cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.6084/m9.figshare.28009754
title: Evolution of a bipolar sexual compatibility system in <i>Marasmius</i>

description: Sexual compatibility in the Basidiomycota is governed by genetic identity at one or two loci, resulting in compatibility systems called bipolar and tetrapolar. The loci are known as <i>HD</i> and <i>P/R</i>, encoding homeodomain transcription factors and pheromone precursors and receptors, respectively. Bipolarity is known to evolve either by linkage of the two loci or by loss of mating-type determination of either the <i>HD</i> or the <i>P/R</i> locus. The ancestor to basidiomycete fungi is thought to have been tetrapolar, and many transitions to bipolarity have been described in different lineages. In the diverse genus <i>Marasmius</i> (Agaricales), both compatibility systems are found, and the system has been shown to follow the infrageneric sections of the genus, suggesting a single origin of bipolarity. Here, we tested this hypothesis using a comprehensive phylogenetic framework and investigated the mode by which bipolarity has evolved in this group. We utilized available genomic data and marker sequences to investigate evolution of sexual compatibility in <i>Marasmius</i> and allied genera. By generating a concatenated multilocus phylogeny, we found support for a single transition to known bipolarity within <i>Marasmius</i>. Furthermore, utilizing genomic data of the bipolar species <i>Marasmius oreades</i>, we found that the <i>HD</i> and <i>P/R</i> loci likely have remained unlinked through this transition. By comparing nucleotide diversity at the <i>HD</i> and <i>P/R</i> loci in <i>Ma. oreades</i>, we show that the <i>HD</i> locus has retained high diversity, and thus likely the function of determining sexual identity, as similarly in other bipolar mushroom-forming fungi. Finally, we describe the genomic architecture of the <i>MAT</i> loci of species of both sexual compatibility systems in Marasmiaceae and related families.
DOI: 10.6084/m9.figshare.28009754.v1
title: Evolution of a bipolar sexual compatibility system in <i>Marasmius</i>

description: Sexual compatibility in the Basidiomycota is governed by genetic identity at one or two loci, resulting in compatibility systems called bipolar and tetrapolar. The loci are known as <i>HD</i> and <i>P/R</i>, encoding homeodomain transcription factors and pheromone precursors and receptors, respectively. Bipolarity is known to evolve either by linkage of the two loci or by loss of mating-type determination of either the <i>HD</i> or the <i>P/R</i> locus. The ancestor to basidiomycete fungi is thought to have been tetrapolar, and many transitions to bipolarity have been described in different lineages. In the diverse genus <i>Marasmius</i> (Agaricales), both compatibility systems are found, and the system has been shown to follow the infrageneric sections of the genus, suggesting a single origin of bipolarity. Here, we tested this hypothesis using a comprehensive phylogenetic framework and investigated the mode by which bipolarity has evolved in this group. We utilized available genomic data and marker sequences to investigate evolution of sexual compatibility in <i>Marasmius</i> and allied genera. By generating a concatenated multilocus phylogeny, we found support for a single transition to known bipolarity within <i>Marasmius</i>. Furthermore, utilizing genomic data of the bipolar species <i>Marasmius oreades</i>, we found that the <i>HD</i> and <i>P/R</i> loci likely have remained unlinked through this transition. By comparing nucleotide diversity at the <i>HD</i> and <i>P/R</i> loci in <i>Ma. oreades</i>, we show that the <i>HD</i> locus has retained high diversity, and thus likely the function of determining sexual identity, as similarly in other bipolar mushroom-forming fungi. Finally, we describe the genomic architecture of the <i>MAT</i> loci of species of both sexual compatibility systems in Marasmiaceae and related families.
DOI: 10.6084/m9.figshare.27623940
title: Morphology, phylogeny, and mitogenomics reveal a new entomopathogenic fungus, <i>Blackwellomyces changningensis</i> (Hypocreales, Clavicipitaceae), from southwestern China

description: Two species of <i>Blackwellomyces</i> (Clavicipitaceae, Hypocreales, Ascomycota) were discovered during an investigation of the diversity of entomopathogenic fungi. A new fungus and one known fungal species that were gathered from Yunnan Province were described in this study. <i>Blackwellomyces changningensis</i>, sp. nov. was described using morphology and phylogenetic evidence from 14 mitochondrial protein-coding gene (PCG) data sets (<i>atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad5, nad6</i>, and <i>nad4L</i>) and six nuclear genes (ITS [ITS4 and ITS5], 18S nuc rDNA [18S], 28S nuc rDNA [28S], <i>tef1-α, rpb1</i>, and <i>rpb2</i>). <i>B. changningensis</i> were found parasitic to Lepidoptera larvae and to produce filiform ascospores with septations. The asexual conidia were ovoid to ellipsoid in shape. Phylogenetic analysis and morphological observations concurred that the fungus belonged to a different species within the genus of <i>Blackwellomyces</i>. The foundation for further taxonomic, genetic, and evolutionary biological studies of the genus <i>Blackwellomyces</i> was laid by this work.
DOI: 10.6084/m9.figshare.27623940.v1
title: Morphology, phylogeny, and mitogenomics reveal a new entomopathogenic fungus, <i>Blackwellomyces changningensis</i> (Hypocreales, Clavicipitaceae), from southwestern China

description: Two species of <i>Blackwellomyces</i> (Clavicipitaceae, Hypocreales, Ascomycota) were discovered during an investigation of the diversity of entomopathogenic fungi. A new fungus and one known fungal species that were gathered from Yunnan Province were described in this study. <i>Blackwellomyces changningensis</i>, sp. nov. was described using morphology and phylogenetic evidence from 14 mitochondrial protein-coding gene (PCG) data sets (<i>atp6, atp8, atp9, cob, cox1, cox2, cox3, nad1, nad2, nad3, nad4, nad5, nad6</i>, and <i>nad4L</i>) and six nuclear genes (ITS [ITS4 and ITS5], 18S nuc rDNA [18S], 28S nuc rDNA [28S], <i>tef1-α, rpb1</i>, and <i>rpb2</i>). <i>B. changningensis</i> were found parasitic to Lepidoptera larvae and to produce filiform ascospores with septations. The asexual conidia were ovoid to ellipsoid in shape. Phylogenetic analysis and morphological observations concurred that the fungus belonged to a different species within the genus of <i>Blackwellomyces</i>. The foundation for further taxonomic, genetic, and evolutionary biological studies of the genus <i>Blackwellomyces</i> was laid by this work.
DOI: 10.5281/zenodo.6885501
title: Supplementary files/DINSOL-v1.0

description: This supplementary file brings all datasets, scripts, and modified source codes that were used during the GMD manuscript written phase. Besides DINSOL output data, the supplementary file also contains some insolation data and dates obtained from PMIPII and a time slice of the Earth's orbital parameters given by Bartlein and Shafer (2019). Further, each folder contains some notes with pieces of information, where we only need to execute the R scripts and generate the Figures and run the statistics presented in the manuscript.
DOI: 10.5281/zenodo.7557354
title: Supplementary files/DINSOL-v1.0

description: This supplementary file brings all datasets, scripts, and modified source codes that were used during the GMD manuscript written phase. Besides DINSOL output data, the supplementary file also contains some insolation data and dates obtained from PMIPII and a time slice of the Earth's orbital parameters given by Bartlein and Shafer (2019). Further, each folder contains some notes with pieces of information, where we only need to execute the R scripts and generate the Figures and run the statistics presented in the manuscript.
DOI: 10.15468/dl.svq3u2
title: Occurrence Download

description: A dataset containing 5137 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Celtis pallida Torr.",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 5137 records from 95 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061601-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.gzw8p7
title: Occurrence Download

description: A dataset containing 91 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Colombia",
 "TaxonKey is Nyctibius maculosus Ridgway, 1912"
 ]
}

 The dataset includes 91 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061602-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5683/sp2/2qrikw
title: More than breathing air: evolution and physiology of amphibious fishes

description: Amphibious fishes are typically considered together with aquatic air-breathers, but we argue that these fishes differ in physiology, ecology, and possibly evolutionary origins. We introduce a scoring system to characterize interspecific variation in amphibiousness, and use this system to highlight important unanswered questions about the evolutionary physiology of amphibious fishes.
DOI: 10.15468/dl.aw6dw5
title: Occurrence Download

description: A dataset containing 116033778 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is United States of America",
 "GadmGid is USA.5_1"
 ]
}

 The dataset includes 116033778 records from 1412 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0061581-241126133413365/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.6jnjyx
title: Occurrence Download

description: A dataset containing 21 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lepidosperma bungalbin R.L.Barrett"
 ]
}

 The dataset includes 21 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0174116-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.t85u9k
title: Occurrence Download

description: A dataset containing 28 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Melocactus deinacanthus Buining & Brederoo"
 ]
}

 The dataset includes 28 records from 14 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0174119-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7l2rz5
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amorphophallus muelleri Blume"
 ]
}

 The dataset includes 74 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069341-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.bwfd2z
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Malaxis molotensis Salazar & de Santiago"
 ]
}

 The dataset includes 5 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0174118-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.dsxx3x
title: Occurrence Download

description: A dataset containing 985320 species occurrences available in GBIF matching the query:
(Query is too complex. Can be viewed on the landing page)

 The dataset includes 985320 records from 1479 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024002-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yoigos
title: Occurrence Download

description: A dataset containing 146 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "or" : [
 "DatasetKey is Atlas des Orchidées de France métropolitaine (2010)",
 "DatasetKey is Données opportunistes capitalisées par la DREAL Corse (OGREVA) - Dreal Corse - Base Ogreva"
 ]
 },
 "TaxonKey is Serapias olbia Verg."
 ]
}

 The dataset includes 146 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015641-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.yxh3w8
title: Occurrence Download

description: A dataset containing 72 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Luina serpentina Cronquist"
 ]
}

 The dataset includes 72 records from 28 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0174117-240321170329656/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.ccwyh1
title: Occurrence Download

description: A dataset containing 74 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Amorphophallus muelleri Blume"
 ]
}

 The dataset includes 74 records from 9 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069342-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.hrc27j
title: Occurrence Download

description: A dataset containing 162 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Italy",
 {
 "or" : [
 "DatasetKey is Herbarium WRSL, Main Collection",
 "DatasetKey is Lund University Biological Museum - Botanical collection (LD)",
 "DatasetKey is Natural History Museum (London) Collection Specimens",
 "DatasetKey is CSIC-Real Jardín Botánico-Colección de Plantas Vasculares (MA)",
 "DatasetKey is NMNH Extant Specimen Records (USNM, US)",
 "DatasetKey is The vascular plants collection (P) at the Herbarium of the Muséum national d'Histoire Naturelle (MNHN - Paris)",
 "DatasetKey is Naturalis Biodiversity Center (NL) - Botany",
 "DatasetKey is Leiner-Herbar Konstanz"
 ]
 },
 "TaxonKey is Isoetes L."
 ]
}

 The dataset includes 162 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015642-190415153152247/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.vh797r
title: Occurrence Download

description: A dataset containing 156 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Boana caingua (Carrizo, 1991)"
 ]
}

 The dataset includes 156 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0019865-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c3cnra
title: Occurrence Download

description: A dataset containing 5979 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasGeospatialIssue is false",
 "Geometry POLYGON((10.45 56.27,10.45 56.29,10.51 56.29,10.51 56.27,10.45 56.27))",
 "PublishingCountry is Denmark"
 ]
}

 The dataset includes 5979 records from 13 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0069348-160910150852091/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.fwc4cn
title: Occurrence Download

description: A dataset containing 382337 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is Lanius cristatus Linnaeus, 1758"
 ]
}

 The dataset includes 382337 records from 174 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024660-231120084113126/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.17639/nott.7560
title: DigiScore Concert as Part of Encuentro Montrealia, Mexico-Canada
title: Three DigiScore commissions

description: Encuentro Montrealia was a collaborative music event held at Mexico's Centre for Music and Sound Arts (CMMAS) and ENES Morelia, partnering with Quebec's leading music technology institutions including Matralab, GRMS, UQAM, and Concordia University. This initiative created a dynamic platform for learning, creative exchange, and dialogue about contemporary music composition through both academic and artistic activities. The event featured the participation of the DigiScore project and its Canadian partner Sandeep Bhagwati from Concordia University. Three international composers were commissioned: Sofía Matus (Mexico), Gabriel Gendín (Argentina) and Andrea Agostini (Italy).
DOI: 10.5524/102687
title: Supporting data for "Lifting the curse from high-dimensional data: Automated projection pursuit clustering for the variety of biological data modalities"

description: Unsupervised clustering is a powerful machine-learning technique widely used to analyze high-dimensional biological data. It plays a crucial role in uncovering patterns, structure, and inherent relationships within complex datasets without relying on predefined labels. In the context of biology, high-dimensional data may include transcriptomics, proteomics, and a variety of single-cell omics data. Most existing clustering algorithms operate directly in the high-dimensional space, and their performance may be negatively affected by the phenomenon known as the curse of dimensionality. Here, we show an alternative clustering approach that alleviates the curse by sequentially projecting high-dimensional data into a low-dimensional representation. We validated the effectiveness of our approach, named APP, across various biological data modalities, including flow and mass cytometry data, scRNA-seq, multiplex imaging data, and T-cell receptor repertoire data. APP efficiently recapitulated experimentally validated cell-type definitions and revealed new biologically meaningful patterns.
DOI: 10.15468/dl.wsp3xv
title: Occurrence Download

description: A dataset containing 1 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Amietia poyntoni Channing & Baptista, 2013",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Specimen, Living Specimen, Observation, Human Observation, Machine Observation, Material sample, Literature Occurrence, Material citation, Occurrence evidence)",
 "Geometry POLYGON ((27.1586 -33.5889,28.2048 -32.9007,25.5395 -32.9007,25.5395 -34.1098,25.6468 -34.1222,25.7787 -34.0734,25.7098 -33.9109,25.8639 -33.797,26.4806 -33.8473,27.1586 -33.5889))"
 ]
}

 The dataset includes 1 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030540-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.7910/dvn/miqwbv
title: Replication Data for: Reevaluating Ideological Asymmetries in Specific Support for the Supreme Court

description: This includes the data and scripts necessary to produce the figures and analysis.
DOI: 10.15468/dl.5dc398
title: Occurrence Download

description: A dataset containing 194 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Asia",
 "Country is China",
 "GadmGid is CHN.15_1",
 "TaxonKey is one of (Rhabdophis tigrinus (Boie, 1826), Lycodon rufozonatus Cantor, 1842, Calamaria septentrionalis Boulenger, 1890, Hydrophis cyanocinctus Daudin, 1803, Sinomicrurus macclellandi (Reinhardt, 1844), Gloydius intermedius (Strauch, 1868), Gloydius brevicauda (Stejneger, 1907), Trimeresurus albolabris Gray, 1842, Gekko hokouensis Pope, 1928, Gekko japonicus (Schlegel, 1836), Gekko swinhonis Günther, 1864)"
 ]
}

 The dataset includes 194 records from 5 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0030542-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5524/102690
title: Supporting data for "Chromosome-level genome assembly and methylome profile yield insights for the conservation of endangered loggerhead sea turtles"

description: Characterising genetic and epigenetic diversity is crucial for assessing the adaptive potential of threatened populations and species in the face of climate change. Sea turtles are particularly vulnerable due to their temperature-dependent sex determination (TSD) system, which heightens the risk of extreme sex ratio bias and extinction under future climate scenarios. High-quality genomic and epigenomic resources will therefore support conservation efforts for these endangered flagship species with such plastic traits.<br>We generated a chromosome-level genome assembly for the loggerhead sea turtle (<i>Caretta caretta</i>) from the globally important Cabo Verde rookery. Using Oxford Nanopore Technology (ONT) and Illumina reads followed by homology-guided scaffolding to the same species, we achieved a contiguous (N50: 129.7 Mbp) and complete (BUSCO: 97.1%) assembly, with 98.9% of the genome scaffolded into 28 chromosomes and 33,887 annotated genes. We also extracted the blood methylome profile from our ONT reads, which was confirmed to be representative of the reference population via whole genome bisulfite sequencing of ten additional loggerheads from the same population. Applying our novel resources, we revealed high conservation of synteny between sea turtle species, reconstructed population size fluctuations in line with major climatic events, and identified microchromosomes as key regions for monitoring genetic diversity and epigenetic flexibility. Isolating 199 TSD-linked genes, we further built a large network of functional protein associations and blood-based methylation patterns.<br>We present a high-quality loggerhead sea turtle genome and methylome from the globally significant East Atlantic population. By leveraging ONT sequencing, we generate genomic and epigenomic resources simultaneously, and showcase the potential of this approach for driving molecular insights for conservation of endangered sea turtles.
DOI: 10.7910/dvn/sowpjm
title: Replication files for: "Judicial Influence and the Importance of Intersecting Identities"

description: Last Tested June 2, 2025 [Stata MP 17.0]

Files include: 
*1- Analysis Dataset: MH_Judicial_Influence_data.dta
*2- Code for models and figures: MH_Judicial_Influence_models.do
*3- Log File: MH_Judicial_Influence.log