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Remote Sensing

MDPI AG

Preprints posted in the last 90 days, ranked by how well they match Remote Sensing's content profile, based on 10 papers previously published here. The average preprint has a 0.01% match score for this journal, so anything above that is already an above-average fit.

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SatCHM (Satellite Canopy Height Model): Leveraging deep learning for site-specific sub-meter canopy height predictions

Mitchell, M.; Abolt, C.; Crennen, Z.; Marcato, A.; Atchley, A.

2026-08-27 ecology 10.64898/2026.08.25.728853 medRxiv
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High-resolution monitoring of forest structure and productivity is essential for effective natural resource management. However, monitoring approaches such as field-based forest inventories or extensive lidar campaigns are costly, time-intensive, and spatially limited. Therefore, inexpensive and accessible methods are needed. SatCHM (Satellite Canopy Height Model) was developed to be an accessible and open-source tool for researchers, allowing for site-specific and temporally flexible predictions of canopy height with limited computational resources. SatCHM requires four inputs: panchromatic satellite imagery, solar and sensor angle metadata of satellite imagery, digital elevation models (DEMs), and lidar-produced CHMs for an area of interest. After SatCHM pre-processes inputs, data is loaded into a collection of convolutional neural networks (CNNs) for image-to-image regression. This ensemble cooperates to yield high-resolution predictions (up to 0.5-meter) of three-dimensional tree structure with discernible tree crowns across a broader defined area of interest. After calculating the mean absolute error for each prediction output, the median of these mean absolute errors was 6.06 meters.

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Performance verification of human field of view occluders for light measurement and simulation

Mardaljevic, J.; de Vries, S. W.; van Duijnhoven, J.

2026-08-10 physiology 10.64898/2026.08.04.742779 medRxiv
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The measurement of light received at the cornea of the eye is a paramount consideration for the understanding of the relation between environmental illumination and the non-image-forming effects of light. The field of view (FOV) at the cornea is less than a full hemisphere, because it is partially occluded by human facial morphology. The International Commission on Illumination (CIE) has defined a standard model of human FOV. A suitably designed physical occluder attached to the sensor (of a light meter) has been proposed as a means of incorporating the effect of human FOV when taking measurements. Similarly, when using simulation to predict light received at the cornea, a geometrical description of the occluder at the eye point(s) can be added to the 3D model of the scene. The first occluder model proposed to represent CIE human FOV was enumerated in terms of: the CIE definition; the radius of the occluder; and, the radius of the light sensor disc. We present a simpler model based only on the CIE definition and the occluder radius. Both models were tested using a virtual goniophotometer. Various sensor response functions describing the spatial sensitivity across the sensor disc, including several we characterized through laboratory measurements, were included in the test. For all functions considered, the performance of the simpler occluder model was equivalent to or better than the model first proposed.

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The Dark Ecology Dataset: Measurements of Aerial Biomass in US Weather Radar from 1995 to 2025

Sheldon, D.; Winner, K.; Deznabi, I.; Bernstein, G.; Bhambhani, P.; Lin, T.-Y.; Desmet, P.; Dokter, A. M.; Horton, K. G.; Nilsson, C.; Van Doren, B. M.; Farnsworth, A.; La Sorte, F. A.; Maji, S.

2026-06-23 ecology 10.64898/2026.06.20.733536 medRxiv
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The US NEXRAD radar network has monitored the aerosphere over the US and its territories continuously since the 1990s and archived nearly 300 million radar volume scans. These data contain a wealth of information about the movements of birds, bats, and insects. Historically, this biological information was difficult to access due to the amount of data and challenges in analyzing it. In the last 15 years, fueled by computational and methodological advances, large-scale aeroecology research has blossomed. However, comprehensive analyses of the NEXRAD archive remain very costly. We collected measurements of biological activity from every volume scan in the NEXRAD archive--nearly 300 million data files total--to assemble a dataset of aerial biomass over the US from 1995 to 2025. The core data are vertical profiles, which summarize biological activity at different heights above the radar station for each volume scan. We also provide time series data products that aggregate vertical profiles to point measurements at radar stations across time. These data products can support a range of aeroecology analyses at significantly reduced effort.

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Toward scalable ambulatory light dosimetry: sensor-placement bias under naturalistic conditions

Zauner, J.; de Vries, S. W.; Didikoglu, A.; van Duijnhoven, J.; Spitschan, M.

2026-08-01 physiology 10.64898/2026.07.28.741277 medRxiv
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BackgroundPersonal light dosimeters enable exposure assessment under free- living conditions, but sensors are rarely positioned near the eyes--the relevant site for visual and non-visual responses. Chest and wrist placement may improve adherence and scalability, yet placement-dependent error and its consequences for derived outcomes remain insufficiently characterised. ObjectiveTo quantify how chest and wrist placement affects time-resolved estimates of eye-level light exposure across naturalistic contexts and derived exposure metrics. MethodsWe analysed concurrent 10-s melanopic equivalent daylight illuminance measurements from identical dosimeter models at the glasses, chest, and wrist across eight sites in seven countries. Melanopic equivalent daylight illuminance was compared at two analytical scales. Generalised additive mixed models quantified time-resolved placement error across contexts (N=787 participant-days), and mixed- effects models compared 54 daily metrics (N=604 participant-days). Hierarchical bootstrap resampling quantified the precision of population-average metric bias across participant numbers and monitoring durations. ResultsBody-worn dosimeters generally underestimated eye-level exposure. Across categorical contexts, estimated mean errors ranged from -23.1% to -4.2% at the chest and from -54.7% to -30.3% at the wrist, with larger errors generally observed at night. Nineteen of 54 chest-derived and 27 of 54 wrist-derived metrics differed nominally from glasses. Among these, median absolute bias was 5% at both placements, but maxima reached 50% and 84%, respectively. Timing outcomes were comparatively insensitive, whereas level and temporal-dynamics outcomes were more sensitive. With seven days per participant, the class-median bias standard deviation reached the 5% precision tolerance with 2-16 participants for all classes except temporal dynamics, which required 33 at the chest and 59 at the wrist. SignificanceDosimeter-placement validity depends on analytical scale and exposure construct. Chest placement can support scalable studies focused on aggregated timing or duration outcomes, whereas wrist placement introduces greater and less predictable bias. Near-eye measurement remains preferable for small- sample studies, time-resolved exposure levels and temporal-dynamics analyses.

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Optimizing Signal Acquisition and Chemometric Pipelines for Micro NIR Plant Identification: Evaluating Spectral Backgrounds and Data Processing in Herbarium Specimens

Alves, T. C.; de Gasper, A. L.

2026-07-07 ecology 10.64898/2026.07.07.736730 medRxiv
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Premise: Rapid and accurate plant species identification is a critical challenge exacerbated by the taxonomic impediment. Although portable near-infrared (Micro NIR) spectroscopy represents a promising solution, the current absence of standardized protocols and a fundamental understanding of how critical acquisition and analysis parameters influence accuracy remain significant barriers. This study focused on the systematic optimization and validation of a comprehensive workflow designed to maximize the reliability of plant identification using this technology. To ensure methodological robustness across diverse foliar matrices, four vascular plant species were strategically selected as a representative test set to encompass morphological extremes, including significant variations in leaf thickness, pubescence, and surface texture. Methods: Using a portable spectrometer on herbarium specimens (exsiccate) of four vascular plant species, we systematically tested five spectral backgrounds, seven pre-processing methods, and four classification models. Subsequently, we optimized the number of spectral readings and evaluated the influence of the leaf scanning surface (adaxial vs. abaxial) on model accuracy. Results: The highest-performing combination was a Shiny Aluminum background, Second Derivative pre-processing, and a Random Forest model, which achieved a mean cross-validated accuracy of 99%. An average of just three spectral readings from the adaxial (upper) leaf face was sufficient to saturate model performance, proving statistically superior to other approaches (p < 0.001). Discussion: This study establishes a validated, high-accuracy protocol for plant species identification from herbarium specimens using portable NIR, offering a powerful tool for biodiversity studies. Direct applicability to fresh plants in the field requires future validation to account for the spectral influence of moisture variability.

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A Bayesian method for estimation of plant soil water content with application to low-cost horticultural robotics

Southgate, A. J.

2026-07-20 plant biology 10.64898/2026.07.14.738550 medRxiv
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Climate change represents a challenge to food security by interfering with the environmental conditions needed for productive plant growth. While technology can be used for partial mitigation, access to technology is inequitable. Low-cost microcontrollers, such as the ESP32, have recently lowered the barrier for entry into prototyping smart devices. ESP32s equipped with capacitive moisture sensors have been suggested for low-cost smart plant watering systems. However, measuring moisture in soil is complex, potentially destructive, and requires careful calibration in order to characterise the response curve mapping soil water content to sensor measurements. Here, we developed a Bayesian method for estimating the inverse response curve from capacitive moisture sensor data, known water doses, and prior uncertainty, bypassing the need for destructive gravimetry. This method constitutes the core calibration module of the open-source OpenHCult software system for low-cost horticultural automation.

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Combining 3D-multispectral and hyperspectral imaging to identify environmental stress treatments imposed during plant growth

Stock, F.; Panda, S.; Poire, R.; Brown, T.; Akram, A.; Zheng, L.; Lei, H.; Zha, R.; Zhao, M.; Isabelle, S.; Martel, M.; Comeau, M.-A.; Hamel, L.-P.; Lavoie, P.-O.; D'Aoust, M. A.; Reithinger, H.; Saxena, P.; Stone, E. A.; Li, H.; Way, D. A.; Atkin, O. K.

2026-08-28 plant biology 10.64898/2026.08.28.747774 medRxiv
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Non-invasive, high-throughput phenotyping tools are needed that can identify environmental effects on plant structure and function to diagnose factors responsible for reduced growth in commercial and non-commercial settings. In this study, we explored whether the integration of 3D-multispectral (3D) and 2D-hyperspectral imaging (HSI), aided by machine learning (ML), could be used to identify environmental stress treatments imposed during plant growth. Controlled environment-grown Nicotiana Benthamiana plants were subjected to a range of abiotic treatments - including different growth irradiances, heat treatment and drought stress - with the treatments resulting in differences in shoot height, biomass, leaf area and spectral reflectance. ML models were trained to identify these treatments using morphological and spectral traits measured at 27, 29, 31, and 34 days after sowing (DAS). A 3D-multispectral scanner was used to obtain information on plant height, biomass, and leaf area. A visible and near-infrared (VNIR) HSI camera provided detailed spectral information for deriving spectral indices including the Normalised Difference Vegetation Index (NDVI), Photochemical Reflectance Index (PRI) and Normalized Difference Red Edge (NDRE). Manual measurements provided baseline comparative data. The 3D-multispectral scanner reliably estimated above-ground traits, with high correlations between manual and scanner-derived measurements. The ML models accurately differentiated among environmental stress treatments, with the fused 3D+HSI model achieving the best overall predictive performance across all evaluated metrics compared with models based on either imaging modality alone. Results demonstrated the effectiveness of combining 3D-multispectral and 2D-HSI data with ML analyses for non-destructive, high-throughput phenotyping. The integration of these techniques enabled non-destructive, high-throughput identification of environmental stress treatments imposed during plant growth.

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WIO-ReefFish: A High-Resolution Dataset for Taxon-Aware Coral Reef Fish Detection in the Western Indian Ocean

Gerard, J.; Branger, L.; Huyghe, F.; Kochzius, M.; Otwoma, L.; Bergacker, S.; op't Roodt, L.; Rumisha, c.; Di Bella, L.

2026-08-20 ecology 10.64898/2026.08.19.745797 medRxiv
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Coral reef fish assemblages are widely used as indicators of ecosystem condition, yet manual annotation of underwater video remains a major bottleneck for scalable biodiversity monitoring. Despite rapid progress in automated detection, ecologically realistic and publicly available datasets remain scarce, particularly for the Western Indian Ocean. Here, we present WIO-ReefFish, a reef fish detection dataset derived from diver-operated line-intercept transects and designed for ecological monitoring under natural survey conditions. WIO-ReefFish comprises 1,000 ultra-high-definition images (3840 $\times$ 2160 pixels) and 6,768 exhaustive bounding-box annotations spanning 24 taxonomic categories, thereby preserving full-frame assemblage structure in complex reef scenes. We also establish a standardized benchmark across nine object detection models under two complementary protocols: class-aware detection and class-agnostic fish localization. Detection performance was consistently higher under the class-agnostic protocol. The best-performing model (RT-DETR) improved from 0.48 mAP50 in the class-aware setting to 0.70 mAP50 when taxonomic constraints were removed, indicating that taxonomic discrimination remains substantially more challenging than fish localisation in reef imagery. Spatially independent evaluation revealed a pronounced generalisation gap, particularly for taxonomic detection, whereas class-agnostic fish localisation remained substantially more robust across transects and countries. Together, these results establish WIO-ReefFish as a realistic benchmark for automated reef fish detection and provide a foundation for more robust computer-vision tools in coral reef biodiversity monitoring. The WIO-ReefFish dataset and associated benchmarking resources are publicly available.

9
Mapping Coastal Forest Retreat Using Convolutional Neural Networks and Different Satellite Imagery

Tajudeen, T. T.; Ardon, M.; Tulbure, M.; Martin, K. L.

2026-08-22 ecology 10.64898/2026.08.18.745552 medRxiv
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Coastal forests are increasingly threatened by saturated soil and elevated salinity levels resulting from sea level rise, saltwater intrusion, and storm surges. In response to rising salinization and flooding, healthy coastal forests that rely on freshwater (both wetland forests and low-elevation upland forests) are transitioning into landscapes dominated by dead or dying trees, known as ghost forests. Situated among salt-tolerant shrubs and grasses, ghost forests eventually become marshes or open water. Here, our main objective was to quantify the dynamics and pathways of these forest landscape conversions, as well as the factors contributing to the changes, which is vital for understanding the progression of coastal ecosystem degradation and forecasting future changes. We focused first on identifying the best method to track forest landscape change by exploring the role of multiple remote sensing indices (i.e., multispectral, bi-seasonal, topographical, and phenological metrics) in enhancing the performance of deep learning models (convolutional neural networks, CNNs) for land cover classification in the coastal plain of North Carolina using surface reflectance of Landsat 8 and Sentinel-2 images. Then, we used the best available data (Landsat 8) to understand long-term change and identify patterns of land cover change from 1985 to 2021. Our study reveals that incorporating phenology and topographical indices enhances the separability of the ghost forests class from all other vegetation classes. In our assessment, the higher-resolution Sentinel-2 data (F1 Score = 96.3) outperformed Landsat images (F1 score = 93.4) for the 2021 co-available year. However, Landsat remains an important tool used due to its long-term data record. Therefore, we used Landsat to determine that 21% of forests were lost between 1985 and 2021, and that the rate of loss is increasing. Between 2010 and 2021, 23,876 ha of forest were converted to marsh, ghost forest, and shrub, which is 1.5 times higher than the 16,968 ha lost between 1985 and 2010. These conversions from forest to ghost forest and marshes were driven primarily by proximity to the channel, salinity, and the increasing rate of relative sea level rise (RSLR), which are the key environmental drivers of observed changes. By quantifying these changes, we highlight regions most vulnerable to environmental stressors, providing a basis for targeted conservation strategies.

10
Global variations of Light Use Efficiency in Forests Jointly Driven by Plant Traits and Climatic Conditions

Zhang, Y.

2026-06-17 ecology 10.64898/2026.06.16.732732 medRxiv
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Forests are essential to the global carbon cycle with light use efficiency (LUE) as a key parameter for assessing carbon sequestration capacity. However, the variations and drivers of LUE remain inadequately understood. Using remote sensing data, we analyzed global LUE patterns across five forest types and identified the main drivers. The global average annual LUE of forests is 0.93 {+/-} 0.36 g C MJ-1 during the period 2001-2022, with an increasing trend of 0.0034 g C MJ-1 yr-1. Among forest types, evergreen broadleaf forests exhibited the highest LUE, followed by evergreen needleleaf forests. Deciduous broadleaf forests and mixed forests showed similar levels, while deciduous needleleaf forests exhibiting the lowest LUE. Variations in LUE were jointly driven by plant traits and climatic conditions, with generalized linear models explaining 86% and 98% of spatial and temporal LUE variations, respectively. These findings highlight the critical role of plant traits and climate in shaping forest LUE, providing insights for enhancing carbon cycle models and informing forest management strategies in the context of global change.

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Recurring daytime and nighttime modes of VOC emissions in a cool-temperate oak forest

Sekimoto, K.; Suyama, Y.; Kita, Y.; Fukuyama, D.; Koss, A.; Matsukami, A.; Tomihira, S.; Yamagishi, H.; Shiojiri, K.; Saito, T.; Yazaki, K.

2026-07-24 physiology 10.64898/2026.07.20.739470 medRxiv
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Plants emit substantial amounts of biogenic volatile organic compounds (VOCs) that link plant physiological activity to ecological interactions and atmospheric chemistry. However, the processes regulating VOC emissions within the forest air and at the interface directly above the canopy remain poorly characterized. In this study, we investigated forest-scale VOC dynamics in a cool-temperate deciduous forest dominated by Quercus crispula using high-time- and high-mass-resolution proton-transfer-reaction time-of-flight mass spectrometry (PTR-ToF-MS) integrated with positive matrix factorization (PMF). This non-targeted, process-oriented framework was applied to forest-interior and canopy-top atmospheres during rain-free summer days in 2024 and 2025 to extract dominant modes of VOC emissions. The PMF consistently resolved two recurring modes characterized by the daytime and nighttime enhancement patterns. The daytime mode was dominated by isoprene and its oxidation products and demonstrated strong light- and temperature-dependence, whereas the nighttime mode was enriched in mono- and sesquiterpenes. The daytime contribution exhibited a pronounced morning-afternoon asymmetry, indicating non-linear physiological and canopy-scale controls. These patterns were reproducible across the years. This study demonstrates that combining PTR-ToF-MS with PMF enables robust, top-down identification of recurring modes of forest VOC variability within and above forest canopies, linking leaf-level physiology and ecosystem-scale atmospheric exchange. HighlightForest-scale VOC emissions were resolved into recurring daytime and nighttime modes using a non-targeted PTR-ToF-MS and PMF framework.

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Fine-scale flight behaviour reveals eagles' response to different uplift sources and highlights observational gaps in high-resolution weather models.

Frisoni, F.; Carrard, T.; U. Gruebler, M.; S. Hatzl, J.; Safi, K.; A. Sprenger, M.; Sumasgutner, P.; Wikelski, M.; Scacco, M.

2026-08-19 ecology 10.64898/2026.08.18.745477 medRxiv
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Understanding how animals respond to their physical environment requires environmental observations at the scale at which behavioural decisions are made. For soaring birds, the coarse resolution of weather products has long hindered the analysis of their behavioural response to fine-scale atmospheric dynamics, forcing uplift sources to be inferred largely from behaviour itself. Here, we combined high-resolution movement data from 24 golden eagles with the kilometre-scale COSMO weather model. We first classified thermal, orographic, and gravity-wave uplifts using independent atmospheric predictors and then quantified the birds' use of each uplift type and their fine-scale behavioural responses. Eagles relied predominantly on thermals, but opportunistically adjusted their use of uplift sources seasonally. The birds' flight behaviour could not reliably indicate which uplift type was primarily used, and thus suggests that both atmospheric processes and behavioural responses are better described as continua than discrete categories. Finally, we compared vertical wind velocities derived from eagles soaring behaviour with those modelled by the COSMO weather model, showing that most of the thermals exploited by eagles remain unresolved at kilometre-scale model resolution. Our results demonstrate how high-resolution weather models provide new insights into bird movement decisions, while also highlighting the potential of soaring birds as biologically embedded atmospheric sensors that could help closing the resolution gap in atmospheric models.

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Vision Normalizing Flows for the probability-informed detection of banana diseases from in-field images

Prusokiene, A.; Prusokas, A.; Retkute, R.

2026-07-21 plant biology 10.64898/2026.07.19.739426 medRxiv
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Banana diseases impose severe production losses in tropical smallholder farming systems, yet accurate in-field visual diagnosis remains difficult: symptom expression varies across cultivars and growth stages, and several diseases produce morphologically overlapping foliar signs. We developed a probabilistic image-recognition framework for detecting five economically important banana diseases -- Xanthomonas Wilt, Banana Bunchy Top Disease, Fusarium Wilt (Panama disease), Yellow Sigatoka, and Black Sigatoka -- from in-field photographs, without any disease-specific fine-tuning of the vision backbone. The approach extracts frozen 1,152-dimensional embeddings from the DINOv3 vision foundation model and couples them with a conditional normalizing flow, trained on four publicly available datasets spanning diseased banana plants, healthy tissue, non-banana vegetation, and general natural imagery. On an independent test set the model achieved F1 scores exceeding 0.98, average precision values of 0.968-0.999, and AUROC values of 0.997-1.000 across all five diseases evaluated as binary detection problems. Multi-class accuracy was near-perfect, with limited confusion between Yellow Sigatoka and Black Sigatoka -- a biologically plausible ambiguity attributable to overlapping early-infection foliar symptoms. Because the normalizing flow estimates explicit conditional probability densities rather than decision boundaries, two complementary log-likelihood ratios can be derived: a disease ratio comparing each disease class against healthy banana, and a plant ratio comparing banana against non-banana imagery. Together these define an interpretable two-dimensional diagnostic space that simultaneously quantifies evidence for disease presence and image relevance, cleanly separating diseased plants, healthy plants, and out-of-distribution images while flagging uncertain predictions for confirmatory testing. Inference on frozen embeddings is lightweight and compatible with smartphone deployment, providing a scalable, uncertainty-aware diagnostic tool for smallholder farming systems and disease surveillance programmes.

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What do satellite vegetation indices actually measure? Photosynthetic capacity rather than transient physiological function across 328 global FLUXNET sites

Zhang, Y.; Ma, X.; Luo, K.; Liu, X.; Cao, C.

2026-08-21 ecology 10.64898/2026.08.21.746123 medRxiv
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A direct empirical relationship between gross primary productivity (GPP) estimated by the eddy covariance method and satellite vegetation indices (VIs) has been widely observed across diverse ecosystems globally. Building on this observed covariation, VIs are frequently utilized as critical parameters - such as the fraction of absorbed photosynthetically active radiation (fPAR) - within light use efficiency (LUE) and greenness-based models for carbon cycle monitoring. However, actual canopy carbon assimilation is jointly governed by slowly evolving structural parameters and highly dynamic functional traits, such as physiological efficiency. The extent to which the macro-scale VI-GPP covariance is driven by structural scaffolding, and how this structural signal decouples from physiological function under environmental stress, remains to be systematically quantified. Here, we synthesized half-hourly eddy covariance measurements from 328 globally distributed sites and paired them with a rigorously angle-normalized Enhanced Vegetation Index (nadir view and fixed solar zenith angle at 30 degrees, EVI_SZA30). By applying a nonlinear light-response curve model across 54,720 high-frequency temporal windows, we mechanistically disentangled observed actual GPP (GPP_EC) into baseline photosynthetic capacity (P_c) and intrinsic quantum yield (alpha). Our results demonstrate that the macroscopic covariance between EVI_SZA30 and GPP_EC (R^2=0.554) is primarily driven by the index's robust ability to track structural capacity (P_c, R^2=0.538). In contrast, EVI_SZA30 exhibits limited sensitivity to high-frequency variations in functional traits like physiological efficiency (alpha, R^2=0.038). Particularly in water-limited biomes (e.g., open shrublands and woody savannas), intense environmental stress triggers rapid stomatal regulation while the physical canopy structure remains relatively stable. Consequently, the correlation between EVI and P_c becomes notably stronger than its correlation with actual GPP_EC, highlighting a pronounced structural-physiological decoupling. Because discrete overpasses by sun-synchronous polar-orbiting satellites face intrinsic temporal constraints in capturing sub-daily physiological down-regulation (e.g., midday photosynthetic depression), future monitoring paradigms could greatly benefit from the continuous, high-frequency observations provided by next-generation geostationary (GEO) satellites to bridge the gap between structural parameters and transient ecosystem function.

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Three-dimensional Imaging of Colonial Cyanobacteria with Optical Coherence Tomography

Sinzato, Y. Z.; Uittenbogaard, R.; Visser, P. M.; Huisman, J.; Jalaal, M.

2026-08-28 ecology 10.64898/2026.08.27.747059 medRxiv
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The morphology of cyanobacterial colonies plays a key role in harmful cyanobacterial blooms, with implications for their vertical migration, resistance against grazing, and light availability. In this study, we introduce the use of Optical Coherence Tomography (OCT) to investigate the three-dimensional morphology of cyanobacterial colonies. The technique enables non-invasive 3D imaging of colonies up to several millimeters in size, providing access to detailed mesoscale morphological features. Gas vesicles inside cells were shown to strongly improve image quality. We describe the sample preparation and image acquisition protocol, as well as an image processing pipeline that extracts mesoscale morphological features and provides a volumetric visualization of colonies. The method was tested for representative colonies of different cyanobacterial species while a dataset of volumetric images and measured mesoscale features was acquired for natural colonies of Microcystis. We demonstrate the utility of 3D imaging by quantifying the effects of irregular colony morphologies on their flotation velocity and the light availability within colonies. We anticipate OCT to become a key imaging technique to monitor populations of cyanobacterial colonies and investigate colony formation, with potential extensions to other colonial and aggregated organisms in freshwater and marine environments.

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Classifying and Mapping Wetland Vegetation Assemblages in Coastal Louisiana with Landsat Imagery, 1985-2025

Snedden, G. A.; Couvillion, B.; Schoolmaster, D. R.

2026-08-18 ecology 10.64898/2026.08.13.744705 medRxiv
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The tidal wetlands of Louisiana comprise about 25% of those found throughout the conterminous United States yet estimates of wetland loss rates in the region between 1932 and 2016 have exceeded 60 km2 yr-1. To mitigate further degradation and wetland loss in the region, a globally unprecedented $50B, 50-year plan for coastal Louisiana is driving restoration efforts, and demand exists from multiple stakeholders for regularly updated, regional-scale, accurate land cover information. We used machine learning (random forests; RF) and cloud computing to develop a new Landsat-based, marsh vegetation community geospatial dataset. The dataset depicts wetland vegetation community types defined in a previous study at annual (1985-2025) time steps at 30-m resolution. An RF algorithm was used to integrate training samples with feature variables derived from Landsat imagery, and the resulting geospatial data product achieved an overall correct classification rate of 78%. The approach for development of the land cover dataset presented here has potential for application in other coastal wetland habitats throughout the world.

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Climatic and non-climatic drivers of rangeland vegetation change in Nepal

Shrestha, U. B.; Joshi, S.

2026-07-10 ecology 10.64898/2026.07.09.737421 medRxiv
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Nepal's rangelands provide multiple benefits, including support for pastoral livelihoods and alpine biodiversity, regulation of water and soil nutrients, and sequestering carbon. Climate change and anthropogenic pressures are altering these rangelands, leading to vegetation and biodiversity change. However, national-scale assessments of rangeland change are limited in Nepal. This study quantified rangeland changes at multiple spatial scales and assessed the climatic and non-climatic drivers of rangeland change. About 80.7% of Nepal's high-altitude rangeland (> 2,000m) outside protected areas showed no significant change. Among areas exhibiting significant annual maximum NDVI trends, 383,281 ha (18.6%) showed positive and 14,702 ha (0.7%) showed negative trends, corresponding the ratio of increase in vegetation greenness and decline in vegetation greenness to 26:1. Climate predicted positive trends covered 627,184 ha (30.5%), whereas residual trends caused by non-climatic drivers covered 94,656 ha (4.6%). Climate induced negative trends covered 47,609 ha (2.3%) while residual trends were observed in 6,260 ha (0.3%). Negative trend pixels were concentrated mainly within the 3,000 to 5,000 m elevation band, with Karnali Province recording the highest proportional climate predicted decline in vegetation greenness (3.4%). At the municipality scale, rangeland change showed no significant relationship with grazing pressure derived from gridded livestock data, suggesting that grazing pressure alone did not explain the non-climatic vegetation signal. These spatially explicit, nationally consistent results identify where rangeland change is occurring and help distinguish climatic and non-climatic drivers of rangeland vegetation change, providing evidence to support targeted rangeland management under Nepal's federal governance structure.

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Biological Footprint of Artificial Light at Night in Rural and Developing Areas

Boyles, J. G.; Merritt, B. J.; Koen, E.; Minnaar, C.

2026-07-14 ecology 10.64898/2026.07.13.737561 medRxiv
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ContextArtificial light at night (ALAN) has profound impacts on individual organisms and entire communities. Still, humans tend to underestimate the true biological (spatial) footprint of ALAN, in part because of our limited sensitivity to light compared to other organisms. ObjectivesWe sought to demonstrate how far ALAN can reach into dark spaces at levels that can impact organismal behavior and physiology using a fundamental physical law, the inverse square law. MethodsWe created a spatially explicit model of light spread on real landscapes, parameterized using increasingly available landscape-scale vegetation data to account for attenuation through forests and blocking by topographic relief. ResultsLighting types common in rural areas can produce biologically important effects more than 1 kilometer from the source, and effects of large lights might stretch 3 kilometers or more. The footprint of a light is determined by the complex and multidimensional interaction between characteristics of the light itself and the environment. For example, attenuation through a dense forest might decrease the footprint of a light more than 90% compared to the same light on a grassland. In complex environments, even small changes in light placement and characteristics can lead to large changes in the biological footprint of the light. ConclusionsDesigners and land stewards must account for lighting type, brightness, directionality, and reflected light to create ecologically responsible lighting. Vertical vegetation and topography strongly influence the propagation of biologically detrimental light, and environmental context is vital when planning and installing lights to minimize the biological impacts.

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Maps of historical forests in France and their temporal continuity since the first half of the 19th century

Dupouey, J.-L.; Berges, L.; Leroy, N.; Lafite, R.; Archaux, F.; Auge, V.; Bec, R.; Bellifa, M.; Bourguignon, J.; Buridant, J.; Burlin, B.; Caubet, S.; Chaleat, A.; Chauchard, S.; Cordonnier, T.; Decocq, G.; Delcamp, M.; Fleury, J.; Gaudin, S.; Gervaise, A.; Gautier, G.; Guilloux, J.; Hamel, A.; Heintz, W.; Janssen, P.; Labonne, S.; Lair, P.; Lallemant, T.; Landmann, G.; Larrieu, L.; Martin, H.; Michel, C.; Mollier, S.; Panaïotis, C.; Renaux, B.; Rochel, X.; Salvaudon, A.; Thomas, M.; Touzet, T.; Vallauri, D.

2026-07-23 ecology 10.64898/2026.07.22.736859 medRxiv
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AbstractIntegrating environmental history is essential for understanding present-day ecosystem dynamics and guiding modern conservation strategies, particularly under the EU Biodiversity Strategy for 2030. This data paper presents the nationwide digitisation and vectorisation of the French General Ordnance survey map (1818-1866), capturing the countrys forest cover at its historical minimum (a pivotal moment known as the "forest transition"). The original manuscript sheets surveyed at a 1:40,000 scale (976 sheets) were scanned, georeferenced and vectorised. They offer higher thematic accuracy than the older Cassini map and are far more feasible for nationwide vectorisation than the highly detailed Napoleonic cadastre. The area-weighted mean survey date is 1843, and the dataset covers 99.6% of modern mainland France. To correct for paper deformation, historical surveying errors and coordinate system transformations, a rigorous workflow was established. This shifted from a global 6-parameter affine transformation (root mean square error of 60 m) to a local elastic transformation based on thousands of control points, for 21% of the territory, which reduced the positioning error to 34 m. We assessed data quality by comparing the General Ordnance Survey maps with the Napoleonic cadastre--the standard reference for 19th-century land-use data--across more than 600 municipalities. The correlation between the two sources regarding forest cover percentages was exceptionally high (r>0.9). Because forests formed large, compact blocks of significant strategic interest to military engineers, they were mapped with high precision. Localised inaccuracies were primarily found in remote areas, most notably in the mountains. The resulting historical vector layer was intersected with contemporary forest data (BD Foret(R) v2, 2005-2019). Historical polygons smaller than 0.5 ha were filtered out to comply with modern FAO forest definitions. This spatial overlay generated a new dataset detailing four distinct land-use trajectories: . ancient forests (44.8% of present day forest): land classified as forest in both the 19th century and the present day (indicating maximum temporal continuity). . recent forests (55.2% of present day forest): land that was non-forested in the 19th century but has since undergone reforestation. . deforested areas (18.9% of 19th-century forest): land recorded as forest in the 19th century but subsequently converted to other land uses. . stable non-forest areas: land that has remained unforested across both periods. Our results suggest that the forest area of mainland France at its historical minimum should be revised upward to 9.9 million ha. A preliminary analysis further indicates that current spatial variation in forest cover is explained more by land-use dynamics occurring since the forest transition than by the initial extent of forest cover. These two open-access national datasets (the 19th-century forest layer and the land-use transition map) open the door to a better understanding of present-day forests : e.g. their biodiversity, soil quality, tree growth and belowground water quality. Furthermore, they provide decision-support tools for conservation planning. Key messageIn this data paper, we provide a map of 19th-century forests in France based on the digitisation of the military topographic map (1818-1866). By overlaying this historical source with the present-day forest map, we built a second map which allows the identification of ancient forests, recent forests, and deforestation. These maps offer avenues for historical ecology and the design of conservation strategies.

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Bathymetric Resolution-Dependent Biases in Antarctic Benthic Biodiversity Models: Hotspots Hold, Counts Shift

Potter, S.; Jansen, J.; Hill, N.; Lucieer, V.

2026-06-24 ecology 10.64898/2026.06.23.734136 medRxiv
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Antarctic benthic organisms are highly diverse and play a critical role in the Southern Ocean ecosystem. Despite decades of sampling, vast areas of the Antarctic continental shelf remain biologically unsurveyed due to logistical and financial constraints, limiting baseline knowledge essential for effective conservation planning. Species distribution models (SDMs) allow biodiversity to be inferred in the absence of biological data by linking benthic community patterns to environmental predictors. However, the resolution of the environmental predictors, particularly bathymetry, varies significantly between regions, casting doubt about how reliably SDMs can be used to predict into regions where only coarse-resolution data are available. Here, we show that SDMs trained on high-resolution data underestimate Antarctic benthic morphospecies richness by up to 18% when applied to aggregated coarse-resolution environmental data (and up to 50% when using satellite-derived ETOPO bathymetry). Using six systematically degraded versions of high-resolution multibeam bathymetry and annotated seafloor imagery across three Antarctic regions, we evaluate SDM performance both with and without additional environmental variables. High-resolution bathymetry captures terrain complexity most effectively, but we find that the spatial distribution of richness hotspots and the median richness per cell remain consistent, provided models are applied at the same resolution at which they were trained. Our results suggest that while high-resolution bathymetry may enhance local predictions, coarse-resolution data may be more robust for regional-scale predictions, such as those used for Antarctic shelf-wide spatial planning.