Find research datasets worth reusing

Data from: Mechanical soil disturbance in a pine savanna has multi-year effects on plant species composition

Data used in the manuscript Mechanical soil disturbance in a pine savanna has multi-year effects on plant species composition accepted for publication in Ecosphere. Data included are species lists for all plots and years, percent cover of species in each plot in 2021, and life-history characteristics (life span, dispersal mechanism, seed bank persistence) of all species. See manuscript for site description and data collection methodology.

Data from: Supervised classification of plant communities with artificial neural networks

This dataset was used to test the performance of artificial neural networks for supervised classification of plant communities, published in:Černá L. & Chytrý M. (2005) Supervised classification of plant communities with artificial neural networks. Journal of Vegetation Science 16, 407-414. https://doi.org/10.1111/j.1654-1103.2005.tb02380.xThe meaning of the individual columns (separated by semicolons) in the file is as follows (for details see the above-mentioned article):<ul><li>Plot no - unique number of the vegetation plot</li><li>Group expert - plot membership in classes 1-11 of the expert  classification</li><li>Subset expert random B - assignment of the plot to the training, selection, test or ignored data subset, using the random selection of the training (and selection) subset, for the expert classification</li><li>Subset expert dg species B - assignment of the plot to the training, selection, test or ignored data subset, using the selection of the training (and selection) subset by  diagnostic species, for the expert classification</li><li>Assignment expert random - a class assignment of the plot by the MLP classifier, when trained with the randomly selected training (and selection) subset, for expert classification</li><li>Assignment expert dg-sp - a class assignment  of the plot by the MLP classifier, when trained with the plots rich in diagnostic species contained in the training (and selection) subset, for expert classification</li><li>Group cluster - plot membership in classes 1-11 of the numerical classification</li><li>Subset cluster random - assignment of the plot to the training, selection, test or ignored data subset, using the random selection of the training (and selection) subset, for numerical classification</li><li>Subset cluster dg species - assignment of the plot to the training, selection, test or ignored data subset, using the selection of the training (and selection) subset by diagnostic species, for expert classification, for numerical classification</li><li>Assignment cluster random - class assignment of the plot by the MLP classifier, when trained with the randomly selected training (and selection) subset, for expert classification, for numerical classification</li><li>Assignment cluster dg-sp - class assignment  of the plot by the MLP classifier, when trained with the plots rich in diagnostic species contained in the training (and selection) subset, for expert classification, for numerical classification </li><li>598 species, with cover/abundance estimates on an ordinal scale of 1-9</li></ul>

Code and data for: The evolution of ontogenetic decision-making in the wood of a clade of tropical plants

Code and data for reproducing the analysis from the manuscript "The evolution of ontogenetic "decision-making" in the wood of a clade of tropical plants". Data includes raw and curated data from cell lineages derived from wood progenitor cells. Python code is provided to generate virtual wood cell lineages using L-systems. It also provides code to determine number of words at different k-mer lengths and to estimate Shannon-Entropy and Lempel-Ziv values, from the coded cell lineages. R code is provided to generate the plots and to adjust linear models of the maximum number of words based on total number of coded cells and mean cell lineage length.

opencc-by-4.0Nov 2023View details →

Dataset underlying the study "Enhanced Susceptibility to Tomato Chlorosis Virus (ToCV) in Hsp90- and Sgt1-Silenced Plants: Insights from Gene Expression Dynamics"

This dataset is underlying the scientific publication titled "Enhanced Susceptibility to Tomato Chlorosis Virus (ToCV) in Hsp90- and Sgt1-Silenced Plants: Insights from Gene Expression Dynamics", published in the <a href="https://www.mdpi.com/1999-4915/15/12/2370">Viruses</a> journal. The dataset includes a time-course transcriptome analysis using RNA-seq of naïve (no whitefly and no virus), mock (non-viruliferous whiteflies) and ToCV (ToCV_viruliferous whiteflies)-treated tomato samples at 2, 7, and 14 days post-infection (dpi) and viral small RNAs derived from Tomato plants infected with ToCV at 14 dpi. The dataset provided here has been deposited in full by the authors in the European Nucleotide Archive (ENA) at EMBL-EBI under accession number PRJEB67704 (<a href="https://www.ebi.ac.uk/ena/browser/view/PRJEB67704">https://www.ebi.ac.uk/ena/browser/view/PRJEB67704</a> The provided information in the dataset are further discussed and interpreted in detail, as well as their subsequent results, in the scientific publication.This research was conducted within the VIRTIGATION project, which is part of the EU Open Research Data pilot. This project has received funding from the European Union's Horizon 2020 research and innovation program under grant agreement No. 101000570.

Plant interaction networks reveal the limits of our understanding of diversity maintenance

Species interactions are key drivers of biodiversity and ecosystem stability. Current theoretical frameworks for understanding the role of interactions make many assumptions which, unfortunately, do not always hold in natural, diverse communities. This mismatch extends to annual plants, a common model system for studying coexistence, where interactions are typically averaged across environmental conditions and transitive competitive hierarchies are assumed to dominate. We quantify interaction networks for a community of annual wildflowers in Western Australia across a natural shade gradient at local scales. Whilst competition dominated, intraspecific and interspecific facilitation were widespread in all shade categories. Interaction strengths and directions varied substantially despite close spatial proximity and similar levels of local species richness, with most species interacting in different ways under different environmental conditions. Contrary to expectations, all networks were predominantly intransitive. These findings encourage us to rethink how we conceive of and categorise the mechanisms driving biodiversity in plant systems.

Functional traits—not nativeness—shape the effects of large mammalian herbivores on plant communities

Large mammalian herbivores (megafauna) have experienced extinctions and declines since prehistory. Introduced megafauna have partly counteracted these losses yet are thought to have unusually negative effects compared to native megafauna. Using a meta-analysis of 3,995 plot-scale plant abundance and diversity responses from 221 studies, we found no evidence that megafauna impacts were shaped by nativeness, 'invasiveness', 'feralness', coevolutionary history, or functional and phylogenetic novelty. Nor was there evidence that introduced megafauna facilitate introduced plants more than native megafauna. Instead, we found strong evidence that functional traits shaped megafauna impacts, with larger-bodied and bulk-feeding megafauna promoting plant diversity. Our work suggests that trait-based ecology provides better insight into interactions between megafauna and plants than concepts of nativeness.

Peatland restoration in Norway – evaluation of ongoing monitoring and identification of plant indicators of restoration success

Norway launched a national action plan on wetland restoration in 2016. So far, 90% of the restoration effort has been on peatland restoration, with about 140 mires restored so far. There are three main restoration goals stated in the action plan: 1) Limit greenhouse gas (GHG) emissions, 2) climate adaptation, and 3) improve ecological condition. Quantifying the outcome of the restoration actions is necessary to evaluate whether the goals of the action plan are met. A vegetation monitoring protocol was suggested before restoration started and has been implemented at five restoration sites. As the peatland restoration effort in Norway is increasing, it is timely to evaluate if the data currently collected can measure peatland restoration outcomes. We evaluate the monitoring protocol based on statistical analyses of the data collected at two sites, describe how indicator species can be identified using generalized composition data used as the basis for classifying habitats in Norway (EcoSyst framework), and suggest the way forward for peatland restoration monitoring in Norway. Data collected according to the monitoring protocol can document changes in species composition at restoration sites but has limitations when the ecological complexity at the sites increases and reference sites are unavailable. We argue that adjusting the monitoring protocol will: 1) Facilitate alignment with existing peatland research; 2) connect better with monitoring programs where data is collected applying EcoSyst framework principles; and 3) enable upscaling to cover the wide variation emerging in peatland restoration.

Competitors alter selection on alpine plants exposed to experimental climate change

Investigating how climate change alters selection regimes is a crucial step towards understanding the potential of populations to evolve in the face of changing conditions. Previous studies have mainly focused on understanding how changing climate directly influences selection, while the role of species' interactions has received little attention. Here, we used a transplant experiment along an elevation gradient to estimate how climate warming and competitive interactions lead to shifts in directional phenotypic selection on morphology and phenology of four alpine plants. We found that warming generally imposed novel selection, with the largest shifts in regimes acting on specific leaf area and flowering time across species. Competitors instead weakened the selection acting on traits that was imposed directly by warming. Weakened or absent selection in the presence of competitors was largely associated with the suppression of absolute means and variation of fitness. Our results suggest that although climate change can impose strong selection, competitive interactions within communities might act to limit selection and thereby stymie evolutionary responses in alpine plants facing climate change.

3D reconstruction of plants using probabilistic voxel carving

This is a companion dataset for the paper titled "3D reconstruction of plants using probabilistic voxel carving." by Feng, J., Saadati, M., Jubery, T., Jignasu, A., Balu, A., Li, Y., Attigala, L., Schnable, P.S., Sarkar, S., Ganapathysubramanian, B. and Krishnamurthy, A., published in Computers and Electronics in Agriculture, 213, p.108248, 2023.

Données brut spectres émission et excitation de différents types de plante

Données brut des différents spectres d'émissions et d'excitations réalisé pour l'étude de la chlorophylle au sein de différents types de plante.

opencc-by-4.0Sep 2023View details →

FIGURE 3 Bibliographic works containing vascular plant nomenclatural events published between 2019 and 2021 in Global access to nomenclatural botanical resources: Evaluating open access availability

FIGURE 3 Bibliographic works containing vascular plant nomenclatural events published between 2019 and 2021 and their use of open access (OA), coverage of top 80% of the International Plant Names Index (IPNI) dataset (journal abbreviations follow IPNI, asterisk indicates that the title is included in the Directory of Open Access Journals).

Amphistomy increases leaf photosynthesis more in coastal than montane plants of Hawaiian ʻilima

Premise of the study The adaptive significance of stomata on both upper and lower leaf surfaces, called amphistomy, is unresolved. A widespread association between amphistomy and open, sunny habitats suggests the adaptive benefit of amphistomy may be greatest in these contexts, but this hypothesis has not been tested experimentally. Understanding amphistomy informs its potential as a target for crop improvement and paleoenvironment reconstruction. Methods We developed a method to quantify "amphistomy advantage", AA, as the log-ratio of photosynthesis in an amphistomatous leaf to that of the same leaf but with gas exchange blocked through the upper surface (pseudohypostomy). Humidity modulated stomatal conductance and thus enabled comparing photosynthesis at the same total stomatal conductance. We estimated AA and leaf traits in six coastal (open, sunny) and six montane (closed, shaded) populations of the indigenous Hawaiian species ʻilima (Sida fallax). Key results Coastal ʻilima benefits 4.04 times more from amphistomy than montane leaves. Evidence was equivocal with respect to two hypotheses – that coastal leaves benefit more because 1) they are thicker and have lower conductance through the internal airspace, and 2) they benefit more because they have similar conductance on each surface, as opposed to most conductance being through the lower surface. Conclusions This is the first direct experimental evidence that amphistomy increases photosynthesis, consistent with the hypothesis that parallel pathways through upper and lower mesophyll increase CO2 supply to chloroplasts. The prevalence of amphistomatous leaves in open, sunny habitats can partially be explained the increased benefit of amphistomy in 'sun' leaves, but the mechanistic basis remains uncertain.

Data from: Promoting success in thin layer sediment placement: effects of sediment grain size and amendments on salt marsh plant growth and greenhouse gas exchange

Thin layer sediment placement (TLP) is a method to mitigate factors resulting in loss of elevation and severe alteration of hydrology, such as sea level rise and anthropogenic modifications, and prolong the lifespan of drowning salt marshes. However, TLP success may vary due to plant stress associated with reductions in nutrient availability and hydrologic flushing or through the creation of acid sulfate soils. This study examined the influence of sediment grain size and soil amendments on plant growth, soil and porewater characteristics, and greenhouse gas exchange for three key US salt marsh plants: Spartina alterniflora, Spartina patens, and Salicornia pacifica. We found that bioavailable nitrogen concentrations (measured as extractable NH4+-N) and porewater pH and salinity were found to have an inverse relationship with grain size, while soil redox was more reducing in finer sediments. This suggests that utilizing finer sediments in TLP projects will result in a more reduced environment with higher nutrient availability, while larger grain-sized sediments will be better flushed and oxidized. We further found that grain size had a significant effect on vegetation biomass allocation and rates of gas exchange, although these effects were species-specific. We found that soil amendments (biochar and compost) did not subsidize plant growth but were associated with increases in soil respiration and methane emissions. Biochar amendments were additionally ineffective in ameliorating acid sulfate conditions. This study uncovers complex interactions between sediment type and vegetation, emphasizing limitations of soil amendments. The findings aid restoration project managers in making informed decisions regarding sediment type, target vegetation, and soil amendments for successful TLP projects.

Drivers of plant diversity, community composition, functional traits and soil processes along an alpine gradient in the central Chilean Andes

The datasets in this repository include plant community surveys, hyperspectral reflectance data at the leaf and canopy level, leaf trait data, and soil chemistry data collected at five sites along an elevation gradient of 2400m-3500m in the Chilean Andes (33°S, 70°W). The purpose of this study was to evaluate the environmental drivers of community assembly processes along the elevation gradient.

Data for: Microbe-induced plant resistance alters aphid inter-genotypic competition leading to rapid evolution with consequences for plant growth and aphid abundance

Plants and insect herbivores are two of the most diverse multicellular groups in the world, and both are strongly influenced by interactions with the belowground soil microbiome. Effects of reciprocal rapid evolution on ecological interactions between herbivores and plants have been repeatedly demonstrated, but it is unknown if (and how) the soil microbiome could mediate these eco-evolutionary processes on a shared host plant. We tested the role of a plant-beneficial soil bacterium (Acidovorax radicis) in altering eco-evolutionary interactions between different aphid genotypes (Sitobion avenae; genotypes Sickte and Fescue) feeding on barley (Hordeum vulgare). We measured fecundity, longevity and population growth of two aphid genotypes reared separately or together (population mixture) on three different barley varieties that were inoculated with or without A. radicis. Results showed that across all plant varieties A. radicis increased plant growth and suppressed aphid populations via reduced longevity and fecundity. The strength of effect was dependent on aphid genotype and barley variety, while the direction of effect was altered by aphid population mixture. Using Lotka-Volterra modelling, we demonstrated that while A. radicis inoculation decreased growth rates for both aphid genotypes it increased the competitiveness of one genotype against the other. In general, in the presence of A. radicis, the Fescue aphid genotype became more inhibitory of Sickte aphids, while Sickte aphids facilitated the growth of Fescue aphids. Our work demonstrates that plant rhizosphere microbiomes exert community-level influences by mediating eco-evolutionary interactions between herbivores and host plants. By altering competitive interaction outcomes among aphids and thus impacting processes such as rapid evolution, soil microbes contribute to the short- and long-term structure and functioning of terrestrial habitats.

Ant handling changes myrmecochore seed coat microbiomes and alters diversity of seed-borne plant pathogenic fungi

The putative benefits to seeds in myrmecochory (ant-mediated seed dispersal) are often cast in a reward context. However, microbes have been mostly overlooked as seed mortality agents in myrmecochory, as have potential treatments provided by ant-handling. We investigated the effects of ant handling on the diversity of seed coat fungal communities of three myrmecochorous plant species. Ant-handling altered measures of both alpha and beta diversity of fungal communities. Ant-handled seeds harbored different overall fungal communities and plant pathogen communities than non-ant-handled seeds. The myrmecochore pathogenic fungal community showed high dissimilarity (high pairwise community turnover) between ant-handled and control seeds, while beta diversity measures for ant-handled seeds and seeds with manually-removed elaiosomes were less dissimilar. Ant handling may offer an additional benefit to myrmecochorous seeds via the reduction of the seed coat pathogenic community, which may be driven by elaiosome removal or as a byproduct of ant cleaning behaviors and chemical secretions.

Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen

The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.

Neutrality in plant–herbivore interactions

Understanding the distribution of herbivore damage among leaves and individual plants is a central goal of plant-herbivore biology. Commonly observed unequal patterns of herbivore damage have conventionally been attributed to the heterogeneity in plant quality or herbivore behavior or distribution. Meanwhile, the potential role of stochastic processes in structuring plant-herbivore interactions has been overlooked. Here, we show that based on simple first principle expectations from metabolic theory, random sampling of different sizes of herbivores from a regional pool is sufficient to explain patterns of variation in herbivore damage. This is despite making the neutral assumption that herbivory is caused by randomly feeding herbivores on identical and passive plants. We then compared its predictions against 765 datasets of herbivory on 496 species across 116° of latitude from the Herbivory Variability Network. Using only one free parameter, the estimated attack rate, our neutral model approximates the observed frequency distribution of herbivore damage among plants and especially among leaves very well. Our results suggest that neutral stochastic processes play a large and underappreciated role in natural variation in herbivory and may explain the low predictability of herbivory patterns. We argue that such prominence warrants its consideration as a powerful force in plant-herbivore interactions.

opencc-zeroFeb 2024View details →

Feeding with plant powders increases longevity and body weight of Western honeybee workers (Apis mellifera)

Beekeepers routinely substitute honey from managed western honeybees, Apis mellifera, colonies with sugar water post-harvest, potentially leading to malnutrition. Although nutritional supplements have been created, a general consensus on proper colony nutrition for beekeeping has yet to be reached. Thus, finding easily obtainable fortified A. mellifera food alternatives is still of interest. Here, we test plant powder-enriched food supplements since a priori evidence suggests plant extracts can enhance dry body weight and longevity of workers. Freshly emerged workers were kept in hoarding cages (N=69 days) and fed either with 50 % (w/v) sucrose solution alone or additionally with one of 12 powders: Laurus nobilis, Quercus spp., Curcuma longa, Hypericum spp., Spirulina platensis, Calendula officinalis, Chlorella vulgaris, Melissa officinalis, Moringa oleifera, Rosa canina, Trigonella foenum-graecum, and Urtica dioica (N=2028 workers total). The dry body weight was significantly increased in Quercus spp., Hypericum spp., Spirunlina platensis, Mellisa officinalis, Moringa oelifera, and Trigonella foenum-graecum treatments. Further, the longevity was significantly increased in Quercus spp., Curcuma longa, Calendulae officinalis, Chlorella vulgaris, Melissa officinalis, Rosa canina, Trigonella foenum-graecum, and Urtica diocia treatments. Given that plant extracts can enhance A. mellifera health, plant powders possibly provide additional macro- (i.e. proteins, lipids, peptides) and micronutrients (minerals and vitamins) thereby enhancing nutrient availability. Further investigations into the mechanisms underlying these effects and field studies are recommended to validate these findings in real-hive scenarios.