cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.q2409
title: Data from: Evolution of neck vertebral shape and neck retraction at the transition to modern turtles: an integrated geometric morphometric approach

description: The unique ability of modern turtles to retract their head and neck into
 the shell through a side-necked (pleurodiran) or hidden-necked
 (cryptodiran) motion is thought to have evolved independently in crown
 turtles. The anatomical changes that led to the vertebral shapes of modern
 turtles, however, are still poorly understood. Here we present
 comprehensive geometric morphometric analyses that trace turtle vertebral
 evolution and reconstruct disparity across phylogeny. Disparity of
 vertebral shape was high at the dawn of turtle evolution and decreased
 after the modern groups evolved, reflecting a stabilization of morphotypes
 that correspond to the two retraction modes. Stem turtles, which had a
 very simple mode of retraction, the lateral head tuck, show increasing
 flexibility of the neck through evolution towards a pleurodiran-like
 morphotype. The latter was the precondition for evolving pleurodiran and
 cryptodiran vertebrae. There is no correlation between the construction of
 formed articulations in the cervical centra and neck mobility. An
 increasing mobility between vertebrae, associated with changes in
 vertebral shape, resulted in a more advanced ability to retract the neck.
 In this regard, we hypothesize that the lateral tucking retraction of stem
 turtles was not only the precondition for pleurodiran but also of
 cryptodiran retraction. For the former, a kink in the middle third of the
 neck needed to be acquired, whereas for the latter modification was
 necessary between the eighth cervical vertebra and first thoracic
 vertebra. Our paper highlights the utility of 3D shape data, analyzed in a
 phylogenetic framework, to examine the magnitude and mode of evolutionary
 modifications to vertebral morphology. By reconstructing and visualizing
 ancestral anatomical shapes we provide insight into the anatomical
 features underlying neck retraction mode, which is a salient component of
 extant turtle classification.
description: Supplementary files
 1-15
DOI: 10.5061/dryad.69pg7
title: Data from: Glacial refugia, recolonisation patterns, and diversification forces in Alpine-endemic Megabunus harvestmen

description: The Pleistocene climatic fluctuations had a huge impact on all life-forms,
 and various hypotheses regarding the survival of organisms during glacial
 periods have been postulated. In the European Alps, evidence has been
 found in support of refugia outside the ice shield (massifs de refuge)
 acting as sources for postglacial recolonisation of inner-Alpine areas. In
 contrast, evidence for survival on nunataks, ice-free areas above the
 glacier, remains scarce. Here, we combine multivariate genetic analyses
 with ecological niche models (ENMs) through multiple timescales to
 elucidate the history of alpine Megabunus harvestmen throughout the ice
 ages, a genus that comprises eight high altitude endemics. ENMs suggest
 two types of refugia throughout the Last Glacial Maximum, inner-Alpine
 survival on nunataks for four species and peripheral refugia for further
 four species. In some geographic regions, the patterns of genetic
 variation are consistent with long-distance dispersal out of massifs de
 refuge, repeatedly coupled with geographic parthenogenesis. In other
 regions, long-term persistence in nunataks may dominate the patterns of
 genetic divergence. Overall, our results suggest that glacial cycles
 contributed to allopatric diversification in Alpine Megabunus, both within
 and at the margins of the ice shield. These findings exemplify the power
 of ENM projections coupled with genetic analyses to identify hypotheses
 about the position and number of glacial refugia and thus to evaluate the
 role of Pleistocene glaciations in driving species-specific responses of
 recolonisation or persistence that may have contributed to observed
 patterns of biodiversity.
description: Bioclimatic variables
 used for ENMs19 bioclimatic variables
 for current conditions, Last Glacial Maximum and mid-Holocene (MIROC and
 CCSM models), extracted from the Wordclim database for the study region
 (European Alps). Additionally, elevation data and the "surface
 area" variable are included (see Materials and Methods for more
 details).ClimateDataset.zipMaxent models for Megabunus speciesMaxent output files of habitat suitability in ASCII format, for current conditions, mid-Holocene and LGM (MIROC and CCSM models), using the selected feature class and regularisation multiplier for each taxon. The habitat suitability scores are average values across 10 cross-validation replicates.MaxentOutputFiles.zipCoordinates and locality namesExcel file containing GPS coordinates and geographic information for each of the 73 localities across the European Alps, where the Megabunus species were sampledMEC-15-1006_sup-table.xlsInput files for Mantel testsDistance matrices (geographic, resistance and genetic distances) for each species that were used for Mantel tests. See Methods section of the manuscript for more details, and Table 1 for population codes.MANTELtest_InputFiles.zip
DOI: 10.5061/dryad.6f8f0
title: Data from: Dynamic population codes of multiplexed stimulus features in primate area MT

description: The middle-temporal area (MT) of primate visual cortex is critical in the
 analysis of visual motion. Single-unit studies suggest that the response
 dynamics of neurons within area MT depend on stimulus features, but how
 these dynamics emerge at the population level, and how feature
 representations interact, is not clear. Here, we used multivariate
 classification analysis to study how stimulus features are represented in
 the spiking activity of populations of neurons in area MT of marmoset
 monkey. Using Representational Similarity Analysis (RSA) we distinguished
 the emerging representations of moving grating and dot field stimuli. We
 show that representations of stimulus orientation, spatial frequency and
 speed are evident near the onset of the population response, while the
 representation of stimulus direction is slower to emerge and sustained
 throughout the stimulus-evoked response. We further found a spatiotemporal
 asymmetry in the emergence of direction representations. Representations
 for high spatial frequencies and low temporal frequencies are initially
 orientation-dependent, while those for high temporal frequencies and low
 spatial frequencies are more sensitive to motion direction. Our analyses
 reveal a complex interplay of feature representations in area MT
 population response that may explain the stimulus-dependent dynamics of
 motion vision.
description: Multivariate classifier
 performance: moving dot field stimuliMultivariate classifier
 performance (proportion correct) when discriminating moving dot field
 stimuli (varying in direction and speed) based on multi electrode
 recordings from marmoset area MT. All data is stored in Matlab data (.mat)
 files that were created with Matlab 2013a.Moving_dot_field_classification_performance.matSpike counts: moving dot field stimuliSpike counts for each electrode from marmoset area MT recorded while the anaesthetised animal was shown moving dot field stimuli. All data is stored in Matlab data (.mat) files that were created with Matlab 2013a.Moving_dot_field_spike_counts.zipMultivariate classifier performance: moving grating stimuliMultivariate classifier performance (proportion correct) when discriminating moving grating stimuli (varying in direction and speed) based on multi electrode recordings from marmoset area MT. All data is stored in Matlab data (.mat) files that were created with Matlab 2013a.Moving_grating_classification_performance.matSpike counts: moving grating stimuliSpike counts for each electrode from marmoset area MT recorded while the anaesthetised animal was shown moving dot field stimuli. All data is stored in Matlab data (.mat) files that were created with Matlab 2013aMoving_grating_spike_counts.zip
DOI: 10.5061/dryad.2td21
title: Data from: Transcriptome characterization and screening of molecular markers in ecologically important Himalayan species (Rhododendron arboreum)

description: Rhododendron arboreum is an ecologically prominent species, which also
 lends commercial and medicinal benefits in the form of palatable juices
 and useful herbal drugs. Local abundance and survival of the species under
 a highly fluctuating climate make it an ideal model for genetic structure
 and functional analysis. However, a lack of genomic data has hampered
 additional research. In the present study, cDNA libraries from floral and
 foliar tissues of the species were sequenced to provide a foundation for
 understanding the functional aspects of the genome and to construct an
 enriched repository that will promote genomics studies in the genera.
 Illumina’s platform facilitated the generation of ∼100 million
 high-quality paired-end reads. De novo assembly, clustering, and filtering
 out of shorter transcripts predicted 113 167 non-redundant transcripts
 with an average length of 1164.6 bases. Of these, 71 961 transcripts were
 categorized based on functional annotations in the Gene Ontology database,
 whereby 5710 were grouped into 141 pathways and 23 746 encoded for
 different transcription factors. Transcriptome screening further
 identified 35 419 microsatellite regions, of which, 43 polymorphic loci
 were characterized on 30 genotypes. Seven hundred and nineteen transcripts
 had 811 high-quality single-nucleotide polymorphic variants with a minimum
 coverage of 10, a total score of 20, and SNP% of 50.
description: Transcripts_RAThe Trinity unigenes assembled from RNA seq of leaf and flower tissue were clustered (95% identity) and filtered to obtain a master file containing only non-redundant transcripts (&gt;500bp).
DOI: 10.5061/dryad.5r09q
title: Data from: The hologenomic basis of speciation: gut bacteria cause hybrid lethality in the genus Nasonia

description: Although the gut microbiome influences numerous aspects of organismal
 fitness, its role in animal evolution and the origin of new species is
 largely unknown. Here we present evidence that beneficial bacterial
 communities in the guts of closely related species of the genus Nasonia
 form species-specific phylosymbiotic assemblages that cause lethality in
 interspecific hybrids. Bacterial constituents and abundance are irregular
 in hybrids relative to parental controls, and antibiotic curing of the gut
 bacteria significantly rescues hybrid survival. Moreover, feeding bacteria
 to germ-free hybrids reinstates lethality and recapitulates the expression
 of innate immune genes observed in conventionally reared hybrids. We
 conclude that in this animal complex, the gut microbiome and host genome
 represent a coadapted “hologenome” that breaks down during hybridization,
 promoting hybrid lethality and assisting speciation.
description: 1.TCA.454Reads.fna file of 16S sequences generated on Roche 454jr1.TCA.454Reads.qual.qual file of 16S reads from Roche 454jrmap fileMap file for 454jr 16S sequencing run. ATTENTION: Correction to map file barcoded sequence on Nov 1, 2013.map_corrected.txt
DOI: 10.6084/m9.figshare.26530669
title: Extensive Alignment Dataset of COVID-19 Gene Primers and Probes Across SARS-CoV-2 Variants

description: <b>This dataset contains a comprehensive analysis of COVID-19 genetic sequences focused on four key genes:</b><b> Spike Glycoprotein,</b><b> Envelope Protein,</b><b> Nucleocapsid Protein,</b><b> and 3' UTR(</b><b>3' </b><b>untranslated region).</b><b> It comprises 20 Excel files,</b><b> each holding 100,</b><b>000 samples.</b><b> A Python script was employed to evaluate primer sets using local alignment against sequences from the NCBI database,</b><b> with lineage determination via the Pangolin tool.</b><b> Each Excel file contains four sheets,</b><b> one per gene,</b><b> with columns for accession ID,</b><b> sample name,</b><b> primer sequences,</b><b> alignment metrics,</b><b> and lineage.</b><b> The dataset includes primer analysis for 2 million sequences across all genes and probe analysis for 1 million sequences in a separate set of 10 Excel files. The dataset contains an additional Excel file that contains the count of </b><b>lineage</b><b> samples to which the primer and the probes were aligned.</b>
DOI: 10.6084/m9.figshare.26530669.v1
title: Extensive Alignment Dataset of COVID-19 Gene Primers and Probes Across SARS-CoV-2 Variants

description: <b>This dataset contains a comprehensive analysis of COVID-19 genetic sequences focused on four key genes:</b><b> Spike Glycoprotein,</b><b> Envelope Protein,</b><b> Nucleocapsid Protein,</b><b> and 3' UTR(</b><b>3' </b><b>untranslated region).</b><b> It comprises 20 Excel files,</b><b> each holding 100,</b><b>000 samples.</b><b> A Python script was employed to evaluate primer sets using local alignment against sequences from the NCBI database,</b><b> with lineage determination via the Pangolin tool.</b><b> Each Excel file contains four sheets,</b><b> one per gene,</b><b> with columns for accession ID,</b><b> sample name,</b><b> primer sequences,</b><b> alignment metrics,</b><b> and lineage.</b><b> The dataset includes primer analysis for 2 million sequences across all genes and probe analysis for 1 million sequences in a separate set of 10 Excel files. The dataset contains an additional Excel file that contains the count of </b><b>lineage</b><b> samples to which the primer and the probes were aligned.</b>
DOI: 10.15468/dl.uftwjs
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Bathytroctes Günther, 1878",
 "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 ((11.7957 -6.2886,12.3365 -7.1504,17.9648 -7.1504,17.9648 1.8496,9.1702 1.8496,8.9648 1.4824,8.9648 -2.2147,9.212 -2.6876,11.2887 -4.7775,11.6694 -5.4096,11.7957 -6.2886))"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010381-250525065834625/datasets/export for details.
DOI: 10.15468/dl.g7dc9w
title: Occurrence Download

description: A dataset containing 35121 species occurrences available in GBIF matching the query:
{
 "and" : [
 "GadmGid is CAN.2_1",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Bombus Latreille, 1802",
 "Year 1990-2025"
 ]
}

 The dataset includes 35121 records from 22 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010382-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.h596q3
title: Occurrence Download

description: A dataset containing 11 records in GBIF matching the query:
SELECT
 kingdom,
 kingdomkey,
 phylum,
 phylumkey,
 class,
 classkey,
 "order",
 orderkey,
 family,
 familykey,
 genus,
 genuskey,
 species,
 specieskey,
 "year",
 IF(ISNULL(familykey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY familykey, "year")) familycount,
 IF(ISNULL(genuskey), NULL, SUM(COUNT(*)) OVER (
 PARTITION BY genuskey, "year")) genuscount,
 COUNT(*) occurrences,
 MIN(GBIF_TEMPORALUNCERTAINTY(eventdate, eventtime)) mintemporaluncertainty,
 MIN(COALESCE(coordinateuncertaintyinmeters, 1000)) mincoordinateuncertaintyinmeters
FROM
 occurrence
WHERE
 occurrence.occurrencestatus = 'PRESENT'
 AND (CAST(occurrence.taxonkey AS INTEGER) = 10842706 OR CAST(occurrence.acceptedtaxonkey AS INTEGER) = 10842706 OR CAST(occurrence.kingdomkey AS INTEGER) = 10842706 OR CAST(occurrence.phylumkey AS INTEGER) = 10842706 OR CAST(occurrence.classkey AS INTEGER) = 10842706 OR CAST(occurrence.orderkey AS INTEGER) = 10842706 OR CAST(occurrence.familykey AS INTEGER) = 10842706 OR CAST(occurrence.genuskey AS INTEGER) = 10842706 OR CAST(occurrence.specieskey AS INTEGER) = 10842706)
 AND occurrence.hasgeospatialissues = FALSE
 AND NOT GBIF_STRINGARRAYCONTAINS(occurrence.issue, 'TAXON_MATCH_FUZZY', TRUE)
 AND (occurrence.distancefromcentroidinmeters &gt;= 2000.0 OR occurrence.distancefromcentroidinmeters IS NULL)
 AND (occurrence.specieskey IS NOT NULL AND occurrence."year" IS NOT NULL)
GROUP BY
 occurrence.kingdom,
 occurrence.kingdomkey,
 occurrence.phylum,
 occurrence.phylumkey,
 occurrence.class,
 occurrence.classkey,
 occurrence."order",
 occurrence.orderkey,
 occurrence.family,
 occurrence.familykey,
 occurrence.genus,
 occurrence.genuskey,
 occurrence.species,
 occurrence.specieskey,
 occurrence."year"

 The dataset's 11 records were derived from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0025782-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.c9euef
title: Occurrence Download

description: A dataset containing 16 species occurrences available in GBIF matching the query:
{
 "and" : [
 {
 "and" : [
 "DatasetKey is one of (VectorNet data Luxembourg 2023-2024, Tick collection_OH ALLIES project_Ireland, OH_SURVector_Hungary_Mosquitoes, VectorNet observations, Investigating the Role of Stable Flies (Stomoxys calcitrans) and Biting Midges (Culicoides spp.) of the genus Culicoides as Potential Mechanical Vectors of African Swine Fever Virus in Lithuania, Poland and Romania, Vector collection_OH surveillance project_Sweden, Monitoring competent vectors of Crimea Congo Haemorragic Fever (ticks) , West Nile and Rift Valley Fever in Spain (mosquitos), OH4Surveillance vector collection in Latvia, OH4Surveillance vector collection in Latvia, One Health Surveillance (OH4S) Vector Collection in Poland - ticks collection, One Health Surveillance (OH4S) Vector Collection in Poland - mosquitoes collection, Mosquito data OH4surveillance Denmark 2024, Tick and moquito collection_OH SURVECTOR project_Slovakia, Vector collection_OH surveillance project Estonia, VectorCollection_SIVIZ_project_Portugal, National tick surveillance in Austria for the detection of tick-borne pathogens 2024 - Project OH SURVector, Results of Tick (Hyalomma and Ixodes ricinus) and Mosquito Surveillance in Croatia in 2024, National mosquito surveillance in Austria for the detection of mosquito-borne pathogens 2024 - Project OH SURVector, VectorDistributionStatus)"
 ]
 },
 {
 "and" : [
 "TaxonKey is one of (Culex pipiens [GBIF Backbone Taxonomy])",
 "Country is one of (Moldova, Republic of)"
 ]
 }
 ]
}

 The dataset includes 16 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005565-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jmd8vu
title: Occurrence Download

description: A dataset containing 7098 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-149.56107 17.20101,-50.43893 17.20101,-50.43893 56.79899,-149.56107 56.79899,-149.56107 17.20101))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Oxytropis lambertii"
 ]
}

 The dataset includes 7098 records from 108 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005563-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5281/zenodo.18411878
title: EEG closed-loop (Behavioural task and data)
DOI: 10.5281/zenodo.18411879
title: EEG closed-loop (Behavioural task and data)
DOI: 10.15468/dl.y695xy
title: Occurrence Download

description: A dataset containing 5537 species occurrences available in GBIF matching the query:
{
 "and" : [
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Erigeron divergens"
 ]
}

 The dataset includes 5537 records from 132 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005564-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.mpdde9
title: Occurrence Download

description: A dataset containing 101093 records in GBIF matching the query:
SELECT
 '579' 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;= 61.2993700571118
 AND decimalLatitude &lt;= 66.79314043790278
 AND decimalLongitude &gt;= 7.910424340471731
 AND decimalLongitude &lt;= 17.960078459264157
 AND "year" &gt;= 2015
 AND "year" &lt;= 2026
 AND (coordinateUncertaintyInMeters &lt;= 100 OR coordinateUncertaintyInMeters IS NULL)
 GROUP BY fish_cell, cell

 The dataset's 101093 records were derived from 254 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005550-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.y65xn5
title: Occurrence Download

description: A dataset containing 0 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Heterosentis brasiliensis",
 "HasCoordinate is true",
 "HasGeospatialIssue is false"
 ]
}

 The dataset includes 0 records from 0 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005566-260126135527185/datasets/export for details.
DOI: 10.15468/dl.qdj5s5
title: Occurrence Download

description: A dataset containing 374 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Dasiphora parvifolia",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 374 records from 21 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005568-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.f2upru
title: Occurrence Download

description: A dataset containing 5 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-8.44170 35.33080,-1.98408 35.33080,-1.98408 37.91270,-8.44170 37.91270,-8.44170 35.33080))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Ponentina martigena"
 ]
}

 The dataset includes 5 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0005569-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.