cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.gr93t
title: Data from: A target enrichment method for gathering phylogenetic information from hundreds of loci: an example from the Compositae

description: Premise of the study: The Compositae (Asteraceae) are a large and diverse
 family of plants, and the most comprehensive phylogeny to date is a
 meta-tree based on 10 chloroplast loci that has several major unresolved
 nodes. We describe the development of an approach that enables the rapid
 sequencing of large numbers of orthologous nuclear loci to facilitate
 efficient phylogenomic analyses. Methods and Results: We designed a set of
 sequence capture probes that target conserved orthologous sequences in the
 Compositae. We also developed a bioinformatic and phylogenetic workflow
 for processing and analyzing the resulting data. Application of our
 approach to 15 species from across the Compositae resulted in the
 production of phylogenetically informative sequence data from 763 loci and
 the successful reconstruction of known phylogenetic relationships across
 the family. Conclusions: These methods should be of great use to members
 of the broader Compositae community, and the general approach should also
 be of use to researchers studying other families.
description: COS alignment
 filesAlignments from all COS
 lociCOS_alignment_files_NEW.zipCOS_sequence_length&number_of_sequencesList of COS sequences with alignment length and number of sequences in each alignment.tree file in newick format for the concatenation of all COS loci, as run in Garli763_loci_tree_newickConcatenation_of_all_763_ COS_alignmentsConcatenated alignment file.Concatenation_of_all_763_COS_alignments_NEW.fasta
DOI: 10.5281/zenodo.18390704
title: Age_depth_model_data

description: Age_depth_model_data. Chronostratigraphic datums used to construct the age–depth model in this study (modified from Khim et al., 2025).
DOI: 10.5281/zenodo.18390703
title: Age_depth_model_data

description: Age_depth_model_data. Chronostratigraphic datums used to construct the age–depth model in this study (modified from Khim et al., 2025).
DOI: 10.5061/dryad.653c9
title: Data from: Contrasting patterns of phenotype-dependent parasitism within and among populations of threespine stickleback

description: Variation in infection rate arises from variation in host exposure and
 resistance to parasites both within and among populations. All things
 being equal, phenotypes that increase exposure risk should covary
 positively with infection among individuals. It might therefore be
 expected that populations with mean phenotypes that increase exposure
 might also have higher rates of infection. However, such positive
 covariance between exposure and infection at the population level might be
 undermined by other factors such as geographic variation in parasite
 abundance or host resistance, negating or reversing in between-population
 comparisons. We studied rates of infection of two parasites among 18
 populations of threespine stickleback (Gasterosteus aculeatus). As
 predicted, within populations, trophic morphology covaries with infection
 of two trophically transmitted parasites: individuals with benthic (or
 limnetic) phenotypes were more likely to be infected with a benthic (or
 limnetic) parasite. However, across populations, the relationship between
 morphology and infection rate was absent (limnetic parasite) or reversed
 (benthic parasite). Our results confirm the importance of
 phenotype-dependent exposure, but stress different factors or processes,
 such as the evolution of reduced susceptibility, might shape variation in
 infection at larger spatial scales.
description: morphological and
 parasitological dataUberDataDryad.csvlake datalakes_summ_prevs.csvraw zooplankton dataData for zooplankton taxa in counts per liter by Lake. Date and depth sampled are shown. Dates where only the year is gven were sampled at sometime within the sampling range for the other lakes.zoops_per_liter.csv
DOI: 10.5061/dryad.h21d3
title: Data from: Pan-Atlantic analysis of the overlap of a highly migratory species, the leatherback turtle, with pelagic longline fisheries

description: Large oceanic migrants play important roles in ecosystems, yet many
 species are of conservation concern as a result of anthropogenic threats,
 of which incidental capture by fisheries is frequently identified. The
 last large populations of the leatherback turtle, Dermochelys coriacea,
 occur in the Atlantic Ocean, but interactions with industrial fisheries
 could jeopardize recent positive population trends, making bycatch
 mitigation a priority. Here, we perform the first pan-Atlantic analysis of
 spatio-temporal distribution of the leatherback turtle and ascertain
 overlap with longline fishing effort. Data suggest that the Atlantic
 probably consists of two regional management units: northern and southern
 (the latter including turtles breeding in South Africa). Although turtles
 and fisheries show highly diverse distributions, we highlight nine areas
 of high susceptibility to potential bycatch (four in the northern Atlantic
 and five in the southern/equatorial Atlantic) that are worthy of further
 targeted investigation and mitigation. These are reinforced by reports of
 leatherback bycatch at eight of these sites. International collaborative
 efforts are needed, especially from nations hosting regions where
 susceptibility to bycatch is likely to be high within their exclusive
 economic zone (northern Atlantic: Cape Verde, Gambia, Guinea Bissau,
 Mauritania, Senegal, Spain, USA and Western Sahara; southern Atlantic:
 Angola, Brazil, Namibia and UK) and from nations fishing in these
 high-susceptibility areas, including those located in international
 waters.
description: Shapefiles of Figs 1 and
 2 and Supplementary figures S1 to S6The folder includes all
 the ArcGIS shapefiles used to make figures 1 and 2 and supplementary
 figures S1 to S6. An excel file is also included which describes which
 field of which shapefile was used to make which figure.Shapefiles.zip
DOI: 10.5061/dryad.1d2k9
title: Data from: "NGS based generation of expressed sequence tags for Lymantria dispar and Lymantria monacha, two closely related lepidopteran species with different responses to parasitism by Glyptapanteles liparidis" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014

description: Introduction: The gypsy moth, Lymantria dispar, and the nun moth,
 Lymantria monacha, are closely related species (Lepidoptera,
 Lymantriidae), co-seasonal and economically important forest pests on
 broadleaf and coniferous trees. In Central Europe, gypsy moth larvae are
 frequently parasitized by the gregarious, endoparasitic wasp
 Glyptapanteles liparidis (Hymenoptera, Braconidae). At oviposition, the
 female wasp injects between 10 and up to 100 eggs into the hemocoel of a
 single host larva, together with venom and calyx fluid containing
 polydnavirus (PDV) particles that subsequently play a critical role in
 suppressing the host immune response so that successful development of the
 parasitoid can proceed (Schopf 2007). These viruses, which are integrated
 in the genomic DNA of the wasp and undergo replication only in the
 female’s ovary, rapidly enter host hemocytes, fat body, and nervous system
 following parasitization, and viral genes are expressed. In L. dispar
 larvae parasitized by G. liparidis, the host’s hemocytes alter their
 behavior, fail to spread properly (thereby inhibiting the encapsulation
 response) and partly undergo programmed cell death (apoptosis), resulting
 in a dramatic drop in the host’s total hemocyte number (Schafellner and
 Schläger 2009).
description: Protocol and
 ScriptsThe pipeline protocol
 and the scripts used for NGS data handlingContigsAnnotationAlignment pools vs singleTable S1Excel fileTableNCBI nt collection BLAST
DOI: 10.5061/dryad.82vg8
title: Data from: The ancient Britons: groundwater fauna survived extreme climate changes over tens of millions of years across NW Europe

description: Global climate changes during the Cenozoic (65.5 - 0 Ma) caused major
 biological range shifts and extinctions. In Northern Europe, for example,
 a pattern of few endemics and the dominance of wide-ranging species is
 thought to have been determined by the Pleistocene (2.59 – 0.01 Ma)
 glaciations. This study, in contrast, reveals an ancient subsurface fauna
 endemic to Britain and Ireland. Using a Bayesian phylogenetic approach we
 found that two species of stygobitic invertebrates (genus Niphargus) have
 not only survived the entire Pleistocene in refugia but have persisted for
 at least 19.5 million years. Other Niphargus species form distinct cryptic
 taxa that diverged from their nearest continental relative between 5.6 and
 1.0 Ma. The study also reveals an unusual biogeographical pattern in the
 Niphargus genus. It originated in Northwest Europe ~88 Ma and underwent a
 gradual range expansion. Phylogenetic diversity and species age are
 highest in Northwest Europe suggesting resilience to extreme climate
 change, and strongly contrasting the patterns seen in surface fauna.
 However, species diversity is highest in Southeast Europe indicating that
 once the genus spread to these areas (~ 25 Ma), geomorphological and
 climatic conditions enabled much higher diversification. Our study
 highlights that groundwater ecosystems provide an important contribution
 to biodiversity and offer insight into the interactions between biological
 and climatic processes.
description: Hanfling Table
 S1Sample locations, taxa
 and Genbank accession numbersSupermatrix alignment
 NiphargusOTUs plus outgroupsSupermatrix of 6 genetic
 loci and 170 taxa used in the phylogenetic analysis (FASTA format). Locus
 = alignment site numbers: 12S = 1-505; 16S = 506-1614; 18S = 1615-4357;
 28S = 4358-6163; CO1 = 6164-7046; EF1a = 7047-7647
DOI: 10.15468/dl.xug3tu
title: Occurrence Download

description: A dataset containing 2752844 species occurrences available in GBIF matching the query:
{
 "and" : [
 "Geometry POLYGON((-20 -38,55 -38,55 38,-20 38,-20 -38))",
 "HasCoordinate is true",
 "HasGeospatialIssue is false",
 "OccurrenceStatus is Present",
 "TaxonKey is Anseriformes"
 ]
}

 The dataset includes 2752844 records from 208 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0001579-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.5tp88
title: Data from: Niche and range size patterns suggest that speciation begins in small, ecologically diverged populations in North American monkeyflowers (Mimulus spp.)

description: Closely related species (e.g., sister taxa) often occupy very different
 ecological niches and can exhibit large differences in geographic
 distributions despite their shared evolutionary history. Budding
 speciation is one process that may partially explain how differences in
 niche and distribution characteristics may rapidly evolve. Budding
 speciation is the process through which new species form as initially
 small colonizing populations that acquire reproductive isolation. This
 mode of species formation predicts that, at the time of speciation, sister
 species should have highly asymmetrical distributions. We tested this
 hypothesis in North American monkeyflowers, a diverse clade with a robust
 phylogeny, using data on geographical ranges, climate, and plant community
 attributes. We found that recently diverged sister pairs have highly
 asymmetrical ranges and niche breadths, relative to older sister pairs.
 Additionally, we found that sister species occupy distinct environmental
 niche positions, and that 80% of sister species have completely or
 partially overlapping distributions (i.e., are broadly sympatric).
 Together, these results suggest that budding speciation has occurred
 frequently in Mimulus, that it has likely taken place both inside the
 range and on the range periphery, and that observed divergences in habitat
 and resource use could be associated with speciation in small populations.
description: occurrence_dataThis file contains raw environmental data for each species used in our analysis.phylogenyThis file contains a nexus formatted file with a subsample of 900 trees from the posterior distribution of trees from the BEAST analysis. Additionally, three log files are included.
DOI: 10.5061/dryad.4t721
title: Data from: Molecular evidence for the monophyly of flatfishes (Carangimorpharia: Pleuronectiformes)

description: Proliferation of phylogenetic studies based on poor taxonomic sampling or
 insufficient molecular evidence usually leads to conflicting results. As a
 consequence, advancement of systematic knowledge yields to confusion. The
 problem is exacerbated for taxonomic groups with historically difficult
 resolution of evolutionary relationships such as the flatfishes. Molecular
 evidence to support monophyly for this emblematic group of fishes and
 their interrelationships has been elusive, and a recent paper published in
 this journal went as far as to claim that flatfish monophyly can be
 rejected with molecular data, implying that the asymmetric body plan
 unique to these fishes had two independent origins. A reanalysis of this
 evidence suggests the contrary and combination of the new data with
 existing datasets unequivocally supports the monophyly of this group based
 on analyses of concatenated data as well as species tree approaches.
 Resolution of difficult phylogenetic problems requires analysis of larger
 datasets with adequate taxonomic coverage and sound hypothesis-testing
 procedures. Proliferation of partial studies claiming extraordinary
 results should be avoided in order to advance the field of molecular
 phylogenetics.
description: COMBINED_DATASET_&_RAxML_TNT_treesNexus file with combined sequence data (from BET and CAM) and the RAxML and TNT trees derived from the analysis of this dataset.GENE_TREES_STAR_SP_TREERAxML gene trees and STAR species tree (newick format).Supplementary_Table_1_Dryad_SynapomorphiesSupplementary Table 1. List of 51 unambiguous molecular synapomorphies supporting pleuronectiform monophyly. The list was extracted from PAUP* using the topology obtained under maximum parsimony in TNT. Character number refers to the position in the concatenated alignment.
DOI: 10.5061/dryad.41b9g
title: Data from: Machine learning-based differential network analysis: a study of stress-responsive transcriptomes in Arabidopsis thaliana

description: Machine learning (ML) is an intelligent data mining technique that builds
 a prediction model based on the learning of prior knowledge to recognize
 patterns in large-scale data sets. We present an ML-based methodology for
 transcriptome analysis via comparison of gene coexpression networks,
 implemented as an R package called machine learning–based differential
 network analysis (mlDNA) and apply this method to reanalyze a set of
 abiotic stress expression data in Arabidopsis thaliana. The mlDNA first
 used a ML-based filtering process to remove nonexpressed, constitutively
 expressed, or non-stress-responsive “noninformative” genes prior to
 network construction, through learning the patterns of 32 expression
 characteristics of known stress-related genes. The retained “informative”
 genes were subsequently analyzed by ML-based network comparison to predict
 candidate stress-related genes showing expression and network differences
 between control and stress networks, based on 33 network topological
 characteristics. Comparative evaluation of the network-centric and
 gene-centric analytic methods showed that mlDNA substantially outperformed
 traditional statistical testing–based differential expression analysis at
 identifying stress-related genes, with markedly improved prediction
 accuracy. To experimentally validate the mlDNA predictions, we selected 89
 candidates out of the 1784 predicted salt stress–related genes with
 available SALK T-DNA mutagenesis lines for phenotypic screening and
 identified two previously unreported genes, mutants of which showed
 salt-sensitive phenotypes.
description: Supplemental Dataset
 1Known Stress-related
 Genes Collected from the TAIR and DRASTIC Databases, their Expression
 Changes in the Stress Microarray Datasets, and the Statistical Results of
 their Gene Ontology (GO) AnnotationsSupplemental Dataset
 2“Informative” Genes
 Obtained from PSOL-based ML Analysis for Gene Co-expression Network
 Construction under Six Studied Stresses in Two TissuesSupplemental Dataset
 3Candidate Stress-related
 Genes Predicted by mlDNASupplemental Dataset
 4List
 of the Candidate Stress-related Genes Evidenced by a High-throughput
 Phenotypic Screening ExperimentSupplemental Dataset
 5Detailed Information for
 Gene Ontology (GO) Modules Enriched with Salt Stress-related
 GenesSupplemental Dataset
 6List
 of Stress Shared GenesSupplemental Dataset
 7List
 of Stress-Specific Genes
DOI: 10.5061/dryad.d9b2t
title: Data from: Static antennae act as locomotory guides that compensate for visual motion blur in a diurnal, keen-eyed predator

description: High visual acuity allows parallel processing of distant environmental
 features, but only when photons are abundant enough. Diurnal tiger beetles
 (Carabidae: Cicindelinae) have acute vision for insects and visually
 pursue prey in open, flat habitats. Their fast running speed causes motion
 blur that degrades visual contrast, forces stop-and-go pursuit, and
 potentially impairs obstacle detection. We demonstrate here that vision is
 insufficient for obstacle detection during running, and show instead, that
 antennal touch is both necessary and sufficient for obstacle detection.
 While running, tiger beetle vision appears to be photon limited in a way
 reminiscent of animals in low light habitats. Such animals often acquire
 wide-field spatial information through mechanosensation mediated by
 longer, more mobile appendages. We show that a nocturnal tiger beetle
 species waves its antennae in elliptical patterns typical of poorly
 sighted insects. While antennae of diurnal species are also used for
 mechanosensation, they are rigidly held forward with the tips close to the
 substrate. This enables timely detection of path obstructions followed by
 an increase in body pitch to avoid collision. Our results demonstrate
 adaptive mechanosensory augmentation of blurred visual information during
 fast locomotion, and suggest that future studies may reveal non-visual
 sensory compensation in other fast-moving animals.
description: antenna
 runsThis Matlab struct
 includes all subject ID and condition info, as well as video tracking and
 scoring data.
DOI: 10.5061/dryad.6nv8d
title: Data from: Deciphering the adjustment between environment and life history in annuals: lessons from a geographically-explicit approach in Arabidopsis thaliana

description: The role that different life-history traits may have in the process of
 adaptation caused by divergent selection can be assessed by using
 extensive collections of geographically-explicit populations. This is
 because adaptive phenotypic variation shifts gradually across space as a
 result of the geographic patterns of variation in environmental selective
 pressures. Hence, large-scale experiments are needed to identify relevant
 adaptive life-history traits as well as their relationships with putative
 selective agents. We conducted a field experiment with 279 geo-referenced
 accessions of the annual plant Arabidopsis thaliana collected across a
 native region of its distribution range, the Iberian Peninsula. We
 quantified variation in life-history traits throughout the entire life
 cycle. We built a geographic information system to generate an
 environmental data set encompassing climate, vegetation and soil data. We
 analysed the spatial autocorrelation patterns of environmental variables
 and life-history traits, as well as the relationship between environmental
 and phenotypic data. Almost all environmental variables were significantly
 spatially autocorrelated. By contrast, only two life-history traits, seed
 weight and flowering time, exhibited significant spatial autocorrelation.
 Flowering time, and to a lower extent seed weight, were the life-history
 traits with the highest significant correlation coefficients with
 environmental factors, in particular with annual mean temperature. In
 general, individual fitness was higher for accessions with more vigorous
 seed germination, higher recruitment and later flowering times. Variation
 in flowering time mediated by temperature appears to be the main
 life-history trait by which A. thaliana adjusts its life history to the
 varying Iberian environmental conditions. The use of extensive
 geographically-explicit data sets obtained from field experiments
 represents a powerful approach to unravel adaptive patterns of variation.
 In a context of current global warming, geographically-explicit
 approaches, evaluating the match between organisms and the environments
 where they live, may contribute to better assess and predict the
 consequences of global warming.
description: Arabidopsis_data_279accessions_8jan14
DOI: 10.5281/zenodo.18390631
title: When Digital Hype Meets Crypto Literacy in Bitcoin Investment Indonesia

description: This study aims to analyze the effects of Fear of Missing Out (FOMO) and Crypto Literacy on Bitcoin investment decisions in Indonesia, with Social Media Exposure serving as a moderating variable. A quantitative approach using Partial Least Squares–Structural Equation Modeling (PLS-SEM) was employed to examine the relationships among variables. The findings reveal that FOMO has a positive effect on Bitcoin investment decisions, confirming the role of psychological factors in driving speculative investment behavior. Crypto Literacy also significantly influences investment decisions, although the level of crypto literacy among Indonesian investors remains relatively low. Social Media Exposure not only has a direct effect but also strengthens the relationships between FOMO and Crypto Literacy with investment decisions, functioning as an amplifier in the dynamics of investment behavior. These findings extend behavioral finance literature by emphasizing the interaction between psychological factors, literacy, and social influence in the context of digital asset investment. This study is expected to contribute insights for investors, regulators, and social media platforms in developing more effective educational strategies, regulations, and consumer protection policies in the digital era.
DOI: 10.5281/zenodo.18390632
title: When Digital Hype Meets Crypto Literacy in Bitcoin Investment Indonesia

description: This study aims to analyze the effects of Fear of Missing Out (FOMO) and Crypto Literacy on Bitcoin investment decisions in Indonesia, with Social Media Exposure serving as a moderating variable. A quantitative approach using Partial Least Squares–Structural Equation Modeling (PLS-SEM) was employed to examine the relationships among variables. The findings reveal that FOMO has a positive effect on Bitcoin investment decisions, confirming the role of psychological factors in driving speculative investment behavior. Crypto Literacy also significantly influences investment decisions, although the level of crypto literacy among Indonesian investors remains relatively low. Social Media Exposure not only has a direct effect but also strengthens the relationships between FOMO and Crypto Literacy with investment decisions, functioning as an amplifier in the dynamics of investment behavior. These findings extend behavioral finance literature by emphasizing the interaction between psychological factors, literacy, and social influence in the context of digital asset investment. This study is expected to contribute insights for investors, regulators, and social media platforms in developing more effective educational strategies, regulations, and consumer protection policies in the digital era.