cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.112cs
title: Data from: Multiple aspects of plasticity in clutch size vary among populations of a globally distributed songbird

description: 1. Plasticity in life-history characteristics can influence many
 ecological and evolutionary phenomena, including how invading organisms
 cope with novel conditions in new locations or how environmental change
 affects organisms in native locations. Variation in reaction norm
 attributes is a critical element to understanding plasticity in life
 history, yet we know relatively little about the ways in which reaction
 norms vary within and among populations. 2. We amassed data on clutch size
 from marked females in eight populations of house sparrows (Passer
 domesticus) from North America and Europe. We exploited repeated measures
 of clutch size to assess both the extent of within-individual phenotypic
 plasticity and among-individual variation and to test alternative
 hypotheses about the underlying causes of reaction norm shape,
 particularly the decline in clutch size with date. 3. Across all
 populations, females of this multibrooded species altered their clutch
 size with respect to date, attempt order, and the interaction of date and
 order, producing a reaction norm in multidimensional environmental space.
 The reaction norm fits that predicted by a model in which optimal clutch
 size is driven by a decline with date hatched in the ability of offspring
 to recruit. Our results do not fit those predicted for other proposed
 causes of a seasonal decline in clutch size. 4. We also found significant
 differences between populations in response to date and the date by
 attempt order interaction. We tested the prediction that the relationship
 with date should be increasingly negative as breeding season becomes
 shorter but found steeper declines in clutch size with date in populations
 with longer seasons, contrary to the prediction. Populations also differed
 in the level of among-individual variation in reaction norm intercept, but
 we found no evidence of among-individual variation in reaction norm slope.
 5. We show that complex reaction norms in life-history characters exhibit
 within- and among-population variance. The nature of this variance is only
 partially consistent with current life-history theory and stimulates
 expansions of such theory to accommodate complexities in adaptive life
 history.
description: Global_archive
DOI: 10.82294/dvngusri6
title: COPUS. Territorio: Cundinamarca. Sector: Educación. Año 2025
title: Dato. Observación estructurada con el protocolo COPUS.

description: Información recopilada durante el año 2025 a partir de observaciones estructuradas realizadas con el protocolo COPUS, dirigidas a educadores artísticos pertenecientes a programas de formación en educación artística y cultural del sector Educación (educación formal) en el departamento de Cundinamarca.
DOI: 10.5061/dryad.ph8s5
title: Data from: Fifty thousand years of arctic vegetation and megafaunal diet

description: Although it is generally agreed that the arctic flora is among the
 youngest and least diverse on Earth, the processes that shaped it are
 poorly understood. Here we present 50 thousand years (kyr) of arctic
 vegetation history, derived from the first large-scale ancient DNA
 metabarcoding study of circumpolar plant diversity. For this interval we
 additionally explore nematode diversity as a proxy for modelling
 vegetation cover and soil quality, and diets of herbivorous megafaunal
 mammals, many of which became extinct around 10 kyr BP (before present).
 For much of the period investigated, arctic vegetation consisted of dry
 steppe tundra dominated by forbs (non-graminoid herbaceous vascular
 plants). During the Last Glacial Maximum (25–15 kyr BP), diversity
 declined markedly, although forbs remained dominant. Much changed after 10
 kyr BP, with the appearance of moist tundra dominated by woody plants and
 graminoids. Our analyses indicate that both graminoids and forbs would
 have featured in megafaunal diets. As such our findings question the
 predominance of a late Quaternary graminoid-dominated arctic “mammoth
 steppe”.
description: Sheep diet
 dataFasta file containing
 the sequence dataovis_sequence_data.fastaMegafauna diet dataFasta file containing sequence data.megafauna_diet_sequence_data.fastaNematoda sequence dataFasta file containing the raw sequence data.nematoda_sequence_data.fastaNematoda filtered sequence dataFasta file containing the filtered sequence data.nematoda_filtered_sequence_data.fastaMegafauna sequence dataFasta file containing the sequence data.megafauna_sequence_data.fastaMegafauna filtered dataTabulated file containing the filtered data.megafauna_filtered_data.txtSheep diet filtered dataTabulated file containing filtered data of sheep diet.ovis_filtered_data.txtFull permafrost datasetcsv file containing the full permafrost dataset.permafrost.fulldata.csvReference database Arctic (gh)Fasta file of the Arctic reference database (P6 loop of the trnL)references.arctic-gh.fastaReference database Arctic (ITSAst)Fasta file of the Arctic reference database (ITSAst)references.arctic-ITSAst.fastaReference database Arctic (ITSCyp)Fasta file of the Arctic reference database (ITSCyp)references.arctic-ITSCyp.fastaReference database Arctic (ITSPoa)Fasta file of the Arctic reference database (ITSPoa)references.arctic-ITSPoa.fastaReference database Boreal (gh)Fasta file of the Boreal reference database (P6 loop of the trnL)references.boreal-gh.fastaReference database EMBL (gh)Fasta file of the EMBL reference database (P6 loop of the trnL)references.embl-gh.fastaReference database EMBL (ITSAst)Fasta file of the EMBL reference database (ITSAst)references.embl-ITSAst.fastaReference database EMBL (ITSCyp)Fasta file of the EMBL reference database (ITSCyp)references.embl-ITSCyp.fastaReference database EMBL (ITSPoa)Fasta file of the EMBL reference database (ITSPoa)references.embl-ITSPoa.fasta
DOI: 10.5061/dryad.jh58p
title: Data from: Habitat collapse due to overgrazing threatens turtle conservation in marine protected areas

description: Marine protected areas (MPAs) are key tools for combatting the global
 overexploitation of endangered species. The prevailing paradigm is that
 MPAs are beneficial in helping to restore ecosystems to more ‘natural’
 conditions. However, MPAs may have unintended negative effects when
 increasing densities of protected species exert destructive effects on
 their habitat. Here, we report on severe seagrass degradation in a
 decade-old MPA where hyper-abundant green turtles adopted a previously
 undescribed below-ground foraging strategy. By digging for and consuming
 rhizomes and roots, turtles create abundant bare gaps, thereby enhancing
 erosion and reducing seagrass regrowth. A fully parametrized model reveals
 that the ecosystem is approaching a tipping point, where consumption
 overwhelms regrowth, which could potentially lead to complete collapse of
 the seagrass habitat. Seagrass recovery will not ensue unless turtle
 density is reduced to nearly zero, eliminating the MPA's value as a
 turtle reserve. Our results reveal an unrecognized, yet imminent threat to
 MPAs, as sea turtle densities are increasing at major nesting sites and
 the decline of seagrass habitat forces turtles to concentrate on the
 remaining meadows inside reserves. This emphasizes the need for policy and
 management approaches that consider the interactions of protected species
 with their habitat.
description: Graphs_Christianen_PRSBData Fig. 1: Gap cover and seagrass biomass between 2003-2011.Fig4_Christianen_PRSBR script and data Fig. 4:Graphical comparison of two fully parameterized models describing the balance between green turtle grazing and seagrass regrowth, and its implications for the response of seagrass to increased turtle density and grazing strategy.Fig_ESM_Christianen_PRSBESM Figure S3. Seagrass biomass and production for gaps of different age or different stage of regrowth.FigESM_Christianen_PRSB.RFigESM2_Christianen_PRSBESM Figure S4. Model 1 ; Seagrass production in a continuous meadow . Seagrass production in a gap mosaic landscape . Model 2 ; Seagrass production in a gap mosaic landscape. where erosion disturbs recovery.Christianen_MS_ESM_revisionElectronic Supported Materials
DOI: 10.5061/dryad.k1t1f
title: Data from: From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes

description: Background: Next-generation sequencing has provided a wealth of plastid
 genome sequence data from an increasingly diverse set of green plants
 (Viridiplantae). Although these data have been useful for reconstructing
 the phylogeny of numerous clades of photosynthetic organisms (e.g., green
 algae, angiosperms, and gymnosperms), their utility for inferring
 relationships across all green plants is uncertain. Viridiplantae
 originated 700-1500 million years ago and may comprise as many as 500,000
 species. This clade represents a major source of photosynthetic carbon and
 contains an immense diversity of life forms, including some of the
 smallest and largest eukaryotes. Here we explore the limits and challenges
 of inferring a comprehensive green plant phylogeny from available complete
 or nearly complete plastid genome data. Results: We assembled
 protein-coding sequence data for 78 genes from 360 diverse green plant
 taxa with complete or nearly complete plastid genome sequences available
 from GenBank. Phylogenetic analyses of the plastid data recovered
 well-supported backbone relationships and strong support for relationships
 that were not observed in previous analyses of major subclades within
 Viridiplantae. However, there also is evidence of systematic error in some
 analyses. In several instances we obtained strongly supported but
 conflicting topologies from analyses of nucleotides versus amino acid
 characters, and the considerable variation in GC content among lineages
 and within single genomes affected the phylogenetic placement of several
 taxa. Conclusions: Analyses of the plastid data recovered a strongly
 supported framework of relationships for green plants. This includes the
 placement of Zygnematophyceace as sister to land plants (Embryophyta) and
 a clade of extant gymnosperms (Acrogymnospermae) with cycads + Ginkgo
 sister to remaining members and with gnetophytes (Gnetophyta) sister to
 non-Pinaceae conifers (Gnecup trees); within the monilophyte clade
 (Monilophyta), relationships are strongly supported with Equisetales +
 Psilotales sister to Marattiales + leptosporangiate ferns. We also
 highlight the challenges of using plastid genome sequences in deep-level
 phylogenomic analyses and provide suggestions for future analyses that
 will likely incorporate plastid genome data for thousands of species. We
 particularly emphasize the importance of exploring the effects of
 different partitioning and character coding protocols for the entire data
 set as well as subsets of the data.
description: Alignments and Partition
 FilesAlignments and partition
 filesAlignmentsandPartitionFiles.zipBootstrap Consensus TreesBootstrap Consensus TreesBSConsensusTrees.zipMLTreeswBLandBSReadMe_Ruhfeletal_Viridiplantae
DOI: 10.5061/dryad.8n6t5
title: Data from: Factors determining forest diversity and biomass on a tropical volcano, Mt. Rinjani, Lombok, Indonesia

description: Tropical volcanoes are an important but understudied ecosystem, and the
 relationships between plant species diversity and compositional change and
 elevation may differ from mountains created by uplift, because of their
 younger and more homogeneous soils. We sampled vegetation over an
 altitudinal gradient on Mt. Rinjani, Lombok, Indonesia. We modeled alpha-
 (plot) and beta- (among plot) diversity (Fisher’s alpha), compositional
 change, and biomass against elevation and selected covariates. We also
 examined community phylogenetic structure across the elevational gradient.
 We recorded 902 trees and shrubs among 92 species, and 67 species of
 ground-cover plants. For understorey, subcanopy and canopy plants, an
 increase in elevation was associated with a decline in alpha-diversity,
 whereas data for ground-cover plants suggested a hump-shaped pattern.
 Elevation was consistently the most important factor in determining
 alpha-diversity for all components. The alpha-diversity of ground-cover
 vegetation was also negatively correlated with leaf area index, which
 suggests low light conditions in the understorey may limit diversity at
 lower elevations. Beta-diversity increased with elevation for ground-cover
 plants and declined at higher elevations for other components of the
 vegetation. However, statistical power was low and we could not resolve
 the relative importance to beta-diversity of different factors.
 Multivariate GLMs of variation in community composition among plots
 explained 67.05%, 27.63%, 18.24%, and 19.80% of the variation (deviance)
 for ground-cover, understorey, subcanopy and canopy plants, respectively,
 and demonstrated that elevation was a consistently important factor in
 determining community composition. Above-ground biomass showed no
 significant pattern with elevation and was also not significantly
 associated with alpha-diversity. At lower elevations communities had a
 random phylogenetic structure, but from 1600 m communities were
 phylogenetically clustered. This suggests a greater role of environmental
 filtering at higher elevations, and thus provides a possible explanation
 for the observed decline in diversity with elevation.
description: Rinjani Elevation
 DatabaseSpreadsheet with all
 dataRinjani
 Elevation database.xlsfinal Rscript
 RinjaniR script for
 analysesSupplementary
 material.zipCompressed file
 supplementary figures and tables
DOI: 10.5061/dryad.f78r2
title: Data from: A Bayesian method for analyzing lateral gene transfer

description: Lateral gene transfer (LGT)—which transfers DNA between two non-vertically
 related individuals belonging to the same or different species—is
 recognized as a major force in prokaryotic evolution, and evidence of its
 impact on eukaryotic evolution is ever increasing. LGT has attracted much
 public attention for its potential to transfer pathogenic elements and
 antibiotic resistance in bacteria, and to transfer pesticide resistance
 from genetically modified crops to other plants. In a wider perspective,
 there is a growing body of studies highlighting the role of LGT in
 enabling organisms to occupy new niches or adapt to environmental changes.
 The challenge LGT poses to the standard tree-based conception of evolution
 is also being debated. Studies of LGT have, however, been severely limited
 by a lack of computational tools. The best currently available LGT
 algorithms are parsimony-based phylogenetic methods, which require a
 pre-computed gene tree and cannot choose between sometimes wildly
 differing most-parsimonious solutions. Moreover, in many studies, simple
 heuristics are applied that can only handle putative orthologs and
 completely disregard gene duplications. Consequently, proposed LGT among
 specific gene families, and the rate of LGT in general remain debated. We
 present a Bayesian MCMC-based method that integrates gene duplication,
 gene loss, LGT, and sequence evolution, and apply the method in a
 genome-wide analysis of two groups of bacteria: Mollicutes and
 Cyanobacteria. Our analyses show that although the LGT rate between
 distant species is high, the net combined rate of duplication and close
 species-LGT is on average higher. We also show that the common practice of
 disregarding reconcilability in gene tree inference overestimates the
 number of LGT and duplication events.
description: Supplementary
 informationsi.pdf
DOI: 10.5061/dryad.55qb2
title: Data from: "454 sequencing of reduced representation libraries to discover single nucleotide polymorphisms (SNPs) in Megabunus harvestmen" in Genomic Resources Notes accepted 1 December 2013 to 31 January 2014

description: Harvestmen or daddy longlegs (Opiliones) are the third-largest and one of
 the oldest arachnid groups, and in recent years, there has been an
 increasing interest in this order. Here we use next-generation sequencing
 of reduced representation libraries to establish nuclear DNA markers. To
 the best of our knowledge this dataset represents the largest genomic
 resource for Megabunus harvestmen available to date.
description: Processing protocol and
 scriptsA data processing
 protocol and all custom python scripts that were used for the analysis of
 the NGS data.FASTA and ALN
 filesThe FASTA files of all
 short reads matching to at least 3 of 4 study species, and the FASTA and
 ALN files of all short reads matching to all 4 species. ALN files were
 generated using Clustal Omega.Distance
 tableGenetic distance table
 of all alignments with matches to 4 species. This table was the basis for
 locus selection for subsequent primer design.Distance table
 purgedDecontamination files
 scripts protocolContains the BLAST
 results of the RRL reads against the NCBI nt collection, and all
 downstream steps performed to remove Homo sapiens
 sequencesDecontaminationFASTA and ALN files purged
DOI: 10.5061/dryad.87d8s
title: Data from: Bayesian estimation of speciation and extinction from incomplete fossil occurrence data

description: The temporal dynamics of species diversity are shaped by variations in the
 rates of speciation and extinction, and there is a long history of
 inferring these rates using first and last appearances of taxa in the
 fossil record. Understanding diversity dynamics critically depends on
 unbiased estimates of the unobserved times of speciation and extinction
 for all lineages, but the inference of these parameters is challenging due
 to the complex nature of the available data. Here, we present a new
 probabilistic framework to jointly estimate species-specific times of
 speciation and extinction and the rates of the underlying birth-death
 process based on the fossil record. The rates are allowed to vary through
 time independently of each other, and the probability of preservation and
 sampling is explicitly incorporated in the model to estimate the true
 lifespan of each lineage. We implement a Bayesian algorithm to assess the
 presence of rate shifts by exploring alternative diversification models.
 Tests on a range of simulated data sets reveal the accuracy and robustness
 of our approach against violations of the underlying assumptions and
 various degrees of data incompleteness. Finally, we demonstrate the
 application of our method with the diversification of the mammal family
 Rhinocerotidae and reveal a complex history of repeated and independent
 temporal shifts of both speciation and extinction rates, leading to the
 expansion and subsequent decline of the group. The estimated parameters of
 the birth-death process implemented here are directly comparable with
 those obtained from dated molecular phylogenies. Thus, our model
 represents a step towards integrating phylogenetic and fossil information
 to infer macroevolutionary processes.
description: Supplementary_InformationTable_S2
DOI: 10.6084/m9.figshare.30294478.v5
title: Residential Energy Dataset with Electric Vehicles,Photovoltaic Generation and Tariff Variability inIreland

description: This dataset presents high-resolution residential energy data collected from four households in the Dingle Peninsula, Ireland, as part of the Dingle Electrification Project. It uniquely integrates household grid imports and exports, rooftop photovoltaic (PV) production, electric vehicle (EV) charging events, EV journey logs, and tariff variability. Data are aligned at 30-minute intervals, covering 2019–2022 for household energy and tariffs, and 2021–2022 for EV usage. Each household was equipped with a 2.1 kWp rooftop PV system, Hyundai Kona Electric vehicle, smart charger, and advanced metering infrastructure. The dataset supports research on smart charging, demand response, renewable integration, and community energy optimization.
DOI: 10.5061/dryad.gv5ss
title: Data from: Factors influencing clinical trial site selection in Europe: the survey of attitudes towards trial sites in Europe (the SAT-EU StudyTM)

description: Objectives: Applications to run clinical trials in Europe fell 25% between
 2007 and 2011. Costs, speed of approvals, and shortcomings of European
 Clinical Trial Directive are commonly invoked to explain this
 unsatisfactory performance. However, no hard evidence is available on the
 actual weight of these factors, nor has it been previously investigated
 whether other criteria may also impact clinical trial site selection.
 Design: The SAT-EU StudyTM was an anonymous, cross-sectional Web-based
 survey that systematically assessed factors impacting European clinical
 trial site selection. It explored 19 factors across investigator-,
 hospital-, and environment-driven criteria, and costs. It also surveyed
 perceptions of the European trial environment. Setting and Participants:
 Clinical Research Organizations (CROs), academic Clinical Trial Units
 (CTUs), and Industry invited to respond. Interventions: None Outcome
 Measures: Primary: Weight assigned to each factor hypothesized to impact
 trial site selection and trial incidence; Secondary: Desirability of
 European countries to run clinical trials Results: Responses were obtained
 from 485 professionals in 34 countries: 49% from BioPharma, 40% from CTUs
 or CROs. Investigator-, environment-, and hospital-dependent factors were
 rated highly important, costs being less important (P&lt;0.0001).
 Within environment-driven criteria, pool of eligible patients, speed of
 approvals, and presence of disease-management networks were significantly
 more important than costs or government financial incentives
 (P&lt;0.0001). The pattern of response was consistent across
 respondent groupings (CTU vs. CRO vs. Industry). Considerable variability
 was demonstrated in the perceived receptivity of countries to undertake
 clinical trials, with Germany, United Kingdom, and the Netherlands rated
 the best trial markets (P&lt;0.0001). Conclusions:
 Investigator-dependent factors and ease of approval dominate trial site
 selection, while costs appear less important. Fostering competitiveness of
 European clinical research may not require additional government
 spending/incentives. Rather, harmonization of approval processes, greater
 visibility of centres of excellence, and reduction of “hidden” indirect
 costs, may bring significantly more clinical trials to Europe.
description: SAT-EU
 SurveySummary_Survey Monkey_10172013_EUROPE_Dryad_UploadVersion
 2Original source of
 information is an excel download from Survey Monkey, which was used to
 collect the survey data.