PLANTS, PEOPLE, PLANET

Cocoa (Theobroma cacao L.) is grown in Cote d'Ivoire (the world's leading producer), almost always in association with trees, yet these cocoa-based agroforestry systems (cocoa AFS) remain characterized largely descriptively, without a robust inferential framework or modern diversity indices. We analyse a survey database covering 474 farms and 103 localities across the three main cocoa-producing zones of Cote d'Ivoire, locally known as " loops " (East/South-East, Centre/Centre-West, South/South-West; surveys 2013-2016), applying a renewed ecological and statistical framework: Hill numbers (q = 0, 1, 2), individual-based Hurlbert rarefaction, multiplicative alpha/beta/gamma diversity partitioning, ordination (PCoA) and PERMANOVA on Bray-Curtis matrices, Ward's hierarchical clustering for a data-driven floristic typology, multivariate MANOVA, and linear mixed models. Across 99 adequately sampled localities (>10 stems), mean taxonomic richness and the Shannon index differed significantly among zones (MANOVA: Wilks' = 0.350; F8,180 = 15.5; p < 0.001), including after standardizing sampling effort by rarefaction (F = 8.72; p < 0.001). Floristic composition differed significantly by zone (PERMANOVA, pseudo-F = 2.85; p = 0.001), though with uneven within-group dispersion (PERMDISP, p = 0.024) that calls for caution in interpretation. The Centre/Centre-West zone showed the highest beta diversity (inter-farm floristic turnover = 16.4, versus 7.2 and 2.2 in the other two zones), revealing a highly heterogeneous mosaic of individual agroforestry choices rather than a homogeneous regional system. A typological classification based on floristic composition distinguishes four cocoa-AFS profiles, ranging from dense, diverse stands to impoverished systems with low densities of associated trees, partially but not fully overlapping with the zonal boundaries. At the scale of the three loops (n = 409 farms with both age and yield recorded), cocoa yield varied significantly by orchard age class (Kruskal-Wallis, H = 18.2; p < 0.001), following a bell-shaped profile peaking around 20-35 years, consistent with the intermediate-age yield optimum suggested qualitatively by the source study; this relationship, robust to log-transformation of yield and to the exclusion of extreme values, nonetheless remains of small magnitude (R2=1.5%) and confers no out-of-sample predictive power under cross-validation, illustrating the need to distinguish statistical significance from predictive utility. This reanalysis provides a reproducible and transferable statistical framework for characterizing West African cocoa AFS, and highlights the potential value of high beta diversity as a possible indicator of landscape resilience.

Smallholder farming systems in sub-Saharan Africa are constrained by declining soil fertility, erosion, and rising fertilizer costs, creating an urgent need for scalable inputs that sustain yields while maintaining soil health. While there is some evidence that microbial inoculants may offer a promising complement to conventional fertility management, field-scale evidence in tropical cereal and tuber systems remains limited. Here, we evaluated a multi-species inoculant composed of 20-22 Bacillus and Streptomyces species on potato and maize across four sites in Rwanda over two growing seasons (2025A and 2025B). Treatments included the inoculant applied at two rates (150 and 250 g ha-1), both alone and in combination with standard fertilization (inorganic fertilizer plus manure), alongside untreated and fertilized controls. Co-application of the inoculant with standard fertilization increased yield and plant biomass beyond fertilization alone, with gains of 6-51% for maize and 3-58% for potato. However, while the inoculant applied alone outperformed untreated controls, it generally did not match standard fertilization. Responses were strongest and most consistent for large-grade potato tubers, and application rate interacted with crop type, whereby the lower dose maximized marketable tuber yield, while maize showed a positive dose-response for grain and biomass. Yield increases were not accompanied by reductions in crop nutrient density, which was instead governed by site-level differences. Altogether, these results indicate that multi-species microbial inoculants are an effective complement to existing fertility practices that may offer, pending further research, a potential pathway to partial fertilizer replacement while sustaining productivity and nutritional quality in smallholder tropical agriculture.

A better understanding factors regulating agricultural production is a research priority, given the pace of environmental change and global human population growth. Fruit orchards may be particularly vulnerable to climate change owing to the strong temperature-dependency of reproduction in temperate trees. In this study, we explored climate influences on the reproductive dynamics of apple (Malus domestica), one of the most widely-grown, economically-important fruit crops worldwide. Observations of individual-tree fruit-set, a key indicator of final yield, were acquired for three apple cultivars in an eight-year census of ~44,900 trees in >5,500 orchards spanning wide climate gradients across the Republic of Korea. With maximum-likelihood models, we quantified temporal and climate-driven patterns in fruit-set, investigated evidence for spatially-synchronized production, and conducted simulations of orchard vulnerability to climate change. We found annual fruit-set oscillated around modal levels and was synchronized between orchards within 25 km. Higher temperatures had contrasting influences, reducing fruit-set during the cold-season (consistent with climate-induced phenological shifts), while increasing fruit-set during the season of bud initiation (prior spring). Simulations predict that higher future temperatures during bud initiation increase average fruit-set, despite the constraints of cold-season warming, but that such enhancements level-off by late-century and are accompanied by heightened volatility. Decelerating fruit-set and greater instability in production have implications for future societal needs, as robust supply systems depend as much on consistent production as on high average output. Our analyses also imply that future climate patterns promoting synchrony in fruit-set among orchards may accentuate the negative consequences of fluctuating production.

Peanut smut, caused by Thecaphora frezzii, is an important constraint to peanut production in Argentina, but quantitative estimates of yield losses across environments remain limited. We quantified the relationship between disease incidence and kernel yield using 922 observations from 26 field studies conducted in Cordoba, Argentina, between 2021 and 2025. Study-specific incidence-yield relationships were analyzed using linear regression, random-effects meta-analysis, and linear mixed-effects models. Peanut smut incidence was consistently associated with yield reduction across studies. The estimated damage coefficient ranged from 24.2 to 28.7 kg ha-{superscript 1} per 1% increase in disease incidence, corresponding to a relative yield reduction of 0.74-0.87% of attainable yield. In contrast, attainable yield varied markedly among studies, ranging from 1,370 to 5,409 kg ha-{superscript 1}. Although an exploratory segmented analysis suggested a breakpoint near 12% incidence, subsequent moderator analyses, study- specific regressions, and normalized response curves provided no evidence of a biologically meaningful change in the damage coefficient across incidence or yield classes. These results indicate that differences among environments were primarily associated with attainable yield rather than with changes in the magnitude of disease-associated yield loss. The resulting damage function provides a quantitative basis for yield-loss assessment and disease management in peanut.

AimHere we aim to disentangle species-specific bioclimatic drivers of forest site productivity and project their future dynamics, providing a spatially explicit basis for anticipating climate-driven shifts in productivity and their implications for forest carbon sequestration. LocationIberian Peninsula. Time period1985-2014 (calibration); 2071-2100 (projected under CMIP6 scenarios). Major taxa studied21 Iberian tree species. MethodsWe used Site Form (SF) maps derived from the Third Spanish National Forest Inventory, spatially interpolating plot-level SF estimates as a continuous productivity index and relating them to 25 bioclimatic variables. Multiple linear regression models were selected via complementary stepwise and subset regression and validated on independent hold-out data (80%/20% split). ResultsValidated [Formula] ranged from 0.46 (Quercus faginea) to 0.97 (Pinus pinaster); 17 of 21 species reached [Formula]. BI013 precipitation of the wettest month), not BI014, was the most frequently retained predictor (15/17); BI014 was retained in only (11/17 models with a near-even sign split. Combining projected changes in mean productivity and habitat extent under SSP5-8.5, fifteen of sixteen applicable species lose total productivity by 2071-2100, six -- including Fagus sylvatica and Betula alba -- collapsing to below 1% of their reference-period value; only Pinus pinaster gains, and only under the lowest-emission pathway (up to 175%) -- under SSP5-8.5 it too loses productivity, albeit less than any other species (35% of its reference-period value retained). Limiting warming to SSP1-2.6 spares Mediterranean pine and oak species but not Euro-Siberian and montane ones. Main conclusionsThese validated, extrapolation-aware models reveal a near-universal, climate-driven collapse in Iberian forest site productivity, with direct implications for the carbon-sink potential currently attributed to these forest types, and provide a route to dynamic, climate-aware carbon-uptake estimates for the region.

Polycultures have long been practiced in traditional agriculture, yet their ecology-based benefits have remained underexplored. Here, under realistic conditions, we experimentally evaluated the productivity and ecological interactions in cultivated milpa, a traditional Mesoamerican polyculture of maize, squash and beans, using a substitutive design in which total plant density was held constant while varying species composition. Specifically, we asked whether productivity gains arose through complementary or selection effects, and whether these gains were associated with changes in arthropod communities and herbivory. We additionally evaluated whether prior cultivation influenced maize performance in the following season. Milpa plots produced significantly higher total yields, more than 2.6 times those of monocultures, despite poor bean performance. In particular, squash and maize equivalent yields increased approximately threefold. We found that these improvements were mainly explained by complementary effects rather than selection effects. Arthropod communities responded in species-specific ways to crop diversity, with predator abundance tracking herbivore presence. However, no consistent patterns emerged between herbivore load, predator abundance and plant damage, suggesting that belowground plant interactions may play a more important role than top-down herbivore control in explaining complementarity effects. In the following season, maize yield increased by [~]30% in plots previously planted with squash or beans, with milpa plots showing intermediate responses. These findings demonstrate that milpa can substantially enhance productivity while generating benefits that extend into the advantages and soil into the following growing season. Overall, our results suggest that complementarity among crops is the primary driver of productivity in milpa under low-input conditions.

Biodiversity aggregators such as GBIF provide unprecedented access to global biodiversity data, yet their representativeness remains uneven across space and taxa. This study examined the spatial and taxonomic structure of global vascular plant data available on GBIF. Six filters were applied to the GBIF vascular plant dataset, resulting in the removal of 54% of all records. Together, the filters explained more than 90% of the identified spatial issues, with duplicate and missing coordinates accounting for most of the variation. A higher number of occurrence records was associated with a greater number of spatial issues. Record distributions became progressively more even at finer taxonomic levels, from orders to species. The time series of occurrences for species, genera, and families increased sharply after 1800 and continued to rise, with no apparent stabilisation. Of the 824 ecoregions covered, 73 accounted for 72% of all occurrence records. These ecoregions spanned all continents but were strongly concentrated in Europe, followed by North America and Oceania. The analyses reveal four key patterns: (1) data volume is positively associated with spatial issues; (2) a small number of taxa account for a large proportion of records, whereas many are represented by relatively few; (3) occurrence data aggregated by GBIF have increased continuously since 1800; and (4) record coverage remains highly uneven across the world's ecoregions. These results highlight the substantial contribution of biodiversity data aggregators to expanding access to biological information while demonstrating the persistent spatial and taxonomic biases that shape their contents. Such biases should be explicitly considered when assessing data completeness and quality and when using aggregated occurrence records to infer global biodiversity patterns.

Juglans neotropica is an endangered South American walnut species for which standardized descriptions of early development are lacking, limiting its effective use in conservation and restoration programs. We developed a BBCH-scale description of early vegetative growth of J. neotropica based on observations under nursery and field conditions in Colombia. Three principal vegetative stages were described: seed germination (stage 0), leaf development (stage 1), and stem elongation (stage 3). Germination was hypogeal and occurred 30-140 d after sowing, occasionally extending to 180 d. During early growth, leaflet morphology, number, and architecture showed consistent and discrete changes between stages 1 and 3, including shifts in apex, base, margin type, and laminar shape. These modifications indicate that early development is organized into distinct ontogenetic phases rather than continuous variation, marking the transition from juvenile to vegetative adult stages. By providing a standardized, development-based framework independent of chronological age, this BBCH scale facilitates accurate identification and monitoring of seedlings in nursery production, restoration projects, and urban forestry programs. More broadly, this approach contributes to the characterization of ontogenetic phase transitions in tropical tree species and supports the use of development-based criteria for managing early establishment and performance.

White lupin (Lupinus albus L.) is a cool-season grain legume with seed crude protein of 33-47%, competitive with soybean (Glycine max L.) meal. It also fixes nitrogen and mobilizes soil phosphorus. Because soybean is a summer crop, white lupin can occupy Southeastern winter fields as a complementary protein source. Breeding for seed protein is limited by the cost and throughput of reference phenotyping. To determine how each is best deployed, we compared the utility of near-infrared spectroscopy (NIRS)-based phenomic selection with genomic selection based on 246,847 SNPs from low-pass, whole genome sequencing in a panel of Auburn University breeding lines and USDA National Plant Germplasm System germplasm. A handheld NIR calibration against Dumas reference protein reached screening-grade accuracy (R2 = 0.81). Under common cross-validation, phenomic predictive ability was 0.93 and genomic was 0.12. The low genomic value was consistent with moderate heritability (H2 = 0.33) and strong genotype-by-year interaction. Beyond predictive ability, NIRS recovered superior accessions the strictest selection intensity, and 40 to 60 reference assays sufficed to calibrate the model. Handheld NIRS is a low-cost tool for protein calibration and early-generation screening, while genomic prediction remains suited to parental selection, together supporting a complementary strategy for legume breeding Plain Language SummarySoybean meal is the main protein source for livestock and fish farms in the United States. Because soybean is a summer crop, many Southeastern fields sit idle or grow low-value cover crops in winter. White lupin, a cool-season legume whose seeds are as protein-rich as soybean meal, makes a good complementary winter crop: it yields high-protein grain while serving as a cover crop that fixes nitrogen and frees up soil phosphorus for later crops. In our early-stage lupin breeding program, measuring seed protein by standard lab methods is slow and costly. We built a calibration that lets a handheld scanner estimate protein from light, and compared it with predicting protein from the plants DNA. The scanner gave accurate, low-cost protein screening from only about 40-60 lab tests, while DNA-based prediction remains suited to guiding parent selection. Used together, these tools offer breeders a practical path to develop high-protein white lupin. Core ideasO_LIHandheld NIRS provides screening-grade prediction of white lupin seed crude protein. C_LIO_LISpectra carried more usable protein signal than markers by measuring seed chemistry directly. C_LIO_LINIRS and genomic prediction serve different stages of a white lupin breeding program. C_LIO_LIAbout 40 to 60 reference assays sufficed to calibrate NIRS to near-full accuracy. C_LI

This study aimed to examine entomologists' perceptions of equity, inclusion, and exclusion within the discipline, identifying perceived challenges and proposed solutions for advancing equity in the field. The present study surveyed 47 self-identified entomologists living in the United States in 2023. Using a mixed-methods design, the study examined entomologists' perceptions of inclusion and exclusion within the discipline through qualitative and quantitative measures. Respondents highlighted needs for race-conscious funding opportunities, comprehensive inclusion efforts through geographically diverse outreach, and access to role models and mentors with similar identities to future entomologists. Findings are discussed in relation to a smaller 2013 study on recruitment and retention of entomologists of color, which offers preliminary historical context. The 2013 respondents emphasized intrinsic and age-based barriers to recruitment (e.g., lack of interest, limited K-12 outreach), the 2023 findings point toward structural inequities and retention needs (e.g., systemic exclusion). The 2013 comparison is interpreted as exploratory given differences in sample size and scope between the two studies. The 2023 study highlights evolving perceptions of persistent inequities in entomology and identifies opportunities to build a more inclusive and representative discipline.

1. Forest canopies harbour strong microclimatic gradients that shape plant performance, species interactions and ecosystem processes. Yet, despite renewed interest sparked by global change, forest canopies remain difficult-to-access experimental spaces. 2. With the goal to expand access to tree canopies as experimental arenas, we designed, built, and tested TreeTOP, a standardized experimental platform that opens canopy space for manipulative ecological experiments, specifically with potted plants. TreeTOP features lightweight aluminum frames placed in mature tree canopies non-invasively, allowing potted plants to be placed in three different heights, ground level, shade canopy, and sun canopy. 3. We implemented TreeTOP using two contrasting infrastructure concepts to demonstrate its applicability in both highly equipped canopy research facilities and forests without permanent canopy infrastructure. One installation relied on a canopy crane, grid power and fully automated irrigation, whereas the second was built by certified tree climbers and was equipped with an autonomous solar-powered, battery-operated irrigation system. At both sites, environmental sensor networks monitor the experiment. 4. TreeTOP successfully reproduced characteristic canopy microclimatic gradients, including increasing light availability, daytime air temperatures and thermal extremes with canopy height. Despite differing infrastructures, both implementations generated comparable microclimatic patterns, demonstrating that standardized canopy experiments are feasible in forests with or without permanent canopy access. By opening canopy space for manipulative experiments, TreeTOP provides a transferable framework for investigating plant performance, phenology, species interactions and microbiome assembly under realistic forest conditions.

Extensive deforestation and disturbance have reshaped forest landscapes in West Africa, including areas surrounding Tai National Park, the largest remaining block of Upper Guinean rainforest. Although many degraded areas are currently undergoing regeneration, the capacity of these secondary forests to recover their biodiversity attributes remains insufficiently assessed within this park. This study quantifies the multidimensional restoration of biodiversity across 125 secondary forest plots and 15 primary forest plots representing 14,731 inventoried individuals in four sectors of the park. Using a Bayesian modelling framework, we estimate recovery trajectories of Shannon diversity, floristic composition, functional traits (wood density, leaf mass per area, seed mass), and conservation-relevant species. The different biodiversity attributes recovered at contrasting rates. Diversity was restored more rapidly ({lambda} = 0.06) than floristic composition ({lambda} = 0.03), and these recovery varied according to environmental variables. Among these, the presence of remnant trees showed the highest median on diversity (0.53 {+/-} 0.61) and floristic composition (0.37 {+/-} 0.17), promoting the rapid recovery of both attributes, followed by prior land use, particularly cocoa farming which also positively influenced the recovery of alpha diversity ({lambda} = 0.03) and floristic composition ({lambda} = 0.02). Regarding functional traits, they displayed contrasting dynamics: specific leaf area and seed mass recovered rapidly along successional gradients, whereas wood density followed a more gradual recovery trajectory. From a conservation perspective, although the proportion of IUCN Red List species remained stable along the successional gradient, old-growth indicator species were significantly more abundant in primary forests. To ensure the long-term conservation of biodiversity, protecting both primary and regenerating forests is essential to preserve the ecological resilience of this park.

Deadwood is a fundamental component of forest ecosystem, supporting biodiversity and driving multiple ecological processes. However, structures that may develop on downed coarse woody debris (CWD) create additional microhabitats that are used by numerous organisms and contribute to small-scale habitat heterogeneity. To date, quality of CWD is commonly characterized by its volume, diameter, tree species or stage of decomposition, while fine-scale structures occurring there remain not surveyed and their role in ecosystem is rarely quantified. Here, we introduce the novel concept of microhabitats on CWD. i.e. Deadwood-related Microhabitats (DreMs), defined as distinct features occurring on CWD that may provide shelter, breeding or foraging sites for forest-dwelling organisms. Using an original catalogue comprising 14 groups and 30 types, we inventoried DreMs on 6,003 CWD across 423 study plots located in best-preserved old-growth forests in Poland. We quantified the frequency and richness of DreMs and assessed the link between CWD characteristics and DreM richness in spruce, beech, willow-poplar, fir-beech and oak-lime- hornbeam forests. All inventoried DreMs occurred on both deciduous and coniferous taxa. The most frequent DreM included bryophyte mats, loose bark patches, insect galleries, fungal fruiting bodies and polypores. DreM richness increased with CWD diameter, more complex architecture and the presence of multiple decay classes within single debris. DreM richness peaked at intermediate decay classes and was higher on deciduous than on coniferous taxa. Our study is the first large-scale qualitative and quantitative assessment of DreMs in temperate forests. By focusing on forests characterized by ecological continuity and minimal human-related disturbance, the results provide a reference for downed deadwood-associated structures. By complementing inventory of tree-related microhabitats, DreMs extend potential monitoring schemes of habitat quality and contribute to biodiversity-oriented forest management. Highlights* Downed coarse woody debris (CWD) hosts Deadwood-related microhabitats (DreMs) * Higher DreM richness is associated with CWD diameter * DreM richness peak at intermediate stages of wood decay * CWD of deciduous taxa support more DreMs than coniferous * Diversified CWD and DreMs increase habitat heterogeneity for forest-dwelling taxa

Amaranthus L. spans aggressive agricultural weeds, ornamentals, and ancient pseudocereals. Species within the genus vary in morphology, environmental tolerance, and sexual systems, making them well-suited for studying reproductive evolution and plant adaptation. To investigate sex chromosome architecture within the genus, we generated chromosome-level assemblies of a monoecious amaranth (Amaranthus spinosus) and three dioecious species (A. acanthochiton, A. arenicola, and A. floridanus) using PacBio high-fidelity (HiFi) long reads. We paired these data with Dovetail Genomics Omni-C sequencing to achieve haplotype resolution for A. spinosus and A. acanthochiton, and we used reference-guided scaffolding for the remaining two species. The assemblies are highly contiguous, with sizes ranging from 394.24 to 607.10 Mbp, contig N50 from 0.63 to 8.76 Mbp, and scaffold N50 from 22.44 to 37.97 Mbp. Evaluation of the assemblies and annotations revealed 96.3 to 97.6%, and 97.6 to 98.3% BUSCO completeness, respectively. Comparative genomic analysis revealed that the Chromosome 1 inversions and Robertsonian fusion previously reported in A. tuberculatus are conserved in A. acanthochiton and consistent with the architecture of A. arenicola and A. floridanus, suggesting that the evolution of dioecy in this clade predates subsequent speciation. In parallel, multiple homologs of Rf1 on Chromosome 3 of A. spinosus, a monoecious species that exhibits spatial separation of male and female flowers and is closely related to the dioecious A. palmeri, were identified. Together, this study provides foundational resources for advancing evolutionary, ecological, and agronomic research across the genus, including herbicide resistance evolution and weediness traits.

BACKGROUNDBlackleg, caused by Leptosphaeria maculans, is a major disease limiting oilseed rape production worldwide, and its management increasingly requires sustainable alternatives to chemical fungicides. In this study, we evaluated the antagonistic activity and plant growth-promoting potential of three endophytic bacteria, Bacillus velezensis Bro5, Bacillus subtilis Bro11, and Pantoea agglomerans Bru13, against a geographically diverse collection of 139 L. maculans isolates from five oilseed rape-producing regions of Argentina. RESULTSDual culture assays revealed strong inhibitory activity by Bro5 and Bro11, with mean inhibition rates of [~]80% across isolates, while Bru13 showed variable inhibition (<75% for most isolates). Greenhouse and growth chamber assays confirmed the protective potential of these strains. At the cotyledon stage, Bro11 and Bro5 reduced lesion size by 47% and 28%, respectively, while their combination achieved a 51% reduction. In greenhouse trials, combined application of Bro5 and Bro11 reduced stem base necrosis by 45% and increased the proportion of plants with [&le;]50% damage to 98%, compared to only 70% in controls. Key disease metrics, including disease index, incidence, and severity, decreased by 60%, 23%, and 26%, respectively. Beyond pathogen suppression, inoculation with the Bro5-Bro11 consortium enhanced plant growth, increasing shoot biomass by 89% at early stages, and improving stem dry weight and diameter by 10% and 35%, respectively, at maturity. CONCLUSIONThese findings highlight the robustness of Bacillus endophytes as biocontrol agents, their capacity to suppress diverse pathogen isolates, and their dual role in plant growth promotion, supporting their potential integration into sustainable blackleg management programs.

Khaya senegalensis (Desr.) A. Juss., the West African savanna mahogany, is listed as Vulnerable on the IUCN Red List due to prolonged commercial and medicinal overexploitation, compounded by failing natural regeneration amid growing deforestation and climate change. Restoration strategies generally rest on the implicit assumption that rigorous selection of seed trees based on their size improves offspring quality. Yet this assumption has never been confronted with the competing hypothesis of a determinism dominated by the planting site, using statistical approaches of adequate power. This study tests the relative contribution of seed-tree dendrometric characteristics (diameter, height) and planting site to germination and juvenile growth (6-24 months) of K. senegalensis, using six complementary analytical approaches: continuous regression, linear mixed models with site x seed-tree interaction, seed-mass mediation analysis, non-linear growth-trajectory modelling, between-site phenotypic plasticity indices, and multi-predictor allometric equations, across two contrasting bioclimatic sites in Cote dIvoire (Korhogo: Sudanian savanna, and Daloa: humid forest) and six seed-tree categories. Converging across all these approaches, the results show that the planting site exerts a decisive influence on germination (71.1% at Korhogo versus 63.9% at Daloa; {chi}{superscript 2} = 6.09; p = 0.014) and on the entire growth trajectory (p < 0.001), whereas no seed-tree characteristic affects offspring performance, whether in continuous regression (p > 0.37), mixed models with interaction (p > 0.29), or through a seed-mass mediation pathway (Sobel test, p = 0.46). An exponential growth model fits better than linear or power-law models ({Delta}AIC = 13.6-14.7 depending on site), and multi-predictor allometric equations (diameter and height) explain 97.4% of the variance in total biomass, versus 94.8% for the single-predictor model. These convergent results indicate that, contrary to the widespread practice of selecting seed trees on size criteria, it is the choice of planting site that truly determines the success of restoring this vulnerable species. A conclusion calling for a reorientation of priorities in reforestation and agroforestry programmes across West Africa.

The global market concentrates extractive pressure on lands held by Indigenous peoples, including peoples living in isolation, for whom free, prior and informed consent cannot be obtained and protection must therefore rest on territorial instruments. Halmahera, Indonesia, holds some of the worlds largest lateritic nickel reserves beneath a lowland rainforest inhabited by the Hongana Manyawa, yet the trajectory of land use and cover change across the island has not been quantified. We characterised land use and cover change over the 17,437 km2 island between 2014 and 2024 using MapBiomas time series, and projected a business-as-usual scenario to 2054 with a stochastic cellular-automata model implemented in Dinamica EGO, calibrated with weights of evidence on eight variables describing mining and logging concessions, transport infrastructure, settlements and previous clearing. Forest covered 83.0% of the island in 2014 and 82.1% in 2024; under unchanged policy it falls to 73.7% by 2054, a net loss of 162 thousand ha, or 11.2% of the 2014 baseline, at gross rates of 47,000-51,000 ha per decade. Deforestation probability is highest within 500 m of previous clearing and declines with distance from settlements, cities and mining sites, while proximity to national parks carries a negative weight of evidence. The frontier is self-propagating and spatially predictable, and legally designated territory retains forest within it. Protecting the Hongana Manyawa consequently depends on excluding extractive licensing from the interior forest ahead of the frontier rather than behind it.

The integration of digital technologies for high-throughput field phenotyping is critical for accelerating crop improvement in agriculture. However, extracting traits from remote sensing data remains constrained by fragmented workflows, manual intervention, and limited interoperability among existing tools, resulting in delays that hinder timely biological insight and decision-making. To address these challenges, we present PhenoStream (Phenotyping Streaming), a scalable, end-to-end cyberinfrastructure designed to automate the full lifecycle of aerial imagery-based phenotyping, from data acquisition to plot- and genotype-level inference. The framework integrates automated data ingestion from distributed field sites, geospatial processing, and AI-enabled trait extraction within a unified, user-accessible graphical interface. Its modular and extensible architecture supports adaptable trait modeling and seamless integration of new data sources, enabling deployment across diverse crops, environments, and experimental designs. We demonstrate the system across a large multi-location field trial network of bioenergy crops, where it enables high-throughput characterization of spatiotemporal growth dynamics, genotype-by-environment (GxE) interactions, and predictive modeling of key agronomic traits. By significantly reducing processing latency and manual effort, the platform facilitates near-real-time analysis and reproducible workflows. This work establishes a generalizable and scalable pathway for operationalizing very-high-spatial resolution aerial phenotyping in agricultural research. By bridging data acquisition and analytics, the end-to-end cyberinfrastructure provides a foundation for integrating heterogeneous and unstructured data streams--including remote sensing, environmental, and management data--toward data-driven decision making in agriculture.

Background/ObjectivesElymus sensu lato (Poaceae) is arguably the largest and most complex genus in the tribe Triticeae. It includes hybrids and polyploids based on x=7 chromosomes, all including the St genome, forming a valuable genepool for forage grass and cereal breeding. Analysis of chloroplast genome diversity and structural dynamics is critical for resolving maternal lineages, reticulate evolution and biodiversity across this agronomically important complex, refining their taxonomy, conservation and exploitation. MethodsWe sequenced the complete chloroplast genome (plastome) of Elymus ciliaris (4x=2n=28; StStYY genome composition) using ultra-long Oxford Nanopore single-molecule reads and compared it to 76 additional chloroplast genomes representing major St-genome lineages in Elymus s.l. (Pseudoroegneria St; Elymus s.s. StH, StY; Thinopyrum StJ/E; Campeiostachys StYH; Kengyilia StYP). We analyzed structure, nucleotide diversity, inverted repeat (IR) dynamics, and phylogenetic signal. ResultsThe E. ciliaris chloroplast genome was 135,004 bp long (38.3% GC) with a canonical quadripartite structure. Single-molecule reads (n=74) revealed heteroplasmy: two Small-Single-Copy (SSC) orientations at 30%:70% frequency, indicating an inversion polymorphism. Across the Elymus group, comparative analysis of chloroplast assemblies showed high structural conservation but lineage-specific IR-boundary shifts. Kengyilia exhibits exceptional IR expansion. Nucleotide diversity hotspots localize to the large single-copy region, especially in StY lineages. Phylogenies recover a monophyletic St-containing clade but do not delineate genera, reflecting reticulate evolution, with North American/Southeast Asian and Eurasian geographic sub-clades. ConclusionsSingle-molecule sequencing uncovered heteroplasmy with an inversion polymorphism in a single plant of Elymus ciliaris, hidden in short read assemblies. There were no other polymorphisms, as expected for chloroplast sequences (except for technical homopolymer variation). Our analyses showed that a Pseudoroegneria-like St chloroplast genome predominates as the maternal donor across Elymus polyploids. Variable regions and IR dynamics offer strong models for chloroplast genome evolution in reticulate lineages and suggest exploiting plastome variation to complement nuclear biodiversity studies.

Cultivar susceptibility strongly influences the epidemiology of vector-borne plant diseases, and understanding cultivar-specific variation can inform management strategies. This is particularly relevant for flavescence doree, an incurable grapevine disease associated with a phytoplasma and transmitted by the leafhopper Scaphoideus titanus. In this study, we investigated the susceptibility of the main Swiss varieties, by combining controlled insect-mediated inoculation experiments with complementary field analyses conducted at progressively finer spatial scales. Together, these approaches allowed us to compare both infection probability and phytoplasma relative titre under standardised transmission conditions with disease incidence and relative titre under natural epidemiological conditions. For most cultivars, laboratory results were broadly consistent with field observations. However, a marked discrepancy emerged in the relative infection pattern between the two main grapevine cultivars grown in Switzerland: Chasselas and Pinot Noir. Under controlled conditions, they did not differ significantly in either their probability of infection or the phytoplasma relative titre, indicating no detectable difference in susceptibility to phytoplasma infection. In contrast, Pinot Noir consistently showed higher disease incidence than Chasselas under natural conditions. This pattern was observed across all spatial scales examined, from regional surveys to neighbouring vineyard plots, and was mirrored by higher phytoplasma relative titres. Importantly, under controlled conditions, S. titanus mortality during the one-week inoculation period was significantly higher on Chasselas than on Pinot Noir, indicating that Chasselas may provide a less favourable host for S. titanus. Together, these findings support the hypothesis that differences in field disease incidence between these cultivars may arise from differences in vector performance rather than intrinsic susceptibility to phytoplasma infection. This highlights the importance of considering plant-vector interactions, alongside susceptibility to infection, when assessing cultivar-specific vulnerability to vector-borne plant diseases.