cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.15468/dl.fhaqsm
title: Occurrence Download

description: A dataset containing 2113 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Vinca",
 "GadmGid is one of (USA.6_1, USA.17_1, USA.27_1, USA.28_1, USA.32_1, USA.35_1, USA.37_1, USA.42_1, USA.44_1, USA.51_1)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "BasisOfRecord is one of (Human Observation, Machine Observation)"
 ]
}

 The dataset includes 2113 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009359-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/13876260
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.34780/8zjhvwdq
title: Kitti Köhler, The biological reconstruction of the population of the Late Neolithic Lengyel culture of Alsónyék-Bátaszék. Appendix 1: Tables 1–132

description: Appendix 1 comprises Tables 1–132. Appendices 2–4 are printed.
DOI: 10.21227/xksh-v784
title: "Innovation Progress and Collaborative Networks in China\u2019s Nuclear Fusion Technology: A Patent Analysis"

description: "Nuclear fusion has emerged as a global strategic priority, with China becoming a pivotal force. However, the internal mechanisms of its innovation ecosystem remain underexplored. This study analyzes 5,144 global patent data points (including 1,366 from China) using the Herfindahl-Hirschman Index (HHI), Latent Dirichlet Allocation (LDA), and Social Network Analysis (SNA) to unveil the system\u2019s structure and evolution. Results indicate: (1) Macro-structure: China\u2019s system exhibits a 'relative concentration' (HHI \u2248 456), significantly higher than the US 'dispersed' model (HHI \u2248 45), characterized by a unique 'Dual-Core' structure led by national institutes. (2) Technological Evolution: A clear strategic shift from \u201cfundamental physics\u201d to \u201cengineering breakthroughs\u201d is identified. (3) Network Structure: The collaborative network is sparse and fragmented, dominated by two \u201cNational Team\u201d clusters (HFIPS and SWIP). (4) Operational Mechanisms: This fragmentation reflects an \u201cordered division of labor\u201d, where research institutes act as system integrators, universities lead in basic science, and enterprises serve as specialized suppliers. Consequently, this study quantitatively characterizes the operational mode of China\u2019s \u201cWhole-of-Nation System\u201d as a mission-oriented, highly concentrated, and specialized division of labor system defined by \u201ccore-periphery\u201d clusters."
DOI: 10.13140/rg.2.2.35051.40486
title: Bollettino sismico Regione Umbria 2022 per Google Earth
DOI: 10.15468/dl.ur8fc3
title: Occurrence Download

description: A dataset containing 31 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Rhabdophis leonardi)",
 "DecimalLatitude is greater than or equal to 0",
 "DecimalLatitude is less than or equal to 60",
 "DecimalLongitude is greater than or equal to 60",
 "DecimalLongitude is less than or equal to 150",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 31 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009361-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.xuagt3
title: Occurrence Download

description: A dataset containing 3891630 species occurrences available in GBIF matching the query:
{
 "TaxonKey" : [
 "is one of (Aphanius baeticus, Aphanius iberus, Salmo trutta)"
 ]
}

 The dataset includes 3891630 records from 757 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0009334-251120083545085/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.34740/kaggle/dsv/12039564
title: Peer-to-Peer Boliviano (BOB) Exchange Data
DOI: 10.15468/dl.d6naqk
title: Occurrence Download

description: A dataset containing 130 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Country is Canada",
 {
 "or" : [
 "Geometry POLYGON((-53.63479 46.22031,-51.83294 46.22031,-51.83294 51.5678,-53.63479 51.5678,-53.63479 46.22031))",
 "Geometry POLYGON((-59.69696 46.35429,-51.43476 46.35429,-51.43476 51.77504,-59.69696 51.77504,-59.69696 46.35429))"
 ]
 },
 "HasGeospatialIssue is false",
 "TaxonKey is Fraxinus nigra Marshall"
 ]
}

 The dataset includes 130 records from 3 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0015982-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.jg2r6b
title: Occurrence Download

description: A dataset containing 12924 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Antigonon leptopus Hook. & Arn.)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present"
 ]
}

 The dataset includes 12924 records from 338 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010673-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.25w2z8
title: Occurrence Download

description: A dataset containing 77 species occurrences available in GBIF matching the query:
{
 "and" : [
 "BasisOfRecord is one of (Human Observation, Occurrence evidence, Observation)",
 "OccurrenceStatus is Present",
 "TaxonKey is Pisonia rotundata Griseb."
 ]
}

 The dataset includes 77 records from 2 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0010674-250525065834625/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.7hm2cf
title: Occurrence Download

description: A dataset containing 14 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is one of (Pingalla lorentzi)",
 "BasisOfRecord is one of (Specimen, Literature Occurrence, Human Observation, Observation)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1991",
 "Year is less than or equal to 2025"
 ]
}

 The dataset includes 14 records from 4 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0024722-250811113504898/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.15468/dl.s5x9sz
title: Occurrence Download

description: A dataset containing 19686 species occurrences available in GBIF matching the query:
{
 "DatasetKey" : [
 "is Prairie Fen Biodiversity Project"
 ]
}

 The dataset includes 19686 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001494-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t7sq1
title: Data from: Genome-wide assessment of population structure and genetic diversity and development of a core germplasm set for sweet potato based on specific length amplified fragment (SLAF) sequencing

description: Sweet potato, Ipomoea batatas (L.) Lam., is an important food crop that is
 cultivated worldwide. However, no genome-wide assessment of the genetic
 diversity of sweet potato has been reported to date. In the present study,
 the population structure and genetic diversity of 197 sweet potato
 accessions most of which were from China were assessed using 62,363 SNPs.
 A model-based structure analysis divided the accessions into three groups:
 group 1, group 2 and group 3. The genetic relationships among the
 accessions were evaluated using a phylogenetic tree, which clustered all
 the accessions into three major groups. A principal component analysis
 (PCA) showed that the accessions were distributed according to their
 population structure. The mean genetic distance among accessions ranged
 from 0.290 for group 1 to 0.311 for group 3, and the mean polymorphic
 information content (PIC) ranged from 0.232 for group 1 to 0.251 for group
 3. The mean minor allele frequency (MAF) ranged from 0.207 for group 1 to
 0.222 for group 3. Analysis of molecular variance (AMOVA) showed that the
 maximum diversity was within accessions (89.569%). Using CoreHunter
 software, a core set of 39 accessions was obtained, which accounted for
 approximately 19.8% of the total collection. The core germplasm set of
 sweet potato developed will be a valuable resource for future sweet potato
 improvement strategies.
description: Sweet_Potato.all.snplistThis file contained all the SNPs developed in this study, you can open the file by using software,like Pilotedit.
DOI: 10.5061/dryad.q29c0
title: Data from: Functional preservation and variation in the cone opsin genes of nocturnal tarsiers

description: The short-wavelength sensitive (S-) opsin gene OPN1SW is pseudogenized in
 some nocturnal primates and retained in others, enabling dichromatic
 colour vision. Debate on the functional significance of this variation has
 focused on dark conditions, yet many nocturnal species initiate activity
 under dim (mesopic) light levels that can support colour vision. Tarsiers
 are nocturnal, twilight-active primates and exemplary visual predators;
 they also express different colour vision phenotypes, raising the
 possibility of discrete adaptations to mesopic conditions. To explore this
 premise, we conducted a field study in two stages. First, to estimate the
 level of functional constraint on colour vision, we sequenced OPN1SW in 12
 wild-caught Philippine tarsiers (Tarsius syrichta). Second, to explore
 whether the dichromatic visual systems of Philippine and Bornean (Tarsius
 bancanus) tarsiers—which express alternate versions of the
 medium/long-wavelength sensitive (M/L-) opsin gene OPN1MW/OPN1LW—confer
 differential advantages specific to their respective habitats, we used
 twilight and moonlight conditions to model the visual contrasts of
 invertebrate prey. We detected a signature of purifying selection for
 OPN1SW, indicating that colour vision confers an adaptive advantage to
 tarsiers. However, this advantage extends to a relatively small proportion
 of prey–background contrasts, and mostly brown arthropod prey amid leaf
 litter. We also found that the colour vision of T. bancanus is
 advantageous for discriminating prey under twilight that is enriched in
 shorter (bluer) wavelengths, a plausible idiosyncrasy of understorey
 habitats in Borneo.
description: Irradiance Spectra
 RSTB.2016.0075Irradiance spectra of
 downwelling twilight in the understorey habitat of Philippine tarsiers
 (Visayas State University, Leyte, Philippines). For irradiance spectra of
 twilight and moonlight in the understorey habitat of Bornean tarsiers, see
 Melin et al. 2012 (doi:10.1002/ajp.21996).Spectral Reflectance
 Data RSTB.2016.0075Reflectance spectra of
 invertebrate prey and their corresponding backgrounds collected at
 tarsier-inhabited sites. Reflectance spectra were measured with a USB2000
 spectrometer calibrated against the WS1 reflectance standard. Spectra were
 processed and smoothed.
DOI: 10.5061/dryad.6vf7j
title: Data from: Mitogenomes and relatedness do not predict frequency of tool-use by sea otters

description: Many ecological aspects of tool-use in sea otters are similar to those in
 Indo-Pacific bottlenose dolphins. Within an area, most tool-using dolphins
 share a single mitochondrial haplotype and are more related to each other
 than to the population as a whole. We asked whether sea otters in
 California showed similar genetic patterns by sequencing mitogenomes of 43
 otters and genotyping 154 otters at 38 microsatellite loci. There were six
 variable sites in the mitogenome that yielded three haplotypes, one found
 in only a single individual. The other two haplotypes contained similar
 percentages (33 and 36%) of frequent tool-users and a variety of diet
 types. Microsatellite analyses showed that snail specialists, the diet
 specialist group that most frequently used tools, were no more related to
 each other than to the population as a whole. The lack of genetic
 association among tool-using sea otters compared with dolphins may result
 from the length of time each species has been using tools. Tool-use in
 dolphins appears to be a relatively recent innovation (less than 200
 years) but sea otters have probably been using tools for many thousands or
 even millions of years.
description: Sea Otter Mitogenomes
 Alignment43 California sea otter
 mitogenomes, mapped and aligned in Geneious 9.0.5SeaOtterMitoGenomes-43Alignment.fastaAnnotations for Sea Otter MitoGenomesAnnotation table for 43 California Sea Otter mitogenomesAnnotations-SeaOtterMitoGenomes.csvMicrosatellite genotypesGenotypes-SOtooluse.txt
DOI: 10.5061/dryad.1pb63
title: Data from: Segmental allotetraploidy generates extensive homeologous expression rewiring and phenotypic diversity at the population level in rice

description: Allopolyploidization, i.e., concomitant merging and doubling of two or
 more divergent genomes in a common nucleus/cytoplasm, is known to
 instantly alter genome-wide transcriptome dynamics, a phenomenon referred
 to as “transcriptomic shock”. However, the immediate effects of
 transcriptomic alteration in generating phenotypic diversity at the
 population level remain under-investigated. Here, we employed the
 MassARRAY-based Sequenom platform to assess and compare orthologous,
 allelic, and homeologous gene expression status in two tissues (leaf and
 root) of a set of randomly chosen individuals from populations of parental
 rice subspecies (indica and japonica), in vitro “hybrids” (parental
 mixes), reciprocal F1 hybrids and reciprocal tetraploids at the 5th-selfed
 generation (S5). We show that hybridization and whole genome duplication
 (WGD) have opposing effects on allelic and homeologous expression in the
 F1 hybrids and tetraploids, respectively. Whereas hybridization exerts
 strong attenuating effects on allelic expression differences in diploid
 hybrids, WGD augments the intrinsic parental differences and generates
 extensive and variable homeolog content which triggers diversification in
 expression patterning among the tetraploid plants. Coupled with the vast
 phenotypic diversity observed among the tetraploid individuals, our
 results provide experimental evidence in support of the notion that
 allopolyploidy catalyzes rapid phenotypic diversification in higher
 plants. Our data further suggest that largely stochastic homeolog content
 reshuffling rather than alteration in total expression level may be an
 important feature of evolution in young segmental allopolyploids, which
 underlies rapid expression diversity at the population level.
description: MassARRAY
 datathe MassARRAY data for
 genotyping analysis of article "Allotetraploidy generates extensive
 homeologous expression rewiring and phenotypic diversity at the population
 level in rice"
DOI: 10.5061/dryad.r1478
title: Data from: Mutualistic strategies minimize coextinction in plant-disperser networks

description: The global decline of mutualists such as pollinators and seed dispersers
 may cause negative direct and indirect impacts on biodiversity.
 Mutualistic network models used to understand the stability of mutualistic
 systems indicate that species with low partner diversity are most
 vulnerable to coextinction following mutualism disruption. However,
 existing models have not considered how species vary in their dependence
 on mutualistic interactions for reproduction or survival, overlooking the
 potential influence of this variation on species' coextinction
 vulnerability and on network stability. Using global databases and field
 experiments focused on the seed dispersal mutualism, we found that plants
 and animals that depend heavily on mutualistic interactions have higher
 partner diversity. Under simulated network disruption, this empirical
 relationship strongly reduced coextinction because the species most likely
 to lose mutualists depend least on their mutualists. The pattern also
 reduced the importance of network structure for stability; nested network
 structure had little effect on coextinction after simulations incorporated
 the empirically derived relationship between partner diversity and
 mutualistic dependence. Our results highlight a previously unknown source
 of stability in mutualistic networks and suggest that differences among
 species in their mutualistic strategy, rather than network structure,
 primarily accounts for stability in mutualistic communities.
description: Data and
 codeThis zip file contains
 an R project file, data, and code to reproduce analyses and simulations.
 Note that some simulations are commented out in the R code due to the long
 run time - the code instead reads in saved .csv files with simulation
 outputs from the "output data" folder.Network
 PRSB.zip
DOI: 10.5061/dryad.713q3
title: Data from: Positive selection on sperm ion channels in a brooding brittle star: consequence of life-history traits evolution

description: Closely related species are key models to investigate mechanisms leading
 to reproductive isolation and early stages of diversification, also at the
 genomic level. The brittle star cryptic species complex Ophioderma
 longicauda encompasses the sympatric broadcast spawning species C3 and the
 internal brooding species C5. Here we used de novo transcriptome
 sequencing and assembly in two closely related species displaying
 contrasting reproductive modes to compare their genetic diversity and to
 investigate the role of natural selection in reproductive isolation. We
 reconstructed 20,146 and 22,123 genes for C3 and C5, respectively, and
 characterized a set of 12,229 orthologs. Genetic diversity was 1.5-2 times
 higher in C3 compared to C5, confirming that species with low parental
 investment display higher levels of genetic diversity. Forty-eight genes
 were the targets of positive diversifying selection during the evolution
 of the two species. Notably, two genes (NHE and TetraKCNG) are
 sperm-specific ion channels involved in sperm motility. Ancestral sequence
 reconstructions show that natural selection targeted the two genes in the
 brooding species. This may result from an adaptation to the novel
 environmental conditions surrounding sperm in the brooding species, either
 directly affecting sperm, or via an increase in male/female conflict. This
 phenomenon could have promoted prezygotic reproductive isolation between
 C3 and C5. Finally, the sperm receptors to egg chemoattractants differed
 between C3 and C5 in the ligand-binding region. We propose that mechanisms
 of species-specific gamete recognition in brittle stars occur during sperm
 chemotaxis (sperm attraction towards the eggs), contrary to other marine
 invertebrates where prezygotic barriers to interspecific hybridization
 typically occur before sperm-egg fusion.
description: assembled_transcriptomesHere you will find the assembled transcriptomes for the brittle star species Ophioderma longicauda C3 (broadcasting species) and Ophioderma longicauda C5 (brooding species)alignmentsHere you will find the alignments in fasta format of the 11 genes evolving under positive selection (the ones listed in Table 3 of the article) and the alignments for the genes involved in fertilization and species recognition in other marine invertebrates (the ones listed in Table 4; e.g. bindin)
DOI: 10.5061/dryad.4ff5n
title: Data from: Pharmacological inactivation does not support a unique causal role for intraparietal sulcus in the discrimination of visual number

description: The “number sense” describes the intuitive ability to quantify without
 counting. Single neuron recordings in non-human primates and functional
 imaging in humans suggest the intraparietal sulcus is an important
 neuroanatomical locus of numerical estimation. Other lines of inquiry
 implicate the IPS in numerous other functions, including attention and
 decision making. Here we provide a direct test of whether IPS has
 functional specificity for numerosity judgments. We used muscimol to
 reversibly and independently inactivate the ventral and lateral
 intraparietal areas in two monkeys performing a numerical discrimination
 task and a color discrimination task, roughly equilibrated for difficulty.
 Inactivation of either area caused parallel impairments in both tasks and
 no evidence of a selective deficit in numerical processing. These findings
 do not support a causal role for the IPS in numerical discrimination,
 except insofar as it also has a role in the discrimination of color. We
 discuss our findings in light of several alternative hypotheses of IPS
 function, including a role in orienting responses, a general cognitive
 role in attention and decision making processes and a more specific role
 in ordinal comparison that encompasses both number and color judgments.
description: LIP
 dataData from the LIP
 experiment.LIP_data.csvVIP dataData from the VIP experiment.VIP_data.csv
DOI: 10.5061/dryad.2nd84
title: Data from: The NBS-LRR architectures of plant R-proteins and metazoan NLRs evolved in independent events

description: There are intriguing parallels between plants and animals, with respect to
 the structures of their innate immune receptors, that suggest universal
 principles of innate immunity. The cytosolic nucleotide binding
 site–leucine rich repeat (NBS-LRR) resistance proteins of plants
 (R-proteins) and the so-called NOD-like receptors of animals (NLRs) share
 a domain architecture that includes a STAND (signal transduction ATPases
 with numerous domains) family NTPase followed by a series of LRRs,
 suggesting inheritance from a common ancestor with that architecture.
 Focusing on the STAND NTPases of plant R-proteins, animal NLRs, and their
 homologs that represent the NB-ARC (nucleotide-binding adaptor shared by
 APAF-1, certain R gene products and CED-4) and NACHT (named for NAIP,
 CIIA, HET-E, and TEP1) subfamilies of the STAND NTPases, we analyzed the
 phylogenetic distribution of the NBS-LRR domain architecture, used
 maximum-likelihood methods to infer a phylogeny of the NTPase domains of
 R-proteins, and reconstructed the domain structure of the protein
 containing the common ancestor of the STAND NTPase domain of R-proteins
 and NLRs. Our analyses reject monophyly of plant R-proteins and NLRs and
 suggest that the protein containing the last common ancestor of the STAND
 NTPases of plant R-proteins and animal NLRs (and, by extension, all NB-ARC
 and NACHT domains) possessed a domain structure that included a STAND
 NTPase paired with a series of tetratricopeptide repeats. These analyses
 reject the hypothesis that the domain architecture of R-proteins and NLRs
 was inherited from a common ancestor and instead suggest the domain
 architecture evolved at least twice. It remains unclear whether the
 NBS-LRR architectures were innovations of plants and animals themselves or
 were acquired by one or both lineages through horizontal gene transfer.
description: Urbach_and_Ausubel_PNAS_2017_20170104Scripts and data files associated with Urbach and Ausubel PNAS 2017