cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh3302704.08fu
title: SH3302704.08FU

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/sh3302705.08fu
title: SH3302705.08FU

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/sh3302706.08fu
title: SH3302706.08FU

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/sh3302707.08fu
title: SH3302707.08FU

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/sh3302708.08fu
title: SH3302708.08FU

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/sh3302709.08fu
title: SH3302709.08FU

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/sh3302710.08fu
title: SH3302710.08FU

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/sh3302711.08fu
title: SH3302711.08FU

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/sh3302712.08fu
title: SH3302712.08FU

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/sh3302713.08fu
title: SH3302713.08FU

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.5q1j0/1
title: C4C Anonymised Data

description: The data is derived form the paper forms completed for each patient within the study. The file contains expansions for each of the codes. for any further information please contact the lead author.
DOI: 10.5061/dryad.6343j/1
title: recomb8.f90: Fortran 90 Code for Main Recursion-Equation Model

description: Fortran 90 code used for the simulations reported in Figures 1-7. Compilation of this code requires the Intel Math Kernel Library Vector Statistical Library.
DOI: 10.5061/dryad.6343j/2
title: recomb_individ2.1.f90: Fortran 90 Code for Individual-Based Model

description: Fortran 90 code used for simulations in Figure 8 and used to verify the recursion-equation model (Table S1).
DOI: 10.5061/dryad.6343j/3
title: recomb2omp3.f90: Fortran 90 Code Used to Calculate Probability of Fixation of Recombination Allele

description: Fortran 90 code used for simulations in Table S5. Compilation of this code requires the Intel Math Kernel Library Vector Statistical Library and an OpenMP library.
DOI: 10.5061/dryad.63m03/3
title: MHCsequences

description: Nucleotide sequences pertaining to 31 MHC I alleles and 5 MHC II alleles used to derive measures in E. stokesii mate choice tests.
DOI: 10.5061/dryad.63m03/4
title: PairData

description: Data used in GLMM analyses for E. stokesii mate choice tests.
DOI: 10.5061/dryad.67qq8/1
title: Concatenated

description: The file “Concatenated.phy” is a concatenated alignment including the genes rbcL and atpF and the non-coding atpF-A and atpA-trnR spacers. It has 37 samples and is 3130 base pairs in length. The taxa are listed as Genus_specificepithet_OTU, where the OTU is the sample number when more than one accession of a species was included in the analysis.

rbcL = 1-1308 bp;
atpF = 1309-1428;
atpF-A spacer = 1429-1510;
atpA = 1511-3025;
atpA-trnR spacer = 3026-3130

The data blocks used in the analyses:
[data_blocks]
rbcL_pos1 = 1-1308\3;
rbcL_pos2 = 2-1308\3;
rbcL_pos3 = 3-1308\3;
atpF_pos1 = 1309-1428\3;
atpF_pos2 = 1310-1428\3;
atpF_pos3 = 1311-1428\3;
atpF-A_spacer     = 1429-1510;
atpA = 1511-3025;
atpA-trnR_spacer = 3026-3130;
 

The “-“ symbols in the middle of the sequence for Adiantopsis_perfasciculata and Adiantopsis_parvisegmenta indicate missing data.
DOI: 10.5061/dryad.8565n/1
title: Field data

description: data for field experiment
DOI: 10.5061/dryad.8565n/2
title: Enclosure data

description: data for enclosure experiment
DOI: 10.5061/dryad.96p8p/1
title: Mannose 10 seconds

description: Force-distance curves at 10 sec contact time between an Acanthamoeba castellanii trophozoite and a mannose-coated cantilever.
DOI: 10.5061/dryad.96p8p/2
title: Mannose 0.5 seconds

description: Force-distance curves at 0.5 sec contact time between an Acanthamoeba castellanii trophozoite and a mannose-coated cantilever.
DOI: 10.5061/dryad.96p8p/3
title: Mannose 5 seconds mannoseblock

description: Force-distance curves at 5 sec contact time between an Acanthamoeba castellanii trophozoite and a mannose-coated cantilever in a mannose containing medium.
DOI: 10.5061/dryad.96p8p/4
title: Mannose 5 seconds

description: Force-distance curves at 5 sec contact time between an Acanthamoeba castellanii trophozoite and a mannose-coated cantilever.
DOI: 10.5061/dryad.ds4gd/14
title: GlobalShellMineralogy

description: Plot of percent occurrences by shell mineralogy.
DOI: 10.5061/dryad.ds4gd/15
title: SOM Table 1

description: Supplementary table of Spearman’s rank correlation tests of changes in tiering by taxonomic groups over time during the Jurassic in Europe.
DOI: 10.5061/dryad.f1b82/1
title: dataset_switchgrass

description: Contains data on switchgrass yield, nitrous oxide and methane flux, nitrate leaching, soil inorganic nitrogen content, and soil gravimetric water content for the first three harvest years (2009-2011) plus soil carbon content and soil bulk density at various times over the study period.
DOI: 10.5061/dryad.f65h2/2
title: GUD_foraging_data

description: GUD foraging data. File is a comma delimited csv. Response variable is "diff.gud", which is described in the article. Contact joeceradini@gmail.com for additional details.
DOI: 10.5061/dryad.f65h2/3
title: PEMA_HabitatSelection_data

description: Used-available data for deer mouse habitat selection analysis at two spatial scales. Response variable is "used", strata = TrackID and cluster = site. Data were analyzed with the clogit function in the survival package in R. Please contact joeceradini@gmail.com for additional details on covariate columns, such as which apply to which spatial scale.
DOI: 10.5061/dryad.f66g0/3
title: Killeen_data_fig3

description: Data for assay 3: column 1= temperature block; column 2=assay temperature; column 3= treatment origin; column 4=selection line identity; column 5=growth rate
DOI: 10.5061/dryad.g23n4/1
title: Supplement data
DOI: 10.5061/dryad.g92d1/1
title: Data for analysis of personality in the Seychelles warbler

description: Each sheet contains the data for each personality trait.
DOI: 10.5061/dryad.gd217/1
title: Mesopredator trait and eelgrass data from three sites in Washington State

description: This file includes raw count and length data for individual mesopredators collected in the field at three sites in Washington State, across three habitat types in three subsites per site.  Except at the first subsite, ten individuals of each species were measured out of the total number counted.  The file also includes functional traits assigned to each species observed in seine samples, using information freely available at FishBase and other sources detailed in the manuscript and supplementary material.  Functional groups based on Gower distances were calculated using the FD package in R, and are also included here.  Finally, we include data on eelgrass morphology including shoot density, biomass, leaf length, sheath length, and sheath width, as well as epiphyte load, measured in 10 0.25m^2 quadrats in eelgrass and edge habitat at each subsite.
DOI: 10.5061/dryad.k1mc5/1
title: Herbivory and plant growth of exotic Lythrum salicaria with differing history of biocontrol exposure

description: Data from greenhouse experiment with exotic populations (18) of Lythrum salicaria (8 genotypes per population), differing in their history of exposure to biocontrol (naïve, recent, release), and subjected to feeding damage(control, herbivory) by specialist biocontrol beetle, Neogalerucella calmariensis. Measured variables: plant height prior to experimental treatment (initialsize); % larval defoliation (larvaldefol); % combined larval and adult defoliation (finaldefol); above-ground biomass at harvest (biomass); number of lateral shoots (latshoots); sum of lengths of shoots regrowing after harvest (regrowshoots). Rack refers to physical units holding randomized groups of replicates ("conetainers" with individual plants).
DOI: 10.5061/dryad.k1r87/1
title: Selection Gradients in the Wild

description: These data compose the information used to generate the empirical patterns shown in the paper. This was done by reclassifying the fitness measures used in the selection gradients collected by Kingsolver et al 2011, and Siepielski et al 2013. Columns have been added to the data for this paper have been indicated in the README file. For original data, consult: [Kingsolver, J., and S. Diamond. 2011. Data from: Phenotypic selection in natural populations: what limits directional selection? Dryad Digit. Repos. doi:10.5061/dryad.7996.] and [Siepielski, A. M., K. M. Gotanda, M. B. Morrissey, S. E. Diamond, J. D. DiBattista, and S. M. Carlson. 2013. The spatial patterns of directional phenotypic selection. Ecol. Lett. 16:1382–92.]
DOI: 10.5061/dryad.mn338/1
title: extracted contigs

description: Fasta files containing the extracted, parasite-derived contigs. Contigs from each Assembly are stored in a separate file.
DOI: 10.5061/dryad.mn338/2
title: predicted amino acids

description: Fasta files containing the predicted amino acid sequences based on the extracted contigs. Sequences from each Assembly are stored in a separate file.
DOI: 10.5061/dryad.mn338/3
title: dataset 1 single genes

description: Fasta files containing the single gene amino acid alignments of dataset 1 prior to processing by Gblocks.
DOI: 10.5061/dryad.mn338/4
title: dataset 1 single genes after gblocks

description: Fasta files containing the single gene amino acid alignments of dataset 1 after processing by Gblocks.
DOI: 10.5061/dryad.n5h64/1
title: Animal tissue carbon and nitrogen content

description: Carbon and nitrogen content as % of dry mass for 391 macro-invertebrate individuals (four feeding types: detritivore, herbivore, omnivore, predator) sampled on the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012. Sites are coded as landscape-transformation system-replicate (two landscapes: Bukit Duabelas and Harapan; four transformation systems: Forest, Jungle rubber, Rubber, Oil palm). Sample.code is an object identifier.
DOI: 10.5061/dryad.n5h64/2
title: Leaf-litter tissue carbon and nitrogen content

description: Carbon and nitrogen content as % of dry mass for 169 leaf-litter specimen sampled on the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012. Sites are coded as landscape-transformation system-replicate (two landscapes: Bukit Duabelas and Harapan; four transformation systems: Forest, Jungle rubber, Rubber, Oil palm). Leaf.sample.code is an object identifier. Rubber.leaf and oilpalm.leaf identify specimens as being rubber or oil palm leaves (1) or not (0).
DOI: 10.5061/dryad.n5h64/3
title: Macro-invertebrate community data per site and feeding type

description: Animal community data for litter macro-invertebrates of four different feeding types (detritivore, herbivore, omnivore, predator) sampled on the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012. Sites are coded as landscape-transformation system-replicate (two landscapes: Bukit Duabelas and Harapan; four transformation systems: Forest, Jungle rubber, Rubber, Oil palm). Dens gives the density as number of individuals m-2, div is the number of morphospecies per core site, bmass is the fresh biomass in mg m-2 and metabolic.demand is the sum of the individual metabolic rates of all individuals found per area in W m-2. For further details on the animal sampling and calculation of metabolic rates see Barnes & Jochum et al., NatCommun, 2014 (doi:10.1038/ncomms6351).
DOI: 10.5061/dryad.n5h64/4
title: Data for main analyses and Figure 3

description: Processed data on leaf litter, detritivore (Det) and predator (Pre) communities sampled on the core sites of the EFForTS project (http://www.uni-goettingen.de/en/310995.html) in the Jambi Province on Sumatra, Indonesia in 2012, used to perform the main analyses and plot Figure 3. Sites are coded as landscape-transformation system-replicate (two landscapes: Bukit Duabelas and Harapan; four transformation systems: Forest, Jungle rubber, Rubber, Oil palm). CN is the unitless ratio of dry-mass carbon to dry-mass nitrogen for leaf litter (single measurements weighted after relative importance of specimens in the local leaf litter) and animal tissue (averaged over measured individuals) per core site. Litter.mass gives the dry litter mass per ground area in g cm-2. Dens gives the density as number of individuals m-2, div is the number of morphospecies per core site, biomass is the fresh biomass in mg m-2 and per-unit-biomass consumer feeding rates were calculated as W mg-1. Note that data are non-logged and non-normalized.
DOI: 10.5061/dryad.np757/1
title: Analysis code and data

description: Code (.Rmd) and data used for analyses.
DOI: 10.5061/dryad.q74p1/1
title: fsc2_runfiles

description: Input files for fastsimcoal2
DOI: 10.5061/dryad.q74p1/2
title: SNP_genotypes

description: Filter 1 SNP genotypes in vcf format
DOI: 10.5061/dryad.q77rs/1
title: alltraitcor

description: Phenotypic data of several life history and stress resistance traits in 3 drosophila species from two environmentally markedly different locations
DOI: 10.5061/dryad.s5935/1
title: Data from Walters et al Functional Ecology 2017