cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15156/bio/sh3292943.08fu
title: SH3292943.08FU

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/sh3292944.08fu
title: SH3292944.08FU

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/sh3292945.08fu
title: SH3292945.08FU

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.90nc6/3
title: Rout_MalesReachAdulthood_Final

description: Generalized linear mixed model (GLMM) to compare the probability that males reached adulthood in a breeding group (versus a non-breeding group or solitary).
DOI: 10.5061/dryad.9gp8g/1
title: "Globally" filtered SNPs

description: VCF file containing 6490 "globally filtered" SNPs for all Eucalyptus microcarpa samples
DOI: 10.5061/dryad.9gp8g/2
title: "Population-level" filtered SNPs

description: VCF file containing 13,113 "population-level filtered" SNPs for Eucalyptus microcarpa samples excluding outlier samples
DOI: 10.5061/dryad.9gp8g/3
title: Metadata for Eucalyptus microcarpa samples

description: Additional data regarding locations and samples belonging to each site
DOI: 10.5061/dryad.9gp8g/4
title: README file

description: README file for Eucalyptus microcarpa data
DOI: 10.5061/dryad.d6jk5.1
title: Data from: A new specimen of Agorophius pygmaeus (Agorophiidae, Odontoceti, Cetacea) from the Early Oligocene Ashley Formation of South Carolina, USA
DOI: 10.5061/dryad.d6jk5.2
title: Data from: A new specimen of Agorophius pygmaeus (Agorophiidae, Odontoceti, Cetacea) from the Early Oligocene Ashley Formation of South Carolina, USA
DOI: 10.5061/dryad.d6jk5.2/1.2
title: Godfrey et al Agorophius matrix

description: NEXUS format data file used for phylogenetic analysis.
DOI: 10.5061/dryad.d6jk5.2/2.2
title: Supplementary Data

description: Additional drawings, dinoflagellate data, and phylogenetic data
DOI: 10.5061/dryad.g703s/4
title: Hydrolight Calculation file

description: Matlab file containing Hydrolight runs for 480 nm using ac-9 casts from NASA's SeaBASS ocean optics database.
DOI: 10.5061/dryad.g9r36/26
title: Cissus rusingensis (paratype) µCT DTS video

description: Video of digital µCT tomograms in transverse section through a fossilized seed (a paratype) of Cissus rusingensis Adams, Collinson, S.Y. Smith & Bamford sp. nov. (KNM specimen R117.1981.476)
DOI: 10.5061/dryad.g9r36/27
title: Cissus psilata µCT DTS video

description: Video of digital µCT tomograms in transverse section through a fossilized seed (the holotype) of Cissus psilata Adams, Collinson, S.Y. Smith & Bamford sp. nov. (NHMUK specimen V68506)
DOI: 10.5061/dryad.hn0dt/1
title: Supplemental Material DeSantis et al: Assessing niche conservatism using a multi-proxy approach

description: Supplemental Materials including Supplemental Figure 1 and Supplemental Tables 1-4.
DOI: 10.5061/dryad.k5n4k/1
title: Fig1

description: Colony forming unit counts for strains competing in two-way competitions and corrected proportions accounting for the evolution of de novo cheats.
DOI: 10.5061/dryad.ks131/1
title: Bt eggplant in the Philippines Raw Data

description: The raw data was obtained from confined field trials of Bt and non-Bt eggplants in Pangasinan, Philippines from 2010 - 2012. The raw data is in MS Excel file with four sheets, namely: (1) Cry1Ac protein expression levels (parts per million dry weight, ppm DW) of different Bt eggplants plant parts for two trials; (2) Cry1Ac protein expression levels (ppm DW) in terminal leaves of Bt eggplants at different growth stages for two trials; (3) percent shoot damage of Bt and non-Bt eggplants for three trials; and, (4) percent fruit damage and larval count of Bt and non-Bt eggplants for three trials.
DOI: 10.5061/dryad.kv072/1
title: GalicianNightSkyBrightnessData_2015

description: Each data file, in txt format, corresponds to a measurement site and contains, in seven columns, the following raw data: Day, Month, Year, Hour, Minute, and Second (in UTC time), and the recorded sky bightness in mag/arcsec^2. An additional file ("Offsets.txt") contains the correction factors to relate the measurements of all sensors to the synthetic common reference sensor of the network.
DOI: 10.5061/dryad.mg529/1
title: Madliger Love_EAP 2016_Control Females

description: Baseline corticosterone (CORT), fitness, and other environmental and reproductive variables associated with control female tree swallows (2010-2012).
DOI: 10.5061/dryad.mk815/1
title: Environmental and similarity datasets

description: source data for linking parasite communities and environmental predictors (one spreadsheet) and list of pairwise similarity data (second spreadsheet)
DOI: 10.5061/dryad.t722h/1
title: PA_Wild_boar_ped

description: 91 Southern Balkan wild boar genotypes in 49508 SNPs in .ped format for PLINK
DOI: 10.5061/dryad.t722h/2
title: PA_Wild_boar_map

description: Information on the 49508 autosomal SNPs in .map file format corresponding to the genotypes in the PA_Wild_boar.ped file for use in PLINK software
DOI: 10.5061/dryad.t722h/3
title: PA_Wild_boar_SNP_structure

description: STRUCTURE file with 91 wild boar SNP genotypes from Southern Balkans
DOI: 10.5061/dryad.t722h/4
title: PA_Wild_boar_info_SNPs

description: Wild boar sample information corresponding to PA_Wild_boar_ped and PA_Wild_boar_SNP_structure
DOI: 10.5061/dryad.t722h/5
title: PA_Wild_boar_micros

description: 555 Southern Balkan wild boar microsatellite genotypes
DOI: 10.5061/dryad.t722h/6
title: PA_Wild_boar_micros_structure

description: STRUCTURE file of 555 Southern Balkan wild boar microsatellite genotypes
DOI: 10.5061/dryad.t722h/7
title: PA_Wild_boar_info_micros

description: Wild boar sample information corresponding to PA_Wild_boar_micros and PA_Wild_boar_micros_structure
DOI: 10.5061/dryad.t722h/8
title: README

description: Short explanation of file content
DOI: 10.17632/dywxyj9xyz.1
title: Filament Network Analysis Software 2.0

description: Filament Network Analysis Software 2.0 with sample data
DOI: 10.17632/fjyd3xvb6j.1
title: Supplemental Information on Kang et al 2016

description: The pdf file contains the equations that could be used to relate remotely sensed vegetation indices to LAI by crop type.
DOI: 10.17632/xycvj95pw9.1
title: Vimentin intermediate filaments template microtubule networks to enhance persistence in cell polarity and directed migration

description: Live cell imaging data for vimentin/microtubules interaction
DOI: 10.5061/dryad.0564q/1
title: Rscripts

description: R scripts and supplementary files for processing the BAMM analyses of the constant rate and diversity-dependent simulations. Please contact Jonathan S. Mitchell with questions about these files.
DOI: 10.5061/dryad.0564q/2
title: constantTrees

description: Constant-rate simulated phylogenies analyzed with two different versions of BAMM under many different model priors. Please contact Jonathan S Mitchell with questions about these files.
DOI: 10.5061/dryad.0564q/3
title: plosTrees1-100

description: First 100 trees from Dan Rabosky's original 2014 PlOS description of BAMM analyzed using three different priors. Please contact Jonathan S Mitchell with questions about these files.
DOI: 10.5061/dryad.0564q/4
title: plosTrees101-300

description: Simulated trees #101 to 300 from Dan Rabosky's original 2014 PLoS description of BAMM analyzed using three different priors. Please contact Jonathan S Mitchell with questions about these files.
DOI: 10.5061/dryad.15d8v/1
title: Materials and Methods and References

description: Materials and Methods and References
DOI: 10.5061/dryad.2435k/19
title: Dryad LOCAL Garrett Creek 2005-2007

description: Garrett Creek, Ottawa County, Oklahoma
DOI: 10.5061/dryad.2435k/20
title: Dryad LOCAL Glover River

description: Glover River, McCurtain County, Oklahoma
DOI: 10.5061/dryad.2435k/21
title: Dryad LOCAL Hauani Creek

description: Hauani Creek, Marshall County, Oklahoma
DOI: 10.5061/dryad.2435k/22
title: Dryad LOCAL Hickory Creek

description: Hickory Creek, Love County, Oklahoma
DOI: 10.5061/dryad.2435k/23
title: Dryad LOCAL Illinois R Lk Frances 2000-2010

description: Illinois River, northeast Oklahoma
DOI: 10.5061/dryad.2435k/24
title: Dryad LOCAL Little Elm Ck 2005-2007

description: Little Elm Creek, Ottawa County, Oklahoma
DOI: 10.5061/dryad.2435k/25
title: Dryad LOCAL Little Glasses Creek

description: Little Glasses Creek, Marshall County, Oklahoma
DOI: 10.5061/dryad.2435k/26
title: Dryad LOCAL Lukfata Slough

description: Lukfata Creek slough, along Hwy 3, McCurtain County, Oklahoma
DOI: 10.5061/dryad.2435k/27
title: Dryad LOCAL Morris Creek

description: Morris Creek, Leflore County, Oklahoma
DOI: 10.5061/dryad.4291s/1
title: Data File S1. Raw genetic interaction datasets - Pair-wise interaction format

description: This folder contains complete SGA genetic interaction data for the following:• A list of all query and array mutant strains represented in the genetic interactionnetwork along with their corresponding fitness estimates• Nonessential x Nonessential network (NxN)• Essential x Essential network (ExE)• Essential x Nonessential network (ExN)• Genetic interactions involving DAmP alleles of essential genes• Genetic interactions for HSP90 and corresponding controlsThe interaction datasets are provided in a tab-delimited format with 11 columns:• Query ORF• Query gene name40• Array ORF• Array gene name• Array Type (DMA or TSA) and Temperature (26oC or 30oC)• Genetic interaction score (ε)• P-value• Query single mutant fitness (SMF)• Array SMF• Double mutant fitness• Double mutant fitness standard deviation
DOI: 10.5061/dryad.4291s/10
title: Data File S10. Correlation analysis of query strain GI degree

description: As a complement to analysis of array strains (fig. S11-S12), GI degrees were calculated for query strains by counting negative interactions (tab 1, interactions with DMA strains; tab 2, interactions with TSA strains) and by counting positive interactions (tab 3, interactions with DMA strains; tab 4, interactions with TSA strains). Essential and nonessential queries were analyzed separately and results are labeled by grouped column headers. Wilcoxon rank-sum tests compared the GI degree in paired gene sets defined by absence and presence of each binary feature tested (top table). If the P-value is significant (&lt; 0.05), the “Test result” column describes the degree of the set of genes for which the listed binary feature is true (compared to the set for which the feature is false). Tests were not performed, indicated by “N/A”, if data were present for fewer than 50 strains; strains with missing data were excluded from the tests. Pearson’s correlation (column labeled “r”) was used to measure associations between GI degree and features that are continuous or counts (bottom table). Uncorrected P-values are shown. The features examined in this analysis are described above (see Methods section entitled, “ Genetic interaction degree and frequency analysis”). Given that analysis of different features required using different statistical tests and some features are not expected to be independent of each other, no multiple hypotheses correction procedures were used. We do note that 31 gene features were tested.
DOI: 10.5061/dryad.4291s/18
title: Data File S8. Mass spectrometric evidence for Ipa1 interactions

description: This file lists proteins identified with high confidence as specific physical interactors with strains expressing Ipa1-GFP from its endogenous locus or Ipa1-HA from a galactose-inducible plasmid.
DOI: 10.5061/dryad.4291s/2
title: Data File S2. Raw genetic interaction datasets - Matrix format

description: This file contains complete SGA genetic interaction data matrix for the following:• Nonessential x Nonessential network (NxN)• Essential x Essential network (ExE)• Combined essential and nonessential network (ExN)
DOI: 10.5061/dryad.4291s/3
title: Data File S3. Genetic interaction profile similarity matrices

description: Matrix files containing genetic interaction profile similarity values (as measured by Pearson correlation) for every pair of mutant strains in the dataset. Similarity values were computed for essential (ExE), non-essential (NxN) and the global similarity network derived from a combined set of all genetic interactions (ExE, NxN, ExN) as described above (see "Constructing genetic interaction profile similarity networks"). Each matrix contains 2 sets of row and column headers, providing a unique allele name for every mutant strain (row & column header #1) as well as a systematic ORF name (row & column header #2).
DOI: 10.5061/dryad.4291s/4
title: Data File S4. GO bioprocess functions predicted by the nonessential and essential similarity networks using a K-nearest neighbor approach

description: This file reports the performance of gene function prediction for non-essential or essential genes based on genetic interaction profiles. For both classes of genes (either nonessential or essential), the performance of a KNN classifier is reported as the Precision at 25% Recall based on interactions derived from TS queries (PR_TSQ) or nonessential deletion queries (PR25_SN). Although analyses were performed using complete genetic interaction profiles (e.g. negative and positive genetic interactions), similar prediction performance was obtained using genetic interaction profiles based on negative interactions alone.
DOI: 10.5061/dryad.4291s/5
title: Data File S5. SAFE analysis_Gene cluster identity and functional enrichments

description: This file lists the results from SAFE analysis of the global genetic profile similarity network (Fig. 1 and Fig. 2). Functional terms enriched within specific network clusters associated with GO biological processes (14) and/or protein complexes (Data File S12). A list of genes comprising each bioprocess-enriched cluster shown on the global similarity network is also provided. Functional terms enriched within specific network clusters associated with cell compartments (17, 119) are all shown on Fig. 2B.
DOI: 10.5061/dryad.4291s/6
title: Data File S6. Genetic profile similarity-based hierarchy analysis

description: The first tab (“Gene to hierarchy cluster mapping”) lists the clusters identified at each level of the genetic interaction-based hierarchy and the deletion and TS allele array mutants assigned to each cluster. Examples of clusters described in the main text are highlighted. The subsequent 9 tabs indicate enrichment of clusters resolved at the specified profile similarity range for specific cell compartments (Cyclops_enrich), biological processes (GO BP_enrich), protein complexes (complex_enrich) and KEGG pathways (KEGG_enrich). The final tab in the file indicates the clusters used to map the functional distribution of negative and positive interactions shown in Fig. 5D.
DOI: 10.5061/dryad.4291s/7
title: Data File S7. Pleiotropic gene analysis

description: This file lists nonessential and essential query genes associated with high confidence pleiotropy scores based on their genetic interactions derived from the TSA (Essential derived pleiotropy) and DMA (Nonessential derived pleiotropy). The file also contains a second list of nonessential and essential query genes that participate in many genetic interactions but exhibited low pleiotropy scores indicating that these genes are more functionally specific.
DOI: 10.5061/dryad.4291s/9
title: Data File S9. High and low interaction degree genes

description: This file lists the negative and positive interaction degree associated with every nonessential deletion (sn#), essential TS (tsq#), and DAmP (damp#) query mutant strain screened against the DMA (“query degree X DMA” tab) and/or TSA (“query degree X TSA” tab). A subset of strains were found to carry a second, spontaneous suppressor mutation that affected fitness of the query mutant strain. Strains carrying a suppressor mutation mapped through SGA analysis are indicated (“-supp”). Query mutants comprising the 20% highest and lowest degree groups of strains are indicated. Furthermore, a “Co-batch signal” rank is provided for every query (see “Co-batch filtering of query mutant strains”). Low ranks correspond to evidence for lingering batch effects. Another column, “ Gene with correlated GI profiles that are co-annotated with the query gene (%)", provides the percent of correlated gene pairs that are co-annotated to the particular query. A low negative interaction degree (e.g. 20% lowest negative interaction degree) coupled with a low co-batch rank (e.g. &lt; ~0.2) and a low fraction of correlated pairs that share a similar functional annotation with a given query strain (e.g. &lt; ~0.15) may be indicative of a low confidence screen. However, these criteria should be considered as loose indicators and not definitive metrics of screen quality and thus, should not be used as strict filters on the global interaction dataset. Another list (“Queries removed - batch effects” tab) indicates ~300 query strains that exhibited severe systematic batch effects and thus were removed from the indicated data set. Finally, two additional tabs provide the negative and positive interaction degree associated with every nonessential (“nonessential array degree” tab) and essential (“essential array degree” tab) array mutant, respectively.
DOI: 10.5061/dryad.488dk/12
title: Halletal.SInb2

description: Mathematica Worksheet 2
DOI: 10.5061/dryad.488dk/13
title: mmc3.R

description: mmc3.R function used to analyse data. Reproduced from Bolker et al. Trends in Ecology & Evolution 24, 127–135 (2009).
DOI: 10.5061/dryad.488dk/14
title: modelCode9

description: MATLAB code for numeric model
DOI: 10.5061/dryad.488dk/15
title: twoSpecies9

description: MATLAB code for numeric model
DOI: 10.5061/dryad.6276d/2
title: HatchingSuccess&ClutchTemperature

description: For king rail clutches in which clutch temperature was measured, hatching success (proportion of eggs hatched) in relation to maximum clutch temperature and time clutch temperature exceeded 43.5ºC.
DOI: 10.5061/dryad.6276d/3
title: IncubationTiming&HatchingSynchrony

description: Hatching rates of king rail nests in relation to Julian first egg date. Over five years at Mackay Island NWR, hatching rates are reported as the number of days during which the eggs hatched and the number of eggs hatched per day.  The day of initiation of incubation in relation to first egg date is reported in cases where known.
DOI: 10.5061/dryad.6276d/4
title: RecessDuration&AmbientTemperature

description: Multiple measures of recess duration (time when nest unattended) at incubated king rail nests during the incubation period, in relation to the mean ambient temperature during the recess interval.
DOI: 10.5061/dryad.6276d/5
title: RecessFrequency&AmbientTemperature

description: Multiple measures per nest of rate of recesses per hour in king rail nests during the incubation period in relation to mean ambient temperature.
DOI: 10.5061/dryad.63nd8/1
title: Simulation Study I Data File

description: Compilation of the simulation data files, generated and analyzed for Simulation Study I.
DOI: 10.5061/dryad.63nd8/2
title: Simulation Study II Data Files

description: Compilation of simulation data files, generated and analyzed for Simulation Study II.
DOI: 10.5061/dryad.63nd8/3
title: GIDS calculation sample

description: GIDS calculation program along with a sample batch file, a sample data file, and output files. See Description.txt for detailed description.
DOI: 10.5061/dryad.6n332/2
title: Bn_complete_genemodels_aa

description: protein sequences
DOI: 10.5061/dryad.72591/1
title: File 1

description: Relative warp scores of upper view
DOI: 10.5061/dryad.91c0t/1
title: Schrey et al. Eastern Fence Lizard and Red Imported Fire Ant Data

description: DNA methylation data and site invasion status along with genetic data for Eastern Fence Lizards
DOI: 10.5061/dryad.bh526/1
title: Database divorce in a year-round territorial bird

description: Database contains raw data used in the analyses included in the manuscript. Each sheet includes data for an specific analysis and has a correspond Read Me tab next to it.
DOI: 10.5061/dryad.c3q5c/1
title: Fasta files for each taxon.

description: Fasta files for each taxon used to generate Bayesian Skyline Plots and population genetic summary statistics.
DOI: 10.5061/dryad.c3q5c/2
title: Bayesian Skyline Plots

description: Excel sheet containing tabs for each lineage/taxon showing time, median, mean, and CI of Ne*t used to construct Bayesian Skyline Plots.
DOI: 10.5061/dryad.ck1m7/1
title: Rana Supplementary Tables

description: Supplementary Data Tables
DOI: 10.5061/dryad.ck1m7/2
title: Rana Supplementary Figures

description: Supplementary Figures
DOI: 10.5061/dryad.ck1m7/4
title: Rana Yuan Nexus file

description: Nexus file of sequences
DOI: 10.5061/dryad.d5h0b/1
title: ECOEVOL_DATA_HIRST

description: survey data, and experimental data