Find research datasets worth reusing

opencc-zeroNov 2023View details →

Data from: Fine-scale genetic structure in the orchid Gymnadenia conopsea is not associated with local density of flowering plants

Premise: Density-dependent pollinator visitation can lead to density-dependent mating patterns and within-population genetic structure. In Gymnadenia conopsea, individuals in low-density patches receive more self-pollen than individuals in high-density patches, suggesting higher relatedness at low density. Ongoing fragmentation is also expected to cause more local matings, potentially leading to biparental inbreeding depression. Methods: To evaluate whether relatedness decreases with local density, we analysed 1315 SNP loci in 113 individuals within two large populations. We quantified within-population genetic structure in one of the populations, recorded potential habitat barriers, and visualized gene flow using estimated effective migration surfaces (EEMS). We further estimated the magnitude of biparental inbreeding depression that would result from matings restricted to within 5 m. Results: There was no significant relationship between local density and relatedness in any population. We detected significant fine-scale genetic structure consistent with isolation-by-distance, with positive kinship coefficients at distances below 10 m. Kinship coefficients were low, and predicted biparental inbreeding depression resulting from matings within the closest 5 m was a modest 1–3%. EEMS suggested that rocks and bushes may act as barriers to gene flow within a population. Conclusions: The results suggest that increased self-pollen deposition in sparse patches does not necessarily cause higher selfing rates, or that inbreeding depression results in low establishment success of inbred individuals. The modest relatedness suggests that biparental inbreeding depression is unlikely to be an immediate problem following fragmentation of large populations. The results further indicate that habitat structure may contribute to governing fine-scale genetic structure in G. conopsea.

opencc-zeroNov 2023View details →

Genetic diversity, genetic differentiation and demographic history of Cryptomeria (Cupressaceae), a Tertiary relict plant in East Asia based on RAD sequencing

Genetic structure and distribution patterns of modern floras are strongly affected by climatic change and geographical isolation. In the present study, we applied restriction-site-associated DNA sequencing (RAD-seq) to analyze the genetic structure and to simulate the demographic history of two extant Cryptomeria species in Japan (C. japonica) and Southeastern China (C. japonica var. sinensis). Thirteen natural populations representing the entire species distributed in East Asia were collected from Japan and China. At the species level, the genetic diversity of Cryptomeria was moderate (Ho = 0.217, He = 0.203) with a significant genetic differentiation among populations (85.30%, P < 0.001), especially between Japan and China lineages (FST = 0.147). Except for the Lushan (LS) population in China, all populations were clustered into two lineages (Japanese and Chinese), which was consistent with their geographical distribution. Approximate Bayesian computations (ABC) model indicated that the current two geographical lineages diverged from a common ancestral lineage and that their divergence time was about 0.417 ~ 0.139 million years ago (Mya). Geographical isolation, climate change in the Quaternary, and human disturbance played important roles in genetic variation and distribution patterns of Cryptomeria in East Asia. Our results shed light on the speciation processes of Cryptomeria and provide a reference for the conservation of this species.

opencc-zeroNov 2023View details →

Data from: Quantifying the impacts of management and herbicide resistance on regional plant population dynamics in the face of missing data

A key challenge in the management of populations is to quantify the impact of interven-tions in the face of environmental and phenotypic variability. However, accurate estima-tion of the effects of management and environment, in large-scale ecological research is often limited by the expense of data collection, the inherent trade-off between quality and quantity, and missing data. In this paper we develop a novel modelling framework, and demographically informed imputation scheme, to comprehensively account for the uncertainty generated by miss-ing population, management, and herbicide resistance data. Using this framework and a large dataset (178 sites over 3 years) on the densities of a destructive arable weed (Alo-pecurus myosuroides) we investigate the effects of environment, management, and evolved herbicide resistance, on weed population dynamics. In this study we quantify the marginal effects of a suite of common management prac-tices, including cropping, cultivation, and herbicide pressure, and evolved herbicide re-sistance, on weed population dynamics. Using this framework, we provide the first empirically backed demonstration that herbi-cide resistance is a key driver of population dynamics in arable weeds at regional scales. Whilst cultivation type had minimal impact on weed density, crop rotation, and earlier cultivation and drill dates consistently reduced infestation severity. Synthesis and applications: As we demonstrate that high herbicide resistance levels can produce extremely severe weed infestations, monitoring of herbicide resistance is a pri-ority for famers across western Europe. Furthermore, developing non chemical control methods is essential to control current weed populations, and prevent further resistance evolution. We recommend that planning interventions that center on crop rotation and incorporate spring sewing and cultivation to provide the best reductions in weed densi-ties. More generally, by directly accounting for missing data our framework permits the analysis of management practices with data that would otherwise be severely compro-mised.

opencc-zeroDec 2022View details →

Data from: Direct and higher-order interactions in plant communities under increasing weather persistence

Climate change is increasing the weather persistence in the mid-latitudes, prolonging both dry and wet spells compared to historic averages. These newly emerging environmental conditions destabilize plant communities, but the role of species interactions in this process is unknown. Here, we tested how direct and higher-order interactions (HOIs) between species may change in synthesized grassland communities along an experimental gradient of increasing persistence in precipitation regimes. Our results indicate that species interactions (including HOIs) are an important determinant of plant performance under increasing weather persistence. Out of the 12 most parsimonious models predicting species productivity, 75 % contained significant direct interactions and 92 % significant HOIs. Inclusion of direct interactions or HOIs respectively tripled or quadrupled the explained variance of target species biomass compared to null models only including the precipitation treatment. Drought was the main driver of plant responses, with longer droughts increasing direct competition but also HOI-driven facilitation. Despite these counteracting changes, drought intensified net competition. Grasses were generally more involved in competitive interactions whereas legumes were more involved in facilitative interactions. Under longer drought, species affinity for nutrient rich or wet environments resulted in more negative direct interactions or HOIs, respectively. We conclude that higher-order interactions, crucially depending on species identity, only partially stabilize community dynamics under increasing weather persistence.

Competition for nitrogen between plants and microorganisms in grasslands: Effect of nitrogen application rate and plant acquisition strategy

Several studies have investigated how nitrogen (N) addition changes N competition between focal plant species and soil microorganisms; still, the impact on community-level plant-microbial N competition and the underlying mechanisms remain unclear. We conducted a short-term (4 h) 15N labeling experiment in an alpine meadow subjected to 7 years of NH4NO3 additions (0, 5, 10, and 15 g N m−2 year−1), by monitoring changes in soil properties (e.g., pH, Al3+, NH4+, NO3−), microbial biomass (MB), plant community composition, root traits (e.g., root length, root area, specific root length), as well as the plant (nine focal species and at the community level) and microbial N uptake. Change in the N competition between the nine focal plant species and microorganisms following N addition depended on the species. At the community level, the N addition rate did not affect plant-microbial competition for NH4 + and NO3 − (P > 0.05). Nitrogen addition directly decreased NH4+competition (β= −0.700) but indirectly increased because of improved plant uptake due to increased N availability(β=1.214). Competition for NO3− was dependent on microbial uptake (β= −0.953) and was influenced by opposing effects of increased N availability (β=1.342) and reduced MB (β= −0.439). Thus, the effects of increased soil N availability and suppressed MB on plant and microbial N competition offset each other, while the plant community had a negligible impact. Such responses should be taken into account for better predictions of the effect of N addition on net primary productivity and ecosystem stability.

Nitrogen redistribution and seasonal trait fluctuation facilitate plant N conservation and ecosystem N retention

<ol> <li>Low available soil nitrogen (N) limits plant productivity in alpine regions, and alpine plants thus resorb and reallocate N from senescing tissues to conserve this limited N during the nongrowing season. However, the destination and extent of N redistribution during plant senescence among above- and below-ground organs, let alone other processes of translocation outside of plants and into the soil components, remain poorly understood. </li> <li>Utilizing the 15N stable isotope as a tracer, we quantified N redistribution among above- and below-ground plant organs and different soil components during senescence in an alpine meadow ecosystem, and explored the relationship between 15N among plant-soil N pools with seasonal fluctuations of plant functional traits.</li> <li>We found a substantial depletion of 15N in fine roots (-40% ± 2.8%) and aboveground tissues (-51% ± 5.1%), and an enhanced 15N storage primarily in coarse roots (+79% ± 27%) and soil organic matter (+37% ± 10%) during plant senescence. In parallel, we observed a temporal variation in plant functional traits, representing a shift from more acquisitive to more conservative strategies as the growing season ends, such as higher coarse root N and coarse root to fine root ratio. The seasonal trait variations were highly correlated with the 15N retention in coarse roots and soil organic matter. Particularly, 15N retention in particulate and mineral-associated organic matter increased by 30% ± 12% and 24% ± 9%, respectively, suggesting a potential pathway through which fine root and microbial mortality contribute to 15N redistribution into soil N pools during senescence.</li> <li> Synthesis. N redistribution and seasonal plant trait fluctuation facilitate plant N conservation and ecosystem N retention in the alpine system. This study suggests a coupled aboveground-belowground N conserving strategy that may optimize the temporal coupling between plant N demand and ecosystem N supply in N-limited alpine ecosystems. </li> </ol>

Data and code for: Species-specific effects of production practices on genetic diversity in plant reintroduction programs

Plant production practices can influence the genetic diversity of cultivated plant materials and, ultimately, their potential to adapt to a reintroduction site. A common step in the plant production process is the application of seed pre-treatment to alleviate physiological seed dormancy and successfully germinate seeds. In production settings, the seeds that germinate more rapidly may be favored in order to fill plant quotas. In this study, we investigated how the application of cold-moist stratification treatments with different durations can lead to differences in the genetic diversity of the propagated plant materials. Specifically, we exposed seeds of three Viola species to two different cold stratification durations, and then we analyzed the genetic diversity of the resulting subpopulations through double-digestion restriction site-associated sequencing (ddRADseq). Our results show that, in two out of three species, utilizing a short stratification period will decrease the genetic diversity of neutral and expressed loci, likely due to the imposition of a genetic bottleneck and artificial selection. We conclude that, in some species, the use of minimal stratification practices in production may jeopardize the adaptive potential and long-term persistence of reintroduced populations and suggest that practitioners carefully consider the evolutionary implications of their production protocols. We highlight the need to consider the germination ecology of target species when selecting the length of dormancy-breaking pre-treatments.

Plant-pollinator interactions in Mediterranean semiarid ecosystems

Pollinators are fundamental for plant reproduction in natural and agricultural ecosystems. However, their populations are declining worldwide, threatening the functioning of the ecosystem service they provide. The factors driving this change are manifold, but land use changes and interspecific transmission of pathogens between managed and wild bees are prominent. In this context, most research efforts have focused on specific taxa and rarely at the community level, limiting our ability to fully understand the effects of global change on the functioning of plant-pollinator interactions in ecosystems. Here, we investigate the impact of human activities (beekeeping and land use intensity) on the spread of an emergent pathogen (Vairimorpha ceranae) in Mediterranean wild bee communities inhabiting landscapes with varying levels of anthropogenic disturbance. Plant-pollinator interactions were sampled in nine one-hectare plots along a gradient of land use (urban structures, croplands and natural vegetation) and beekeeping intensity. We analised the impact of human disturbances on pollination networks and pathogen prevalence and applied a network approach to examine whether total effects of species in networks (i.e. direct plus indirect interactions) explain pathogen spread through bee communities. We found that V. ceranae prevalence in honey bees is not a good predictor of the pathogen spread through bee communities. There seems to be a temporal mismatch between pathogen dynamics in managed and wild bees. Networks with more diversity of interactions and more plants showed less pathogen prevalence, but total effect analyses (i.e. combining direct and indirect interactions) failed to explain pathogen transmission across pollination networks. Croplands increased wild bee density, and interactions and species diversity in networks while shrublands had the opposite effect. Our results highlight the importance of studying pathogen dynamics at the community level and analysing species interaction patterns to improve our understanding of pathogen spread through communities.

Soil toxicity and species dominance rather than nutrient availability drive plant species richness in swamp forests of Central Europe

Aim: A resource-based conceptual model of plant diversity (RBCM) assumes direct relationships between resource supply and the diversity of a local plant assembly. However, the RBCM largely ignores variation imposed by soil toxicity due to climatic effects. Both soil-limiting resources and soil toxicity vary along climatic gradients but their net and interactive effects on plant species diversity remain unknown. We asked how climatic gradients shape resource availability, soil toxicity and dominance of herb-layer graminoids, and how these predictors control local species diversity of herbs and bryophytes. Location: Swamp forests, Central Europe Taxon: Vascular plants, bryophytes Methods: Alpha taxonomic diversity of vascular plants and bryophytes was counted for 101 vegetation plots sampled in temperate swamp forests distributed along an 800-km geographical gradient across the Continental, Alpine and Pannonian biogeographical regions. Path analysis (structural equation modelling) was used to quantify the direct and indirect effects of climatic variables (potential evapotranspiration; PET), limiting resources (soil N/P, Ca, C/N, proxies for light and water availability), and soil toxicity (Mn) on graminoid dominance and community diversity. Results: PET negatively influenced species richness of both groups analysed either directly or indirectly through its positive effect on the cover of graminoid species. Alpha diversity of herbs was additionally reduced by soil toxicity (Mn). Limiting resources correlated either with species dominance (canopy shading, soil Ca) or with PET (soil N/P ratio), but they did not control species richness pattern. Main Conclusions: Climate, soil toxicity and species dominance determined alpha diversity instead of the expected importance of soil limiting resources. These results are key to advancing the theoretical framework of the RBCM. Increased soil toxicity (Mn) in well-watered regions favours the dominance of plant competitors at the expense of less tolerant species. This implies a potential threat to wetland diversity under ongoing climate change.

opencc-by-4.0Dec 2023View details →

A root-specific NLR network confers resistance to plant parasitic nematodes - genomic sequences and annotations

Sequence and annotation data associated with "A root-specific NLR network confers resistance to plant parasitic nematodes"

opencc-zeroDec 2022View details →

Data from: Abiotic legacies mediate plant-soil feedback during early vegetation succession on rare earth element mine tailings

An increasing number of studies have shown how feedback interactions between plants and soil can influence primary and secondary succession. However, very little is known about the patterns and mechanisms of such plant-soil feedbacks on stressed mine tailings ecosystem, which can be severely contaminated by a range of toxic elements. In a two-phase plant-soil feedback experiment based on the rare earth element (REE) mine tailing soil, we investigated biotic (changes in bacterial and fungal community) and abiotic legacies (changes in chemical properties) of three pioneer grass species, and examined feedback effects of three grasses, two legumes and two woody plants with different root traits. Positive plant-soil feedback was found in Miscanthus sinensis, Paspalum thunbergii and Tephrosia candida, and neutral feedback was observed in other four plants. These effects corresponded with an increase of nutrients and total organic carbon, as well as a decrease of acidity and extractable aluminum and REEs. There were less signs of biotic changes in the conditioned tailings. The correlation analysis suggested a relationship between responses to soil legacies and root traits, as well as root economics spectrum. On the mine tailings, acquisitive species with higher specific root length appeared to have greater potential for positive feedback. Synthesis and application: Our study shows that early succession on contaminated REE mine tailings may lead to more positive plant-soil feedback than predicted based on results of non-contaminated soils, mainly due to the alleviation of abiotic stress in tailings. Therefore, the improvement of specific abiotic soil stress and the trait-based selection of acquisitive plants should be preferentially considered to promote the primary restoration of degraded land.

opencc-by-4.0Dec 2023View details →

Bipartite plant-pollinator diurnal and nocturnal networks for three mountain systems of the Iberian Peninsula.

Dataset generated for the article "Addition of nocturnal pollinators modifies the structure of pollination" networks" (DOI:10.1038/s41598-023-49944-y).  Diurnal and nocturnal plant-flower visitor networks (hereafter, plant-pollinator networks) were built for each site during the flowering season of 2010 (Picos de Europa) and 2011 (Sierra de Guadarrama and Sierra Nevada). To build the diurnal networks, interactions between plants and floral visitors were recorded along diurnal transects at each site, where all insects contacting the reproductive structures of the flowers were recorded. The sampled area differed between sites from 500 × 250 m in Picos de Europa to 150 × 100 m in Sierra Nevada and 100 × 60 m in Sierra de Guadarrama. These differences were dependent on the small-scale heterogeneity of vegetation. The transects were evenly distributed throughout the study area. The length of the transects varied depending on the size of the study area. Diurnal transects were performed from 10 to 18 h on sunny days with mild wind conditions for pollinator activity. Nocturnal plant-pollinator networks were built for each site by trapping moths using light traps and analysing their pollen loads. Light traps consisted of a UV light surrounded by three white triangular sheets. Moths landing on the sheets were immediately trapped and stored in individual vials with a small piece of tissue and some drops of ethyl acetate. For more details on the methodology see original publication.

Dataset of global plant-soil feedback

Plant-soil feedback (PSF) is an important mechanism determining plant community dynamics and structure. Understanding the geographic patterns and drivers of PSF is essential for understanding the mechanisms underlying geographic plant diversity patterns. We compiled a large dataset containing 5969 observations of PSF from 202 studies to demonstrate the global patterns and drivers of PSF for woody and non-woody species. Overall, PSF was negative on average and was influenced by plant attributes and environmental settings. Woody species PSFs did not vary with latitude, but non-woody PSFs were more negative at higher latitudes. PSF was consistently more positive with increasing aridity for both woody and non-woody species, likely due to increased mutualistic microbes relative to soil-borne pathogens. These findings were consistent between field and greenhouse experiments, suggesting that PSF variation can be driven by soil legacies from climates. Our findings call for caution to use PSF as an explanation of the latitudinal diversity gradient and highlight that aridity can influence plant community dynamics and structure across broad scales through mediating plant soil-microbe interactions.

Plant size, latitude, and phylogeny explain within-population variability in herbivory

Interactions between plants and herbivores are central in most ecosystems, but their strength is highly variable. The amount of variability within a system is thought to influence most aspects of plant-herbivore biology, from ecological stability to plant defense evolution. Our understanding of what influences variability, however, is limited by sparse data. We collected standardized surveys of herbivory for 503 plant species at 790 sites across 116° of latitude. With these data, we show that within-population variability in herbivory increases with latitude, decreases with plant size, and is phylogenetically structured. Differences in the magnitude of variability are thus central to how plant-herbivore biology varies across macroscale gradients. We argue that increased focus on interaction variability will advance understanding of patterns of life on Earth.

Establishment from seed is more important for exotic than for native plant species

Climate change has initiated the movement of both native and non-native (exotic) species across the landscape. Exotic species are hypothesized to establish from seed more readily than comparable native species. We tested the hypothesis that seed limitation is more important for exotic species than native grassland species. We compared seed limitation and invasion resistance over three growing seasons between 18 native and 18 exotic species, grown in both monocultures and mixtures in a field experiment. Half of the plots received a seed mix of the contrasting treatment (i.e. exotic species were seeded into native plots, and native species were seeded into exotic plots), and half served as controls. We found that 1) establishment in this perennial grassland is seed limited, 2) establishment from seed is greater in exotic than native species, and 3) community resistance to seedling establishment was positively related diversity of extant species, but only in native communities. Native-exotic species diversity and composition differences did not converge over time. Our results imply that native-to-exotic transformations occur when diversity declines in native vegetation and exotic seeds arrive from adjacent sites, suggesting that managing for high diversity will reduce transformations to exotic dominance.

FLAMITS: FLAMmability plant traiTS database

FLAMITS database contains 19,972 records of 40 flammability variables (classified according to the measured component of flammability). For each record, relevant details of the flammability experiment are included, such as the burning device, the ignition source, and the burned plant part. In addition, FLAMITS compiles taxonomic and functional data of the studied species and information on the study site (locality, geographic coordinates, biome, biogeographic realm, and fire activity). We compiled data from 295 studies located in 39 countries and distributed across 12 biomes worldwide over the last 62.5 years (1961 to 15th May 2023). The dataset has 1790 plant taxa from 186 families, 833 genera, and 1790 species.

Data from: Plant pathogenic bacterium Ralstonia solanacearum can rapidly evolve tolerance to antimicrobials produced by Pseudomonas biocontrol bacteria

Soil-borne plant pathogens significantly threaten crop production due to lack of effective control methods. One alternative to traditional agrochemicals is microbial biocontrol, where pathogen growth is suppressed by naturally occurring bacteria that produce antimicrobial chemicals. However, it is still unclear if pathogenic bacteria can evolve tolerance to biocontrol antimicrobials and if this could constrain the long-term efficacy of biocontrol strategies. Here we used an in vitro experimental evolution approach to investigate if the phytopathogenic Ralstonia solanacearum bacterium, which causes bacterial wilt disease, can evolve tolerance to antimicrobials produced by Pseudomonas bacteria. We further asked if tolerance was specific to pairs of R. solanacearum and Pseudomonas strain and certain antimicrobial compounds produced by Pseudomonas. We found that while all R. solanacearum strains could initially be inhibited by Pseudomonas strains, this inhibition decreased following successive subculturing with or without Pseudomonas supernatants. Using separate tolerance assays, we show that the majority of R. solanacearum strains evolved increased tolerance to multiple Pseudomonas strains. Mechanistically, evolved tolerance was most likely linked to reduced susceptibility to orfamide lipopeptide antimicrobials secreted by Pseudomonas strains in our experimental conditions. Some levels of tolerance also evolved in the control treatments, which was likely correlated response due to adaptations to the culture media. Together, these results suggest that plant-pathogenic bacteria can rapidly evolve increased tolerance to bacterial antimicrobial compounds, which could reduce the long-term efficacy of microbial biocontrol.

opencc-by-4.0Dec 2023View details →

Supplementary Materials - Integrating Spatial Analyses and Microbotanical Remains: A Methodological Approach for Investigating Plant Processing Activities and Domestic Spaces at Neolithic Çatalhöyük.

Supplementary Materials I, II, and III - Integrating Spatial Analyses and Microbotanical Remains: A Methodological Approach for Investigating Plant Processing Activities and Domestic Spaces at Neolithic Çatalhöyük.   Supplementary I contains the raw data for the microbotanical analyses on Buildings 80 and 131. It consists of laboratory track sheets and the raw counts of phytoliths and starch grains from each building. Supplementary II contains: a) A detailed description of all the starch grain typologies encountered in this research along with references from modern reference collections; b) A visual example of each of the phytolith morphotypes identified and c) The variogram and the Kriging error variances. Supplementary III refers to the R code, building shape files (Mask), and spatial data utilized to produce the Kriging and IDW stipital objects.

opencc-byDec 2016View details →

A scan of the freshly planted plot

Quick scan using 80 photos of the garden plot using Visual SfM and an iPhone while watering the garden this morning. Source: Objaverse 1.0 / Sketchfab

Data from: Nitrogen deposition suppresses ephemeral post-fire plant diversity

Fire is a dominant force shaping patterns of plant diversity in Mediterranean-type ecosystems. In these biodiversity hotspots, including California's endangered coastal scrub, many species remain hidden belowground as seeds and bulbs, only to emerge and flower when sufficient rainfall occurs after wildfire. The unique adaptations possessed by these species enable survival during prolonged periods of unfavorable conditions, but their continued persistence could be threatened by nonnative plant invasion and environmental change. Furthermore, their fleeting presence aboveground makes evaluating these threats in situ a challenge. For example, nitrogen (N) deposition resulting from air pollution is a well-recognized threat to plant diversity worldwide, but impacts on fire-following species are not well understood. We experimentally evaluated the impact of N deposition on post-fire vegetation cover and richness for three years in stands of coastal sage scrub that had recently burned in a large wildfire in southern California. We installed plots receiving four levels of N addition that corresponded to the range of N deposition rates in the region. We assessed the impact of pre-fire invasion status on vegetation dynamics by including plots in areas that had previously been invaded by nonnative grasses, as well as adjacent uninvaded areas. We found that N addition reduced native forb cover in the second year post-fire while increasing the abundance of nonnative forbs. As is typical in fire-prone ecosystems, species richness declined over the three years of the study. However, N addition hastened this process, and native forb richness was severely reduced under high N availability, especially in previously invaded shrublands. An indicator species analysis also revealed that six functionally and taxonomically diverse forb species were especially sensitive to N addition. Our results highlight a new potential mechanism for the depletion of native species through the suppression of ephemeral post-fire biodiversity.