cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18286457
title: Global atmospheric boundary layer wind speed profile dataset derived from Aeolus observations from July 2020 to April 2023

description: Global-ABLWind is a global atmospheric boundary layer (ABL) wind speed profile dataset based on the first spaceborne LiDAR Aeolus covering the height range from 100 m to 2000 m above ground level at 100 m vertical resolution, spanning the period from July 2020 to April 2023.

The Aeolus has two receivers that simultaneously capture the signal from both the Rayleigh (Ray) and Mie channels. Similarly, this dataset also includes two versions based on Aeolus observations from different channels

The temporal and spatial resolution is identical to that of the Aeolus L2C product. The dataset is distributed as monthly NetCDF files, with filenames following the convention "Global-ABLWind_XXX_V1_YYYY_MM.nc", where XXX represents the channel (Ray or Mie), YYYY refers to the year, and MM is the month of the year.




standard_name (Variable name)
Dimensions
Units
Description


time
1
seconds since YYYY-MM-01 00:00:00
Average time of Aeolus observations used for the current wind profile, derived from the Aeolus L2C product


latitude
1
degrees_north
Average latitude of Aeolus observations used for the current wind profile, derived from the Aeolus L2C product


longitude
1
degrees_east




Average longitude of Aeolus observations used for the current wind profile, derived from the Aeolus L2C product




height
1
m
Height above ground level (AGL), fixed vertical grid from 100 m to 2000 m at 100 m intervals


wind_speed (ws)
2
m s⁻¹
Horizontal wind speed
DOI: 10.5061/dryad.59zw3r26b
title: Data for: Increased male mating success in the presence of prey and rivals in a sexually cannibalistic mantis

description: Pre-copulatory sexual cannibalism—or cannibalism without mating—is
 expected to promote the evolution of male strategies that enhance mating
 success and reduce the risk of cannibalism, such as preferentially
 approaching feeding females. Sexual selection on male competitiveness has
 the potential to alter male mating decisions in the face of cannibalism
 risk, but such effects are poorly understood. We investigated the effect
 of prey availability and male-male competition on mating incidence in the
 highly cannibalistic Springbok mantis, Miomantis caffra. We found that
 matings were initiated more rapidly and more often in the presence of
 prey, suggesting that females distracted with foraging may be less of a
 threat. Competition between males also hastened the onset of copulation
 and led to higher mating success, with very large effects occurring in the
 presence of both prey and competitors, indicating that intrasexual
 competition may intensify attraction to foraging females. Taken together,
 our results suggest that pre-copulatory cannibalism has selected for male
 preference for foraging females, and that males adjust their mating
 strategy to both the risk of competition and the threat of cannibalism.
description: Data were collected in a fully factorial laboratory
 experiment.
DOI: 10.5061/dryad.x95x69phg
title: Trophic cascade in a marine protected area

description: An ultimate benefit of marine protected areas (MPAs) is to reverse trophic
 cascades caused by human-driven collapse of critical ecological
 interactions. Here we demonstrate, that despite a small-scale (0.28 km2),
 and not being fully protected, a MPA with strict fishing management and
 habitat enhancement by artificial reefs (ARs) in southwest Japan can lead
 to well-established macroalgal communities on widespread sea urchin
 barrens through cascading effects of predator recovery. Areas with low
 urchin densities occurred in and around daytime lobster (Panulirus
 japonicus) shelters primarily formed by quarry-rock ARs inside the MPA. We
 confirmed in the laboratory that lobsters preyed on two dominant sea
 urchins (Echinometra sp. A and Heliocidaris crassispina), with size- and
 species-dependent predation. The area with few urchins extended farther
 (~65 m) from an AR with numerous lobsters than from a natural shelter
 (patch reef) with far fewer lobsters. Causation of this pattern was
 confirmed by a tethering experiment showing that predation on urchins was
 similarly high at and near lobster shelters but decreased at ~100 m from
 the AR to a similar level as at an unprotected site. Time-lapse
 photography revealed that predation on tethered urchins was due mostly to
 the largest size class of lobsters (&gt; 100 mm carapace length),
 which comprised only 7% of the population, highlighting the importance of
 large-sized lobsters in controlling urchin abundance in localized areas
 adjacent to urchin-dominated barrens. Despite an ongoing once-a-year
 fishing event permitted within the MPA, lobster populations were
 persistent, demonstrating that the cascading effect of the lobsters on
 urchins and ultimately macroalgae was robust to temporary reductions in
 predator population size. Erect macroalgal cover was not simply accounted
 for by snapshot urchin density or biomass, suggesting a hysteresis effect
 of the phase shifts between macroalgal dominance and urchin barren states.
DOI: 10.5061/dryad.dr7sqv9xj
title: Climate-assisted persistence of tropical fish vagrants in temperate marine ecosystems

description: Rising temperatures and extreme climatic events are propelling tropical
 species into temperate marine ecosystems, but not all species can persist.
 Here, we used the heatwave-driven expatriation of tropical black
 rabbitfish (Siganus fuscescens) to the temperate environments of Western
 Australia to assess the ecological and evolutionary mechanisms that may
 entail their persistence. Population genomic assays for this rabbitfish
 indicated little genetic differentiation between tropical residents and
 vagrants to temperate environments due to high migration rates, which were
 likely enhanced by the marine heatwave. DNA metabarcoding revealed a
 diverse diet for this species based on phytoplankton and algae, as well as
 an ability to feed on regional resources, including kelps. Irrespective of
 future climate scenarios, these macroalgae-consuming vagrants may
 self-recruit in temperate environments and further expand their geographic
 range by 2100. This expansion may compromise the health of the kelp
 forests that form Australia’s Great Southern Reef. Overall, our study
 demonstrates that projected favourable climatic conditions, continued
 large-scale genetic connectivity between populations, and diet versatility
 are key for tropical range-shifting fish to establish in temperate
 ecosystems.
description: See included README file and Gajdzik et al. 2021 published in
 Communications Biology.
description: We have provided two types of data files, associated metadata,
 and supporting documentation: 1) metabarcoding data for diet analysis and
 2) SNP data for population genetic analysis. For #1,
 metabarcoding data for diet analysis, we here provide: (i) raw Illumina
 MiSeq read 1 file in .fastq format (file name
 "MSRun289_LIG23_S1_L001_R1_001.fastq"), (ii) raw Illumina MiSeq
 read 2 file in .fastq format (file name
 "MSRun289_LIG23_S1_L001_R2_001.fastq"), (iii) demultiplexed
 metabarcoding reads from stomach samples of each rabbitfish indivual in
 fasta format (zip folder "Demultiplexed_samples_fasta_format"),
 (iv) metadata for each stomach sample (file name
 "Metadata_dietary_metabarcoding_rabbitfish"), and (v)
 oligonucleotide and index sequences used for demultiplexing in fasta
 format (zip folder
 "Oligo_sequence_indices_fasta_format"). For
 #2, SNP data for population genetic analysis, we here provide: (i) raw SNP
 data as provided by https://www.diversityarrays.com/ (file name
 "DArTseq_data_rabbitfish_Gajdzik_et_al") and (ii) metadata for
 each <em>Siganus fuscescens</em> individual caught from 13
 sites across seven regions in Western Australia (file name
 "Metadata_DArTseq_Gajdzik_et_al").
DOI: 10.5061/dryad.3xsj3txfx
title: Seed re-dispersal experiments

description: These data files hold the results from a redispersal experiment where
 seeds of the Perennial plant, Sternbergia clusiana, were presented to
 three species of desert ants and seed fate was followed after the
 seeds were taken into the nest. The other data set includes information
 regarding the distribution of this plant, at three life stages, with
 respect to the distribution of shurbs. These data were used to test
 indirectly whether the shrub's environment may be beneficial for the
 survival, growth and reproductive success of the target plant. More
 details in the associated manuscript.
description: These data were the results of an experiment where seeds were
 presented to three species of desert ants and seed fate was followed after
 the seeds were taken into the nest. More details in the associated
 manuscript.
DOI: 10.5061/dryad.n8pk0p2tv
title: Data from: Computational fluid dynamics confirms drag reduction associated with trilobite queuing behaviour

description: Queuing behaviour has been documented in marine arthropods from Cambrian
 to modern oceans. One possible explanation of this behaviour is drag
 reduction, with trilobites in the following positions hypothesized to
 produce less drag than those leading. In this study, we evaluate the
 hydrodynamics of queuing behaviour in the Devonian trilobite
 Trimerocephalus chopini using computational fluid mechanics. Our results
 show that the drag forces of the trilobites following in the queue were
 substantially lower than those produced by the leader (75.1% lower at 2 cm
 s-1). Drag reduction is positively correlated with the movement speed of
 the trilobites, but decreases with increasing distance from the leader.
 Our results support the hypothesis that the queuing behaviour of
 trilobites was an adaptation for reducing hydrodynamic drag. This drag
 reduction effect compensated for the energy cost of movement, which would
 have been particularly advantageous during migration.
DOI: 10.5061/dryad.kkwh70s3w
title: Perl scripts from: The genomes of ancient date palms germinated from 2,000-year-old seeds

description: Seven date palm seeds (Phoenix dactylifera L.), radiocarbon dated
 from the fourth century BCE to the second century CE, were recovered from
 archaeological sites in the Southern Levant and germinated to yield viable
 plants. We conducted whole-genome sequencing of these germinated ancient
 samples and used single-nucleotide polymorphism data to examine the
 genetics of these previously extinct Judean date palms. We find that the
 oldest seeds from the fourth to first century BCE are related to modern
 West Asian date varieties, but later material from the second century BCE
 to second century CE showed increasing genetic affinities to present-day
 North African date palms. Population genomic analysis reveals that by
 ∼2,400 to 2,000 y ago, the P. dactylifera gene pool in
 the Eastern Mediterranean already contained introgressed segments from the
 Cretan palm Phoenix theophrasti, a crucial genetic feature of the
 modern North African date palm populations. The P.
 theophrasti introgression fraction content is generally higher in
 the later samples, while introgression tracts are longer in these ancient
 germinated date palms compared to modern North African varieties. These
 results provide insights into crop evolution arising from an analysis of
 plants originating from ancient germinated seeds and demonstrate what can
 be accomplished with the application of a resurrection genomics approach.
description: Perl scripts from Gros-Balthazard et al. (2021) PNAS - The
 genomes of ancient date palms germinated from 2,000-year-old
 seeds Usage may be found within each script.
 1. vcf2polymorphism_count.pl<br> This script counts the
 number of biallelic snps in a subset of samples in a vcf.
 2. vcf2private_alleles.pl<br> This script evaluate a vcf
 for private alleles. 3.
 vcf2singleton_mutation_profiles2.pl<br> This script reports
 sample-specific mutation profiles at singleton sites.
 4. vcf2singleton_indels.pl<br> This script reports
 singleton indels from an input vcf.
DOI: 10.15468/dl.smsx9e
title: Occurrence Download

description: A dataset containing 301026 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Salix alba",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 301026 records from 2154 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002750-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pxu8ys
title: Occurrence Download

description: A dataset containing 72274 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-13.46929 35.74753,71.3364 35.74753,71.3364 72.23402,-13.46929 72.23402,-13.46929 35.74753))",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Mantis religiosa (Linne, 1758)"
 ]
}

 The dataset includes 72274 records from 1748 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0013849-250515123054153/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.eqxwaj
title: Occurrence Download

description: A dataset containing 29 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Hebecarpa robinsonii"
 ]
}

 The dataset includes 29 records from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008505-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jtqtsf
title: Occurrence Download

description: A dataset containing 79 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Semenovia transiliensis",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 79 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008507-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pwf3bc
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Eleutherodactylus darlingtoni"
 ]
}

 The dataset includes 31 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008506-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.de3xaq
title: Occurrence Download

description: A dataset containing 4698 records in GBIF matching the query:
SELECT
 '223' AS fish_cell,
 GBIF_MGRSCode(1000, decimalLatitude, decimalLongitude, 0) AS cell, -- NO randomization
 COUNT(DISTINCT speciesKey) AS species_richness
 FROM occurrence
 WHERE hasCoordinate = TRUE
 AND speciesKey IS NOT NULL
 AND NOT ARRAY_CONTAINS(issue, 'ZERO_COORDINATE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_OUT_OF_RANGE')
 AND NOT ARRAY_CONTAINS(issue, 'COORDINATE_INVALID')
 AND NOT ARRAY_CONTAINS(issue, 'COUNTRY_COORDINATE_MISMATCH')
 AND decimalLatitude &gt;= 8.098015256935714
 AND decimalLatitude &lt;= 12.166598047573723
 AND decimalLongitude &gt;= 95.37679782651514
 AND decimalLongitude &lt;= 101.18668076201917
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 4698 records were derived from 117 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008490-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.symz7w
title: Occurrence Download

description: A dataset containing 22 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Blicca bjoerkna",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1905",
 "Year is less than or equal to 1909"
 ]
}

 The dataset includes 22 records from 6 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008509-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.13140/rg.2.2.31371.96808
title: PRINCIPIA FRACTALIS Comprehensive Research Data Report Supporting Evidence for Peer-Reviewed Publication
DOI: 10.5281/zenodo.14252310
title: OMAnnotator: a novel approach to building an annotated consesus genome sequence

description: Archive for the associated paper "OMAnnotator: a novel approach to building an annotated consensus genome sequence". This archive contains all sequence data inputs and outputs, sequence processing scripts, analysis scripts and results. Note that paths within scripts will need to be changed to reflect the path to where you download the archive on your machine.

OMAnnotator is a tool to combine input annotations from different sources, using evolutionary relationships as a tie-breaker. It involves three steps: data preparation for orthology infernece using the OMAnnotator prepare_data module, orthology inference using the OMA Standalone software, and consensus annotation extraction (based on inferred orthology) using the OMAnnotator extract_consesnus module.

Three tar-zipped files are provided: 



Proof_of_Principle_Dros_Annotations.tar.gz contains all data from the Proof of Principle testing on the Drosophila melanogaster reference.

OMAnnotator_Other_Species.tar.gz contains all data from using OMAnnotator to re-annotate three species.

25_species_OMA_Data.tar.gz contains the full OMA Standalone instance for the Proof of Principle run with 25 related species (reported in the main manuscript). 


Within the Proof_of_Principle_Dros_Annotations.tar.gz and OMAnnotator_Other_Species.tar.gz folders, folders from the orthology inference step (OMA Standalone) of OMAnnotator have the prefix 'Data_OMA', which contain the related species set ('tar.gz' files) downloaded from OMA browser. These related species sets were used to infer orthology in the OMA Standalone step. Thus, these related species files can be unzipped to create an OMA folder and reproduce the OMA Standalone run. See https://github.com/DessimozLab/OMAnnotator for sample slurm scripts to run the OMA Standalone step. For the Proof of Principle run with 25 species (reported in the main manuscript), the full OMA Standalone instance is provided instead (25_species_OMA_Data.tar.gz). 

The folders OMAnnotator_env.gz and OMAnnotator_Scripts.gz contain the environment and OMAnnotator.py versions used to generate the study results.
DOI: 10.5281/zenodo.18216923
title: OMAnnotator: a novel approach to building an annotated consesus genome sequence

description: Archive for the associated paper "OMAnnotator: a novel approach to building an annotated consensus genome sequence". This archive contains all sequence data inputs and outputs, sequence processing scripts, analysis scripts and results. Note that paths within scripts will need to be changed to reflect the path to where you download the archive on your machine.

OMAnnotator is a tool to combine input annotations from different sources, using evolutionary relationships as a tie-breaker. It involves three steps: data preparation for orthology infernece using the OMAnnotator prepare_data module, orthology inference using the OMA Standalone software, and consensus annotation extraction (based on inferred orthology) using the OMAnnotator extract_consesnus module.

Three tar-zipped files are provided: 



Proof_of_Principle_Dros_Annotations.tar.gz contains all data from the Proof of Principle testing on the Drosophila melanogaster reference.

OMAnnotator_Other_Species.tar.gz contains all data from using OMAnnotator to re-annotate three species.

25_species_OMA_Data.tar.gz contains the full OMA Standalone instance for the Proof of Principle run with 25 related species (reported in the main manuscript). 


Within the Proof_of_Principle_Dros_Annotations.tar.gz and OMAnnotator_Other_Species.tar.gz folders, folders from the orthology inference step (OMA Standalone) of OMAnnotator have the prefix 'Data_OMA', which contain the related species set ('tar.gz' files) downloaded from OMA browser. These related species sets were used to infer orthology in the OMA Standalone step. Thus, these related species files can be unzipped to create an OMA folder and reproduce the OMA Standalone run. See https://github.com/DessimozLab/OMAnnotator for sample slurm scripts to run the OMA Standalone step. For the Proof of Principle run with 25 species (reported in the main manuscript), the full OMA Standalone instance is provided instead (25_species_OMA_Data.tar.gz). 

The folders OMAnnotator_env.gz and OMAnnotator_Scripts.gz contain the environment and OMAnnotator.py versions used to generate the study results.
DOI: 10.15468/dl.35msg5
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Seseli intricatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 10 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008513-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.e69hbz
title: Occurrence Download

description: A dataset containing 18 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Blicca bjoerkna",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1910",
 "Year is less than or equal to 1914"
 ]
}

 The dataset includes 18 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0008514-260120142942310/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18225112
title: Behavior in focus: A video-based ethogram of social behaviors in rewilded horses and its applications for conservation
DOI: 10.5281/zenodo.18225113
title: Behavior in focus: A video-based ethogram of social behaviors in rewilded horses and its applications for conservation
DOI: 10.5281/zenodo.18356952
title: Hui o ka Wai Ola Water Quality Data

description: This dataset is the quarterly report for the Hui o Ka Wai Ola citizen-science based water quality program. Included are physical and chemical data that were collected and analyzed every two or three weeks beginning from June 6, 2016 to December 31, 2025. New results will be posted as available. Please see huiokawaiola.com for more information. 

The goal of the Hui o Ka Wai Ola program is to increase the capacity for monitoring water quality in Maui coastal waters by generating reliable data to assess long-term water-quality conditions and detect temporal trends. These data augment the data produced by the Hawaii Department of Health Clean Water Branch beach monitoring program on Maui.

Please use the most recent version, as it is the latest quality assured data available from the group.
description: Visit huiokawaiola.com for full methods and most recently data and analysis.