cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.6c03bm4
title: Data from: Manipulating saltmarsh microtopography modulates the effects of elevation on sediment redox potential and halophyte distribution

description: 1. Halophyte distributions on saltmarshes are strongly related to
 elevation in the tidal frame. However, collinearity between elevation, the
 consequent inundation regime, and sediment waterlogging/redox potential
 obscures the proximate causes of distribution patterns. We sought to
 distinguish the effects of elevation per se from those of waterlogging by
 manipulating microtopography. 2. We experimentally manipulated elevation
 by ±15 cm at locations that spanned the elevation ranges of three
 saltmarshes recently reactivated by managed coastal realignment.
 Experimental plots were initially cleared of any vegetation. Elevation and
 sediment redox potential were determined for each plot. We planted five
 perennial species (Armeria maritima, Atriplex portulacoides, Limonium
 vulgare, Plantago maritima and Triglochin maritima) in half of the plots,
 recording survival over four years, and monitored natural colonisation of
 the other plots. 3. Overall, redox potential increased with elevation.
 Sediments were more oxidising in raised plots and more reducing in lowered
 plots. Redox reductions in lowered plots were in line with those that
 would be predicted from the overall redox/elevation relationship, but
 increases in raised plots were greater than predicted from elevation
 alone. 4. Plant colonisation and survival was poorer in lowered plots and,
 for most species, improved in raised plots. This can, in part, be
 attributed to the concomitant alterations in redox potential and elevation
 in the tidal frame, but microtopographic manipulation also had substantial
 independent effects on plant performance, including on the survival of all
 planted species and the colonisation of Puccinellia maritima, Salicornia
 europaea agg. and Tripolium pannonicum. 5. Synthesis: Microtopography can
 have effects on sediment chemistry and plant performance similar in
 magnitude to those of overall tidal elevation. Understanding how its
 effects modulate the relationship between tidal elevation, redox and other
 environmental conditions helps clarify the abiotic factors that
 fundamentally determine halophyte colonisation and survival. These results
 support the use of topographic manipulation to enhance the diversity of
 created saltmarshes.
description: Mossman_etal_JEcol_UnplantedplotsData on the abundance (cover) of the six most abundant species that colonised unplanted experimental plots. Plots (1 m by 1 m) were raised (treatment R) by 15 cm, lowered (L) by 15 cm or at the marsh surface (F). Plots were established in winter 2009 and vegetation sampled at the end of the growing season in 2013.Mossman_etal_JEcol_PlantedplotsData on the number of individuals that survived (out of 10) in experimental plots. Plots (1 m by 1 m) were raised (Treatment R) by 15 cm, lowered (L) by 15 cm or at the marsh surface (F). Plots were established in winter 2009, individuals planted in spring/summer 2010, and survival assessed at the end of the growing season in 2013.
DOI: 10.5061/dryad.727r289
title: Data from: Adjustments in control of mitochondrial respiratory capacity while facing temperature fluctuations

description: As the world's climate changes, life faces an evolving thermal
 environment. Mitochondrial oxidative phosphorylation (OXPHOS) is critical
 to ensure sufficient cellular energy production, and it is strongly
 influenced by temperature. The thermally-induced changes to the regulation
 by specific steps within the OXPHOS process are poorly understood. In our
 study, we used the eurythermal species of planarian Dugesia tigrina to
 study the thermal sensitivity of the OXPHOS process at 10, 15, 20, 25,
 30&[deg]C. We conducted cold acclimation experiments where we
 measured the adjustment of specific steps at two assay temperatures (10
 and 20&[deg]C) following four weeks of acclimation under normal
 (22&[deg]C) or low (5&[deg]C) temperature conditions. At
 the low temperature, the contribution of the NADH pathway to the maximal
 OXPHOS capacity, in a combined pathway (NADH and succinate) was reduced.
 There was partial compensation by an increased contribution of the
 succinate pathway. As the temperature decreases, OXPHOS becomes more
 limited by the capacity of the phosphorylation system. Acclimation to the
 low temperature resulted in positive adjustments of the NADH pathway
 capacity due, at least in part, to an increase in complex I activity. The
 acclimation also resulted in a better match between OXPHOS and
 phosphorylation system capacities. Both of these adjustments following
 acclimation were specific to the low assay temperature. We conclude that
 there is substantial plasticity in the mitochondrial OXPHOS process
 following thermal acclimation in D. tigrina, and this is likely
 contributing to the wide thermal range of the species.
description: Dugesia tigrina
 mitochondria and temperature-Data shareAdjustments in Control
 of Mitochondrial Respiratory Capacity while Facing Temperature
 FluctuationsDugesia-Acclimation-2019-05-16-Data share.xls
DOI: 10.5061/dryad.174v48d
title: Data from: Plant adaptation to different climates shapes the strengths of chemically-mediated tritrophic interactions

description: How plant traits evolve along geographical and climatic gradients has
 recently received increased attention because of anticipated climate
 change and associated shifts in insect distribution, whether they are
 herbivores or predators. This issue is particularly relevant for traits
 related to growth and anti-herbivore defence of plants, because both sets
 of traits are closely tied to fitness, and because being sessile
 organisms, plants tend to experience strong local selection. Despite
 widespread recognition that the abiotic environment imposes selection on
 plant traits, how temperature and water availability independently select
 for allocation to growth and defence against herbivores is not well
 resolved; and even more so, when considering underground herbivory and
 tritrophic interactions involving plant herbivores and their predators. To
 address heritable, climate-driven, variation of root traits mediating
 tritrophic interactions, we performed a common garden experiment with four
 populations of the red fescue (Festuca rubra) encompassing the four
 corners of a precipitation by temperature gradient matrix. We found that
 plants originating from wetter and warmer conditions, in addition to
 producing more biomass, also produced a blend of volatile organic
 compounds more attractive for predatory nematodes of root insect
 herbivores. Moreover, across populations, variation in nematode attraction
 was mediated by balancing the emissions of attractive and repulsive
 volatile compounds. Our work builds toward better understating how plant
 adaptation to climate interacts with adaptations to herbivores and their
 predators.
description: Bioassay
 dataPlant trait (biomass and
 volatile data), and entomopathogenic nematode choice
 dataLaureline_Norway.csv
DOI: 10.5061/dryad.6b2c0n3
title: Data from: Relating national levels of crop damage to population size indices of large grazing birds: implications for management

description: 1. Populations of large grazing birds have increased in Europe during at
 least five decades, raising conflicts between conservation and farming
 interests. Managing these conflicts requires knowledge about the currently
 unknown relationship between population sizes and crop damage levels. 2.
 We analyzed unique data on reported, inspected and compensated crop damage
 caused by geese, swans and cranes together with data from population
 surveys in Sweden to investigate how bird abundance related to damage
 levels at the national scale between 2000 and 2015. 3. Over the study
 period, the annual number of damage reports, yield loss and costs for
 compensation increased. These crop damage levels were positively related
 to national population indices of common crane, barnacle and greylag
 goose. The shape of these relationships varied between species and
 encompassed considerable uncertainty. However, on a year-to-year basis
 (detrended data) we found no evident association between damage levels and
 bird numbers. 4. Yield loss and compensation costs per reported damage did
 not increase with higher population indices of greylag goose, but they did
 so for barnacle goose. 5. Synthesis and applications: We present a novel
 study towards the understanding of the relationships between different
 crop damage level indicators (damage reports, yield loss and compensation
 costs) and population numbers of large grazing birds. We identified a
 positive relationship with high uncertainty for all cases. We also
 identified the need to 1) better synchronize the monitoring of damages and
 bird numbers in time and space and 2) further study the relationships
 between damage levels and bird numbers at smaller (local and regional) and
 larger (flyway) spatial scales to reduce the uncertainty of the
 relationship and to gain a more holistic understanding of the system.
description: RawData_Models
DOI: 10.5281/zenodo.18392268
title: simulated few million CLAS12 e+P data

description: Dataset contents

This Zenodo record publishes a set of GEMC-produced HIPO files containing simulated detector response (and associated Monte Carlo truth where available) intended for:





Track reconstruction development and validation (algorithm development, regression testing, performance studies)




Data-preparation workflows for ML / foundation-model experiments



Primary data format: HIPOPrimary generator/simulation toolchain: GEMC (Geant4-based), with configuration and job recipes tracked in the linked repository.

How the data were produced (provenance)

The HIPO files were generated by running GEMC with a controlled detector and physics configuration, producing simulated detector hits / digitization and exporting to HIPO for downstream reconstruction and analysis.

Generation and configuration details are documented in:





Software repository: https://code.jlab.org/cmorean/gemc-trackreco



At minimum, the production procedure includes:





Selection of geometry and detector configuration (TODO)




Event generation (TODO)




Transport and detector response simulation (Geant4 via GEMC)




Digitization / hit formatting and export to HIPO



Reproducibility note: This record is intended to be reproducible from the repository, pinned via commit hashes/tags and/or container images when available (TODO).

File organization

The deposition contains:





*.hipo — simulated events in HIPO format



Intended use

This dataset is designed to support:





Reconstruction algorithm development (including track finding/fitting, detector alignment studies, and performance comparisons)




Controlled ML experiments where ground-truth labels and stable simulation conditions are required




Data “readiness” studies for large-scale QCD-related ML pipelines, including provenance-aware dataset curation and repeatable training/evaluation splits



It is not intended to represent a final physics result; it is a simulation-derived dataset intended for method development and evaluation under a known configuration.
DOI: 10.5281/zenodo.18392267
title: simulated few million CLAS12 e+P data

description: Dataset contents

This Zenodo record publishes a set of GEMC-produced HIPO files containing simulated detector response (and associated Monte Carlo truth where available) intended for:





Track reconstruction development and validation (algorithm development, regression testing, performance studies)




Data-preparation workflows for ML / foundation-model experiments



Primary data format: HIPOPrimary generator/simulation toolchain: GEMC (Geant4-based), with configuration and job recipes tracked in the linked repository.

How the data were produced (provenance)

The HIPO files were generated by running GEMC with a controlled detector and physics configuration, producing simulated detector hits / digitization and exporting to HIPO for downstream reconstruction and analysis.

Generation and configuration details are documented in:





Software repository: https://code.jlab.org/cmorean/gemc-trackreco



At minimum, the production procedure includes:





Selection of geometry and detector configuration (TODO)




Event generation (TODO)




Transport and detector response simulation (Geant4 via GEMC)




Digitization / hit formatting and export to HIPO



Reproducibility note: This record is intended to be reproducible from the repository, pinned via commit hashes/tags and/or container images when available (TODO).

File organization

The deposition contains:





*.hipo — simulated events in HIPO format



Intended use

This dataset is designed to support:





Reconstruction algorithm development (including track finding/fitting, detector alignment studies, and performance comparisons)




Controlled ML experiments where ground-truth labels and stable simulation conditions are required




Data “readiness” studies for large-scale QCD-related ML pipelines, including provenance-aware dataset curation and repeatable training/evaluation splits



It is not intended to represent a final physics result; it is a simulation-derived dataset intended for method development and evaluation under a known configuration.
DOI: 10.5061/dryad.f8s1f6m
title: Data from: Revealing higher than expected diversity of Harpacticoida (Crustacea:Copepoda) in the North Sea using MALDI-TOF MS and molecular barcoding

description: The North Sea is one of the most extensively studied marine regions of the
 world. Hence, large amounts of molecular data for species identification
 are available in public repositories, and expectations to find numerous
 new species in this well-known region are rather low. However, molecular
 reference data for harpacticoid copepods from this area in particular but
 also for this group in general is scarce. By assessing COI barcodes and
 MALDI-TOF mass spectra for this group of small crustaceans, it was
 discovered that there is a huge unknown diversity in this area. In total,
 COI sequences for 548 specimens from 115 species of harpacticoid copepods
 are presented. Over 19% of these were new to science and ten MOTUs were
 found to be part of cryptic species complexes. MALDI-TOF mass spectra were
 assessed for 622 specimens from 75 species. Because results were in
 concordance with species delimitation by COI barcoding and also enabled
 recognition of possible cryptic species, the discriminative power of this
 technique for biodiversity assessments is highlighted. Findings imply,
 species diversity in this group may be largely underestimated and total
 species number can be expected to be much higher than previously assumed.
description: Data matrix with
 metadataThis .csv file contains
 the mass spectra data of all specimens investigated in this study as it
 was used for the analyses described. The data was processed as reported in
 the manuscript and finally hellinger transformed. Moreover, the file
 contains the sampling data on all contained specimens including sampling
 date, station number, latitude and longitude as well as sampling depth and
 species names in columns. The mass spectra data is provided in a matrix
 with specimens as rows and peak intensities in columns. Column names
 indicate the size of the measured proteins in Dalton.MALDI data matrix with
 MetaData.csvData_matrix_before_binningThis .csv data contains the mass spectra "raw data". Data was processed as described in the manuscript until the peak binning. Hence, this file contains the measurements of peaks without aligning them using peak binning.MALDI TOF raw spectraThis .zip archive contains the raw measurements of all specimens investigated in this study. For each specimen there is a separate folder containing subfolders for each measurement that was carried out.
DOI: 10.5061/dryad.6ts275n
title: Data from: Wildfire alters the structure and seasonal dynamics of nocturnal pollen-transport networks

description: Wildfires drive global biodiversity patterns and affect plant–pollinator
 interactions, and are expected to become more frequent and severe under
 climate change. Post‐fire plant communities often have increased floral
 abundance and diversity, but the effects of wildfires on the ecological
 process of pollination are poorly understood. Nocturnal moths are globally
 important pollinators, but no previous study has examined the effects of
 wildfire on nocturnal pollination interactions. We investigated the
 effects of wildfire on nocturnal pollen‐transport networks. We analysed
 the abundance and species richness of moths and flowers, and the structure
 of these networks, at three burned and three unburned sites in Portugal
 for two years, starting eight months after a large fire. Nocturnal
 pollen‐transport networks had lower complexity and robustness following
 the fire than at nearby unburned sites. Overall, 70% of individual moths
 carried pollen, and moths were found to be transporting pollen from 83% of
 the flower species present. Burned sites had significantly more abundant
 flowers, but less abundant and species‐rich moths. Individual moths
 transported more pollen in summer at burned sites, but less in winter;
 however, total pollen transport by the moth assemblage at burned sites was
 just 20% of that at unburned sites. Interaction turnover between burned
 and unburned networks was high. Negative effects of fire upon moths will
 likely permeate to other taxa through loss of mutualisms. Therefore, if
 wildfires become more frequent under climate change, community resilience
 may be eroded. Understanding the responses of ecological networks to
 wildfire can inform management that promotes resilience and facilitates
 whole‐ecosystem conservation.
description: Raw pollinator and
 pollen transport dataRaw, unprocessed data on
 individual insects sampled in light traps and pollen transport sampled
 from those insects.BanzaDataNoct.csvRaw plant transect dataRaw, unprocessed data on floral abundance sampled during transects.PlantTransects.csvPollen transport matrixPollinator and pollen transport data, wrangled into matrix format for ease of analysis.MatrixNoct.txtFloral abundance matrixFloral abundance data, wrangled into matrix format for ease of analysis.PlantTransects.txtPlant species metadataMetadata for all plant species detected on floral transects or in pollen analysis, listed family-level taxonomy and growth strategy (i.e. annual, perennial etc.).AllPlantSpecies_strategy.csvMoth species metadataMetadata for all moth species identified in the study, listing family-level taxonomy and resolution of ID.AllSpeciesEdited.csvCoordinatesGeographic locations of field sampling plots.Season orderMetadata file listing the nine sampling seasons by name and giving their correct chronological order.SeasonOrder.csvTrap timesMetadata file giving the time of day (in decimal hours) at which light traps were turned on and off during each sampling session.TrapTimes.csv
DOI: 10.5061/dryad.0hn97r5
title: Data from: Population genetic structure and connectivity of the seagrass Thalassia hemprichii in the Western Indian Ocean is influenced by predominant ocean currents

description: This study is the first large-scale genetic population study of a
 widespread climax species of seagrass, Thalassia hemprichii, in the
 Western Indian Ocean (WIO). The aim was to understand genetic population
 structure and connectivity of T. hemprichii in relation to hydrodynamic
 features. We genotyped 205 individual seagrass shoots from 11 sites across
 the WIO, spanning over a distance of ~2,700 km, with twelve microsatellite
 markers. We assessed clonality and visualized genetic diversity and
 genetic population differentiation. We used Bayesian clustering approaches
 (TESS) to trace spatial ancestry of populations and used directional
 migration rates (DivMigrate) to identify sources of gene flow. We
 identified four genetically differentiated groups; (1) samples from the
 Zanzibar channel, (2) Mozambique, (3) Madagascar, and (4) the east coast
 of Zanzibar and Kenya. Significant pairwise population genetic
 differentiation was found among many sites. Isolation by distance was
 detected for the estimated magnitude of divergence (DEST), but the three
 predominant ocean current systems (i.e. East African Coastal Current,
 North East Madagascar Current and the South Equatorial Current) also
 determine genetic connectivity and genetic structure. Directional
 migration rates indicate that Madagascar acts as an important source
 population. Overall clonality was moderate to high with large differences
 among sampling sites, indicating relatively low, but spatially variable
 sexual reproduction rates. The strongest genetic break was identified for
 three sites in the Zanzibar channel. Although isolation by distance is
 present, this study suggests that the three regionally predominant ocean
 current systems (i.e. East African Coastal Current, North East Madagascar
 Current and the South Equatorial Current) rather than distance determine
 genetic connectivity and structure of T. hemprichii in the WIO. If the
 goal is to maintain genetic connectivity of T. hemprichii within the WIO,
 conservation planning and implementation of marine protection should be
 considered at the regional scale – across national boarders.
description: Thalassia_MLGsThis file contains the genotyping data based on microsatellites for the seagrass Thalassia hemprichii in the Western Indian Ocean. The file contains multi locus genotypes (MLGs), i.e. duplicates clones within sites have been removed. The analysis was based on 12 microsatellites and their names are shown in the first line of the file. Sample names are given in column 1, and sampling sites in column 2.
DOI: 10.5061/dryad.6hm5760
title: Data from: Mycorrhizae alter constitutive and herbivore-induced volatile emissions by milkweeds

description: Plants use volatile organic compounds (VOCs) to cue natural enemies to
 their herbivore prey on plants. Simultaneously, herbivores utilize
 volatile cues to identify appropriate hosts. Despite extensive efforts to
 understand sources of variation in plant communication by VOCs, we lack an
 understanding of how ubiquitous belowground mutualists, such as arbuscular
 mycorrhizal fungi (AMF), influence plant VOC emissions. In a full
 factorial experiment, we subjected plants of two milkweed (Asclepias)
 species under three levels of AMF availability to damage by aphids (Aphis
 nerii). We then measured plant headspace volatiles and chemical defenses
 (cardenolides) and compared these to VOCs emitted and cardenolides
 produced by plants without herbivores. We found that AMF have plant
 species-specific effects on constitutive and aphid-induced VOC emissions.
 High AMF availability increased emissions of total VOCs, two green leaf
 volatiles (3-hexenyl acetate and hexyl acetate), and methyl salicylate in
 A. curassavica, but did not affect emissions in A. incarnata. In contrast,
 aphids consistently increased emissions of 6-methyl-5-hepten-2-one and
 benzeneacetaldehyde in both species, independent of AMF availability. Both
 high AMF availability and aphids alone suppressed emissions of individual
 terpenes. However, aphid damage on plants under high AMF availability
 increased, or did not affect, emissions of those terpenes. Lastly, aphid
 feeding suppressed cardenolide concentrations only in A. curassavica, and
 AMF did not affect cardenolides in either plant species. Our findings
 suggest that by altering milkweed VOC profiles, AMF may affect both
 herbivore performance and natural enemy attraction.
description: Mycorrhizae alter
 milkweed constitutive and herbivore-induced volatile
 emissionsThe file
 “AMFVolatiles.xslx” contains the raw data used in our publication
 “Mycorrhizae Alter Constitutive and Herbivore-Induced Volatile Emissions
 by Milkweeds”. Missing values are denoted with “NA”. Please see the README
 file for more detail about the data file.AMFVolatiles.xlsx