cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.4tmpg4f7n
title: Development of a multi-excitation fluorescence (MEF) imaging method to improve the information content of benthic coral reef surveys

description: Benthic surveys are a key component of monitoring and conservation efforts
 for coral reefs worldwide. While traditional image-based surveys rely on
 manual annotation of photographs to characterise benthic composition,
 automatic image annotation based on computer vision is becoming
 increasingly common. However, accurate classification of some benthic
 groups from reflectance images presents a challenge to local ecologists
 and computers alike. Most coral reef organisms produce one or a
 combination of fluorescent pigments, such as Green Fluorescent Protein
 (GFP)-like proteins found in corals, chlorophyll-a found in all
 photosynthetic organisms, and phycobiliproteins found in red macroalgae,
 crustose coralline algae (CCA) and cyanobacteria. Building on the
 potential of these pigments as a target for automatic image annotation, we
 developed a novel imaging method based on off-the-shelf components to
 improve classification of coral and other biotic substrates using a
 multi-excitation fluorescence (MEF) imaging system. We used RGB cameras to
 image the fluorescence emission of coral and algal pigments stimulated by
 narrow-waveband blue and green light, and then combined the information
 into 3-channel pseudocolour images. Using a set of a priori rules defined
 by the relative pixel intensity produced in different channels, the method
 achieved successful classification of organisms into three categories
 based on the dominant fluorescent pigment expressed, facilitating
 discrimination of traditionally problematic groups. This work provides a
 conceptual foundation for future technological developments that will
 improve the cost, accuracy and speed of coral reef surveys.
DOI: 10.15468/dl.hm2dpr
title: Occurrence Download

description: A dataset listing the 464 species recorded in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((172.64806 -43.38585,172.62365 -43.3804,172.59669 -43.38067,172.57603 -43.38734,172.56025 -43.39972,172.5499 -43.41755,172.54605 -43.43511,172.55834 -43.45319,172.57562 -43.46136,172.59208 -43.46721,172.61236 -43.47211,172.62684 -43.47007,172.64774 -43.4653,172.65821 -43.45973,172.67332 -43.45211,172.68258 -43.43527,172.68171 -43.41123,172.6759 -43.39799,172.66348 -43.38975,172.64806 -43.38585))",
 "TaxonKey is one of (Insecta, Arachnida, Athoracophoridae, Rhytididae, Onychophora)"
 ]
}

 The dataset's 464 records were derived from 20 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002565-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.z612jm69d
title: Melanin-based ornament darkness positively correlates with across-season nutritional condition

description: Sexually dimorphic ornamental traits are widely regarded as indicators of
 nutritional condition. However, variation of nutritional condition outside
 the reproductive and the ornament production seasons has rarely been
 considered, although it affects the generality of information content,
 especially for ornaments that may be used across the year. We measured
 several indicators of migratory and moult condition in male and female
 blackcaps (Sylvia atricapilla) during their autumn migration, and
 quantified their crown reflectance. We detected robust correlations
 between migratory and moult condition indices, and the correlation
 structure was similar in the two sexes. Furthermore, the across-season
 measure of body condition was positively related to the darkness of the
 black crown in males, while being unrelated to reflectance traits of the
 reddish crown in females. Our results reinforce the possibility that some
 melanin-based ornaments may be year-round indicators of individual quality
 via their dependence on nutritional condition.
description: Key to variable names can be found in the second sheet of the
 Excel file.
DOI: 10.5061/dryad.xwdbrv1c5
title: Estimating the time since admixture from phased and unphased molecular data

description: After admixture, recombination breaks down genomic blocks of contiguous
 ancestry. The breakdown of these blocks forms a new `molecular
 clock', that ticks at a much faster rate than the mutation clock,
 enabling accurate dating of admixture events in the recent past. However,
 existing theory on the break down of these blocks, or the accumulation of
 delineations between blocks,  so called `junctions', has
 mostly been limited to using regularly spaced markers on phased data.
 Here, we present an extension to the theory of junctions using the
 Ancestral Recombination Graph that describes the expected number of
 junctions for any distribution of markers along the genome. Furthermore,
 we provide a new framework to infer the time since admixture using
 unphased data. We demonstrate both the phased and unphased methods on
 simulated data and show that our new extensions have improved accuracy
 with respect to previous methods, especially for smaller population sizes
 and more ancient admixture times. Lastly, we demonstrate the applicability
 of our method on three empirical datasets, including labcrosses of yeast
 (Saccharomyces cerevisae) and two  case studies of hybridization
 in swordtail fish and Populus trees.
description: This contains all code used for the manuscript, including code to
 simulate underlying data, analyze empirical data, and also code to
 visualize the results and reproduce the figures from the main text. The
 code is organized per figure and each folder is named according to the
 associated figure. See associated Zenodo Related Works for code.
 Each folder typically contains 3 files:<br> -
 data.zip<br> - simulate.R<br> - plot_figure.R
 data.zip contains the underlying (often simulated) data<br>
 simulate.R contains the scripts used to generate data.zip<br>
 plot_figure.R contains the code to summarise the simulated data, and
 create the figure found in the main text. In some
 cases, additional scripts can be found to analyze the data, in particular
 for the three empirical datasets.<br> The raw data used in the
 empirical data analysis was not included here, but can be found in the
 references used, or in the additional README files in the relevant
 folders. Furthermore, the code for the junctions R
 package was amended as well, which can be installed either from CRAN using
 'install.packages('junctions')', or installed from the
 local tar file included in this dryad repository.<br> For
 completeness, the Supplementary file available via de journal's
 website has been added here as well.
DOI: 10.6084/m9.figshare.31164676
title: Modeling Injury Severity Among Motor Vehicle Occupants Using a Safe System–Aligned, Population-Based Framework: Evidence from Ohio Crash Data (2017–2023)

description: This dataset supports a multilevel Safe System analysis of motor vehicle crashes in Ohio between 2017 and 2023. Derived from the Ohio Department of Public Safety’s traffic crash reports, the dataset includes over 41,000 cases involving suspected serious injuries (SSIs) and fatalities. Each case is described across three hierarchical levels—Crash, Unit (vehicle), and Person—enabling multivariate modeling of injury severity. Data cleaning and validation were performed in R, and Vehicle Identification Numbers (VINs) were decoded using the NHTSA VIN Decoder to determine vehicle year and safety feature availability.Risk factors were coded into four Safe System domains—People, Vehicle, Road, and Speed—allowing both individual and combined effects to be examined. Key risk factors include impaired or distracted driving, non-use of seat belts, vehicle model year prior to 2010, road departures, and unsafe speed. Each injury case is annotated for the presence or absence of 12 system-level risk factors, enabling advanced modeling of injury probability based on factor combinations. This dataset facilitates exploration of systemic contributors to crash severity and supports the development of data-informed, integrated countermeasures to reduce severe and fatal outcomes. The structure, coding, and metadata make it readily adaptable for replication by other jurisdictions.
DOI: 10.6084/m9.figshare.31164676.v1
title: Modeling Injury Severity Among Motor Vehicle Occupants Using a Safe System–Aligned, Population-Based Framework: Evidence from Ohio Crash Data (2017–2023)

description: This dataset supports a multilevel Safe System analysis of motor vehicle crashes in Ohio between 2017 and 2023. Derived from the Ohio Department of Public Safety’s traffic crash reports, the dataset includes over 41,000 cases involving suspected serious injuries (SSIs) and fatalities. Each case is described across three hierarchical levels—Crash, Unit (vehicle), and Person—enabling multivariate modeling of injury severity. Data cleaning and validation were performed in R, and Vehicle Identification Numbers (VINs) were decoded using the NHTSA VIN Decoder to determine vehicle year and safety feature availability.Risk factors were coded into four Safe System domains—People, Vehicle, Road, and Speed—allowing both individual and combined effects to be examined. Key risk factors include impaired or distracted driving, non-use of seat belts, vehicle model year prior to 2010, road departures, and unsafe speed. Each injury case is annotated for the presence or absence of 12 system-level risk factors, enabling advanced modeling of injury probability based on factor combinations. This dataset facilitates exploration of systemic contributors to crash severity and supports the development of data-informed, integrated countermeasures to reduce severe and fatal outcomes. The structure, coding, and metadata make it readily adaptable for replication by other jurisdictions.
DOI: 10.5061/dryad.5x69p8d1k
title: Allochthonous resources are less important for faunal communities on highly productive, small tropical islands

description: Ecosystems are interconnected by energy fluxes that provide resources for
 the inhabiting organisms along the transition zone. Especially where
 in-situ production is low, ecosystems can become highly dependent on
 external resources. The dependency on external input becomes less
 pronounced in systems with elevated in-situ production, where only
 consumer species close to the site of external input remain subsidized,
 whereas species distant to the input site rely on the in-situ production
 of the ecosystem. It is largely unclear though if this pattern is
 consistent over different consumer species and trophic levels in one
 ecosystem, and whether consumer species that occur both proximate to and
 at a distance from the input site differ in their dependency on external
 resource inputs between sites. Using stable isotope analysis, we
 investigated the dependency on external marine input for common
 ground-associated consumer taxa on small tropical islands with high
 in-situ production. We show that marine input is only relevant for strict
 beach-dwelling taxa, while the terrestrial vegetation is the main carbon
 source for inland-dwelling taxa. Consumer species that occurred both close
 (beach) and distant (inland) to the site of marine input showed similar
 proportions of marine input in their diets. This supports earlier findings
 that the relevance of external resources becomes limited to species close
 to the input site in systems with sufficient in-situ production. However,
 it also indicates that the relevance of external input is also
 species-dependent, as consumers occurring close and distant to the input
 site depended equally strong or weak on marine input.
DOI: 10.5061/dryad.8sf7m0ckd
title: Genomic evidence of past and future climate-linked loss in a migratory Arctic fish

description: Despite widespread biodiversity losses, an understanding of how most taxa
 will respond to future climate change is lacking. Here we integrate
 genomics and environmental modelling to assess climate change responses in
 an ecologically and economically important Arctic species. Environmentally
 associated genomic diversity and machine learning are used to identify
 highly vulnerable populations of anadromous (migratory) Arctic charr, and
 we reconstruct estimates of effective population size spanning the
 twentieth century to identify past climate-associated declines. We uncover
 past region-wide declines in effective population size that correspond to
 decreases in temperature and community biomass in the Northwest Atlantic.
 We find vulnerable populations near the southern range limit, indicating
 northward shifts and a possible loss of commercially important
 life-history variation in response to climate change. The genomic approach
 used here to investigate climate change response identifies past and
 future declines that impact species persistence, ecosystem stability and
 food security in the Arctic.
description: Plink (ped/map/raw) files: 16,431 polymorphic SNPs from 744
 individuals and 28 populations of Arctic Charr from northeastern
 Canada. Enviro_results_WorldClim.csv: coordinates and
 environmental data from WorldClim for all individuals under current
 conditions
DOI: 10.5061/dryad.r4xgxd29n
title: How do species barriers decay? concordance and local introgression in mosaic hybrid zones of mussels

description: The Mytilus complex of marine mussel species forms a mosaic of hybrid
 zones, found across temperate regions of the globe. This allows us to
 study "replicated" instances of secondary contact between
 closely-related species. Previous work on this complex has shown that
 local introgression is both widespread and highly heterogeneous, and has
 identified SNPs that are outliers of differentiation between lineages.
 Here, we developed an ancestry-informative panel of such SNPs. We then
 compared their frequencies in newly-sampled populations, including samples
 from within the hybrid zones, and parental populations at different
 distances from the contact. Results show that close to the hybrid zones,
 some outlier loci are near to fixation for the heterospecific allele,
 suggesting enhanced local introgression, or the local sweep of a shared
 ancestral allele. Conversely, genomic cline analyses, treating local
 parental populations as the reference, reveal a globally high concordance
 among loci, albeit with a few signals of asymmetric introgression.
 Enhanced local introgression at specific loci is consistent with the early
 transfer of adaptive variants after contact, possibly including asymmetric
 bi-stable variants (Dobzhansky-Muller incompatibilities), or haplotypes
 loaded with fewer deleterious mutations. Having escaped one barrier,
 however, these variants can be trapped or delayed at the next barrier,
 confining the introgression locally. These results shed light on the decay
 of species barriers during phases of contact.
DOI: 10.25338/b84w6z
title: Landscape simplification increases vineyard pest outbreaks and insecticide use

description: Diversifying agricultural landscapes may mitigate biodiversity declines
 and improve pest management. Yet landscapes are rarely managed to suppress
 pests, in part because researchers seldom measure key variables related to
 pest outbreaks and insecticides that drive management decisions. We used a
 13-year government database to analyze landscape effects on European
 grapevine moth (Lobesia botrana) outbreaks and insecticides across ~400
 Spanish vineyards. At harvest, we found pest outbreaks increased four-fold
 in simplified, vineyard-dominated landscapes compared to complex
 landscapes in which vineyards are surrounded by semi-natural habitats.
 Similarly, insecticide applications doubled in vineyard-dominated
 landscapes but declined in vineyards surrounded by shrubland. Importantly,
 pest population stochasticity would have masked these large effects if
 numbers of study sites and years were reduced to typical levels in
 landscape pest-control studies. Our results suggest increasing landscape
 complexity may mitigate pest populations and insecticide applications.
 Habitat conservation represents an economically and environmentally sound
 approach for achieving sustainable grape production.
DOI: 10.5061/dryad.xksn02vdh
title: Data from: Limited contributions of plant pathogens to density-dependent seedling mortality of mast fruiting Bornean trees

description: Fungal pathogens are implicated in driving tropical plant diversity by
 facilitating strong, negative density-dependent mortality of conspecific
 seedlings (C-NDD). Assessment of the role of fungal pathogens in mediating
 coexistence derives from relatively few tree species and predominantly the
 Neotropics, limiting our understanding of their role in maintaining
 hyper-diversity in many tropical forests. A key question is whether fungal
 pathogen-mediated C-NDD seedling mortality is ubiquitous across diverse
 plant communities. Using a manipulative shadehouse experiment, we tested
 the role of fungal pathogens in mediating C-NDD seedling mortality of
 eight mast fruiting Bornean trees, typical of the species rich forests of
 South East Asia. We demonstrate species-specific responses of seedlings to
 fungicide and density treatments, generating weak negative
 density-dependent mortality. Overall seedling mortality was low and likely
 insufficient to promote overall community diversity. Although conducted in
 the same way as previous studies, we find little evidence that fungal
 pathogens play a substantial role in determining patterns of seedling
 mortality in a SE Asian mast fruiting forest, questioning our
 understanding of how Janzen-Connell mechanisms structure the plant
 communities of this globally important forest type.
DOI: 10.5061/dryad.pzgmsbcjf
title: Data from: Ecological convergence of secondary phytochemicals along elevational gradients

description: Biologists still strive to identify the ecological and evolutionary
 drivers of phytochemical variation that mediate biotic interactions. We
 hypothesized that plant species growing at sites characterized by high
 herbivore pressure would converge to produce highly toxic blends of
 secondary metabolites, independent of phylogenetic constraints. To address
 the role of shared evolutionary history and ecological niches in driving
 variation in plant phytochemistry, we combined targeted metabolomics with
 insect herbivore bioassays and with a set of growth-related traits of
 several Cardamine species growing along the entire elevational gradient of
 the Alps. We observed that Cardamine phytochemical profiles grouped
 according to previously-established growth form categorizations within
 specific abiotic conditions, independently of phylogenetic relationship.
 We also showed that novel indices summarizing functional phytochemical
 diversity better explain plant resistance against chewing and sap-feeding
 herbivores than classic diversity indices. We conclude that multiple
 functional axes of phytochemical diversity should be integrated with the
 functional axis of plant growth forms to study phenotypic convergence
 along large-scale ecological gradients.
DOI: 10.5281/zenodo.18390520
title: TP53 Mutations Orchestrate an Immunosuppressive Malignant-Myeloid Niche to Dictate Therapeutic Vulnerability in PDAC

description: Data about TP53 Mutations Orchestrate an Immunosuppressive Malignant-Myeloid Niche to Dictate Therapeutic Vulnerability in PDAC review
DOI: 10.5281/zenodo.18390521
title: TP53 Mutations Orchestrate an Immunosuppressive Malignant-Myeloid Niche to Dictate Therapeutic Vulnerability in PDAC

description: Data about TP53 Mutations Orchestrate an Immunosuppressive Malignant-Myeloid Niche to Dictate Therapeutic Vulnerability in PDAC review
DOI: 10.5061/dryad.08kprr50t
title: Modelling mycorrhizal fungi dispersal by the mycophagous swamp wallaby (Wallabia bicolor)

description: Despite the importance of mammal-fungal interactions, tools to estimate
 the mammal-assisted dispersal distances of fungi are lacking. Many mammals
 actively consume fungal fruiting bodies, the spores of which remain viable
 after passage through their digestive tract. Many of these fungi form
 symbiotic relationships with trees and provide an array of other key
 ecosystem functions. We present a flexible, general model to predict the
 distance a mycophagous mammal would disperse fungal spores. We modelled
 the probability of spore dispersal by combining animal movement data from
 GPS-telemetry with data on spore gut-retention time. We test this model
 using an exemplar generalist mycophagist, the swamp wallaby (Wallabia
 bicolor). We show that swamp wallabies disperse fungal spores hundreds of
 metres—and occasionally up to 1265 m—from the point of consumption,
 distances that are ecologically significant for many mycorrhizal fungi. In
 addition to highlighting the ecological importance of swamp wallabies as
 dispersers of mycorrhizal fungi in eastern Australia, our simple modelling
 approach provides a novel and effective way of empirically describing
 spore dispersal by a mycophagous animal. This approach is applicable to
 the study of other animal-fungi interactions in other ecosystems.
description: Methods are described in the published article.
DOI: 10.5061/dryad.j3tx95xbs
title: Environmental DNA reveals aquatic biodiversity of an urban backwater area, southeast coast of India.

description: Strong conservational management needs comprehensive data on the status of
 biodiversity. However, effective methods to document aquatic biodiversity
 are either lacking or less in use. Environmental DNA (eDNA), often
 released by the organisms into the environment (e.g. water, soil) offers a
 great opportunity for examining the biota in aquatic ecosystems. Here, we
 have conducted a metagenomics study on eDNA sample collected from
 Muttukadu, Tamil Nadu, India to portray the biodiversity in a backwaters
 featured environment. Shotgun metagenomic approach with Illumina® NextSeq
 500 sequencing yielded 88.4 million raw reads. The processed clean data
 were assigned as 80% prokaryotes, 0.4% eukaryotes, ̴ 2 % viruses and ~ 17
 % remain as unknown or un-identified. Using this approach, we detected 112
 families across the major phyla of eukaryotes. The approach has the
 potential to discover small micro-eukaryote, unseen species and, our data
 represents major phyla from both estuarine and marine environments.
  This includes phyla that are of conservational significance and
 ecologically sensitive. Given the sensitivity, efficacy, and the
 cost-effectiveness of the method, we suggest this tool for an introductory
 understanding of biodiversity structure in a backwater environment during
 biomonitoring assessments.
DOI: 10.15468/dl.crb328
title: Occurrence Download

description: A dataset containing 457 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Cathormion umbellatum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 457 records from 17 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002576-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.