cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.m346b576
title: Data from: DNA from soil mirrors plant taxonomic and growth form diversity

description: Ecosystems across the globe are threatened by climate change and human
 activities. New rapid survey approaches for monitoring biodiversity would
 greatly advance assessment and understanding of these threats. Taking
 advantage of next-generation DNA sequencing, we tested an approach we call
 metabarcoding: high-throughput and simultaneous taxa identification based
 on a very short (usually less than 100 base pairs) but informative DNA
 fragment. Short DNA fragments allow the use of degraded DNA from
 environmental samples. All analyses included amplification using
 plant-specific versatile primers, sequencing and estimation of taxonomic
 diversity. We tested in three steps whether degraded DNA from dead
 material in soil has the potential of efficiently assessing biodiversity
 in different biomes. First, soil DNA from eight boreal plant communities
 located in two different vegetation types (meadow and heath) was
 amplified. Plant diversity detected from boreal soil was highly consistent
 with plant functional and structural diversity estimated from conventional
 above-ground surveys. Second, we assessed DNA persistence using samples
 from formerly cultivated soils in temperate environments. We found that
 number of crop DNA sequences retrieved strongly varied with years since
 last cultivation, and crop sequences were absent from nearby, uncultivated
 plots. Third, we assessed the universal applicability of DNA metabarcoding
 using soil samples from tropical environments: a large proportion of
 species and families from the study site was efficiently recovered. The
 results open unprecedented opportunities for large-scale DNA-based
 biodiversity studies across a range of taxonomic groups using standardized
 metabarcoding approaches.
description: Yoccoz_et_al_Table_S1Supplementary Table with description of the results obtained for the Boreal site.Yoccoz_et_al_Table_S2Supplementary Table showing the results obtained for the Tropical site.Boreal_sequence_datafasta file.Tropical_sequence_dataFasta file.Temperate_sequence_dataFasta file.Temperate_sequence_data_filteredTab file.
DOI: 10.5061/dryad.3q3b7740
title: Data from: A field test for host fruit odour discrimination and avoidance behaviour for Rhagoletis pomonella flies in the western United States

description: Prezygotic isolation due to habitat choice is important to many models of
 speciation-with-gene-flow. Habitat choice is usually thought to occur
 through positive preferences of organisms for particular environments.
 However, avoidance of non-natal environments may also play a role in
 choice and have repercussions for postzygotic isolation that preference
 does not. The recent host shift of Rhagoletis pomonella (Diptera:
 Tephritidae) from downy hawthorn, Crataegus mollis, to introduced apple,
 Malus domestica, in the eastern U.S. is a model for speciation-with-gene
 flow. However, the fly is also present in the western U.S. where it was
 likely introduced via infested apples &lt; 60 years ago. R. pomonella
 now attacks two additional hawthorns in the West, the native C. douglasii
 (black hawthorn) and the introduced C. monogyna (English ornamental
 hawthorn). Flight tunnel tests have shown that western apple-, C.
 douglasii-, and C. monogyna-origin flies all positively orient to fruit
 volatile blends of their respective natal hosts in flight tunnel assays.
 Here, we show that these laboratory differences translate to nature
 through field trapping studies of flies in the state of Washington.
 Moreover, western R. pomonella display both positive orientation to their
 respective natal fruit volatiles and avoidance behaviour (negative
 orientation) to non-natal volatiles. Our results are consistent with the
 existence of behaviourally differentiated host races of R. pomonella in
 the West. In addition, the rapid evolution of avoidance behaviour appears
 to be a general phenomenon for R. pomonella during host shifts, as the
 eastern apple and downy hawthorn host races also are antagonized by
 non-natal fruit volatiles.
description: TableS1SimetalBlackHawSite2010TableS2SimetalAppleSite2011
DOI: 10.5061/dryad.jf04r362
title: Data from: Shared spatial effects on quantitative genetic parameters: accounting for spatial autocorrelation and home range overlap reduces estimates of heritability in wild red deer

description: Social structure, limited dispersal and spatial heterogeneity in resources
 are ubiquitous in wild vertebrate populations. As a result, relatives
 share environments as well as genes, and environmental and genetic sources
 of similarity between individuals are potentially confounded. Quantitative
 genetic studies in the wild therefore typically account for easily
 captured shared environmental effects (e.g. parent, nest or region).
 Fine-scale spatial effects are likely to be just as important in wild
 vertebrates, but have been largely ignored. We used data from wild red
 deer to build ‘animal models’ to estimate additive genetic variance and
 heritability in four female traits (spring and rut home range size,
 offspring birth weight and lifetime breeding success). We then,
 separately, incorporated spatial autocorrelation and a matrix of home
 range overlap into these models to estimate the effect of location or
 shared habitat on phenotypic variation. These terms explained a
 substantial amount of variation in all traits and their inclusion resulted
 in reductions in heritability estimates, up to an order of magnitude up
 for home range size. Our results highlight the potential of multiple
 covariance matrices to dissect environmental, social and genetic
 contributions to phenotypic variation, and the importance of considering
 fine-scale spatial processes in quantitative genetic studies.
description: Red Deer
 PedigreeRed Deer
 PedigreeDeerPed.pedBirth weight dataANIMAL: Identity of female | MOTHER | Sex: Sex of offspring | BirthYear: Birth Year of offspring | BirthWt:Birth weight of offspring | MumAVCOL: Average column location of female | MumAVROW: Average row location of female | MumAge: Female's age | MumRegion: Female's region | MumReps: Female's reproductive statusLBS dataANIMAL: Identity of female | MOTHER | LBS: Lifetime breeding success | BirthYear: Birth Year of female | AVCOL: Average column location of female | AVROW: Average row location of female | Region:Female's regionRut home range size dataANIMAL: Identity of female | MOTHER | HOMERANGE: Rut home range size | Year: Year of observation | NoFixes: Number of locations used to calculate home range | AGE: Age of female | REGION: Female's region | LOCALPOP: Local population densityRut home range data.DATSpring home range size dataANIMAL: Identity of female | MOTHER | HOMERANGE: Rut home range size | Year: Year of observation | AGE: Age of female | REGION: Female's region | LOCALPOP: Local population density | REPS: Reproductive status of female | AVCOL: Average column location of female | AVROW: Average row location of femaleSpring home range data.datRut home range overlap matrixruthroverlap.grmSpring home range overlap matrixsproverlap.grm
DOI: 10.5061/dryad.b4d75m52
title: Data from: Biodiversity soup: metabarcoding of arthropods for rapid biodiversity assessment and biomonitoring

description: 1) Traditional biodiversity assessment is costly in time, money, and
 taxonomic expertise. Moreover, data are frequently collected in ways (e.g.
 visual bird lists) that are unsuitable for auditing by neutral parties,
 which is necessary for dispute resolution. 2) We present protocols for the
 extraction of ecological, taxonomic and phylogenetic information from bulk
 samples of arthropods. The protocols combine mass trapping of arthropods,
 mass-PCR amplification of the COI barcode gene, pyrosequencing, and
 bioinformatic analysis, which together we call ‘metabarcoding.’ 3) We
 construct seven communities of arthropods (mostly insects) and show that
 it is possible to recover a substantial proportion of the original
 taxonomic information. We further demonstrate, for the first time, that
 metabarcoding allows for the precise estimation of pairwise community
 dissimilarity (beta diversity) and within-community phylogenetic diversity
 (alpha diversity), despite the inevitable loss of taxonomic information
 inherent to metabarcoding. 4) Alpha and beta diversity metrics are the raw
 materials of ecology and the environmental sciences, facilitating
 assessment of the state of the environment with a broad and efficient
 measure of biodiversity.
description: Sequences after initial
 processing in QIIME (seqs.fna, library 1)Raw sequence data from
 the Roche 454 GS FLX sequencer, region 1 (split_library_output_1). These
 data are the output of the command: split_libraries.py -m 454_Map.txt -f
 1.TCA.454Reads.fna -q 1.TCA.454Reads.qual -o split_library_output_1/ -l
 100 -L 700 -H 9 -M 2 -b 10seqs.fnaSequences after initial processing in QIIME (seqs.fna, library 2)Raw sequence data from the Roche 454 GS FLX sequencer, region 2 (split_library_output_2). These data are the output of the command: split_libraries.py -m 454_Map.txt -f 2.TCA.454Reads.fna -q 2.TCA.454Reads.qual -o split_library_output_2/ -l 100 -L 700 -H 9 -M 2 -b 10 -n 55100seqs.fna
DOI: 10.5061/dryad.td03p886
title: Data from: Phylogenetic conservatism in plant phenology

description: Phenological events – defined points in the life cycle of a plant or
 animal – have been regarded as highly plastic traits, reflecting flexible
 responses to various environmental cues. The ability of a species to
 track, via shifts in phenological events, the abiotic environment through
 time might dictate its vulnerability to future climate change.
 Understanding the predictors and drivers of phenological change is
 therefore critical. Here, we evaluated evidence for phylogenetic
 conservatism – the tendency for closely related species to share similar
 ecological and biological attributes – in phenological traits across
 flowering plants. We aggregated published and unpublished data on timing
 of first flower and first leaf, encompassing ˜4000 species at 23 sites
 across the Northern Hemisphere. We reconstructed the phylogeny for the set
 of included species, first, using the software program Phylomatic, and
 second, from DNA data. We then quantified phylogenetic conservatism in
 plant phenology within and across sites. We show that more closely related
 species tend to flower and leaf at similar times. By contrasting mean
 flowering times within and across sites, however, we illustrate that it is
 not the time of year that is conserved, but rather the phenological
 responses to a common set of abiotic cues. Our findings suggest that
 species cannot be treated as statistically independent when modelling
 phenological responses. Synthesis. Closely related species tend to
 resemble each other in the timing of their life-history events, a likely
 product of evolutionarily conserved responses to environmental cues. The
 search for the underlying drivers of phenology must therefore account for
 species' shared evolutionary histories.
description: Generic level
 phylogenetic treeGeneric level
 phylogenetic tree for 1246 plant species. The tree was calibrated using
 penalized likelihood.nceas_genera_pl.divDNA matrixDNA matrix based on 7 different DNA regions for the 1246 generanceas_genus.phy.gz
DOI: 10.5061/dryad.231g746f
title: Data from: Complex patterns of host switching in New World Arenaviruses

description: We empirically tested the long-standing hypothesis of codivergence of New
 World arenaviruses (NWA) with their hosts. We constructed phylogenies for
 NWA and all known hosts and used them in reconciliation analyses. We also
 constructed a phylogenetic tree of all Sigmodontinae and Neotominae
 rodents and tested whether viral–host associations were phylogenetically
 clustered. We determined host geographical overlap to determine to what
 extent opportunity to switch hosts was limited by host relatedness or
 physical proximity. With the exception of viruses from North America, no
 phylogenetically codivergent pattern between NWA and their hosts was
 found. We found that different virus clades were clustered differently and
 that Clade B with members pathogenic to humans was randomly distributed
 across the rodent phylogeny. Furthermore, viral relatedness within Clade B
 was significantly explained by the geographic overlap of their hosts’
 ranges rather than host relatedness, indicating that they are capable of
 host switching opportunistically. This has important bearings on their
 potential to become panzootic. Together, these analyses suggest that NWA
 have not codiverged with their hosts and instead have evolved
 predominantly via host switching.
description: New World Arenavirus Z
 protein alignmentAlignment of the Z
 protein of 51 NWA sequences, labelled with Genbank accessions
 numbers.NWA-Z.nexNew World Arenavirus -L protein alignmentAlignment of the L protein of 37 NWA sequences, labelled with Genbank accessions numbers.NWA-L.nexNew World Arenavirus -Nucleoprotien alignmentAlignment of the nucleoprotien of 64 NWA sequences, labelled with Genbank accessions numbers.NWA-NP.nexNew World Arenavirus -Glycoprotein alignmentAlignment of the glycoprotein of 62 NWA sequences, labelled with Genbank accessions numbers.NWA-GP.nexSigmodontinae and Neotominae Mitochondria Cytochrome B alignmentSigmodontinae and Neotominae Mitochondria Cytochrome B alignment. 523 taxa aligned with Genbank accession number and current taxonomy indicated for each sequence.SigmodontinaeNeotominaeHosts_mt-cyb.phyR script for phylogeneitcally informed mantel testsOriginal R script provided by the authors of the following paper as supplementary material Harmon, L.J & Glor, R.E. (2010) This script has been modified by O.Missa to suit working from a genetic distance Matrixphylo.perm.mantel.tests.txt
DOI: 10.5061/dryad.4r9h61v8
title: Data from: Genetic effects on mating success and partner choice in a social mammal

description: Mating behavior has profound consequences for two phenomena - individual
 reproductive success and the maintenance of species boundaries - that
 contribute to evolutionary processes. Studies of mating behavior in
 relation to individual reproductive success are common in many species,
 but studies of mating behavior in relation to genetic variation and
 species boundaries are less commonly conducted in socially complex
 species. Here, we leveraged extensive observations of a wild yellow baboon
 (Papio cynocephalus) population that has experienced recent gene flow from
 a close sister taxon, the anubis baboon (Papio anubis), to examine how
 admixture-related genetic background affects mating behavior. We
 identified novel effects of genetic background on mating patterns,
 including an advantage accruing to anubis-like males and assortative
 mating among both yellow-like and anubis-like pairs. These genetic effects
 acted alongside social dominance rank, inbreeding avoidance, and age to
 produce highly nonrandom mating patterns. Our results suggest that this
 population may be undergoing admixture-related evolutionary change, driven
 in part by nonrandom mating. However, the strength of the genetic effects
 is mediated by behavioral plasticity and social interactions, emphasizing
 the strong influence of social context on mating behavior in socially
 complex species.
description: dryaddataRaw data Excel file containing outcomes of potential consortship events and potential predictors of consortship occurence, as well as a README tab explaining these predictors.
DOI: 10.15468/dl.jbd9bm
title: Occurrence Download

description: A dataset containing 902 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Continent is Europe",
 "DatasetKey is International Barcode of Life project (iBOL)",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "TaxonKey is Gammarus roeselii"
 ]
}

 The dataset includes 902 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001722-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.7dk0m36r
title: Data from: Reconstruction of paternal genotypes over multiple breeding seasons reveals male green turtles do not breed annually

description: For species of conservation concern, knowledge of key life-history and
 demographic components, such as the number and sex ratio of breeding
 adults, is essential for accurate assessments of population viability.
 Species with temperature-dependent sex determination can produce heavily
 biased primary sex ratios, and there is concern that adult sex ratios may
 be similarly skewed or will become so as a result of climate warming.
 Prediction and mitigation of such impacts are difficult when life-history
 information is lacking. In marine turtles, owing to the difficultly in
 observing males at sea, the breeding interval of males is unknown. It has
 been suggested that male breeding periodicity may be shorter than that of
 females, which could help to compensate for generally female-biased sex
 ratios. Here we outline how the use of molecular-based paternity analysis
 has allowed us, for the first time, to assess the breeding interval of
 male marine turtles across multiple breeding seasons. In our study rookery
 of green turtles (Chelonia mydas), 97% of males were assigned offspring in
 only one breeding season within the 3-year study period, strongly
 suggesting that male breeding intervals are frequently longer than 1 year
 at this site. Our results also reveal a sex ratio of breeding adults of at
 least 1.3 males to each female. This study illustrates the utility of
 molecular-based parentage inference using reconstruction of parental
 genotypes as a method for monitoring the number and sex ratio of breeders
 in species where direct observations or capture are difficult.
description: microsatellite
 dataExcel spreadsheet of
 genotypes at 13 microsatellite data for females, offspring and inferred
 males. Locus names are included in the first row. Missing data is
 indicated by 0.microsatellite
 genotypes
DOI: 10.15468/vxptfo
title: Duke University Herbarium Fungal Collection

description: The Duke Fungal Herbarium was established by Duke mycologist Dr. Rytas Vilgalys in the early 1990's. The Herbarium consists mainly of Basidiomycete collections with special emphasis on Agaricomycetes. Specimens of Septobasidium, collected by Dr. Daniel Henk for his dissertation research, and dissertation research vouchers of truffles (Tuber) of Dr. Greg Bonito are accessioned in our holdings. Rich in new collections from Australia, New Zealand, Italy, Newfoundland and Labrador, Columbia, South Africa and the United States. Significant collections from Papua New Guinea, France, Costa Rica and China.
DOI: 10.5061/dryad.r3gr75qs
title: Data from: Eriocaulon madayiparense (Eriocaulaceae) - a new species from the foot hills of the Western Ghats of India

description: Eriocaulon madayiparense Swapna, Rajesh, Manju & Prakashkumar sp.
 nov. is described and illustrated from the Madayipara, a lateritic midland
 of Kannur District of Kerala. The species is allied to E. eurypeplon
 Koernicke, in its two free male and female sepals, female sepals being
 keeled and acute and not exceeding the floral bracts, acuminate leaf apex
 and setiform appendages appearing in vertical rows, but differs mainly
 inyellow seeds with solitary appendage arising from transverse radial
 walls, curved and connate with the adjacent ones of the same vertical row
 forming longitudinal parallel ribs on the surface of seeds.
description: Eriocaulon madayiparense
 FigureEriocaulon madayiparense
 Type specimen
DOI: 10.5061/dryad.s672t4gh
title: Data from: Dispersal and gene flow in the rare, parasitic Large Blue butterfly Maculinea arion

description: Dispersal is crucial for gene flow and often determines the long-term
 stability of meta-populations, particularly in rare species with
 specialized life cycles. Such species are often foci of conservation
 efforts because they suffer disproportionally from degradation and
 fragmentation of their habitat. However, detailed knowledge of effective
 gene flow through dispersal is often missing, so that conservation
 strategies have to be based on mark–recapture observations that are
 suspected to be poor predictors of long-distance dispersal. These
 constraints have been especially severe in the study of butterfly
 populations, where microsatellite markers have been difficult to develop.
 We used eight microsatellite markers to analyse genetic population
 structure of the Large Blue butterfly Maculinea arion in Sweden. During
 recent decades, this species has become an icon of insect conservation
 after massive decline throughout Europe and extinction in Britain followed
 by reintroduction of a seed population from the Swedish island of Öland.
 We find that populations are highly structured genetically, but that gene
 flow occurs over distances 15 times longer than the maximum distance
 recorded from mark–recapture studies, which can only be explained by
 maximum dispersal distances at least twice as large as previously
 accepted. However, we also find evidence that gaps between sites with
 suitable habitat exceeding ∼20 km induce genetic erosion that can be
 detected from bottleneck analyses. Although further work is needed, our
 results suggest that M. arion can maintain fully functional
 metapopulations when they consist of optimal habitat patches that are no
 further apart than ∼10 km.
description: Ugelvig&al_GeographicDistanceMatrixThe file contains pairwise geographic distances between individual samples, based on unique coordinates generated in the clustering program TESS.Ugelvig&al_MicrosatRawdata
DOI: 10.5281/zenodo.18387834
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).