landscape reveals a frustrated evolutionary network for self-aminoacylating RNA
DOI: 10.5061/dryad.nm1189t.2/1.2
title: Correlation of Fitness Effects - script

description: Python script to calculate the correlation of fitness effects in a given ribozyme family.
DOI: 10.5061/dryad.nm1189t.2/2.2
title: Correlation of Fitness Effects - source file

description: Excel source file used as input for the script ActivityCorrelationGamma.py.
DOI: 10.5061/dryad.nm1189t.2/3.2
title: k-seq Analysis - script

description: Python script to calculate catalytic kinetics for a population of sequences, using the k-Seq methodology.
DOI: 10.5061/dryad.nm1189t.2/4.2
title: k-seq Analysis - example input files

description: Input files for k-seq Analysis: kseq_rounds is example-rounds.txt, normalization_list is example-normalization.txt, substrate_concs is example-subst-concs.txt, rounds_to_average is example-rnds-to-avg.txt and rounds_to_error is example-rnds-to-err.txt.
DOI: 10.5061/dryad.q5n39p4.1
title: Data from: PER-SIMPER - a new tool for inferring community assembly processes from taxon occurrences
DOI: 10.5061/dryad.q5n39p4.1/1.1
title: R PerSIMPER function

description: Based on a presence/absence matrix, this function allows the identification of the first-order process of assembly underlying a set of taxonomic assemblages. Its use should therefore be limited to the comparison of significantly distinct taxonomic sets. But at the same time connected enough to allow the potential dispersal of species between these different sets. The PER-SIMPER method distinguishes the main ecological assembly process (between species dispersal capacity and niche richness) at the origin of the observed taxonomic differences between two (or more) compared sets of assemblages. The PER-SIMPER method is associated with the calculation of the E index (the logarithm of the sum of squared deviations between empirical and simulated SIMPER profiles) to assist in distinguishing the result of PER-SIMPER analyses.
DOI: 10.5061/dryad.q5n39p4.1/2.1
title: Help notes PER-SIMPER

description: Help notes of the PER-SIMPER R function. R function included too.
DOI: 10.5061/dryad.q5n39p4.2/3.2
title: PerSIMPERgroups
DOI: 10.5061/dryad.q5n39p4.2/4.2
title: PerSIMPERmatrix
DOI: 10.5061/dryad.q6m40r0/1
title: count table

description: A four column (descriptors) x 478018 rows (records) data table of phytoplankton species specific counts. Column 1: sampleID [character] - unique ID code for each phytoplankton saample; Column 2: name [character] - valid taxonomic latin name of the taxon; Column 3: AphiaID [integer] - WORMS unique ID code for the taxon; Column 4: biomass [numeric] - biomass of the taxon in the particular sample (µg / L). The records are linked with the sample table by the sampleID code, and with the taxon table by the AphiaID code.
DOI: 10.5061/dryad.q6m40r0/2
title: sample table

description: A 7 columns (descriptors) x 15640 rows (samples) data table, containing the meta data about each phytoplankton sample used in the analysis. Column 1: sampleID - unique sample ID [characters], linking with the sampleID in the count table. Column 1: date [character] - date and year when the sample was taken; Column 3: basin [character] - sample location, either bs (the Baltic Sea) or chesa (the Chesapeake Bay); Column 4: lon [numeric] - longitude coordinate (degrees); Column 5: lat [character] - latitude coordinate (degrees); Column 6: Temp [numeric] - water temperature (°C) of the sample; Column 7: Salin [numeric] - salinity of the sample
DOI: 10.5061/dryad.q6m40r0/3
title: taxon table

description: 1384 rows (taxa) x  24 columns (descriptors). Column 1: AphiaID [integer] unique ID code for each taxon, linking with the AphiaID of the count table. Column 2: name [character] - name of the taxon, corresponding to the AphiaID in the WORMS database and linking with the name in the count table; Columns 3 - 23 [character] names of the respective taxonomic ranks of the respective taxon; Column 24: rank [character] - the lowest rank of identification of the taxon
DOI: 10.5061/dryad.q8kh0p9/1
title: Sato et al_JApplEcol_surrogate-workshop-data

description: This data file includes two xls spreadsheets with the workshop data for Figure 1 and Table S1 of Sato,CF et al. The use and utility of surrogates in biodiversity monitoring programmes.
DOI: 10.5061/dryad.t2m0hg0/1
title: Individual sample information

description: Data file includes information on sample ID, sex, age, date collected, geographic locality, morphological measurements, genomic hybrid index, and species identification.
DOI: 10.17632/7btwptx393.1
title: Data for: DETERMINANTS OF TRANSPARENCY IN HONDURAN MUNICIPALITIES

description: FINANCIAL TRANSPARENCY IN HONDURAN MUNICIPALITIES
DOI: 10.17632/hfd4b8zfw6.2
title: Data for: Empirical forward price distribution from Bitcoin option prices

description: Data from Deribit exchange snapped at 5-minutes intervals from 9 to 18 dec 2018. Format is json. Contains option and futures data. USD Libor data is included but not used in the report.
DOI: 10.17632/jwkpw42pn9.1
title: Data for: 3356520
DOI: 10.17632/rzf9xgzkrr.1
title: Data for: 3314856
DOI: 10.17632/s8h8g968xy.1
title: Data for: Petrological and geochemical evidence for the formation of organic-rich siliceous rocks of the late Permian Dalong Formation, lower Yangtze region, southern China

description: Geochemical data for siliceous rocks of the Dalong Formation within the lower Yangtze region, southeastern China. Abbreviations: CC, Caicun section; CQ, Changqiao section; NS, Niushan section.
DOI: 10.17632/xwcd87zyx5.1
title: Data for: Forest resources conservation in the protected areas through co-management: Analyzing multi-temporal satellite imagery and stakeholders’ perceptions

description: The data file has two sheets: (1) Perception data and (2) GIS data related to the study sites.
DOI: 10.5061/dryad.1c9g5mm.1/14.1
title: min10.nex

description: Concatenated nexus alignment for the dataset containing minimum 10 samples per locus. See "params_Darter_m10.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.1/15.1
title: min20.nex

description: Concatenated nexus alignment for the dataset containing minimum 20 samples per locus. See "params_Darter_m20.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.1/16.1
title: min30.nex

description: Concatenated nexus alignment for the dataset containing minimum 30 samples per locus. See "params_Darter_m30.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1c9g5mm.1/17.1
title: params_Darter_m4_RAxML

description: Pyrad parameter file for minimum 4 samples per locus assembly.
DOI: 10.5061/dryad.1c9g5mm.1/20.1
title: params_Darter_m30_RAxML

description: Pyrad parameter file for minimum 30 samples per locus assembly.
DOI: 10.5061/dryad.1c9g5mm.1/21.1
title: Figure A1

description: Figure A1. Species trees inferred by tetrad, with bootstrap support values = 100% unless indicated. Nodes with less than 50% boostrap support have been collapsed. White nodes represent topological conflicts between the tetrad min4 tree and min30 tree. Gray nodes represent topological conflicts between either of the tetrad trees and the RAxML tree (Fig. 1). Black nodes represent topological conflicts between the tetrad min4 tree and m30 tree plus conflict between either of the tetrad trees and the concatenated RAxML tree.
DOI: 10.5061/dryad.1c9g5mm.1/23.1
title: Figure A3

description: Figure A3. Primary concordance tree. Species sampled for each clade are indicated below the clade names. Nodes are labeled with concordance factors, 95% CI in parentheses. Dotted lines indicate conflicting topologies with concordance factor 95% CIs that overlap with the concordance factor 95% CI of a bipartition in the primary concordance tree.
DOI: 10.5061/dryad.1c9g5mm.1/27.1
title: Table A5

description: Table A5. Results of the first set of D-statistic tests, grouped by P2 taxa + P3 clade. Proportion of D-statistic tests significantly different from 0 after adjusting for multiple comparisons (alpha = 0.05).
DOI: 10.5061/dryad.1c9g5mm.1/9.1
title: min4.phy

description: Concatenated phylip alignment for the dataset containing minimum 4 samples per locus. See "params_Darter_m4.txt" for more information on assembly parameters.
DOI: 10.5061/dryad.1vm20t6/1
title: NanSound_Ecol&Evol