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opencc-zeroMay 2024View details →

Data for: Post-translational regulation of photosynthetic activity via the TOR kinase in plants

Chloroplasts are the powerhouse of the plant cell, and their activity must be matched to plant growth to avoid photo-oxidative damage. We have identified a post-translational mechanism linking the eukaryotic Target of Rapamycin (TOR) kinase that promotes growth and the guanosine tetraphosphate (ppGpp) signaling pathway of prokaryotic origins that regulates chloroplast activity, and photosynthesis in particular. We find that RelA SpoT Homologue 3 (RSH3), a nuclear-encoded enzyme responsible for ppGpp biosynthesis, interacts directly with the TOR complex via a plant-specific N-terminal region which is phosphorylated in a TOR-dependent manner. Downregulating TOR activity causes a rapid increase in ppGpp synthesis in RSH3 overexpressors and reduces photosynthetic capacity in an RSH-dependent manner in wild-type plants. The TOR-RSH3 signaling axis therefore regulates the equilibrium between chloroplast activity and plant growth, setting a precedent for the regulation of organellar function by TOR.

opencc-by-4.0May 2024View details →

RGB-Depth raw hyperstacks of both resistant and susceptible plant batches with the Pepper-TSWV pathosystem.

RGB-Depth raw hyperstacks of both resistant and susceptible plant batches with the Pepper-TSWV pathosystem. Hyperstacks are uploaded with the following structure: (Time,Width,Height,Channels)=(753,130,335,4). The time scale corresponds to one image every fifteen minutes, i.e. 96 images per day.

opencc-zeroMay 2024View details →

Data from: Data for habitat quality or quantity? Niche marginality across 21 plants and animals suggests differential responses between highland and lowland species to past climatic changes

Climatic changes can affect species distributions, population abundance, and evolution. Such organismal responses could be determined by the amount and quality of available habitats, which can vary independently. In this study, we assessed changes in habitat quantity and quality independently to generate explicit predictions of the species' responses to climatic changes between Last Glacial Maximum (LGM) and present day. We built ecological niche models and distribution models for 21 reptile, mammal, and plant taxa from the Baja California peninsula inhabiting lowland or highland environments. Geological data suggests the CCSM global circulation model is a better representation of LGM climate for the Baja California peninsula. Significant niche divergence was detected for all clades within species, along with significant differences in the niche breadth and area of distribution between northern and southern clades. Most clades showed a reduction in distribution area towards LGM. Further, niche marginality (used as a measure of habitat quality) was higher during LGM for most clades, except for northern highland species. Our results suggest that changes in habitat quantity and quality can affect organismal response independently. This allows the prediction of genomic signatures associated with changes in effective population size and selection pressure that could be explicitly tested to support our models.

opencc-zeroMay 2024View details →

Assessing the links between pollinators and the genetic and epigenetic features of plant species with contrasting distribution ranges

In flowering plants, pollinators contribute to gene flow while they also respond to variation in plant traits together determined by genetic, epigenetic and environmental sources of variation. Consequently, a correlation between abundance and diversity of pollinators and the genetic and epigenetic characteristics of plant populations such as diversity or distinctiveness is expected. However, no study has explored these long-term dimensions of plant-pollinator interactions. Mediterranean narrow endemics often exhibit unexpectedly high levels of population genetic and epigenetic diversity. We hypothesize that pollinators may contribute to explain this pattern. Specifically, given the higher sensitivity of small, isolated population to gene flow, we expect a stronger association of pollinators with population genetic and epigenetic variability in narrow endemics than in widely distributed congeners. We studied five pairs of congeneric plant species, consisting of one narrow endemic with a restricted distribution and one widespread congener, found in the Sierra de Cazorla mountains (SE Spain). We characterized the pollinators in up to three populations per species to estimate their diversity and visitation rates. Additionally, we calculated the genetic and epigenetic diversity and distinctiveness of each population using AFLP markers and methylation-sensitive AFLP markers (MSAP), respectively. We assessed the relationship between pollinator diversity and visitation rates. The diversity of pollinators did not vary according to the plant´s distribution range, but visitation rate was higher in widespread species. As predicted, only narrow endemics showed a significant association between pollinators and their population genetic and epigenetic characteristics. Specifically, higher pollinator diversity and visitation rates entailed higher population genetic diversity and lower epigenetic distinctiveness. This work shows the importance of investigating the relationship between pollinator diversity and population genetics and epigenetics to better understand the evolution of plant rarity.

Heat Stress and Microbial Stress Induced Defensive Phenol Accumulation in Medicinal Plant Sparganium stoloniferum

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Species-dependent responses of crop plants to polystyrene microplastics

Only recently there has been a strong focus on the impacts of <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/microplastics">microplastics</a> on terrestrial crop plants. This study aims to examine and compare the effects of microplastics on two monocotyledonous (barley, Hordeum vulgare and wheat, Triticum aestivum), and two dicotyledonous (carrot, Daucus carota and lettuce, Lactuca sativa) <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/plant-specie">plant species</a> through two complimentary experiments. First, we investigated the effects of low, medium, and high (103, 105, 107 particles per mL) concentrations of 500 nm <a href="https://www.sciencedirect.com/topics/earth-and-planetary-sciences/polystyrene">polystyrene</a> microplastics (PS-MPs) on seed germination and early development. We found species-dependent effects on the early development, with microplastics only significantly affecting lettuce and carrot. When acutely exposed during germination, PS-MPs significantly delayed the germination of lettuce by 24%, as well as promoted the shoot growth of carrot by 71% and decreased its biomass by 26%. No effect was recorded on monocot species. Secondly, we performed a chronic (21 d) hydroponic experiment on lettuce and wheat. We observed that PS-MPs significantly reduced the shoot growth of lettuce by up to 35% and increased its biomass by up to 64%, while no record was reported on wheat. In addition, stress level indicators and defence mechanisms were significantly up-regulated in both lettuce and wheat seedlings. Overall, this study shows that PS-MPs affect plant development: impacts were recorded on both germination and growth for dicots, and responses identified by biochemical markers of stress were increased in both lettuce and wheat. This highlights species-dependent effects as the four crops were grown under identical conditions to allow direct comparison. For future research, our study emphasizes the need to focus on crop specific effects, while also working towards knowledge of plastic-induced impacts at environmentally relevant conditions.

Data from: Climate refugia along Lake Superior's shores: Disjunct arctic-alpine plants rely on cool shoreline temperatures but are unlikely to persist under climate warming

Climate refugia can serve as remnant habitat or stepping stones for species dispersal under climate warming. The largest freshwater lake by surface area, Lake Superior, USA and Canada, serves as a model system for understanding cooling-mediated local refugia, as its cool water temperatures and wave action have maintained shoreline habitats suitable for southern disjunct populations of arctic-alpine plants since deglaciation. Here we seek to explain spatial patterns and environmental drivers of arctic-alpine plant refugia along Lake Superior's shores, and assess future risk to refugia under moderate (+3.5 °C) and warmest (+5.7 °C) climate warming scenarios. First, we examined how the interactive effects of summer surface water temperatures and wind affected onshore temperatures, resulting in areas of cooler refugia. Second, we developed an ecological niche model for presence of disjunct arctic-alpine refugia (pooling 1253 occurrences from 58 species) along the lake's shoreline. Third, we fit species distribution models for 20 of the most common arctic-alpine disjunct species and predicted presence to identify refugia hotspots. Finally, we used the two climate warming scenarios to predict changes in presence of refugia and disjunct hotspots. Bedrock type, elevation above water, inland distance, July land surface temperature from MODIS/Terra satellite, and near-shore depth of water were the best predictors of disjunct occurrences. Overall, we predicted 2,236 km of the shoreline (51%) as disjunct refugia habitat for at least one species under current conditions, but this was reduced to 20% and 7% with moderate (894 km) and warmest (313 km) climate change projections.

Code and data for: Evolutionary assembly of the plant terrestrialization toolkit from protein domains

Evolutionary assembly of the plant terrestrialization toolkit from protein domains <ul> <li>We want to trace the evolutionary predisposition the green lineage had at the time of terrestrialization.</li> <li>Terrestrialization is a complete change in environment from water, and these acted like new and/or intensified stress factors on the green lineage.</li> <li>Thus, in order to trace the evolutionary predisposition which led to successful overcoming of challenges of a new environment, we carefully annotate, dissect and analyse the stress proteome of the extant Green lineage.</li> </ul> Key Concepts <ul> <li>Already existing Concept: <ul> <li>Orthology</li> </ul> </li> <li>New/Redefined Concept <ul> <li>Embryophytic Domain: Protein domain which has an Embryophytic ancestor, that is, present in at least one Bryophyte species and at least one Tracheophyte species</li> <li>Latent Genetic Potential (LGP): Key (functional) Embryophytic protein domains having Last Common Ancestor (LCA) prior to the LCA of protein with corresponding function</li> </ul> </li> </ul> Data: (Figure 1 A) <ul> <li>We take 6 species from Cholorophyte algae lineage, 7 from Streptophyte algae lineage, 5 from Bryophyte lineage and 14 from Tracheophyte lineage. 5 species from Cyanobacteria were taken as an outgroup lineage.</li> </ul> Stress-annotation (Figure 1B) <ul> <li>First 57,796 orthogroups were obtained from 37 proteome. This is computed by using OrthoFinder2.</li> <li>Next we need to annotate stress-related proteins across our dataset. Following are existing ways of annotation: <ul> <li>Extensive experiments have been done on A.thaliana and P.patens in the green lineage. Thus, we stress-annotated 37 proteomes using TAIR10 and PEATmoss respectively. From this method, we stress-annotated 4,902 orthogroups</li> <li>Eggnogmapper is a known tool with an extensive database used for gene ontology purposes. We stress-annotated 17,349 orthogroups.</li> </ul> </li> <li>In order to avoid experimental bias and tool-based randomness we overlap the two methods to have our final stress-annotation. We finally filtered 2,475 stress-annotated orthogroups from 57,796 orthogroups.</li> </ul> Overview of Stress-annotation (Figure 1C, 1D) <ul> <li>To have an overview of stress-annotation, overlaps of stress-annotated protein domains, proteins and orthogroups across our dataset lineages and various response to stresses are shown.</li> </ul> Distribution of Stress-annotation (Figure 2) <ul> <li>Using the overlap annotation approach explained earlier, the stress-annotated orthogroups and corresponding protein domains are in Figure 2A. A standard pattern is observed in both, that is, the unique number of stress orthogroups and protein domains increase from Cyanobacteria to Tracheophytes. The number of proteins and average number of protein domains also increases similarly.</li> <li>Top 10 bursts of protein domains from one lineage to the next is shown in Figure 2B.</li> </ul> Changes in stress-annotation with respect to Protein Domains (Figure 3) <ul> <li>Figure 3 is a 4-dimensional plot with the following parameters: Species(37), Protein Domains (100), Number of Orthgogroups with Protein Domain (size of circle), Number of Proteins with Protein Domain (Color of circle). The plot is sorted from top to bottom based on the number of orthogroups, and the top 100 protein domains are chosen for the plot.</li> <li>This plot is used to express an overview of the most significant occurances of sub- and neo-functionalizations. Here, each orthogroup is considered to be a protein family. 2 protein families can have an overlapping number of functions. That is why there are more than 1 orthogroup which have the same protein domain.</li> </ul> Assembling LGP from protein domains (Figure 4) - refer to Key Concepts to understand LGP <ul> <li>In Figure 1A, we show 2 categories (x/y) of orthogroups at each node (a,b,c,d,e,f). The number y for example at node b indicates the number of orthogroups (4) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP (or key Embryophytic protein domains) in Charophyceae. The number x at node b indicates the number of orthogroups (131) in Tracheophyta+Bryophyta+Zygnemaotphyceae that have LGP in all the rest of the lineages (Charophyceae+Klebsormidiophyceae+Chlorokybophyceae+Mesostigmatophyceae+Chlorophytes) in the figure.</li> <li>Since we are concerned about the LGP for Land Plants (Embryophytes), we look at node a. Next, we functionally annotate 96 orthogroups. 50 annotations that occur the most number of times is shown in Figure 4B.</li> <li>In Figure 4C, we can see in which species the key Embryophytic Domains are present whose proteins and protein families are only seen in Embryophytes.</li> </ul> Thus, from the final figure we can trace the LGP present at the time of terrestrialization in the LCA of Land Plants. Database files: These are intermediate files used in code for different figures. Following is the link to access them:<a href="https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c" rel="nofollow">https://data.mendeley.com/datasets/mnrn7j7hrw/draft?a=b981b40f-01a8-48ff-9d6a-151f6223810c</a> [OR]<a href="https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA" rel="nofollow">https://owncloud.gwdg.de/index.php/s/dH3Y4MAHSfbmhrA</a>

Neighbor-detection causes shifts in allocation across multiple organs to prepare plants for light competition

To maximize their fitness, plants have to adjust their allocation strategy according to their abiotic and biotic environments. Plants can use the ratio of red to far-red light (R:FR) to sense neighbors, allowing them to modify their growth in response to aboveground competition. In this study, we used supplemental FR light to artificially lower the R:FR of the lower leaves of common sunflowers (Helianthus annuus) to examine how plants change their growth in response to the threat of neighbors. We combined this treatment with a nitrogen fertilization treatment to investigate how responses to neighbor-detection interact with nitrogen limitation. Plants grown in low R:FR increased in height at the expense of root growth, resulting in nitrogen limitation that restricted leaf growth. However, we found that plants reduced their nitrogen investment into leaves in low R:FR. By weakening the nitrogen sink strength of these lower leaves before they experienced low photosynthetically active radiation, plants were able to preemptively allocate nitrogen to leaves higher in the canopy. Plants responded to the perception of neighbors by simultaneously diverting resources from root growth to stem elongation and from leaves threatened by neighbors to leaves that would pose a threat to neighbors. This whole-plant response to neighbor-detection enables plants to change their allocation in a way that simultaneously manages their limited nitrogen and prepares them for future light competition.

Selection favors high spread and asymmetry of flower opening dates within plant individuals

Natural selection on traits expressed repeatedly by individuals is usually investigated with a focus on mean values, although within-individual trait distributions often differ also in other aspects, such as their spread and shape. In plants producing multiple flowers during a season, there might not be a single optimal flowering time, but rather an optimal distribution of flower opening dates. This optimal distribution might depend on both resource allocation patterns and interactions with the abiotic and biotic environment. In this study, we quantified mean, variance, skewness and kurtosis of 495 individual flowering schedules (5287 flowers) over three years, and assessed phenotypic selection on these aspects of the within-individual distribution of opening dates in the perennial herb Lathyrus vernus. We also explored how selection on within-individual variation in flowering schedules was related to effects on two fitness components: fruit set and the proportion of seeds escaping pre-dispersal predation. Within-individual variation in phenology was larger than, or at least similar to, among-individual variation in all years. We found phenotypic selection on several aspects of individual flowering schedules. In one year, selection favoured plants with higher variance in opening dates, and this coincided with a higher fruit set in plants with an increased spread of the flowering schedule. In two of the study years, selection favoured a higher asymmetry of the flowering schedule, and plants with more right-skewed distributions had higher fruit set and higher proportions of seeds escaping predation. Both fruit set and seed predation increased with an earlier mean flowering, resulting in no net selection on mean flowering date. Synthesis. Our results suggest that phenotypic selection on the spread and shape of flower opening date distributions might be at least as important as selection on the mean flowering date. In a broad sense, this implies that we should consider the entire trait distribution if we aim to understand the evolution of traits that are expressed multiple times within individuals.

opencc-by-4.0May 2024View details →

Understanding woody plant encroachment: A plant functional trait approach

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Data from: Evolutionary déjà vu? A case of convergent evolution in an ant-plant association

Obligatory ant-plant symbioses often appear to be single evolutionary shifts within particular ant lineages; however, convergence can be revealed once natural history observations are complemented with molecular phylogenetics. Here we describe a remarkable example of convergent evolution in an ant-plant symbiotic system. Exclusively arboreal, Myrmelachista species can be generalized opportunists nesting in several plant species or obligately symbiotic, live-stem nesters of a narrow set of plant species. Instances of specialization within Myrmelachista are known from northern South America and throughout Middle America. In Middle America, a diverse radiation of specialists occupies understory treelets of lowland rainforests. The morphological and behavioural uniformity of specialists suggests that they form a monophyletic assemblage, diversifying after a single origin of specialization. Using ultraconserved element phylogenomics and ancestral state reconstruction, we show that shifts from opportunistic to obligately symbiotic evolved independently in South and Middle America. Furthermore, our analyses strongly support a remarkable case of convergence within the Middle American radiation, with two independently evolved specialist clades, arising nearly simultaneously from putative opportunistic ancestors during the late Pliocene. This repeated evolution of a complex phenotype suggests similar mechanisms behind trait shifts from opportunists to specialists, generating further questions about the selective forces driving specialization.

Monthly production and open-circuit string voltage measurements after 10-year operation of three photovoltaic plants in Southern Spain affected by severe potential-induced degradation

Data are formated in a spreadsheet file.  Data are presented from three photovoltaic plants in Southern Spain (Córdoba province - Northern Andalucía) designed and installed by the same person, with the same photovoltaic module and the same model of inverter, deployed at the same time (end 2009). The plants are severely affected by potential-induced degradation (PID), so that secondary effects produce some by-pass diodes to activate, producing three families of open-circuit voltage (Voc) in the modules (~40V), (~26V) and (~12V) of a total of nominal Voc of 42,6V.  Monthly production is shown along 11 years (2010-2021), and the measurements of the open-circuit voltage of the strings after 10 years of operation along with the voltage range of the modules of each string. Sheet 1: configuration of the architecture of the three photovoltaic plants and the features of the photovoltaic module installed. Sheet 2: energy production for 11 years of opetation. In the last years some recovery is shown in plant 1 and 2 because a repowering project. Sheet 3: partial climate data of the towns were the plants are located. Sheet 4: open-circuit voltages of the strings and number of modules in each string with open-circuit voltage in the ranges (~40V) and (<=26V) in plant 1, july-2018. Sheet 5: open-circuit voltages of the strings and number of modules in each string with open-circuit voltage in the ranges (~40V), (~26V) and (~12V) in plant 2, july-2020.

Simulation results for "Integration of Plant and Microbial Oil Processing at Oilcane Biorefineries for More Sustainable Biofuel Production" publication

Simulation results for "Integration of Plant and Microbial Oil Processing at Oilcane Biorefineries for More Sustainable Biofuel Production" publication.

African wood density database with matches to the taxonomic backbone data sets of World Flora Online (version 2023.12) and the World Checklist of Vascular Plants (version 11)

The African Wood Density Database provides air-dry wood density data for over 750 tree species grown in Africa. This archive provides taxonomic matches with recent versions of World Flora Online (WFO; <a href="../records/10425161">version 2023.12 downloaded from Zenodo</a>; Borch et al. <a href="https://onlinelibrary.wiley.com/doi/10.1002/tax.12373">2020</a>) and the World Checklist of Vascular Plants (WCVP; <a href="https://sftp.kew.org/pub/data-repositories/WCVP/Archive/">version 11 downloaded from the Kew data depository</a>; Govaerts et al. <a href="https://doi.org/10.1038/s41597-021-00997-6">2021</a>). Matching was done via the WorldFlora package (<a href="https://cran.r-project.org/package=WorldFlora">version 1.14-3</a>; Kindt <a href="https://bsapubs.onlinelibrary.wiley.com/doi/full/10.1002/aps3.11388">2020</a>), using similar scripts as documented in this Rpub: <a href="https://rpubs.com/Roeland-KINDT/1134151">https://rpubs.com/Roeland-KINDT/1134151</a>.   <ul> <li>Carsan, S. Orwa, C. Harwood, C. Kindt, R. Stroebel, A. Neufeldt, H. and Jamnadass, R. 2012. African Wood Density Database. World Agroforestry Centre, Nairobi. <a href="https://apps.worldagroforestry.org/treesnmarkets/wood/">https://apps.worldagroforestry.org/treesnmarkets/wood/#</a> </li> <li>Borsch, T., Berendsohn, W., Dalcin, E., Delmas, M., Demissew, S., Elliott, A., Fritsch, P., Fuchs, A., Geltman, D., Güner, A., Haevermans, T., Knapp, S., le Roux, M.M., Loizeau, P.-A., Miller, C., Miller, J., Miller, J.T., Palese, R., Paton, A., Parnell, J., Pendry, C., Qin, H.-N., Sosa, V., Sosef, M., von Raab-Straube, E., Ranwashe, F., Raz, L., Salimov, R., Smets, E., Thiers, B., Thomas, W., Tulig, M., Ulate, W., Ung, V., Watson, M., Jackson, P.W. and Zamora, N. (2020), World Flora Online: Placing taxonomists at the heart of a definitive and comprehensive global resource on the world's plants. TAXON, 69: 1311-1341. <a href="https://doi.org/10.1002/tax.12373">https://doi.org/10.1002/tax.12373</a></li> <li>Govaerts, R., Nic Lughadha, E., Black, N. et al. The World Checklist of Vascular Plants, a continuously updated resource for exploring global plant diversity. Sci Data 8, 215 (2021). <a href="https://doi.org/10.1038/s41597-021-00997-6">https://doi.org/10.1038/s41597-021-00997-6</a></li> <li>Kindt, R. 2020. WorldFlora: An R package for exact and fuzzy matching of plant names against the World Flora Online taxonomic backbone data. Applications in Plant Sciences 8(9): e11388. <a href="https://doi.org/10.1002/aps3.11388">https://doi.org/10.1002/aps3.11388</a></li> </ul>   Original funding for the database was provided by the Carbon Benefits Project (CBP) supported by The Global Environment Facility (GEF). Development of the 2024 version was supported by the Darwin Initiative to project DAREX001 of Developing a Global Biodiversity Standard certification for tree-planting and restoration, by Norway’s International Climate and Forest Initiative through the Royal Norwegian Embassy in Ethiopia to the Provision of Adequate Tree Seed Portfolio project in Ethiopia, by the Green Climate Fund through the IUCN-led Transforming the Eastern Province of Rwanda through Adaptation project and through the Readiness proposal on Climate Appropriate Portfolios of Tree Diversity for Burkina Faso, by the Bezos Earth Fund to the Bezos Quality Tree Seed for Africa in Kenya and Rwanda project and by the German International Climate Initiative (IKI) to the regional tree seed programme on The Right Tree for the Right Place for the Right Purpose in Africa. When using African Wood Density database in your work, cite the 2012 version (Carsan et al. <a href="https://apps.worldagroforestry.org/treesnmarkets/wood/">2012</a>) as well as this repository using the DOI.

Flower position within plants influences reproductive success both directly and via phenology

<div> This data set includes data from recordings of 5883 individual flowers of the perennial herb Lathyrus vernus belonging to 558 flowering events (i.e. one plant individual flowering in one year) over three years (1987-1989). It includes data on phenology, reproductive succress and seed predation of individual flowers, as well as data on the position of the flower within the raceme, and of the raceme within the plant. The data wree collected in a population of L. vernus located in a deciduous forest in southeast Sweden (58.9496 N, 17.6097 E).    </div>

Data for "The effect of drought on agronomic and plant physiological characteristics of cocksfoot (Dactylis glomerata L.) cultivars "

Data for " The effect of drought on agronomic and plant physiological characteristics of cocksfoot (Dactylis glomerata L.) cultivars " Data include all raw data necessary for the analyses of the manuscript.  These include data on climatic parameters the experiment design, the growth, the fresh and dry matter yield, the crude protein content, the water use and the water use efficiency.   Description of the data and file structure The data are divided into two sheets.  The first contains data necessary for the analyses presented in the main text.  The second includes data about temperature solar radiation and Vapor Pressure.

EstablishMed: a dataset of transition probabilities for woody plant establishment in the Mediterranean Region

Motivation: Plant establishment is the result of sequential demographic processes, namely post-dispersal seed survival, seed germination, seedling survival and sapling survival. These processes can be quantified as transition probabilities between life stages through field experiments, and their product provides an overall establishment probability. This information is essential to understand demography within populations and plant colonization potential under global change scenarios. The Mediterranean Region constitutes a biodiversity hotspot characterised by severe summer droughts, which suppose a critical demographic bottleneck for perennial plant establishment. Despite many studies have quantified transition probabilities of woody species in this region, information is scattered through literature and has not yet been compiled. To fill this gap, we collated data from a systematic literature review and completed them with new unpublished data to create the EstablishMed dataset. Main types of variables contained: EstablishMed is a compilation of 4728 records of transition probabilities that quantify demographic processes operating during plant establishment. All records belong to native species and were obtained in situ under field conditions. Each record includes information about the specific spatiotemporal context of the study (i.e., year, site, population, habitat and microhabitat) and the experimental procedures employed (e.g., degree of protection against natural enemies). In addition, we included taxonomic and trait information of the study species (i.e., seed mass, dispersal syndrome and life form), and the bioclimate of the study sites. Spatial location and grain: The dataset covers the whole Mediterranean Region. The finest spatial resolution corresponds to microhabitat types within populations. Time period and grain: Data were extracted from 271 studies originated between 1991 and 2024. Major taxa and level of measurement: 134 woody species from 80 genera and 39 families. Software format: EstablishMed is available in .csv format in Dryad repository.

Data from: Trends in plant cover derived from vegetation-plot data using ordinal zero-augmented beta regression

Questions. Plant cover values in vegetation-plot data are bounded between 0 and 1, and cover is typically recorded in discrete classes with non-equal intervals. Consequently, cover data are skewed and heteroskedastic, which hampers the application of conventional regression methods. Recently developed ordinal beta regression models consider these statistical difficulties. Our primary question is if we can detect species trends in vegetation-plot time series data with this modelling approach. A second question is whether trends in cover have additional value compared to trends in occurrence, which are easier to assess for practitioners. Location. The Netherlands, Western Europe. Methods. We used vegetation-plot data collected from 10.000 fixed plots which were surveyed once every four years during 1999-2022. We used the ordinal zero-augmented beta regression (OZAB) model, a hierarchical model consisting of a logistic regression for presence and an ordinal beta regression for cover. We adapted the OZAB model for longitudinal data and produced estimates of cover and occurrence for each four-year period. Thereafter we assessed trends in cover and in occurrence across all periods. Results. We found evidence of a trend in cover in 318 out of the 721 species (44%) with sufficient data. Most species showed similar directional trends in occurrence and percent cover. No trend in occurrence was detected for 64 species that had evidence of a trend in cover. Declining species had stronger relative changes in cover than in occurrence. Conclusions. Our model enables researchers to detect trends in cover using longitudinal vegetation-plot data. Cover trends often corroborated trends in occurrence, but we also regularly found trends in cover even in the absence of evidence for trends in occurrence. Our approach thus contributes to a more complete picture of (changes in) vegetation composition based on large monitoring datasets.