cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.15804014
title: Simulated dataset

description: The uploaded files contain gene trees generated under three distinct topological scenarios. Each archive includes trees simulated under five transfer rates (0.1%, 0.4%, 0.7%, 1%, and 2%). All gene trees meet the following criteria: (1) each subgeneric clade is monophyletic and includes at least four extant species; and (2) each species is constrained to a maximum of 10 gene leaf nodes. 2v2.zip, 3v3.zip, 3v4.zip

The uploaded file Poaceae_case.zip contains the following materials related to the Poaceae RI detection: (1) Manully_scignificant_gene_tree: A folder containing gene trees in the Poaceae RI detection. (2) Poaceae_config.txt: The configuration file used as input for the analysis. (3) Poaceae_tree_V16.out.consistance.significant: A list of significant ancient introgression events. (4) Poaceae_tree_V16.out.consistance.significant.all.out: A list of both significant ancient and recent introgression events. (5) Poaceae_tree_V16.out.consistance.significant.gene.list: A gene list corresponding to the significant results. (6) Poaceae_tree_V16.out.consistance.significant.OG.node.nwk: Tree structures of each OG-like group showing significant gene flow events. (7) Poaceae_tree_V16.out.OG.node. nwk and Poaceae_tree_V16.out. p_value: Respectively, the tree structures of each OG-like group for all detected gene flow events, and the statistical assessment distinguishing incomplete lineage sorting (ILS) from introgression.
DOI: 10.5281/zenodo.15877093
title: Simulated dataset

description: The uploaded files contain gene trees generated under three distinct topological scenarios. Each archive includes trees simulated under five transfer rates (0.1%, 0.4%, 0.7%, 1%, and 2%). All gene trees meet the following criteria: (1) each subgeneric clade is monophyletic and includes at least four extant species; and (2) each species is constrained to a maximum of 10 gene leaf nodes. 2v2.zip, 3v3.zip, 3v4.zip

The uploaded file Poaceae_case.zip contains the following materials related to the Poaceae RI detection: (1) Manully_scignificant_gene_tree: A folder containing gene trees in the Poaceae RI detection. (2) Poaceae_config.txt: The configuration file used as input for the analysis. (3) Poaceae_tree_V16.out.consistance.significant: A list of significant ancient introgression events. (4) Poaceae_tree_V16.out.consistance.significant.all.out: A list of both significant ancient and recent introgression events. (5) Poaceae_tree_V16.out.consistance.significant.gene.list: A gene list corresponding to the significant results. (6) Poaceae_tree_V16.out.consistance.significant.OG.node.nwk: Tree structures of each OG-like group showing significant gene flow events. (7) Poaceae_tree_V16.out.OG.node. nwk and Poaceae_tree_V16.out. p_value: Respectively, the tree structures of each OG-like group for all detected gene flow events, and the statistical assessment distinguishing incomplete lineage sorting (ILS) from introgression.
DOI: 10.15468/dl.bkfesk
title: Occurrence Download

description: A dataset containing 3 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cinara cupressi",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 3 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010348-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vjkrck
title: Occurrence Download

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

 The dataset includes 29 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010347-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.apkf7u
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia holbrooki",
 "Country is Côte d’Ivoire",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010349-250711103210423/datasets/export for details.
DOI: 10.15468/dl.n2kyd5
title: Occurrence Download

description: A dataset containing 5343 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Epilobium palustre",
 "Geometry POLYGON((-8.00174339329464 54.1998526673513, 0.202120938926891 54.1998526673513, 0.202120938926891 61.2628565887411, -8.00174339329464 61.2628565887411, -8.00174339329464 54.1998526673513))",
 "CoordinateUncertaintyInMeters is 0,101",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5343 records from 49 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010350-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.tfrtdw
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is BOLD:ADX0109"
 ]
}

 The dataset includes 5 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010352-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.59m7zp
title: Occurrence Download

description: A dataset containing 10 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia holbrooki",
 "Country is Cyprus",
 "HasCoordinate is true"
 ]
}

 The dataset includes 10 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010351-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jfjp3k
title: Occurrence Download

description: A dataset containing 4 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia holbrooki",
 "Country is Egypt",
 "HasCoordinate is true"
 ]
}

 The dataset includes 4 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010353-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ycg8ns
title: Occurrence Download

description: A dataset containing 3230 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bejaria resinosa"
 ]
}

 The dataset includes 3230 records from 130 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010354-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.r8rc28
title: Occurrence Download

description: A dataset containing 352 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ilex nummularia"
 ]
}

 The dataset includes 352 records from 50 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010357-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.9bkswr
title: Occurrence Download

description: A dataset containing 3914 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Crataegus coccinea"
 ]
}

 The dataset includes 3914 records from 206 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010356-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.qtfkjt
title: Occurrence Download

description: A dataset containing 186 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Spilogale pygmaea"
 ]
}

 The dataset includes 186 records from 23 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010358-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.myw7v9
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia holbrooki",
 "Country is Ethiopia",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010360-250711103210423/datasets/export for details.
DOI: 10.15468/dl.95ukxu
title: Occurrence Download

description: A dataset containing 47 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ptyomaxia syntaractis"
 ]
}

 The dataset includes 47 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010361-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.z6c8e4
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Carassius auratus",
 "Country is Zimbabwe",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010362-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.wg56va
title: Occurrence Download

description: A dataset containing 92 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Harttia carvalhoi"
 ]
}

 The dataset includes 92 records from 10 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010363-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.v2q25e
title: Occurrence Download

description: A dataset containing 587 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Mexico",
 "OccurrenceStatus is Present",
 "TaxonKey is Capra hircus"
 ]
}

 The dataset includes 587 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010365-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jsytrc
title: Occurrence Download

description: A dataset containing 7 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Icerya purchasi",
 "Country is Chile",
 "HasCoordinate is true"
 ]
}

 The dataset includes 7 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010364-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.k9esvc
title: Occurrence Download

description: A dataset containing 166 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Bombus inexspectatus"
 ]
}

 The dataset includes 166 records from 7 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010366-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.pdjt4h
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Gambusia holbrooki",
 "Country is Micronesia (Federated States of)",
 "HasCoordinate is true"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010367-250711103210423/datasets/export for details.
DOI: 10.4121/6678651a-df94-4db4-b74a-b6c22f3035e3
title: Delft3D FM numerical models for North Sea case studies with varying tidal and non-tidal forcing included in Coastal Engineering article: "The importance of time-varying, non-tidal currents in modelling in-situ sand wave dynamics"

description: This dataset contains the model input and output for the Delft3D FM model runs used in the research article:Overes, P. H. P., Borsje, B. W., Luijendijk, A. P., & Hulscher, S. J. M. H. (2024). The importance of time-varying, non-tidal currents in modelling in-situ sand wave dynamics. Coastal Engineering, 189, 104480. https://doi.org/10.1016/j.coastaleng.2024.104480The aim of the study is to assess the impact of realistic fluctuations of non-tidal currents on in-situ sand wave dynamics. This is done through comparison of the results of various 2DV hydro-morphodynamic Delft3D FM sand wave models with different forcing. The models include two case study locations in the Dutch North Sea (HKZ and Texel, see publication for details). For each of the case study location models with different hydrodynamic forcing are set up, which include different combinations of tidal components and a full forcing run which also takes meteorological forcing and density driven effects into account. From the morphological results it is concluded that the time-varying, non-tidal currents, which are included in the full forcing run, but not in the tidal runs, have a significant effect on the dynamics of sand waves. The dataset includes the model input and output for these different runs. For the specifics about the different files reference is made to the user manual(s): https://content.oss.deltares.nl/delft3dfm2d3d/<br>
DOI: 10.4121/6678651a-df94-4db4-b74a-b6c22f3035e3.v1
title: Delft3D FM numerical models for North Sea case studies with varying tidal and non-tidal forcing included in Coastal Engineering article: "The importance of time-varying, non-tidal currents in modelling in-situ sand wave dynamics"

description: This dataset contains the model input and output for the Delft3D FM model runs used in the research article:Overes, P. H. P., Borsje, B. W., Luijendijk, A. P., & Hulscher, S. J. M. H. (2024). The importance of time-varying, non-tidal currents in modelling in-situ sand wave dynamics. Coastal Engineering, 189, 104480. https://doi.org/10.1016/j.coastaleng.2024.104480The aim of the study is to assess the impact of realistic fluctuations of non-tidal currents on in-situ sand wave dynamics. This is done through comparison of the results of various 2DV hydro-morphodynamic Delft3D FM sand wave models with different forcing. The models include two case study locations in the Dutch North Sea (HKZ and Texel, see publication for details). For each of the case study location models with different hydrodynamic forcing are set up, which include different combinations of tidal components and a full forcing run which also takes meteorological forcing and density driven effects into account. From the morphological results it is concluded that the time-varying, non-tidal currents, which are included in the full forcing run, but not in the tidal runs, have a significant effect on the dynamics of sand waves. The dataset includes the model input and output for these different runs. For the specifics about the different files reference is made to the user manual(s): https://content.oss.deltares.nl/delft3dfm2d3d/<br>
DOI: 10.15468/dl.esvexx
title: Occurrence Download

description: A dataset containing 2144 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Belamcanda chinensis"
 ]
}

 The dataset includes 2144 records from 143 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010368-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ndwfv6
title: Occurrence Download

description: A dataset containing 3452 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Ilex pubescens"
 ]
}

 The dataset includes 3452 records from 55 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010369-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.21954/ou.rd.29530013
title: Supplementary materials for PhD thesis "Reverse engineering gene regulatory networks: Elucidation of trancriptome organization, gene function and gene regulation in mammalian systems"

description: This dataset comprises the files contained on a CD-ROM which was attached to the thesis when it was submitted in 2010. It was uploaded to ORDO in 2025 for preservation purposes. For more information, please refer to the thesis “Reverse engineering gene regulatory networks: Elucidation of trancriptome organization, gene function and gene regulation in mammalian systems” via ORO.
DOI: 10.21954/ou.rd.29530013.v1
title: Supplementary materials for PhD thesis "Reverse engineering gene regulatory networks: Elucidation of trancriptome organization, gene function and gene regulation in mammalian systems"

description: This dataset comprises the files contained on a CD-ROM which was attached to the thesis when it was submitted in 2010. It was uploaded to ORDO in 2025 for preservation purposes. For more information, please refer to the thesis “Reverse engineering gene regulatory networks: Elucidation of trancriptome organization, gene function and gene regulation in mammalian systems” via ORO.
DOI: 10.6084/m9.figshare.27152817
title: <b>Using animal tracking for early detection of mass poisoning events</b>

description: 1 Amidst the sixth mass extinction, some animal groups, such as vultures, the only obligate scavengers among vertebrates, are disappearing at an unprecedented rate. Vulture populations worldwide are declining, primarily due to poisoning. As many vulture species are social foragers, they can congregate in large numbers to scavenge at a carcass, potentially increasing their exposure to poisoning risk. Current anti-poisoning prevention and mitigation measures are insufficient to tackle this threat. There is an urgent need for new effective strategies to prevent mass vulture mortality.2 In this study, we applied agent-based modelling using white-backed vulture (<i>Gyps africanus</i>) data from Namibia to: (1) quantify the impact of different foraging strategies on vulture poisoning risk, and (2) evaluate the cost-effectiveness of using vultures as sentinels for poisoning detection. This approach involves GPS tracking of various numbers of vultures and using the data to quickly detect poisoning incidents and decontaminate carcasses. These actions help mitigate further vulture mortality and prevent mass poisoning.3 Our findings demonstrate that social foraging significantly increases the risk of poisoning among white-backed vultures. However, GPS tracking of individual vultures enables earlier detection of poisoning events, thereby reducing associated mortalities. Poisoning mitigation effectiveness improves with both the number of tracked individuals and the speed of decontamination response. According to our agent-based model tailored to our study system and species, tracking approximately 5% of the population (25 individuals) offers a good balance between cost and effectiveness, requiring an estimated budget of USD 60,000. Using this strategy and approach, and assuming a response time within two hours, up to 45% of poisoning-related deaths could be prevented.4<i> Synthesis and applications</i>: Our results suggest that, in order to reduce mortality incidences from poisoning in our study system and species, it is sufficient to track a small proportion of the vulture population, which would act as sentinels for the rest. By evaluating the costs and ecological benefits of alternative strategies, varying in number of birds tagged or response time, we provide evidence-based solutions that practitioners can use to design conservation plans. These findings are therefore instrumental in supporting vulture and scavenger conservation policy and practice.
DOI: 10.6084/m9.figshare.27152817.v1
title: <b>Using animal tracking for early detection of mass poisoning events</b>

description: 1 Amidst the sixth mass extinction, some animal groups, such as vultures, the only obligate scavengers among vertebrates, are disappearing at an unprecedented rate. Vulture populations worldwide are declining, primarily due to poisoning. As many vulture species are social foragers, they can congregate in large numbers to scavenge at a carcass, potentially increasing their exposure to poisoning risk. Current anti-poisoning prevention and mitigation measures are insufficient to tackle this threat. There is an urgent need for new effective strategies to prevent mass vulture mortality.2 In this study, we applied agent-based modelling using white-backed vulture (<i>Gyps africanus</i>) data from Namibia to: (1) quantify the impact of different foraging strategies on vulture poisoning risk, and (2) evaluate the cost-effectiveness of using vultures as sentinels for poisoning detection. This approach involves GPS tracking of various numbers of vultures and using the data to quickly detect poisoning incidents and decontaminate carcasses. These actions help mitigate further vulture mortality and prevent mass poisoning.3 Our findings demonstrate that social foraging significantly increases the risk of poisoning among white-backed vultures. However, GPS tracking of individual vultures enables earlier detection of poisoning events, thereby reducing associated mortalities. Poisoning mitigation effectiveness improves with both the number of tracked individuals and the speed of decontamination response. According to our agent-based model tailored to our study system and species, tracking approximately 5% of the population (25 individuals) offers a good balance between cost and effectiveness, requiring an estimated budget of USD 60,000. Using this strategy and approach, and assuming a response time within two hours, up to 45% of poisoning-related deaths could be prevented.4<i> Synthesis and applications</i>: Our results suggest that, in order to reduce mortality incidences from poisoning in our study system and species, it is sufficient to track a small proportion of the vulture population, which would act as sentinels for the rest. By evaluating the costs and ecological benefits of alternative strategies, varying in number of birds tagged or response time, we provide evidence-based solutions that practitioners can use to design conservation plans. These findings are therefore instrumental in supporting vulture and scavenger conservation policy and practice.
DOI: 10.15468/dl.cy9gpb
title: Occurrence Download

description: A dataset containing 335 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((9.89907 46.01502,13.50006 46.01502,13.50006 48.02734,9.89907 48.02734,9.89907 46.01502))",
 "HasCoordinate is true",
 "TaxonKey is Eristalis nemorum"
 ]
}

 The dataset includes 335 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010370-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6wefh9
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Ctenopharyngodon idella",
 "Country is Albania",
 "HasCoordinate is true"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010373-250711103210423/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.