cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.5172532/2
title: Cysteine_protease_alignment

description: The sequence alignment prepared in MEGA7 with default settings.
DOI: 10.5061/dryad.7m07n0r/2
title: tree_nexus

description: A phylogenetic tree of 53 species generated using maximum likelihood method of estimation and based on a concatenated sequence of 9 nuclear genes and 4 mitochondrial genes obtained from GenBank (see supplementary table S1).
DOI: 10.5061/dryad.7v72n64/1
title: Kernbach_ALANViremiaCORTMortalityRawData2019

description: CSV document that contains the raw data for viremia, CORT, body mass, and survival parameters.
DOI: 10.5061/dryad.7v72n64/2
title: Kernbach_GeneOntology_ALAN2dpevs6dpe

description: Gene ontology data for transcriptomic data for ALAN exposed days compared between days 2 and 6 post-exposure
DOI: 10.5061/dryad.7v72n64/3
title: Kernbach_GeneOntology_6dpeALANvsCtrl

description: Gene ontology for transcriptomic data comparing ALAN exposed and control birds on day 6
DOI: 10.5061/dryad.7v72n64/4
title: Kernbach_GeneOntology_Ctrl2dpevs6dpe

description: Gene ontology transcriptomic results for control birds on day 2 post-exposure and day 6 post-exposure
DOI: 10.5061/dryad.7v72n64/5
title: Kernbach_GeneOntology_2dpeALANvsCtrl

description: Gene ontrology for transcriptomic results comparing ALAN exposed and control birds on day 2 post-exposure
DOI: 10.5061/dryad.7v72n64/6
title: Kernbach_DiffExp2dpeALANvsCtrl

description: Differential expression of genes comparing ALAN exposed and control birds on day 2 post-exposure
DOI: 10.5061/dryad.7v72n64/7
title: Kernbach_DiffExp6dpeALANvsCtrl

description: Differential expression on genes compared between ALAN exposed and control birds on day 6 post-exposure
DOI: 10.5061/dryad.8f57ck3/1
title: Karvonen et al. Evolutionary Applications Data
DOI: 10.5061/dryad.9k862c8/1
title: Genetic and environmental data, and R code

description: Genetic and environmental data, and R code
DOI: 10.5061/dryad.h7nj6qn/1
title: EvolApp sim data

description: Summary simulation data for figures
DOI: 10.5061/dryad.m88k1c2/1
title: Supp data

description: Data for individual hyrax involved in mating related and mate guarding interactions.
DOI: 10.5061/dryad.n4ts139/1
title: Clutch Data 2015-2016

description: Metadata on clutches collected in 2015 and 2016 including inferred dam and sire, parental relatedness, parental inbreeding, clutch size, and hatching success. Both raw and quality controlled data.
DOI: 10.5061/dryad.n4ts139/2
title: Genotype data

description: Microsatellite genotype calls for all genotyped individuals from Archbold Biological Station including hatchlings and eggs from clutches examined in this study.
DOI: 10.5061/dryad.n4ts139/3
title: Hatchling phenotypic data

description: Phenotypic data for all viable hatchlings collected for this study. Carapace and plastron measurements (in mm) and mass was measured for both the 2015 and 2016 cohort. Locomotor performance data on a 1m track was measured for the 2016 cohort only. Locomotor data (latency time, total time, initial speed, average speed, and max speed) is averaged across trials for each individual.
DOI: 10.5061/dryad.nr51124/4
title: 4. Sequenced fungal cultures and corresponding ESVs.

description: Each row in the table corresponds to one out of 473 representative fungal cultures that were sequenced. Seed lot and seed number from which the culture was obtained are indicated in the first two columns, and the assigned morphotype in the third column. Column “ESV” indicates the ESV sequence with which the ITS2 region of sequenced fungal culture mapped and the column “Identity (%)” indicates the percentage of the overlap between two sequences. Last six columns indicate the taxonomical assignment ("Division", "Phylum", "Class", "Order", "Family", "Genus", "Species") of each sequenced culture.
DOI: 10.5061/dryad.nr51124/5
title: 5. Sample x ESV matrix

description: The matrix represents number of reads of each fungal ESV (columns) in each seed lot (rows). The information about the taxonomy and origin of each seed lot is provided in last three columns ("Species", "Group" and "Continent").
DOI: 10.5061/dryad.nr51124/6
title: 6. ESV taxonomy and guilds

description: The table provides information about the taxonomy (division; phylum; class; order; family; genus; species) of each of 1905 obtained fungal ESVs in the study and assigned guilds.
DOI: 10.5061/dryad.nr51124/7
title: 7. Infestation of seeds with insects

description: The table contains the information about presence ("Exit holes PA" and "Larvae PA") and number of exit holes and insect larvae ("Exit holes" and "Larvae") in each of 100 assessed seeds per seed lot. Column "Infestation" indicates combined presence of exit holes and/or larvae in a seed. Columns "Group" and "Species" indicate the taxonomy and column "Continent" the origin of a seed lot.
DOI: 10.5061/dryad.nr51124/8
title: 8. Insect taxonomy

description: Each row corresponds to one of 79 insects revealed from seeds in this study. For each insect the seed lot in which it was found ("Seed lot ID"), tree taxonomy (columns "Species" and "Group) and origin of a seed lot (column "Continent") are indicated in first four columns. The information about the insect order as a result of morphological identification (column “Insect order”) and the results of molecular identification (column “Insect taxonomy”) and the percentage of identity match with the reference sequence are provided.
DOI: 10.5061/dryad.q50dc8d/1
title: Bd_México-Bolom et al.
DOI: 10.5061/dryad.vg5712f/1
title: Shovon et al...

description: 1. Environmental Variables: Eight environmental variables were initially selected for this study. Later 4 of them (canopy openness, clay, soil C/N ratio and soil moisture) were selected for the model selection. Third row shows the unit of the environmnetal variables. 2. Community Weighted Mean Community weighted mean of seven individual traits are given here. These traits are: LA (Leaf Area), SLA (Specific Leaf Area), LDMC (Leaf Dry Matter Content), SRL (Specific Root Length), RDMC (Root Dry Matter Content), RD (Rooting Depth) and Height (Maximum Height). Third row shows the unit of the variables. 3. Functional Dispersion Functional Dispersion of seven individual traits are given here. These traits are: LA (Leaf Area), SLA (Specific Leaf Area), LDMC (Leaf Dry Matter Content), SRL (Specific Root Length), RDMC (Root Dry Matter Content), RD (Rooting Depth) and Height (Maximum Height). These variables are unit-less.
DOI: 10.17632/5tndf4p6rj.1
title: FIGURE 4

description: Figure 4: Screenshot media content information and distribution map of Dayak tribe Borneo
DOI: 10.17632/9b6pgjxv85.4
title: FIGURE 2

description: Figure 2: The 5R Adaptation framework for mobile cultural heritage
DOI: 10.17632/p5hyx6b9mx.1
title: Effects of phytoestrogens in the treatment of menopausal depressive disorders: A systematic review and meta-analysis

description: 1. Search Strategies 2.Detailed extraction of data for each included literature 3.Detailed information of risk of bias
DOI: 10.17632/sfy7wt9wz7.1
title: Data for: A Biased Sampling Approach to Accelerate Backward Monte Carlo Atmospheric Radiative Transfer Simulations and its Application to Arctic Heterogeneous Cloud and Surface Conditions
DOI: 10.17632/tc6kr6jsvp.1
title: FIGURE 3

description: Figure 3: Screenshot mobile culture heritage apps for literation Dayak tribe Borneo
DOI: 10.5061/dryad.144h1s1/1
title: Fig 3

description: Raw data associated with Figure 3
DOI: 10.5061/dryad.144h1s1/2
title: Fig 5

description: All the data in Figure 5
DOI: 10.5061/dryad.144h1s1/3
title: Fig 6-7

description: Data found in BOTH figures 6-7 (the SR cells)
DOI: 10.5061/dryad.1t38n12/1
title: SupplementaryDataTopt
DOI: 10.5061/dryad.2v1kr38/10
title: Outlier tests data files

description: Data files used for outlier selection tests (OutFLANK, PCadapt and Bayescan).
DOI: 10.5061/dryad.2v1kr38/11
title: R script: outlier selection tests

description: R script used to run outlier selection tests on the raw RAD sequencing data from Jenkins et al. (2018) https://doi.org/10.1007/s12686-018-1001-8. Raw reads archived on Dryad (https://doi.org/10.5061/dryad.2pc6v).
DOI: 10.5061/dryad.2v1kr38/12
title: Miscellaneous data files

description: Zip file containing miscellaneous data files including post-filtered SNP genotypes in adegenet and genepop format, HWE results in RData format, and LD results in RData format.
DOI: 10.5061/dryad.2v1kr38/7
title: Assignment data files

description: Data files used in the assignment analyses.
DOI: 10.5061/dryad.2v1kr38/8
title: R script: assignment

description: R script used to analyse population assignment using the package assignPOP.
DOI: 10.5061/dryad.2v1kr38/9
title: R script: plot allele frequencies

description: R script used to plot population allele frequencies.
DOI: 10.5061/dryad.5rq1h6n/1
title: alpha_analyses_data

description: Data used for analyses of individual quadrats (alpha scale). Details on each column can be found in the readme file.
DOI: 10.5061/dryad.5rq1h6n/2
title: beta_analyses_data

description: Data used for pairwise analyses of quadrats (beta scale). Details on each column can be found in the readme file.
DOI: 10.5061/dryad.69325t8/1
title: CarterRudolf_Dryad

description: data on experimental communities of amphibians testing effects of shifts in hatching timing/phenology on competitive outcomes
DOI: 10.5061/dryad.7v72n64/10
title: Kernbach_WGCNAoverview

description: Overview of WGCNA results for transcriptomic data
DOI: 10.5061/dryad.7v72n64/11
title: Kernbach_WGCNA_modulemembership

description: Module membership of differentially expressed genes from the transcriptomic data
DOI: 10.5061/dryad.7v72n64/12
title: Kernbach_WGCNA_blue

description: Genes belonging to the blue module.
DOI: 10.5061/dryad.7v72n64/13
title: Kernbach_WGCNA_purple

description: Genes belonging to the purple module.
DOI: 10.5061/dryad.7v72n64/14
title: Kernbach_WGCNA_tan

description: Genes belonging to the tan module.
DOI: 10.5061/dryad.7v72n64/15
title: Kernbach_WGCNA_turquoise

description: Genes belonging to the turquoise module.
DOI: 10.5061/dryad.7v72n64/16
title: Kernbach_WGCNA_yellow

description: Genes belonging to the yellow module.
DOI: 10.5061/dryad.7v72n64/8
title: Kernbach_DiffExpCtrl2dpes6dpe

description: Differential expression of genes in control birds between days 2 ad 6 post-exposure
DOI: 10.5061/dryad.7v72n64/9
title: Kernbach_DiffExpALAN2dpevs6dpe

description: Differential expression of genes in ALAN exposed birds between days 2 ad 6 post-exposure
DOI: 10.5061/dryad.c4f07h6.1
title: Data from: A mirage of cryptic species: genomics uncover striking mito-nuclear discordance in the butterfly Thymelicus sylvestris
DOI: 10.5061/dryad.c4f07h6.2
title: Data from: A mirage of cryptic species: genomics uncover striking mito-nuclear discordance in the butterfly Thymelicus sylvestris
DOI: 10.5061/dryad.c4f07h6.2/1.2
title: Wolbachia loci alignment

description: Alignment of Wolbachia fragments found in the ddRADseq data.
DOI: 10.5061/dryad.c4f07h6.2/2.2
title: ddRADseq data, alignment

description: ddRADseq data aligned. The first number of the labels indicates the mitochondrial lineage.
DOI: 10.5061/dryad.hr45320/2
title: Schindler Supplemental Materials

description: Supplementary information
DOI: 10.5061/dryad.k69gf52/1
title: Database_ID 19-0168.R1

description: File with the raw data (excel format).
DOI: 10.5061/dryad.mn8v722/1
title: Data from Keiser et al - Tadpole bacterial acquisition
DOI: 10.5061/dryad.rn2j5p0/1
title: ABM Simulation Code Bartlett and Rozins et al 2019

description: Annotated R script documentation implementation of agent-based model of pathogen spread across apiaries, as described in 'Industrial bees: the impact of apicultural intensification on local disease prevalence' Bartlett, Rozins et al. 2019. Journal of Applied Ecology. Note this only includes the implementation of the simulation code - downstream output file reading and analysis not provided.
DOI: 10.5441/001/1.hs79pk45/1
title: Landscape-dependent optimisations in pelicans_Functional Ecology

description: Efrat R, Hatzofe O, Nathan R (2019) Landscape-dependent time versus energy optimisations in pelicans migrating through a large ecological barrier. Functional Ecology. doi:10.1111/1365-2435.13426
description: 1. During migration, birds are often forced to cross ecological barriers, facing challenges due to scarcity of resources and suitable habitats. While crossing such barriers, birds are expected to adjust their behaviour to reduce time, energy expenditure and associated risks. 2. We studied the crossing of the Sahara Desert by the Great White Pelican (Pelecanus onocrotalus), a large wetland‐specialist. We focused on decisions made by migrating pelicans along different parts of the southbound autumn migration, their response to local environmental conditions, and the implications for time and energy optimisations. We compared the observed pelicans' migration routes with simulated “direct‐pass” (shortest, mostly across the desert) and “corridor‐pass” (along the Nile River) routes, and used GPS, body acceleration and atmospheric modelling to compare flight behaviour along the Nile River versus the desert. 3. The observed route was significantly shorter and faster than the simulated corridor‐pass route and not significantly different from the simulated direct‐pass one. Daily flights over the desert were longer than along the Nile River, with flying time extending to late hours of the day despite unfavourable atmospheric conditions for soaring‐gliding flight. Moreover, the pelicans behavioural response to atmospheric conditions changed according to the landscape over which they flew. Overall, the pelicans showed stronger behavioural adjustments to atmospheric conditions over the desert than along the Nile River. 4. Our findings suggest that migrating pelicans primarily acted as time minimisers while crossing the Sahara Desert, whereas energetic optimisation was only considered when it did not substantially compromise time optimisation. The pelicans took the almost shortest possible route, only following the Nile River along its south‐oriented parts, and frequently staged overnight in the desert far from water, despite being large, wet‐habitat specialists. Correspondingly, their behavioural response to atmospheric conditions changed according to the landscape over which they were flying, switching between time (over the desert) and energy (over the Nile River) optimisation strategies. Our results suggest that the interaction between landscape and atmospheric conditions depict a flexible, yet primarily time‐dominated, migration optimisation strategy.
DOI: 10.5441/001/1.hs79pk45/2
title: Landscape-dependent optimisations in pelicans_Functional Ecology-reference-data

description: Efrat R, Hatzofe O, Nathan R (2019) Landscape-dependent time versus energy optimisations in pelicans migrating through a large ecological barrier. Functional Ecology. doi:10.1111/1365-2435.13426
description: 1. During migration, birds are often forced to cross ecological barriers, facing challenges due to scarcity of resources and suitable habitats. While crossing such barriers, birds are expected to adjust their behaviour to reduce time, energy expenditure and associated risks. 2. We studied the crossing of the Sahara Desert by the Great White Pelican (Pelecanus onocrotalus), a large wetland‐specialist. We focused on decisions made by migrating pelicans along different parts of the southbound autumn migration, their response to local environmental conditions, and the implications for time and energy optimisations. We compared the observed pelicans' migration routes with simulated “direct‐pass” (shortest, mostly across the desert) and “corridor‐pass” (along the Nile River) routes, and used GPS, body acceleration and atmospheric modelling to compare flight behaviour along the Nile River versus the desert. 3. The observed route was significantly shorter and faster than the simulated corridor‐pass route and not significantly different from the simulated direct‐pass one. Daily flights over the desert were longer than along the Nile River, with flying time extending to late hours of the day despite unfavourable atmospheric conditions for soaring‐gliding flight. Moreover, the pelicans behavioural response to atmospheric conditions changed according to the landscape over which they flew. Overall, the pelicans showed stronger behavioural adjustments to atmospheric conditions over the desert than along the Nile River. 4. Our findings suggest that migrating pelicans primarily acted as time minimisers while crossing the Sahara Desert, whereas energetic optimisation was only considered when it did not substantially compromise time optimisation. The pelicans took the almost shortest possible route, only following the Nile River along its south‐oriented parts, and frequently staged overnight in the desert far from water, despite being large, wet‐habitat specialists. Correspondingly, their behavioural response to atmospheric conditions changed according to the landscape over which they were flying, switching between time (over the desert) and energy (over the Nile River) optimisation strategies. Our results suggest that the interaction between landscape and atmospheric conditions depict a flexible, yet primarily time‐dominated, migration optimisation strategy.
DOI: 10.17632/6t79jgswmg.1
title: Data for: Paleostress and statistical analysis using quartz veins from mineralized and non-mineralized zones: application for exploration targeting

description: Four Supplementary data files have been uploaded and are referred to in the text. Detailed captions have been included in each individual supplementary data pdf. Brief description of the content of each supplementary data file is provided below: Supplementary data-1 is a table giving coefficient of determination for different statistical distributions of vein thickness for different transects. Supplementary data-2: Thickness vs. corrected cumulative number of veins per unit length graphs for each transect in the mineralized and non-mineralized zones of the Gadag region (Southern India). Supplementary data-3: Thickness vs. probability density function of vein distribution for each transect in mineralized and non-mineralized zone. Supplementary data-4: Lower hemisphere equal area projections of poles to vein orientations for each outcrop in the mineralized and non-mineralized zone of the study area.
DOI: 10.17632/dxxmj48nfv.1
title: Data for: Chronostratigraphy of the Baringo-Tugen-Barsemoi (HSPDP-BTB13-1A) Core – 40Ar/39Ar Dating, Magnetostratigraphy, Tephrostratigraphy, Sequence Stratigraphy and Bayesian Age Modeling

description: Supporting paleomagnetic, ArAr, and stratigraphic data for the BTB13 age model.
DOI: 10.17632/fx8w6mnr95.1
title: Data for: In-situ fabrication of dispersion nuclear fuel pellets with a core-shell structure

description: The experimental and theoretical data of the shell thickness obtained under different mixing process parameters
DOI: 10.17632/kwfxt6j4m5.1
title: Data for: NeuroBel: Spanish screening test for oral psycholinguistics disabilities in elderly people with mild cognitive impairment, and early stage of Alzheimer´s disease

description: Database of 75 elderly Spanish participants with and with out cognitive impairment. Including sociodemographic characteristics and MMSE scores and neurobel scores in differents psycholinguistics tasks.
DOI: 10.17632/kwfxt6j4m5.2
title: Data for: NeuroBel: Spanish screening test for oral psycholinguistics disabilities in elderly people with mild cognitive impairment, and early stage of Alzheimer´s disease

description: Database of 75 elderly Spanish participants with and with out cognitive impairment. Including sociodemographic characteristics and MMSE scores and neurobel scores in differents psycholinguistics tasks.
DOI: 10.17632/m9z269s8mr.1
title: Data for: Formation of highly oxygenated multifunctional compounds from cross-reactions of carbonyl compounds in the atmospheric aqueous phase

description: UV spectra of PA and GL under different conditions, the data by FTICRMS of PA and PA-GL under 12 hours of irradiation and the comparison of the mass spectra between FTICRMS and Orbitrap
DOI: 10.5061/dryad.144h1s1/10
title: Fig 8 2of2

description: All the data in Figure 8, part 2 of 2
DOI: 10.5061/dryad.144h1s1/4
title: Fig 8 1of2

description: All the data in Figure 8, part 1 of 2
DOI: 10.5061/dryad.144h1s1/5
title: Fig 7 part 1 of 3

description: All the data in Figure 7, part 1 of 3
DOI: 10.5061/dryad.144h1s1/6
title: Fig 6

description: All the data in Figure 6
DOI: 10.5061/dryad.144h1s1/7
title: 14dpf boundaries

description: Data that describes the boundaries of 14dpf fish. No associated figure.
DOI: 10.5061/dryad.144h1s1/8
title: Fig 7 2 of 3

description: All the data in Figure 7, part 2 of 3
DOI: 10.5061/dryad.144h1s1/9
title: Fig 7 part 3 of 3

description: All the data in Figure 7, part 3 of 3
DOI: 10.5061/dryad.293kp3d/1
title: Laumer_ProcB

description: Supplemental data and analysis files from:

"Revisiting metazoan phylogeny with genomic sampling of all phyla"

Laumer, Christopher, Fernández, Rosa, Lemer, Sarah, Combosch, David, Kocot, Kevin, Riesgo, Ana, Andrade, Sonia, Sterrer, Wolfgang, Sørensen, Martin, Giribet, Gonzalo

Data are grouped into directories as follows:

a.) IQtree_analyses - all ML trees presented in the supplemental figures, including profile mixture-model and LG4X (in its own subdirectory). Matrices follow the naming convention detailed below for the PhyloBayes analysis. The analyses shown in Figure S1 were based on the matrix titled "FcC_supermatrix.fas".

b.) Matrix_construction - a series of subdirectories containing the original MARE and taxon-based matrix reduction runs (named as in Figure 1). The set of trimmed orthologue alignments containing 50 or 100 or more taxa are kept in "Genes_3824" and "Genes_1034", respectively; the latter also contains files used in the MARE reduction for the pan-metazoa matrix. A set of RAxML gene trees for the individual orthologue alignments are held in the "Indiv_Gene_trees_UPhO" directory. Example python scripts for taxon specific submatrix construction are also contained in this directory.

c.) PhyloBayes_analyses. Taxon-specific matrix analyses are named as such. "Metazoa_BMGE" contains all analyses based on the 43,011 site matrix where taxon removal was performed only after BMGE-trimming; "metazoa_pre-red" contains the analyses on the 53,167 site matrix where taxa were removed prior to BMGE-trimming. All recoded matrix files contain the string "dayhoff6" in the filename. Where retained (for the recoded PhyloBayes analyses only), the very large ".chain" files have been removed in the interest of space, and are available on request.

d.) Original_proteomes - containing peptide fasta files with their original headers used as inputs for the OrthoFinder analysis.

e.) Orthology_analysis - Containing all files and ad-hoc scripts used to derive the original orthology set, as well as several preliminary test analyses. The actual set used to derive the 5511 UPhO orthologue analysis is contained in "filtered_gappy/cut_1", with the actual orthogroups contained in "UPhO_orthogroups.csv". This is a large directory with many files.
DOI: 10.5061/dryad.7q22r2m/1
title: dataup

description: Soil Hydraulic parameters of 15 columns modelled in the paper. These data include summrized version output of drip infiltrometer data used for inverse modelling.
DOI: 10.5061/dryad.7v72n64/17
title: ReadME File

description: README file describing labels from all datasets.
DOI: 10.5061/dryad.945c410/1
title: Data of THz absorption coefficients and BA contents is named as data.mat.
DOI: 10.5061/dryad.945c410/2
title: X is the first derivative spectra of THz absorption coefficients
DOI: 10.5061/dryad.945c410/3
title: Y is BA contents
DOI: 10.5061/dryad.945c410/4
title: fz is the frequency
DOI: 10.5061/dryad.945c410/5
title: DemoBPNN is the program of BPNN
DOI: 10.5061/dryad.945c410/6
title: DemoGRNN is the program of GRNN algorithm
DOI: 10.5061/dryad.bs03tq7/1
title: mafft-nexus-edge-trimmed-clean-50p_noPartitionTaxonsets

description: Nexus file for phylogenetic analyses