cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.bvq83bkd2
title: Ineffective integration of multiple antipredator defences in a rotifer: a low-cost insurance?

description: To maximize survival, prey often integrates multiple anti-predator
 defenses. How the defenses interact to reduce predation risk is, however,
 poorly known. We used the rotifer Brachionus calyciflorus to investigate
 how morphological (spines) and behavioral (floating) defenses are
 integrated against a common predatory rotifer, Asplanchna brightwellii,
 and if their combined use improves survival. To this end, we assessed the
 cost of the behavioral defense and the efficiency of both defenses,
 individually and combined, as well as their mutual dependency. The results
 show that the behavioral defense is costly in reducing foraging activity,
 and that the two defenses are used simultaneously, with the presence of
 the morphological defense enhancing the use of the behavioral defense, as
 does the pre-exposure to predator cues. However, while the morphological
 defense reduces predation risk, the behavioral defense does not, thus,
 adding the costly behavioral defense to the morphological defense does not
 improve survival. It is likely that the cost of the behavioral defense is
 low given its reversibility – compared to the cost of misidentifying the
 predator species – and that this has promoted the adoption of both
 defenses, as general low-cost insurance rather than as a tailored strategy
 toward specific predators. Thus, the optimal strategy in the rotifer
 appears to be to express both morphological and behavioral defenses when
 confronted with the cues of a potential predator.
description: the data is collected from four lab experiments.
 For details of the dataset please read our manscript
 "Ineffective integration of
 multiple antipredator defenses in a rotifer: a low-cost
 insurance?"  
  
description: the data is collected from four lab experiments.
 For details of the dataset please read our manscript
 "Ineffective integration of
 multiple antipredator defenses in a rotifer: a low-cost
 insurance?"
DOI: 10.5061/dryad.n02v6wx1d
title: Sib-mating enhances fitness in a haplodiploid beetle

description: Inbreeding is generally avoided in animals due to the risk of inbreeding
 depression following an increase in homozygous deleterious alleles and
 loss of heterozygosity. Species that regularly inbreed challenge our
 understanding of the fitness effects of these risks. We investigated
 fitness consequences of extended inbreeding in the haplodiploid date-stone
 beetle, Coccotrypes dactyliperda. We hypothesized that continuous
 inbreeding could result in reduced fitness, while outbreeding would either
 increase fitness due to heterosis or lower fitness if co-adapted gene
 complexes are disrupted. We established three breeding treatments with
 beetles from two geographically separated populations: Sib-mating
 (inbreeding), and outbreeding within- and between-populations.
 Between-population outbreeding groups of both populations had lower
 fecundity and collapsed before the experiment ended, while sib-mated and
 within-population breeding groups persisted for ten generations. Sib-mated
 females had higher fecundity than within- and between-population
 outbreeding females. Inbreeding coefficients of sib-mated groups were
 higher than the other treatment groups, yet sib-mated beetles remained
 genetically polymorphic at the population level. Thus, there was no
 inbreeding depression, while crossing between distant populations led to
 outbreeding depression. Our findings are consistent with the life history
 of C. dactyliperda, in which sib-mating predominates within the date seed,
 but occasional within-population outbreeding may occur following local
 dispersal.
description: A breeding experiment over 10 generations with three breeding
 treatments: sib-mating, outbreeding within a local population, and
 outbreeding between distant populations. Variables
 measured were fecundity and adult body size. In select
 generations, genetic markers were used to determine the level of
 heterozygosity and inbreeding coefficients of beetles in the experimental
 treatments and in the original populations.
description: Excel
DOI: 10.5061/dryad.tdz08kq33
title: The topological nature of tag jumping in environmental DNA metabarcoding studies (sequencing raw data)

description: Metabarcoding of environmental DNA constitutes a state-of-the-art tool for
 environmental studies. One fundamental principle implicit in most
 metabarcoding studies is that individual sample amplicons can still be
 identified after being pooled with others – based on their unique
 combinations of tags – during the so-called demultiplexing step that
 follows sequencing. Nevertheless, it has been recognized that tags can
 sometimes be changed (i.e. tag jumping), which ultimately leads to sample
 crosstalk. Here, using four DNA metabarcoding datasets derived from the
 analysis of soils and sediments, we show that tag jumping follows very
 specific and systematic patterns. Specifically, we find a strong
 correlation between the number of reads in blank samples and their
 topological position in the tag matrix (described by vertical and
 horizontal vectors). This observed spatial pattern of artefactual
 sequences could be explained by polymerase activity, which leads to the
 exchange of the 3’ tag of single stranded tagged sequences through the
 formation of heteroduplexes with mixed barcodes. Importantly, tag jumping
 substantially distorted our datasets – despite our use of methods
 suggested to minimize this error. We developed a topologic model to
 estimate the noise based on the counts in our blanks, which suggested that
 40-80% of the taxa in our soil and sedimentary samples were likely false
 positives introduced through tag jumping. We highlight that the amount of
 false positive detections caused by tag jumping strongly biased our
 community analyses. 
description: Sequencing data in fastq format. Multiplexed libraries,
 information on tags, primers and protocols can be found in the published
 paper and its supplementary information.
DOI: 10.15124/a033ed32-ff01-4c85-a1de-8955d48b0891
title: Exploring pre-catalyst scope and selectivity in Negishi coupling of aryl iodides in deep eutectic solvents - Raw data

description: Raw data supporting the paper "Exploring pre-catalyst scope and selectivity in Negishi coupling of aryl iodides in deep eutectic solvents". The archive contains data on: NMR spectra and GC data.
DOI: 10.5061/dryad.4qrfj6qdf
title: Primer sequences for H3N2 canine influenza virus full-length amplification, polymerase activity assay, and rescue

description: Influenza A viruses in animal reservoirs repeatedly cross species barriers
 to infect humans. Once an animal-borne virus with novel antigenicity
 acquired the efficient human-to-human transmissibility, it will become
 epidemic in the population. Dogs are the closest animal companions to
 humans, and canine respiratory tract expresses both SAα2,3-(avian type)
 and α2,6-Gal (human type) receptors. However, the role of dogs in the
 ecology of influenza viruses is unclear. H3N2 avian influenza viruses were
 transmitted to dogs around 2006 and have formed stable lineages. The
 long-term epidemic of avian-origin H3N2 virus in canines offers the best
 models to investigate the effect of dogs on the evolution of influenza
 viruses. Here, we carried out a systematic and comparative identification
 of the biological characteristics of H3N2 canine influenza viruses (CIVs)
 isolated in worldwide over 10 years. We found that during the adaptation
 of H3N2 CIVs to dogs, H3N2 CIVs became to recognize the human-like
 SAα2,6-Gal receptor, gradually increased HA acid stability and replication
 ability in human airway epithelial cells, and acquired a 100% transmission
 rate via respiratory droplet in ferret model, which were essential
 hallmarks of being adapted to humans. We also identified that the
 frequency of substitutions related to human adaptation has gradually
 increased in H3N2 CIVs and determined four cumulative molecular changes
 responsible for the increased airborne transmission ability in ferrets.
 Our results suggested that canines may serve as an intermediate for the
 adaptation of avian influenza virus to humans. Continuous surveillance
 coordinated with risk assessment for CIVs is necessary.
description: This study designed the primer dataset by Primer Premier 6.0.
 Some primer sequences are used for virus genome amplification and
 sequencing, while others are used for virus rescue and polymerase activity
 assay.
description: No special programs or software are required to open the data
 files.
DOI: 10.15468/dl.bewafq
title: Occurrence Download

description: A dataset containing 33 species occurrences available in GBIF matching the query:
{
 "and" : [
 "TaxonKey is Eurypetalum unijugum",
 "HasCoordinate is true",
 "BasisOfRecord is one of (Specimen)"
 ]
}

 The dataset includes 33 records from 8 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003307-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.1zcrjdfw0
title: Data from: GABABR silencing of nerve terminals

description: Control of neurotransmission efficacy is central to theories of how the
 brain computes and stores information. Neuromodulators are critical in
 this problem as they locally influence synaptic strength and can operate
 on a wide range of time scales. Presynaptic function is heavily influenced
 by G-protein coupled receptors (GPCRs) that in part restrict voltage-gated
 calcium (Ca2+) influx in the active zone. Here, using quantitative
 analysis of both single bouton Ca2+ influx and exocytosis, we
 uncovered an unexpected non-linear relationship between the magnitude of
 action potential driven Ca2+ influx and the concentration of
 external Ca2+ ([Ca2+]e). We find that this unexpected
 relationship is leveraged by neuromodulator signaling when operating at
 the nominal physiological set point for [Ca2+]e, 1.2 mM, to achieve
 complete silencing of nerve terminals. These data imply that the
 information throughput in neural circuits can be readily modulated in an
 all-or-none fashion at the single synapse level when operating at the
 physiological set point.
DOI: 10.5061/dryad.x95x69pnp
title: Higher spring phenological sensitivity to forcing temperatures of Asian compared to European tree species under low and high pre-chilling conditions Datasets

description: Winter chilling, spring forcing temperature and photoperiod are the most
 important drivers explaining the spatial and temporal variability of
 spring phenology in temperate trees. However, how these factors interact
 with each other on dormancy release and spring budburst date remains
 unclear and varies greatly depending on species. Our knowledge is also
 limited as to whether heat accumulation of forcing temperatures that
 trigger bud break in spring is a linear or non-linear process. Here, we
 aimed at experimentally quantifying the effect of chilling, forcing,
 photoperiod and their interactions on the budburst dates of nine different
 temperate tree species from East Asia (near Beijing, China) and Central
 Europe (near Zurich, Switzerland), including six phylogenetically related
 species (same genus). We conducted a full factorial experiment in climate
 chambers using two chilling (low and high, i.e., 0 vs. 56 days at 2C after
 sampling at the end of December), four forcing (5, 10, 15, and 20C), and
 two photoperiod (8 vs. 16 h) treatments simultaneously in Beijing and
 Zurich. We found that species growing near Beijing responded more readily
 to forcing conditions than species of the same genus growing near Zurich
 regardless of chilling treatment. Budburst timing of most species but
 European beech was marginally, if at all, affected by photoperiod.
 Furthermore, our results suggest that linear heat accumulation, as
 commonly used with the growing degree hours (GDH) model, could result in
 accurate prediction of budburst date depending on the temperature
 threshold used as a basis for heat accumulation. Our results also
 demonstrate the important role of chilling in shaping the sensitivity and
 rate of forcing accumulation to trigger budburst and suggest that
 species-specific sigmoid relationship for accumulating heat that accounts
 for prior chilling exposure may yield better predictions of budburst
 dates. Our results suggest that deciduous trees may have adapted their
 chilling and forcing requirements in regards to the predictability of
 winter-spring transition and late spring frosts. A less predictable
 winter-spring transition, as observed in Central Europe, could have driven
 species evolution towards higher chilling and forcing requirements
 compared to species growing in a more predictable climate of Northeastern
 Asia. Our cross-continental experiment therefore suggests that the spring
 phenology of East Asian species is tighter coupled to spring forcing
 temperature than Central European forests.
description: Exposure of twig cuttings to different chilling, forcing, and
 photoperiods to disentangle those different drivers of temperate tree
 spring phenology. Evaluated are days to budburst and growing degree hours
 (GDH) to budburst for 9 deciduous tree species 3 from East-Asia and 6 from
 Central Europe.
description: The data could be accessed with any text editor.
DOI: 10.5061/dryad.q2bvq83p7
title: Codes and data for: Clustering optimisation method for highly connected biological data

description: Currently, data-driven discovery in biological sciences resides in finding
 segmentation strategies in multivariate data that produce sensible
 descriptions of the data. Clustering is but one of several approaches and
 sometimes falls short because of difficulties in assessing reasonable
 cutoffs, the number of clusters that need to be formed or that an approach
 fails to preserve topological properties of the original system in its
 clustered form. In this work, we show how a simple metric for connectivity
 clustering evaluation leads to an optimised segmentation of biological
 data. The novelty of the work resides in the creation of a simple
 optimisation method for clustering crowded data. The resulting clustering
 approach only relies on metrics derived from the inherent properties of
 the clustering. The new method facilitates knowledge for optimised
 clustering, which is easy to implement.We discuss how the clustering
 optimisation strategy corresponds to the viable information content
 yielded by the final segmentation. We further elaborate on how the
 clustering results, in the optimal solution, corresponds to prior
 knowledge of three different data sets. This is the dataset and the codes
 required to conduct the above-mentioned analysis.
DOI: 10.5061/dryad.xgxd254km
title: Fire favors sexual precocity in a Mediterranean pine

description: Wildfires are a natural disturbance in many ecosystems. Consequently,
 plant species have acquired traits that allow them to resist and
 regenerate in an environment with recurrent fires. A key trait in
 fire-prone ecosystems is the age at first reproduction (maturity age);
 populations of non-resprouting species cannot persist when fire interval
 is shorter than this age. Maturity age is variable among individuals, so
 we hypothesize that short fire intervals select for early seed production
 (precocity). We selected 13 plots with different fire regimes in eastern
 Spain, all dominated by Pinus halepensis (a non-resprouting serotinous
 species). Then, we evaluated the age at first reproduction and the size of
 the canopy seed bank of each individual pine. Our results show a
 significant effect of fire regime on the onset of reproduction in this
 species, suggesting a selection towards higher precocity in populations
 subject to shorter fire intervals. Due to this higher precocity, pines
 stored more cones, and therefore, increased their potential for post-fire
 regeneration. We provide the first field evidence that fire can act as a
 driver of precocity. Being precocious in fire-prone environments is
 adaptive because it increases the probability of having a significant seed
 bank when the next fire arrives.
description: We selected 13 sites dominated
 by <em>Pinus halepensis</em> trees in the Valencia region
 (eastern Spain) across a range of altitudes and climatic conditions. In
 each site, we established 4 transects, spaced by at least 100 m. In each
 transect, we haphazardly selected and georeferenced 10 trees, separated by
 at least 10 m. For each tree, we measured its basal diameter (10 cm above
 ground) and the distance to the two closest trees. Then, we compute the
 annual growth rate as the basal diameter (cm) divided by the age (years)
 and the average of the distances to the 2 closest trees. Afterward, we
 estimated the age of each tree by counting whorls. For reproductive trees,
 we also estimated the age of each cone following the same method of
 counting whorls (avoiding immature cone cohorts; i.e., the last or last
 two cohorts depending on the sampling season) and recorded whether they
 were open (non-serotinous), closed (serotinous cones), or from the last
 cohort considered (closed but serotiny unknown). The retention of branches
 and cones in this species allowed us to estimate the age of the young tree
 and its cones (even if they were open), and therefore the age at first
 reproduction (tree age - age of the first cone) and the total number of
 stored cones (i.e. closed cones; an estimation of the canopy seed bank)
 for each tree. Please see “materials and methods” section within the paper
 for more details.
DOI: 10.5061/dryad.8gtht76sn
title: Broad diversity in monoterpene-sesquiterpene balance across wild sunflowers: implications of leaf and floral volatiles for biotic interactions

description: • Premise of the study: As plant lineages diversify across
 environmental gradients, species are predicted to encounter divergent
 biotic pressures. This study investigates the evolution of volatile
 secondary metabolism across Helianthus genus.   •
 Methods: Leaves and petals of 40 species of wild Helianthus were
 analyzed via gas chromatography-mass-spectrometry to describe volatile
 secondary metabolite profiles. • Key results: Across all species,
 500 compounds were identified including 40% sesquiterpenes, 18%
 monoterpenes, 3% diterpenes, 4% fatty acid derivatives, and 35% other
 compounds such as phenolics and small organic compounds. Qualitatively,
 annuals and species from more arid western climates had leaf compositions
 with a higher proportion of total monoterpenes, while erect perennials and
 species from more mesic eastern habitats contained a higher proportion of
 total sesquiterpenes. Among species, mass-based leaf monoterpene and
 sesquiterpene abundance were identified as largely orthogonal axes of
 variation by principal components analysis. Leaf and petal profiles were
 not strongly correlated. • Conclusions: Wide diversity in
 volatile metabolism was observed among wild Helianthus, indicating value
 of this genus as a model system, and a rich genetic resource. The
 independence of leaf and petal volatile profiles indicates a low level of
 phenotypic integration between vegetative and reproductive structures,
 implying vegetative defense and reproductive defense or pollinator
 attraction functions mediated by terpenoid profiles in these two organs
 can evolve without major tradeoffs. The major biosynthetic pathways
 manufacturing major terpenoids identified in wild Helianthus have been
 well described to date, providing a road map to deeper inquiry into the
 drivers of this diversity.
description: Greenhouse study of wild sunflower species. Tissue sampled and
 analyzed by solid phase microextraction gas chromatography-mass
 spectrometry. Chromatographic data processed to generate individual,
 tissue, and species mean profile data. Phylogenetic comparative methods
 used.
description: Data files are CSV, no proprietary software required.
DOI: 10.5061/dryad.0p2ngf24r
title: The time course of acclimation to the stress of triose phosphate use limitation

description: Triose-phosphate utilization (TPU) limits the maximum rate at which plants
 can photosynthesize. However, TPU is almost never found to be limiting
 photosynthesis under ambient conditions for plants. This, along with
 previous results showing adaptability of TPU at low temperature, suggest
 that TPU capacity is regulated to be just above the photosynthetic rate
 achievable under the prevailing conditions. A set of experiments were
 performed to study the adaptability of TPU capacity when plants are
 acclimated to elevated CO2 concentrations. Plants held at 1500 ppm CO2
 were initially TPU-limited. After 30 hours, they no longer exhibited TPU
 limitations, but they did not elevate their TPU capacity. Instead, the
 maximum rates of carboxylation and electron transport declined. A time
 course of regulatory responses was established. A step increase of CO2
 first caused PSI to be oxidized, but after 40 s, both PSI and PSII had
 excess electrons as a result of acceptor-side limitations. Electron flow
 to PSI slowed, and the proton motive force increased. Eventually,
 non-photochemical quenching reduced electron flow sufficiently to balance
 the TPU limitation. Over several minutes rubisco deactivated contributing
 to regulation of metabolism to overcome the TPU limitation.
description: This data was collected in laboratory in East Lansing MI using
 LI-COR LI-6800 instruments modified to be able to take optical and
 fluorescent measurements. Rubisco activation measurements were collected
 via scintillation counts for radioactive C14. Data was split, processed
 using R scripts, and then collated into tables that are presented in this
 dataset.
description: All data presented here is in comma-delimited text formats and
 should be openable by all coding languages and any text or tabular file
 viewer. Some demonstrative graphs are presented as PDFs. Files are
 organized into zipped files based on experiment and data type.
DOI: 10.15468/dl.bweuhz
title: Occurrence Download

description: A dataset containing 9747802 species occurrences available in GBIF matching the query:
{
 "and" : [
 "DatasetKey is Macro-moth distribution records for the UK from Butterfly Conservation, up to 2019",
 "TaxonKey is Geometridae",
 "HasCoordinate is true",
 "OccurrenceStatus is Present",
 "HasGeospatialIssue is false",
 "Year is greater than or equal to 1950"
 ]
}

 The dataset includes 9747802 records from 1 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0003300-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.280gb5mss
title: Single vesicle fusion experiments illustrating the inhibition of the calcium triggered release by the inhibitory peptide SP9

description: Synaptic neurotransmitter release is mediated by an orchestra of
 presynaptic proteins that precisely control and trigger fusion between
 synaptic vesicles and the neuron terminal at the active zone upon an
 action potential. Critical to this process are the neuronal SNAREs
 (Soluble N-ethylmaleimide sensitive factor Attachment protein REceptor),
 the Ca2+-sensor synaptotagmin, the activator/regulator complexin, and
 other factors. Here we present the data for single vesicle fusion
 experiments with synaptic vesicles in absence and presence of the
 inhibitory peptide SP9 that illustrate the inhibition of calcium-triggered
 release. 
description: See README.md file.
description: See README.me file.