cometadata/datacite-titles-descriptions-related-identifiers huggingface dataset:
DOI: 10.5061/dryad.w3r2280vk
title: Biomass potential via light interception of novel miscanthus hybrids from field trials

description: New biomass crop hybrids for bioeconomic expansion require yield
 projections to determine their potential for strategic land use planning
 in the face of global challenges. Our biomass growth simulation
 incorporates radiation interception and conversion efficiency. Models
 often use leaf area to predict interception which is demanding to
 determine accurately, so instead, we use low-cost rapid light interception
 measurements using a simple lab-made line ceptometer and relate the
 dynamics of canopy closure to thermal time, and to measurements of
 biomass. We apply the model to project the European biomass potentials of
 new market-ready hybrids for 2020–30. Field measurements are easier to
 collect, the calibration is seasonally dynamic and reduces influence of
 weather variation between field sites. The model obtained is conservative,
 being calibrated by crops of varying establishment and varying maturity on
 less productive (marginal) land. This results in conservative projections
 of miscanthus hybrids for 2020-30 based on 10% land use conversion of the
 least (productive) grassland and arable for farm diversification, which
 show a European potential of 80.7–89.7 Mt y-1 biomass, with potential for
 1.2-1.3 EJ y-1 energy and 36.3–40.3 Mt y-1 carbon capture, with seeded M.
 sacchariflorus x sinensis displaying highest yield potential. Simulated
 biomass projections must be viewed in light of the field measurements on
 less productive land with high soil water deficits. We are attempting to
 model results from an ambitious and novel project combining new hybrids
 across Europe with agronomy which has not been perfected on less
 productive sites. Nevertheless, at a time of energy sourcing issues,
 seed-propagated miscanthus hybrids for the upscaled provision of bioenergy
 offer an alternative source of renewable energy. If European countries
 provide incentives for growers to invest, seeded hybrids can improve
 product availability and biomass yields over the current commercial
 miscanthus variety.
description: The dataset was collected via (1) the GRACE
 field trial for novel miscanthus hybrids (observed standing crop biomass,
 light interception, harvest yield) (2) data analysis
 and modelled extraction of a best-fit curve (light interception)
 (3) calibration data and validation data were used in the
 Bioenergy model MiscanFor (Hastings et al, 2009 https://doi.org/10.1111/j.1757-1707.2009.01007.x; Shepherd et al, 2020 https://doi.org/10.1111/gcbb.12671) The GRACE project contained more sites and more genotypes than the study for this paper, so data for relevant genotypes, years and locations have been extracted, analysed and used for model calibration and validation.
description: Excel (.csv files) and ArcGIS coverages (zipped)
DOI: 10.5061/dryad.rv15dv4br
title: Invertebrates on fungal fruit bodies

description: Fungi and invertebrates comprise a major part of biodiversity in dead wood
 ecosystems and invertebrates depend on fungi to utilise the dead wood
 resource. Many invertebrates also visit the long‐lived fruit bodies of
 wood‐decay fungi to feed on spores, the hymenium or other invertebrates.
 However, as traditional sampling methods are labour‐intensive, we know
 little of these interactions. In this study, we use time‐lapse cameras to
 monitor invertebrates visiting the hymenium of a common wood‐decay fungus,
 Fomitopsis pinicola, and explain their activity in terms of temporal
 variation, temperature and presence of Gyrophaena boleti, a highly
 abundant fungivorous beetle living primarily in fruit bodies of F.
 pinicola. The most common invertebrates on F. pinicola fruit bodies were
 Coleoptera, Araneae, Diptera, Gastropoda and Chilopoda. The invertebrate
 activity exhibited strong temporal variation with higher abundance during
 night and, for Coleoptera, earlier in the season. We discuss how this
 might correlate with the sporulation period of F. pinicola. The presence
 of G. boleti had a positive impact on the predatory Lordithon lunulatus
 and Ipidia binotata, and a negative impact on the fungivorous Thymalus
 limbatus and Peltis ferruginea. Chilopoda and L. lunulatus were ephemeral
 visitors, while the fungivorous Coleoptera and Araneae stayed the longest.
 We estimated the invertebrates' visitation frequency and duration,
 which would be time‐consuming to obtain with traditional methods. We offer
 improvements to our method and urge future research on invertebrate–fungus
 interactions to quantify invertebrate visits to fungal fruit bodies.
description: Monitoring of 19 Fomitopsis pinicola fruit body hymenia with
 time-lapse cameras taking pictures every ten minutes throughout the day
 from April-September in 2019 and 2020. The cameras have in-built flash and
 thermometers. Images were manually annotated to the lowest possible
 invertebrate taxonomic rank.
description: R and Microsoft Excel
DOI: 10.17632/hb6t2v6nsn.1
title: ICCE CTD location data

description: During the International Circumnavigation Expedition (ICCE) 2024-25, CTD measurements were collected in both polynya and non-polynya regions to investigate water-mass characteristics.
DOI: 10.6078/d1wt6w
title: Single and half-cell RNA-sequencing in Stentor coeruleus control and beta-tubulin knockdown cells

description: Stentor coeruleus are giant single-celled ciliates that reach
 lengths of up to 1 mm. Because of their large size, these cells are easy
 to manipulate and they also possess the ability to heal wounds and
 regenerate. These properties are ideal for investigating subcellular
 pattern formation, as we can physically dissect the cells into anterior
 and posterior halves. We used single and half-cell RNA-sequencing to assay
 for changes in transcript localization upon knocking down beta-tubulin, an
 important component of the microtubule cytoskeleton. 
description: After conducting RNAi knockdown of beta-tubulin
 in <em>Stentor </em><em>coeruleus</em>, we
 bisected the cells using a glass needle. Within 20 minutes of bisection,
 the whole cells and bisected cells were lysed and prepped for sequencing
 with the NEBNext Single Cell/Low Input Library Prep Kit for Illumina (Cat.
 No. E6420).
DOI: 10.60893/figshare.apl.31047451
title: Supplementary Materials

description: Supplementary Materials
DOI: 10.60893/figshare.apl.31047451.v1
title: Supplementary Materials

description: Supplementary Materials
DOI: 10.17632/rdy682rmdr
title: Effect of Planting Pattern and Intercropping Density on the Quality of Pandanus amaryllifolius Roxb

description: Pandanus amaryllifolius Roxb., an aromatic tropical spice crop, exhibits quality intricately linked to its key volatile constituents. Due to uncertainties surrounding the synergistic effects of intercropping systems and planting densities on these phytochemicals, this investigation implemented field trials encompassing three intercropping configurations with coconut(Cocos nucifera L.) , rubber (Hevea brasiliensis ) and areca nut (Areca catechu L.), alongside three planting density levels. Findings indicated that the intercropping of areca catechu with low planting density yielded optimal results, notably enhancing volatile compound concentrations and overall quality. This research elucidates the underlying synergistic mechanisms and offers valuable insights for the development of high-quality cultivation strategies.
DOI: 10.17632/rdy682rmdr.1
title: Effect of Planting Pattern and Intercropping Density on the Quality of Pandanus amaryllifolius Roxb

description: Pandanus amaryllifolius Roxb., an aromatic tropical spice crop, exhibits quality intricately linked to its key volatile constituents. Due to uncertainties surrounding the synergistic effects of intercropping systems and planting densities on these phytochemicals, this investigation implemented field trials encompassing three intercropping configurations with coconut(Cocos nucifera L.) , rubber (Hevea brasiliensis ) and areca nut (Areca catechu L.), alongside three planting density levels. Findings indicated that the intercropping of areca catechu with low planting density yielded optimal results, notably enhancing volatile compound concentrations and overall quality. This research elucidates the underlying synergistic mechanisms and offers valuable insights for the development of high-quality cultivation strategies.
DOI: 10.5061/dryad.z34tmpgjg
title: Effects of the entomopathogenic fungus Mucor hiemalis BO-1 on the physical functions and transcriptional signatures of Bradysia odoriphaga larvae

description: Mucor hiemalis BO-1 is an entomopathogenic fungus that infects Bradysia
 odoriphaga, a destructive root maggot. M. hiemalis BO-1 possesses stronger
 pathogenicity to the larvae than to other stages of B. odoriphaga and
 provides satisfactory field control. However, the physiological response
 of B. odoriphaga larvae to infection and the infection mechanism of M.
 hiemalis are unknown. We detected some physiological indicators of
 diseased B. odoriphaga larvae infected by M. hiemalis BO-1. These included
 changes in consumption, nutrient contents and digestive and antioxidant
 enzymes. We performed transcriptome analysis of diseased B. odoriphaga
 larvae and found that M. hiemalis BO-1 showed acute toxicity to B.
 odoriphaga larvae and was as toxic as some chemical pesticides. The food
 consumption of diseased B. odoriphaga after inoculation with M. hiemalis
 spores decreased significantly, and there was a significant decrease in
 total protein, lipid and carbohydrates in diseased larvae. Key digestive
 enzymes (protease, α-amylase, lipase and cellulase) were significantly
 inhibited during infection. Peroxidase maintained high activity, and the
 activity of other antioxidant enzymes (catalase, superoxide dismutase and
 glutathione S-transferases) first increased and then decreased. Combined
 with the transcriptional signatures of diseased B. odoriphaga larvae, M.
 hiemalis BO-1 infection resulted in decreased food consumption, reduced
 digestive enzyme activity and altered energy metabolism and material
 accumulation. Infection was also accompanied by fluctuations in immune
 function, such as cytochrome P450 and the Toll pathway. Therefore, our
 results laid a basis for the further study of the interactions between M.
 hiemalis BO-1 and B. odoriphaga and promoted the genetic improvement of
 entomopathogenic fungi.
DOI: 10.15468/dl.v665vw
title: Occurrence Download

description: A dataset containing 474574 species occurrences available in GBIF matching the query:
{
 "Geometry" : [
 "POLYGON ((151.193848 -32.2732, 151.11145 -32.782656, 151.853027 -32.745703, 151.907959 -32.170963, 151.193848 -32.2732))"
 ]
}

 The dataset includes 474574 records from 160 constituent datasets; see https://api.gbif.org/v1/occurrence/download/0002818-260126135527185/datasets/export for details.
 
Data from some individual datasets included in this download may be licensed under less restrictive terms.
DOI: 10.5061/dryad.t4b8gtj5t
title: High-intensity fires may have limited medium-term effectiveness for reversing woody plant encroachment in an African savanna

description: 1. Woody thickening or “bush encroachment” is a growing concern in
 savannas worldwide and can reportedly be reversed by applying
 high-intensity fires. Preliminary findings following experimental fires in
 2010 and 2013 indicated that woody plant cover declined one year after
 high-intensity fires, but increased after low-intensity fires. However,
 the longer-term outcomes of high-intensity fires are largely unknown. 2.
 To establish longer-term outcomes, we re-assessed sites subjected to Low,
 Medium and High-intensity fire treatments 10 years after the initial
 experimental fires. We compared woody vegetation structure in 2010 with
 that in 2020 using both ground surveys and airborne LiDAR. 3. Ground
 surveys revealed increases in the number of stems and individual shrubs
 (&lt; 10 m tall) over 10 years, and decreases in shrub height, with no
 significant differences between treatments. Large trees (≥ 10 m) declined
 by about 65% in number due to ongoing high mortality across treatments
 over 10 years. 4. LiDAR surveys revealed significant but very small
 differences in woody plant height and cover between treatments after 10
 years. Median height was around 2 m in all treatments, and 90th percentile
 tree height was moderately taller in the Low fire treatment. Mean canopy
 cover was about 55% in all treatments. The treatments, therefore, did not
 result in a meaningful reversal of woody encroachment with no discernible
 difference between the treatment sites after 10 years. 5. Synthesis and
 applications. The application of high-intensity fires did not reverse
 woody encroachment in the longer term. In addition, the application of
 such treatments would be impractical at a large scale. Within a framework
 of Strategic Adaptive Management, the next logical step would be to
 attempt a different approach. In this case, it is intended to use early or
 late wet season burns to increase the mortality of shrubs when they are in
 a more vulnerable phenological state. This study illustrates the
 importance of ongoing long-term monitoring, review and adaptation for
 finding practical ways to achieve desired ecological outcomes.
description: Data was collected using both ground surveys as well as airborne
 LiDAR.
DOI: 10.5061/dryad.4qrfj6qf5
title: Transgenerational plasticity in a zooplankton in response to elevated temperature and parasitism

description: Organisms are increasingly facing multiple stressors, which can
 simultaneously interact to cause unpredictable impacts compared to a
 single stressor alone. Recent evidence suggests that phenotypic plasticity
 can allow for rapid responses to altered environments, including biotic
 and abiotic stressors, both within a generation and across generations
 (transgenerational plasticity). Parents can potentially ‘prime’ their
 offspring to better cope with similar stressors, or, alternatively, might
 produce offspring that are less fit because of energetic constraints. At
 present, it remains unclear exactly how biotic and abiotic stressors
 jointly mediate the responses of transgenerational plasticity, and whether
 this plasticity is adaptive. Here we test the effects of biotic and
 abiotic environmental changes on within- and trans-generational plasticity
 using a Daphnia-Metschnikowia zooplankton-fungal parasite system. By
 exposing parents and their offspring consecutively to the single and
 combined effects of elevated temperature and parasite infection, we showed
 that transgenerational plasticity induced by temperature and parasite
 stress influenced host fecundity and lifespan; offspring of mothers that
 were exposed to one of the stressors were better able to tolerate elevated
 temperature, compared to offspring of mothers that were exposed to neither
 or both stressors. Yet the negative effects caused by parasite infection
 were much stronger, and this greater reduction in host fitness was not
 mitigated by transgenerational plasticity. We also showed that elevated
 temperature led to a lower average immune response and that the
 relationship between immune response and lifetime fecundity reversed under
 elevated temperature: the daughters of exposed mothers showed decreased
 fecundity with increased hemocyte production at ambient temperature, but
 the opposite relationship at elevated temperature. Together, our results
 highlight the need to address questions at the interface of multiple
 stressors and transgenerational plasticity, and the importance of
 considering multiple fitness-associated traits when evaluating the
 adaptive value of transgenerational plasticity under changing
 environments.
description: We conducted a fully factorial experiment over two generations in
 the laboratory to assess the adaptive significance of transgenerational
 plasticity in the
 host <em>Daphnia </em><em>dentifera </em>in
 response to the single or combined effects of elevated temperatures and/or
 parasite exposure.
description: All analyses were performed in R (version 4.1.2).
DOI: 10.5061/dryad.hqbzkh1m7
title: Widespread introgression of MHC genes in Iberian Podarcis lizards

description: Major Histocompatibility Complex (MHC) genes are crucial for the adaptive
 immune response of jawed vertebrates. Their variation, reaching extreme
 levels, is driven mainly by an arms race between hosts and pathogens. One
 hypothesized mechanism contributing to MHC polymorphism is adaptive
 introgression, the exchange of genetic variants between hybridizing
 species favoured by selection, yet its effect on MHC variation is poorly
 understood. Detection of adaptive MHC introgression, though challenging,
 may be facilitated by the analysis of species complexes forming multiple
 hybrid zones. Here, we investigated MHC introgression in six hybrid zones
 formed by seven species of Podarcis lizards inhabiting the
 Iberian Peninsula. To differentiate adaptive introgression from neutral
 introgression, we compared the patterns of gene exchange in MHC and
 genome-wide markers. We found elevated sharing of MHC alleles in the
 proximity of contact beyond the areas of detectable genome-wide admixture
 in most hybrid zones and, in half of them, asymmetric MHC exchange. In
 general, the elevated MHC allele sharing between species pairs with
 abutting ranges compared to geographically isolated species pairs also
 supports the prevalence of introgression. Collectively, our results
 demonstrate widespread MHC introgression in the Iberian Podarcis complex
 and suggest its adaptiveness. Contrary to previous results from Triturus
 newts, we did not observe differences in the rate of introgression between
 MHC classes. Our work adds support to the emerging view of adaptive
 introgression as a key mechanism shaping MHC diversity. It also raises
 questions about the effect of elevated MHC variation and factors leading
 to the asymmetry of adaptive introgression.
description: Details can be found in Gaczorek et al. (2023) "Widespread
 introgression of MHC genes in Iberian Podarcis lizards."
description: R software is needed to reproduce the attached R script.
DOI: 10.5061/dryad.nzs7h44w6
title: Data from: Tracing the origin of Oriental beech stands across Western Europe and reporting hybridization with European beech – implications for assisted gene flow

description: The benefits and risks of human-aided translocation of individuals within
 the species range, assisted gene flow (AGF), depend on the genetic
 divergence, on the rate and direction of hybridization, and on the climate
 transfer distance between the host and donor populations. In this study,
 we explored the use of Oriental beech (Fagus sylvatica subsp. orientalis),
 growing from Iran to the Balkans, for AGF into European beech populations
 (F. sylvatica subsp. Sylvatica) that increasingly suffer from climate
 warming. Using samples from natural populations of Oriental and European
 beech and microsatellite loci, we identified 5 distinct genetic clusters
 in Oriental beech with a divergence (FST) of 0.15 to 0.25 from European
 beech. Using this knowledge, we traced the origin of 11 Oriental beech
 stands in Western Europe established during the 20th century. In two
 stands of Greater Caucasus origin, we found evidence for extensive
 hybridization, with 18% and 41% of the seedlings having hybrid status.
 Climate data revealed higher seasonality with warmer and drier summers
 across the native Oriental beech sites in comparison to the planting sites
 in Western Europe. Accordingly, we found that bud burst of Oriental beech
 occurred four days earlier than in European beech. Overall, our results
 suggest that AGF of Oriental beech could increase the genetic diversity of
 European beech stands and may foster introgression of variants adapted to
 expected future climatic conditions. Our study showcases the evaluation of
 the benefits and risks of AGF and call for similar studies on other native
 tree species.
description: See the Methods section of Kurz et al. 2023.
DOI: 10.5061/dryad.0gb5mkm59
title: Bayesian models' outputs for: A new method to explicitly estimate the shift of optimum along gradients in multispecies studies

description: This repository contains data to reproduce analysis presented in the
 paper: B. Mourguiart, B. Liquet, K. Mengersen, T. Couturier, J. Mansons,
 Y. Braud, A. Besnard . A new method to explicitly estimate the shift of
 optimum along gradients in multispecies studies. Journal of Biogeography,
 (in press). The paper introduces a new formulation of a Bayesian
 hierarchical linear model that explicitly estimates optimum shifts for
 multiple species having symmetrical response curves. This new formulation,
 called Explicit Hierarchical Model of Optimum Shifts (EHMOS), is compared
 to a mean comparison method and a Bayesian generalized linear mixed model
 (GLMM) using simulated and real datasets. Fitting the models to the
 simulated data took several days. Here we provide the models' outputs
 needed to reproduce the results presented in the paper without re-running
 the models. 
description: The software R is required to open the data files.
DOI: 10.5061/dryad.qjq2bvqkw
title: Phenotype images of Gryllus personatus and five resulting morphological measurements

description: Sexual size dimorphism (SSD) and sexual shape dimorphism (SShD) are of
 interest to evolutionary ecology, but the two phenomena can very easily be
 conflated by not taking a multivariate approach to measuring size. In our
 study we draw attention to this problem by measuring four body size
 dimensions (maxillae span, head width, pronotum length and mean hind femur
 length) in lab-reared individuals of the badlands cricket (Orthoptera,
 Gryllinae, Gryllus personatus) and conducting a variety of multivariate
 analyses to test whether there is SSD and/or SShD. We found that males had
 wider heads and maxillae than females, and females had longer pronota and
 hind femora than males. This difference in the direction of sexual
 dimorphism indicates SShD. However, multivariate methods failed to detect
 SSD, instead confirming that the sexes primarily differ in body shape. We
 suggest that orthopterists studying sexual dimorphism minimally measure
 head width, pronotum length and hind femur length as a standard that will
 allow a more repeatable and generalizable assessment of the prevalence and
 direction of both SSD and SShD.
description: The attached dataset consists of: 1)
 all of the photographs (*.jpg) from which the measurements were taken, 2)
 a reference photograph (ReferenceScale2mm_WildM56X.jpg) of a 2-mm-long
 stage micrometer taken with the same microscope (Wild M5) and at the same
 magnification (6X), and 3) a spreadsheet (*.csv) containing our
 measurements, which form the basis for analyses in our published
 article. Photographs were
 prepared by dissecting individual crickets that had been euthanized by
 freezing, and placing them in standardized positions under a Wild M5
 stereomicroscope as in Judge and Bonnano 2008 (https://doi.org/10.1371/journal.pone.0003980). Images were taken with a digital camera (Infinity Lumenera) as in Dupuis et al. 2020 (https://doi.org/10.1093/biolinnean/blaa094). Landmarks (see Figure 1 in Judge and Bonanno 2008, https://doi.org/10.1371/journal.pone.0003980) were placed on the photos using SB Morphometrics (http://life.bio.sunysb.edu/morph/index.html) and converted to linear measurements as described in Dupuis et al. 2020.  Photograph files have a consistent naming system of five letters, three numbers, and then one or two letters. For example, GPEFA001FL.jpg, where GPE is consistent for all and refers to the species, F means the individual is female (M for male), A means the individual is an adult (J for juvenile), 001 is individual 1 (ranges from 001 to 168), and FL means femur left indicating the photo subject (other subjects: FR for femur right, HP for head posterior, and P for pronotum).
description: Image files can be opened and landmarks placed with the freely
 available SB Morphometrics (http://life.bio.sunysb.edu/morph/index.html). The data csv file is accessible by most spreadsheet programs.