cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.11jp5/1
title: SNP file PoPoolation2 format

description: Within the Aha_09_11_18_19_21_31_N1_N3_N4v3_rc file you can find the 2,178,204 SNPs as well as some small insertions and deletions in in the format of PoPoolation2 (Kofler et al. 2011).
DOI: 10.5061/dryad.3jt35/1
title: SubgenIrisPlast Dataset

description: SubgenIrisPlast is an aligned dataset of seven plastid markers comprising almost 8,000 sequenced bp for 87 Iris taxa. Seventy-one taxa, representing each of the six sections and about 80% of the recognized species in subgenus Iris, and 11 outgroup taxa were included in the study. Also included were five Asian species that share some morphological characteristics with subgenus Iris but are typically considered in other subgenera. This dataset is utilized in the publication: Wilson, C. 2017. Sectional relationships in the Eurasian bearded Iris (subgen. Iris) based on phylogenetic analyses of sequence data. Syst. Bot.
DOI: 10.5061/dryad.3qm6v/1
title: LecideaceaeMcCuneEtAl2017-ITS

description: DNA sequence data, ITS, alignment.
DOI: 10.5061/dryad.3qm6v/2
title: LecideaceaeMcCuneEtAl2017-nuLSU

description: DNA sequence data, nuLSU, alignment
DOI: 10.5061/dryad.3t423/10
title: Stacey (restrictus, conicus, vitricola clades)
DOI: 10.5061/dryad.3t423/11
title: starBEAST
DOI: 10.5061/dryad.3t423/4
title: RNA polymerase beta alignmnent of sect. Restricti
DOI: 10.5061/dryad.3t423/5
title: concatenated alignmnent of sect. Restricti
DOI: 10.5061/dryad.3t423/6
title: concatenated alignmnent of subg. Aspergillus
DOI: 10.5061/dryad.3t423/7
title: partitioned analysis of sect. Restricti tree
DOI: 10.5061/dryad.3t423/8
title: partitioned analysis of subg. Aspergillus tree
DOI: 10.5061/dryad.3t423/9
title: Stacey (penicillioides clade)
DOI: 10.5061/dryad.404rm/1
title: SNP_seq_data

description: Sequence data is in phylip format. Site ID name for each sample can be found the sampling site GPS coordinate file
DOI: 10.5061/dryad.404rm/2
title: Genotype_msats

description: Genotype data is in GeAlEx format. Site ID for each sample can be found in the sampling site GPS coordinate file.
DOI: 10.5061/dryad.404rm/3
title: Sampling site GPS coordinates
DOI: 10.5061/dryad.44894/1
title: Lourenco_etal_MolEcol_genotype_database

description: Dataset containing genotypes of 15 microsatellite loci genotyped in 16 populations of Salamandra salamandra in Oviedo.
DOI: 10.5061/dryad.44c0r/1
title: Data from Pimsler, Jackson, and Lozier. 2017. Population genomics reveals a candidate gene involved in bumble bee pigmentation. Ecology and Evolution.

description: ZIP file containing folders of input and output files for SNP data, outlier analyses, and confirmation re-sequencing alignments.
DOI: 10.5061/dryad.63m03/1
title: MHCgenotypes

description: Contains MHC I genotypes for 47 adult E. stokesii and MHC II genotypes for 46 adult E. stokesii, utilised in mate choice tests.
DOI: 10.5061/dryad.63m03/2
title: MICSATgenotypes

description: Microsatellite genotype data (six loci) for adult E. stokesii, utilised in mate choice tests.
DOI: 10.5061/dryad.65n35/1
title: Experiment 1 data
DOI: 10.5061/dryad.65n35/2
title: Experiment 2 data
DOI: 10.5061/dryad.7kc09/1
title: Aikens_etal_2017_Data

description: This zip folder contains three data files, please see README.pdf and the associated publication for more information.
DOI: 10.5061/dryad.dc863/6
title: VegClass

description: VegClass is an ArcMap version 10.4.1 shapefile of polygon-features (SpatialPolygonsDataFramein R) with four attributes giving the “Subarea” of the study area, the area in ha (“area_ha”) of the polygon-feature, the functional class of the polygon in 1972 (“Veg1972”), and the functional class of the polygon in 2012 (“Veg2012”). Projection is UTM zone6 with datum of WGS84. Please see VegClass_README.rtf for further details.
DOI: 10.5061/dryad.ds4gd/10
title: Globalrandomization

description: Text file of R script to perform a 10,000 randomization permutation shuffling time bins of global occurrences.
DOI: 10.5061/dryad.ds4gd/11
title: Europerandomization

description: Text file of R script to perform a 10,000 randomization permutation shuffling time bins of European occurrences.
DOI: 10.5061/dryad.ds4gd/12
title: RegionalShuffle

description: Text file of R script to perform a 10,000 randomization permutation shuffling occurrences by regions.
DOI: 10.5061/dryad.ds4gd/13
title: ShellMineralogy

description: Text file of R script to calculate the percent occurrences by shell mineralogy.
DOI: 10.5061/dryad.ds4gd/5
title: percentConfidenceInterval

description: R function to calculate confidence intervals on percentages based on David Raup's method.
DOI: 10.5061/dryad.ds4gd/6
title: percentEcolTrait

description: R function used to calculate the percent ecologic traits.
DOI: 10.5061/dryad.ds4gd/7
title: Regional Occurrence Percentages

description: Text file with R script that calculates the percent occurrences of individual ecological traits in each region.
DOI: 10.5061/dryad.ds4gd/8
title: Global Occurrence Percentages

description: Text file of R script used calculate the global percent occurrence of individual ecological traits.
DOI: 10.5061/dryad.ds4gd/9
title: Europe Environments Occurrence Percentages

description: Text file of R script used to calculate percent occurrences of individual ecological traits by European depositional environment.
DOI: 10.5061/dryad.f65h2/1
title: PEMA_MarkRecap_Survival

description: Mark-recapture data used to estimate deer mouse apparent survival using a Huggins robust design model. The file is a tab delimited text file. The data are set up to be analyzed in RMark (R interface for program MARK). The capture histories have 2 dummy occasions, 9 and 10, that were necessary for processing the data as robust design with RMark. Those occasions, and the dummy survival interval, were all fixed to zero so they did not affect estimates. Please contact joeceradini@gmail.com for additional details.
DOI: 10.5061/dryad.f66g0/1
title: Killeen_fig1

description: Data for figure 1. Column 1=treatment; column 2=temperature; column 3=day of experiment; column 4=proportion of populations alive
DOI: 10.5061/dryad.f66g0/2
title: Killeen_data_fig2

description: column 1=Assay; column 2=treatment origin; column 3=assay temperature; column 4=selection line identity; column 5=growth rate
DOI: 10.5061/dryad.hj1p1/19
title: Figure S16

description: FIG. S16. Ancestral state reconstruction for the character: “Appendages long (mm)”, on the phylogenetic hypothesis based on psbA-trnH. Circles denote the state and circles in the nodes show the proportional likelihood visually.
DOI: 10.5061/dryad.hj1p1/20
title: Figure S17

description: FIG. S17. Ancestral state reconstruction for the character: “Appendages long (mm)”, on the phylogenetic hypothesis based on ITS. Circles denote the state and circles in the nodes show the proportional likelihood visually.
DOI: 10.5061/dryad.hj1p1/21
title: Figure S18

description: FIG. S18. Ancestral state reconstruction for the character: “Relation between the width of the appendage and width of the gland”, on the phylogenetic hypothesis based on psbA-trnH. Circles denote the state and circles in the nodes show the proportional likelihood visually.
DOI: 10.5061/dryad.hj1p1/22
title: Figure S19

description: FIG. S19. Ancestral state reconstruction for the character: “Relation between the width of the appendage and width of the gland”, on the phylogenetic hypothesis based on ITS. Circles denote the state and circles in the nodes show the proportional likelihood visually.
DOI: 10.5061/dryad.hj1p1/23
title: Figure S20

description: FIG. S20. Ancestral state reconstruction for the character: “Sonoran biome and adjacent areas”, on the phylogenetic hypothesis based on psbA-trnH. Circles denote the state and circles in the nodes show the proportional likelihood visually.
DOI: 10.5061/dryad.hj1p1/24
title: Figure S21

description: FIG. S21. Ancestral state reconstruction for the character: “Sonoran biome and adjacent areas”, on the phylogenetic hypothesis based on ITS. Circles denote the state and circles in the nodes show the proportional likelihood visually.
DOI: 10.5061/dryad.hk16k/1
title: R script for creating isocapes and probabilistic maps of salmon otolith values
DOI: 10.5061/dryad.jq6t1/1
title: PointLocalityRecords

description: The point localities where each species was observed is provided in a separate comma separated value (csv) file. The 3 columns of the file are (1) an abbreviated species name, (2) longitude of observation, (3) latitude of observation.
DOI: 10.5061/dryad.kt364/1
title: Nuclear genotypes at 10 microsatellite loci and additional information regarding the larvae sampled

description: nuclear data (10 microsatellites) of Baetis alpinus larvae sampled on several dates/assigned to different cohorts in two basins of the Swiss Alps (Val Roseg and Lötschental).
DOI: 10.5061/dryad.kt364/2
title: life history data

description: Larval size measurements of Baetis alpinus species group individuals collected in Roseg and Lötschental (2012 and 2013)
DOI: 10.5061/dryad.kt364/3
title: Stream temperature data

description: Tributary (hourly logged) and glacial main-stream (predicted from hydrological station) temperature estimates at Val Roseg and Lötschental sites
DOI: 10.5061/dryad.kt364/4
title: Periphyton biomass estimates

description: Periphyton biomass estimates in Val Roseg and Lötschental (2013)
DOI: 10.5061/dryad.kt364/5
title: Water Chemistry, conductivity and monthly mean temperatures

description: Water Chemistry, conductivity and monthly mean temperatures in Val Roseg and Lötschental (mostly 2013)
DOI: 10.5061/dryad.mf886/1
title: Species abundance data for predators and decomposers/primary consumers

description: Species abundance data for both predators (first tab, 60 species) and decomposers/primary consumers (second tab, 73 species). Site information (time since logging) is located in the last column for each data set. See Appendix S2E for corresponding trait data and for phylogenetic relationships.
DOI: 10.5061/dryad.nq67q/16
title: Genomic differentiation between sympatric Timema populations and species (part 06 of 09)

description: This is the seventh part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.
DOI: 10.5061/dryad.nq67q/17
title: Genomic differentiation between sympatric Timema populations and species (part 07 of 09)

description: This is the eighth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.
DOI: 10.5061/dryad.nq67q/18
title: Genomic differentiation between sympatric Timema populations and species (part 08 of 09)

description: This is the ninth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.
DOI: 10.5061/dryad.nq67q/19
title: Genomic differentiation between sympatric Timema populations and species (part 09 of 09)

description: This is the tenth part of a 10 part split file. To extract contents, download all parts and concatenate. Resultant file wgs_speciation_continuum.tar.bz2 (md5sum 5ed0d1765fc6a527fe1dc82daf7b208a). For further details, please see the associated README file.
DOI: 10.5061/dryad.nq67q/7
title: Genotyping-by-sequencing (GBS) and stages of speciation
DOI: 10.5061/dryad.nq67q/8
title: Phylogenetic inference and molecular dating
DOI: 10.5061/dryad.nq67q/9
title: Evolution of reproductive isolation and phenotypic differentiation through time
DOI: 10.5061/dryad.vd127/1
title: Microsatellite Data
DOI: 10.5061/dryad.01f10/1
title: R code

description: The R code for reproducing the statistical analyses and figures in the paper. The data are available in the 'SuppInfo_TablesS1-S6.xlsx' file and the R script reads from this file. Alternatively, the data are also available in .csv format.
DOI: 10.5061/dryad.01f10/2
title: Figure S1-S3

description: Figure S1 Richness of fungal OTUs at different clustering dissimilarity cut-offs.
Figure S2 Fungal OTUs significantly affected by cropping system.
Figure S3 Comparison of potential pathogens between cropping systems.
DOI: 10.5061/dryad.01f10/3
title: Table S1-S6 (xlsx)

description: Table S1 Sample identifying barcodes.
Table S2 Species identification for fungal operational taxonomic units (OTUs).
Table S3 Characteristics of organically and conventionally managed wheat fields (explanatory variables).
Table S4 OTU table. Abundance of fungal OTUs (no. of ITS copies/ng wheat DNA) across 22 wheat fields.
Table S5 Real-time PCR data per extraction replicate.
Table S6 OTU table. Read counts per extraction replicate.
DOI: 10.5061/dryad.01f10/4
title: Table S1-S6 (csv)

description: Supplementary data files in csv format.
DOI: 10.5061/dryad.231b9/1
title: Data from: Ecological speciation by temporal isolation in a population of the stonefly Leuctra hippopus (Plecoptera, Leuctridae)

description: Data from the paper "Ecological speciation by temporal isolation in a population of the stonefly Leuctra hippopus (Plecoptera, Leuctridae)", by Boumans, Hogner, Brittain & Johnsen. Ecology and Evolution: xxx. DOI: xxx.

Included are the following files:

Files used in the software program STRUCTURE, for different subsets of the data (see paper):
-AFLP_data.csv
-RAD matrix 1.csv
-RAD matrix 1a.csv
-RAD matrix 2.csv
-RAD matrix 2a.csv

Samples sorted by % missing data for the above four RAD matrices:
-Samples sorted by missing data.csv

Stacks sumstats output files for Matrix 1a and 2a:
-Stacks_sumstats_output_RAD_data_matrix 1a.csv
-Stacks_sumstats_output_RAD_data_matrix 2a.csv
DOI: 10.5061/dryad.3539k/1
title: ripr_analysis_code_annotated

description: The R code used for the analysis in the paper, including drawing the figures.
DOI: 10.5061/dryad.3539k/2
title: reviewer data from Molecular Ecology

description: This file contains the reviewer data for Molecular Ecology. The other data files called by the analysis code are from Petchey et al (2014), see http://dx.doi.org/10.5061/dryad.36r69
DOI: 10.5061/dryad.4g74f/1
title: Full data set

description: Empirical data set for river locations, predation level, group sizes, number of approaches by the focal individual, and which stimulus was first approached by the focal individual. Data are labelled accordingly.
DOI: 10.5061/dryad.5dk62/1
title: Cushman14Oct16Figure2rubraMorphData

description: Morphological data matrix for figure 2 and morphological analysis.
DOI: 10.5061/dryad.5dk62/2
title: Cushman14Oct16Figure3bartramianaMorphData

description: Morphological data matrix for A. bartramiana complex analysis and figure 3.
DOI: 10.5061/dryad.5dk62/3
title: Cushman14Oct16Figure5cusickiiMorphData

description: Morphological data matrix for the Amelanchier cusickii morphological analysis and figure 5.
DOI: 10.5061/dryad.5dk62/4
title: Cushman14Oct16Figure6ETSalignment

description: DNA sequence alignment for ETS region and Figure 6.
DOI: 10.15156/bio/sh081523.07fu
title: SH081523.07FU

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/sh081524.07fu
title: SH081524.07FU

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/sh081525.07fu
title: SH081525.07FU

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/sh081526.07fu
title: SH081526.07FU

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/sh081527.07fu
title: SH081527.07FU

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/sh081528.07fu
title: SH081528.07FU

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/sh081529.07fu
title: SH081529.07FU

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.