cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5281/zenodo.18387833
title: DIVINE: Andalusia Agroclimatic Information Network Historic Datasets - CORDOBA - (June 24 - May 25)

description: This dataset contains high-resolution daily agroclimatic data from the RIA (Red de Información Agroclimática de Andalucía) network, managed by IFAPA. The data has been collected as part of the DIVINE project to support research in precision agriculture, water management, and climate adaptation in Southern Spain.

The dataset covers the period from June 1, 2024, to May 31, 2025, providing key parameters such as temperature (mean, max, min), humidity, wind speed, solar radiation, precipitation, and calculated ETo (Evapotranspiration) using the Penman-Monteith method.

Geographic Coverage and Station Distribution: The dataset includes part of the processed records from 123 monitoring stations distributed across the 8 provinces of Andalusia. In this case the data includes the ones in Córdoba.

Data Format:





Format: JSON (JavaScript Object Notation).




Naming Convention: 34 [Province_ID] [Station_ID] DIVINE [Station_Name] ([Province]).json




Coordinate System: WGS84 (included within the metadata of individual station files).



Source: Data retrieved from the official IFAPA RIAWS API (Junta de Andalucía).
DOI: 10.5061/dryad.2sr417nv
title: Data from: Linking the investigations of character evolution and species diversification

description: Variation in diversification rates is often studied by investigating
 traits related to species' ecology and life history. Often, however,
 it is unknown whether these traits evolve gradually or in punctuated
 bursts during speciation. Using phylogenetic data and species'
 present-day trait information, we present a novel approach to assess the
 mode of character change while accounting for trait-dependent speciation
 and extinction. Our model, "Binary-State Speciation and Extinction -
 node enhanced state shift" (BiSSE-ness), estimates both the rate of
 change occurring along lineages and the probability of change occurring
 during speciation, as well as independent speciation and extinction rates
 for each character state. Using simulations, we found that BiSSE- ness is
 able to distinguish along-lineage and speciational change and to estimate
 accurately the parameters associated with character change and
 diversification rates. We applied BiSSE-ness to an empirical primate data
 set, finding evidence for along-lineage changes in primate mating systems
 and social behaviours, whereas shifts in habitat were associated with
 speciation. In cases where trait changes may be linked to the speciation
 process itself (e.g., niche-related traits), BiSSE-ness provides a
 suitable framework in which to simultaneously address questions regarding
 species' diversification and character change.
description: BiSSE-nessContains the directories of data files and R code to complete BiSSE-ness using the R package diversitree.
DOI: 10.5061/dryad.4h402262
title: Data from: Diversity measures in environmental sequences are highly dependent on alignment quality—data from ITS and new LSU primers targeting basidiomycetes

description: The ribosomal DNA comprised of the ITS1-5.8S-ITS2 regions is widely used
 as a fungal marker in molecular ecology and systematics but cannot be
 aligned with confidence across genetically distant taxa. In order to study
 the diversity of Agaricomycotina in forest soils, we designed primers
 targeting the more alignable 28S (LSU) gene, which should be more useful
 for phylogenetic analyses of the detected taxa. This paper compares the
 performance of the established ITS1F/4B primer pair, which targets
 basidiomycetes, to that of two new pairs. Key factors in the comparison
 were the diversity covered, off-target amplification, rarefaction at
 different Operational Taxonomic Unit (OTU) cutoff levels, sensitivity of
 the method used to process the alignment to missing data and insecure
 positional homology, and the congruence of monophyletic clades with OTU
 assignments and BLAST-derived OTU names. The ITS primer pair yielded no
 off-target amplification but also exhibited the least fidelity to the
 expected phylogenetic groups. The LSU primers give complementary pictures
 of diversity, but were more sensitive to modifications of the alignment
 such as the removal of difficult-to align stretches. The LSU primers also
 yielded greater numbers of singletons but also had a greater tendency to
 produce OTUs containing sequences from a wider variety of species as
 judged by BLAST similarity. We introduced some new parameters to describe
 alignment heterogeneity based on Shannon entropy and the extent and
 contents of the OTUs in a phylogenetic tree space. Our results suggest
 that ITS should not be used when calculating phylogenetic trees from
 genetically distant sequences obtained from environmental DNA extractions
 and that it is inadvisable to define OTUs on the basis of very
 heterogeneous alignments.
description: PONE_mesquiteThis data file contains 3 alignments of fungal ITS rDNA sequences and 9 alignments of fungal LSU rDNA sequences amplified and cloned from total genomic DNA isolated from Ah horizon forest soil of the Hainich-Dün Biodiversity Exploratory.
DOI: 10.5061/dryad.383
title: Data from: Stability of Cladistic Relationships between Cetacea and Higher-Level Artiodactyl Taxa

description: Over the past ten years, the phylogenetic relationships among higher level
 artiodactyl taxa have been examined with multiple data sets. Many of these
 data sets suggest that Artiodactyla (even-toed ungulates) is paraphyletic
 and that Cetacea (whales) represents a highly derived
 "artiodactyl" subgroup. In this report, phylogenetic
 relationships between Cetacea and artiodactyls are tested with a
 combination of 15 published data sets plus new DNA sequence data from two
 nuclear loci, interphotoreceptor retinoid binding protein (IRBP) and von
 Willebrand factor (vWF). The addition of the IRBP and vWF character sets
 disrupts none of the relationships supported by recent cladistic analyses
 of the other 15 data sets. Simultaneous analyses support three critical
 clades: (Cetacea + Hippopotamidae), (Cetacea + Hippopotamidae +
 Ruminantia), and (Cetacea + Hippopotamidae + Ruminantia + Suina).
 Perturbations of the combined matrix show that the above clades are stable
 to a variety of disturbances. A chronicle of phylogenetic results over the
 past three years suggests that cladistic relationships between Cetacea and
 artiodactyls have been stable to increased taxonomic sampling and to the
 addition of over 1,400 informative characters from 15 data sets.
description: Gatesy et al Data Set
 1Gatesy1.htmGatesy et al Data Set 2Gatesy2.htm
DOI: 10.5061/dryad.8v7f3br5
title: Data from: Drosophila FoxP mutants are deficient in operant self-learning

description: Intact function of the Forkhead Box P2 (FOXP2) gene is necessary for
 normal development of speech and language. This important role has
 recently been extended, first to other forms of vocal learning in animals
 and then also to other forms of motor learning. The homology in structure
 and in function among the FoxP gene members raises the possibility that
 the ancestral FoxP gene may have evolved as a crucial component of the
 neural circuitry mediating motor learning. Here we report that genetic
 manipulations of the single Drosophila orthologue, dFoxP, disrupt operant
 self-learning, a form of motor learning sharing several conceptually
 analogous features with language acquisition. Structural alterations of
 the dFoxP locus uncovered the role of dFoxP in operant self-learning and
 habit formation, as well as the dispensability of dFoxP for operant
 world-learning, in which no motor learning occurs. These manipulations
 also led to subtle alterations in the brain anatomy, including a reduced
 volume of the optic glomeruli. RNAi-mediated interference with dFoxP
 expression levels copied the behavioral phenotype of the mutant flies,
 even in the absence of mRNA degradation. Our results provide evidence that
 motor learning and language acquisition share a common ancestral trait
 still present in extant invertebrates, manifest in operant self-learning.
 This ‘deep’ homology probably traces back to before the split between
 vertebrate and invertebrate animals.
description: flight
 performanceSemicolon delimited text
 file containing all the individual flight performance data (in s) for wild
 type Canton S and the three insertion mutant lines (Fig.
 2)flight_performance.txthabit-formationSemicolon delimited text file containing all the individual data for the habit-formation experiment (Fig. 4d).self-learningSemicolon delimited text file containing all the individual performance index data for all self-learning experiments (Fig. 3a2, 4b).world-learningSemicolon delimited text file containing all the individual performance index data for all world-learning experiments (Fig. 3b2, 4a).RT-PCR GelsAll full RT-PCR gels for mutants and RNAi experiments, heads (Figs. 3/4) and thoraxes (no figure in publication). Eight JPG files in a ZIP container.rt-pcr.zip
DOI: 10.15468/s4vf7q
title: Fort Lewis College Herbarium

description: The fungal collection of FLD contains approximately 1700 specimens of principally wood decay and macrofungi with a geographic focus on southwestern Colorado and the greater southwestern United States. The collection was started and built up by Dr. J. Page Lindsey who worked at Fort Lewis College from 1978-2009. FLD also includes a vascular plant collection consisting of ca. 17,000 specimens. The vascular plant collection is fully databased and searchable via the Southwest Environmental Information Network (https://swbiodiversity.org/seinet/).
DOI: 10.5061/dryad.qj8t7r0q
title: Data from: The velvet spiders: an atlas of the Eresidae (Arachnida, Araneae)

description: The family Eresidae C. L. Koch, 1850 is reviewed at the genus level. The
 family comprises nine genera including one new genus. They are: Adonea
 Simon, 1873, Dorceus C. L. Koch, 1846, Dresserus Simon, 1876, Eresus
 Walckenaer, 1805, Gandanameno Lehtinen, 1967, Loureedia gen. n., Paradonea
 Lawrence, 1968, Seothyra Purcell, 1903, and Stegodyphus Simon, 1873. A key
 to all genera and major lineages is provided along with corresponding
 diagnoses, as well as descriptions of selected species. These are
 documented with collections of photographs, scanning electron micrographs,
 and illustrations. A new phylogeny of Eresidae based on molecular sequence
 data expands on a previously published analysis. A species of the genus
 Paradonea Lawrence, 1968 is sequenced and placed phylogenetically for the
 first time. New sequences from twenty Gandanameno Lehtinen, 1967 specimens
 were added to investigate species limits within the genus. The genus
 Loureedia gen. n. is proposed to accommodate Eresus annulipes Lucas, 1857.
 Two species, Eresus semicanus Simon, 1908 and Eresus jerbae El-Hennawy,
 2005, are synonymized with Loureedia annulipes comb. n. One new species,
 Paradonea presleyi sp. n. is described. Eresus algericus El-Hennawy, 2004
 is transferred to Adonea Simon, 1873. The female of Dorceus fastuosus C.
 L. Koch, 1846 is described for the first time. The first figures depicting
 Paradonea splendens (Lawrence, 1936) are presented.
description: Milleretal_ZookeysMatrixPhylogenetic data matrix based on aligned molecular sequence data including commands for running analysis in Mr Bayes.Milleretal_EresidaeKML (Keyhole Markup Language) file for viewing specimen occurence records interactively in Google Earth (http://earth.google.com/).Milleretal_EresidaeSupplementaryDocsElectronic supplementary documents. Figure S1.: Bayesian phylogenetic tree. Figure S2: Photographs of copulatory organs from Gandanameno specimens used in molecular phylogenetic analysis. Figure S3: Photographs of copulatory organs from Gandanameno specimens used in molecular phylogenetic analysis.
DOI: 10.5061/dryad.p12305b2
title: Data from: Patterns and evolution of nucleotide landscapes in seed plants

description: Nucleotide landscapes, which is the way base composition is distributed
 along a genome, strongly vary among species. The underlying causes of
 these variations have been much debated. Though mutational bias and
 selection were initially invoked, GC-biased gene conversion (gBGC), a
 recombination-associated process favoring the G and C over A and T bases,
 is increasingly recognized as a major factor. As opposed to vertebrates,
 evolution of GC content is less well known in plants. Most studies have
 focused on the GC-poor and homogeneous Arabidopsis genome and the much
 more GC-rich and heterogeneous rice (Oryza sativa) genome and has often
 been generalized as a dicot/monocot dichotomy. This vision is clearly
 phylogenetically biased and does not allow understanding the mechanisms
 involved in GC-content evolution in plants. To tackle these issues, we
 used EST data from more than 200 species and provided the most
 comprehensive description of gene GC content across the seed plant
 phylogeny so far available. As opposed to the classically assumed
 dicot/monocot dichotomy, we found continuous variations in GC content from
 the probably ancestral GC-poor and homogeneous genomes to the more derived
 GC-rich and highly heterogeneous ones, with several independent enrichment
 episodes. Our results suggest that gBGC could play a significant role in
 the evolution of GC content in plant genomes.
description: tpc093674SupplementalDS4List of Genbank accession used for the EST dataset of the articletpc093674SupplementalDS5Acession numbers for the complete genome dataset of the article
DOI: 10.5061/dryad.8fp2pc88
title: Data from: A missense mutation in AGTPBP1 was identified in sheep with a lower motor neuron disease

description: A type of lower motor neuron (LMN) disease inherited as autosomal
 recessive in Romney sheep was characterized with normal appearance at
 birth, but with progressive weakness and tetraparesis after the first week
 of life. Here, we carried out genome-wide homozygosity mapping using
 Illumina Ovine SNP50 BeadChips on lambs descended from one carrier ram,
 including 19 sheep diagnosed as affected and 11 of their parents that were
 therefore known carriers. A homozygous region of 136 consecutive
 single-nucleotide polymorphism (SNP) loci on chromosome 2 was common to
 all affected sheep and it was the basis for searching for the positional
 candidate genes. Other homozygous regions shared by all affected sheep
 spanned eight or fewer SNP loci. The 136-SNP region contained the sheep
 ATP/GTP-binding protein 1 (AGTPBP1) gene. Mutations in this gene have been
 shown to be related to Purkinje cell degeneration (pcd) phenotypes
 including ataxia in mice. One missense mutation c.2909G&gt;C on exon
 21 of AGTPBP1 was discovered, which induces an Arg to Pro substitution
 (p.Arg970Pro) at amino-acid 970, a conserved residue for the catalytic
 activity of AGTPBP1. Genotyping of this mutation showed 100% concordant
 rate with the recessive pattern of inheritance in affected, carrier,
 phenotypically normal and unrelated normal individuals. This is the first
 report showing a mutant AGTPBP1 is associated with a LMN disease in a
 large mammal animal model. Our finding raises the possibility of human
 patients with the same etiology caused by this gene or other genes in the
 same pathway of neuronal development.
description: LMNSNPdataThis data achieve including all the genotypes for each SNP for each animal. The files were created from the original genotyping file using "awk" or "sort" commands.
DOI: 10.15468/paoyy3
title: Intermountain Herbarium (fungi, not lichens), Utah State University

description: The geographic focus of the Intermountain Herbarium is the area between the Sierra Nevada and the Rocky Mountains. The fungal collection includes both macrofungi and plant pathogens. Most of the macrofungi are from northern Utah. Dr. Bradley R. Kropp is Curator emeritus of Fungi.
DOI: 10.5061/dryad.b0c8470m
title: Data from: Estimating speciation and extinction rates for phylogenies of higher taxa

description: Speciation and extinction rates can be estimated from molecular
 phylogenies. Recently, a number of methods have been published showing
 that these rates can be estimated even if the phylogeny is incomplete,
 that is, if not all extant species are included. We show that the accuracy
 of such methods strongly depends on making the correct assumptions about
 how the sampling process was performed. We focus on phylogenies that are
 incomplete because some subclades (e.g., genera and families) are each
 represented as a single lineage. We show that previous methods implicitly
 assumed that such subclades are defined by randomly (or in an extreme
 deterministic way) choosing the edges that define the subclades from the
 complete species phylogeny. We show that these methods produce biased
 results if higher taxa are defined in a different manner. We introduce
 strict higher level phylogenies where subclades are defined so that the
 phylogeny is fully resolved from its origin to time xcut, and fully
 unresolved thereafter, so that for all subclades, stem age &gt; xcut
 &gt; crown age. We present estimates of speciation and extinction
 rates from a phylogeny of birds in which this subclade definition was
 applied. However, for most higher level phylogenies in the literature, it
 is unclear how higher taxa were defined, but often such phylogenies can be
 easily transformed into strict higher level phylogenies, as we illustrate
 by estimating speciation and extinction rates from a near-complete but
 only partly resolved species-level phylogeny of mammals. The accuracy of
 our methods is verified using simulations.
description: GroupTaxaAppendixSupplementary InformationSFig1Supplementary Figure 1SFig2Supplementary Figure 2
DOI: 10.5061/dryad.gd031k26
title: Data from: Dynamic antagonism between phytochromes and PIF-family bHLHs induces selective reciprocal responses to light and shade in a rapidly responsive transcriptional network in Arabidopsis

description: Plants respond to shade-modulated light-signals, via the phytochrome (phy)
 system, by adaptive changes, collectively termed the shade avoidance
 syndrome (SAS). To examine the roles of the Phy-Interacting bHLH Factors,
 PIF1, 3, 4 and 5, in relaying this information to the transcriptional
 network, we compared the genome-wide expression profiles of wild-type and
 quadruple pif (pifq) mutants in response to shade. The data identify a
 subset of genes, enriched in transcription-factor-encoding loci, that
 respond rapidly (within 1 h), in a PIF-dependent manner, to the shade
 signal, and that contain promoter-located G-box-sequence motifs (CACGTG),
 known to be preferred PIF binding sites. These genes are thus potential
 direct targets of phy-PIF signaling that function in the primary
 transcriptional circuitry controlling downstream response-elaboration. A
 second subset of PIF-dependent, early-response genes, lacking G-box
 motifs, are enriched for auxin-responsive loci, suggestive of being
 indirect targets of phy-PIF signaling involved in the rapid cell-expansion
 known to be induced by shade. A meta-analysis comparing deetiolation- and
 shade-responsive transcriptomes identifies a further subset of
 G-box-containing genes that reciprocally display rapid repression and
 induction in response to light and shade signals at the inception of
 deetiolation and shade-avoidance, respectively. Collectively, these data
 define a core set of transcriptional and hormonal (auxin, cytokinin)
 processes that appear to be dynamically poised to react rapidly to changes
 in the light environment via perturbations in the mutually antagonistic
 actions of the phys and PIFs. Data from comparative analysis of the
 quadruple pifq and all triple pif-mutant combinations in response to light
 and shade, confirm that the PIF-quartet members act with overlapping
 redundancy on seedling morphogenesis and transcriptional regulation, but
 that the individual PIFs contribute differentially to these responses.
description: Supplemental Dataset
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DOI: 10.5061/dryad.d3t16pd2
title: Data from: Pleistocene and ecological effects on continental-scale genetic differentiation in the bobcat (Lynx rufus)

description: The potential for widespread, mobile species to exhibit genetic structure
 without clear geographic barriers is a topic of growing interest. Yet the
 patterns and mechanisms of structure – particularly over broad spatial
 scales – remain largely unexplored for these species. Bobcats occur across
 North America and possess many characteristics expected to promote gene
 flow. To test whether historical, topographic, or ecological factors have
 influenced genetic differentiation in this species, we analyzed 1 KB mtDNA
 sequence and 15 microsatellite loci from over 1700 samples collected
 across its range. The primary signature in both marker types involved a
 longitudinal cline with a sharp transition, or suture zone, occurring
 along the Great Plains. Thus, the data distinguished bobcats in the
 eastern U.S. from those in the western half, with no obvious physical
 barrier to gene flow. Demographic analyses supported a scenario of
 expansion from separate Pleistocene refugia, with the Great Plains
 representing a zone of secondary contact. Substructure within the two main
 lineages likely reflected founder effects, ecological factors,
 anthropogenic/topographic effects, or a combination of these forces. Two
 prominent topographic features, the Mississippi River and Rocky Mountains,
 were not supported as significant genetic barriers. Ecological regions and
 environmental correlates explained a small but significant proportion of
 genetic variation. Overall, results implicate historical processes as the
 primary cause of broad-scale genetic differentiation, but contemporary
 forces seem to also play a role in promoting and maintaining structure.
 Despite the bobcat’s mobility and broad niche, large-scale landscape
 changes have contributed to significant and complex patterns of genetic
 structure.
description: Unique mtDNA haplotypes
 (n=73)Nexus file containing
 the sequences (949 bp) of the 73 unique ND5 mtDNA haplotypes discovered
 among 1128 bobcat samples. Also included in the file is the sequence
 "lynx" that was used as an outgroup (Canada lynx, Genbank
 accession AY598481).N73andOut.nexIndividual mtDNA sequences (n=1128)Nexus file containing the 949 bp mtDNA ND5 sequences for each of the 1128 bobcat samples analyzed. Sequence name corresponds to the sample ID.FinalSEQset.nexMicrosatellite and Spatial Coordinate Data (n=1702)Tab-delimited file containing microsatellite data, spatial coordinates, and other information for 1702 bobcat samples used in this study.SampleData.txtTableS2Summary of mtDNA and microsatellite genetic variation for 52 a priori "sample groups". Note that this table also appears as an Excel file in online supplementary information associated with this article in Molecular Ecology.
DOI: 10.5281/zenodo.15263400
title: Using Digital Prompts to Support Physics Students Self-Regulated Learning

description: csv file pre-post student survey data and learning outcome in a business-as-usual condition (student id starting in SP23) and intervention condition (student id starting in SP24).