Biology subjects

Barbier, N.

Publications and source records attributed to Barbier, N..

4 recordsLinked to original sources

bioRxiv2024

The global spectrum of tree crown architecture

Trees can differ enormously in their crown architectural traits, such as the scaling relationships that link their height and crown size to their stem diameter. Yet despite the importance of crown architecture in shaping the structure and function of woody ecosystems, we lack a complete picture of what drives this incredible diversity in crown shapes. Using data from >500,000 globally distributed trees, we explored how climate, disturbance, competition, functional traits, and evolutionary history constrain the height, crown size and shape of the worlds tree species. We found that variation in height scaling relationships was primarily controlled by water availability and light competition. Conversely, crown width was predominantly shaped by exposure to wind and fire, while also covarying with other functional traits related to mechanical stability and photosynthesis. Additionally, several plant lineages had crown architectures that defy their environments, such as the exceedingly slender dipterocarps of Southeast Asia, or the extremely wide crowns of legumes in African savannas. Our study charts the global spectrum of tree crown architectural types. It provides a roadmap for integrating crown architecture with vegetation models and remote sensing observations, so that we may better understand the processes that shape the 3D structure of woody ecosystems.

ecology↗

bioRxiv2024

Improved tests for the origin of allometric scaling across tree architectures

The scaling of organismal metabolic rates with body size is one of the most prominent empirical patterns in biology. For over a century, the nature and causes of metabolic scaling have been the subject of much focus and debate. West, Brown, and Enquist (WBE) proposed a general model for the origin of metabolic scaling from branching vascular networks. However, recent empirical tests of WBE vascular scaling predictions in plants and animals have reported deviations caused by variability in network geometry. After clarifying the core assumptions of the WBE model, we revisit the methods and conclusions of recent tests conducted in trees, finding support for key WBE predictions in woody plant architecture. To do this, we apply an approach that better captures: i) network branching self-similarity and ii) leaf area as a proxy of plant metabolic capacity. The WBE model also predicts curvature in metabolic scaling in smaller organisms, and we introduce a novel method that accounts for curvature in plant branching geometry. Together, these advances allow more direct measurements of metabolic scaling than previous work, and we apply them to a dataset of diverse laser-scanned tree architectures. Analyses reveal the predicted interspecific [3/4] metabolic scaling across tree crowns, with intraspecific variation within individual tree crowns. Scaling variability is consistent with WBE predictions for curvature from asymptotic growth and underlying variation in branching geometry. We conclude that linking fine-scale branching variation to metabolic scaling allometries remains a challenge, while our results support the foundational hypotheses of the WBE model. Author summaryTrees survive in a variety of habitats and lifestyles across Earth. They are also characterized by a stunning array of sizes and shapes that make trees objects of vast cultural, economic, and ecological importance. At the same time, the need to link vascular plant function with traits and environment is more pressing than ever. Size (body mass) is fundamentally linked to plant functioning within ecosystems through allometric relationships. Allometric relationships emerge from the geometry of branch networks in trees, which are increasingly well-characterized with remote-sensing data. We use a dataset of laser-scanned tree crowns to test allometric predictions that link size to key traits, particularly metabolic capacity, understood as total leaf area. Our results indicate that i) scanning technology can provide accurate assessments of branch allometry with proper data preparation, and ii) studying branch allometries provides an organizing framework for interpreting natural variation in tree architecture.

plant biology↗

bioRxiv2024

Major change in swine influenza virus diversity in France owing to emergence and widespread dissemination of a newly introduced H1N2 1C genotype in 2020

Swine influenza A viruses (swIAV) are a major cause of respiratory disease in pigs worldwide, presenting significant economic and health risks. These viruses can reassort, creating new strains with varying pathogenicity and cross-species transmissibility. This study aimed to monitor the genetic and antigenic evolution of swIAV in France from 2019 to 2022. Molecular subtyping revealed a marked increase in H1avN2 cases from 2020 onwards, altering the previously stable subtypes distribution. Whole-genome sequencing and phylogenetic analyses of H1av (1C) strains identified ten circulating genotypes, including five new genotypes, marked by a significant predominance of the H1avN2#E genotype. It was characterized by an HA-1C.2.4, an N2-Gent/84, and internal protein-encoding genes belonging to a newly defined genogroup within the Eurasian avian-like (EA) lineage, the EA-DK subclade. H1avN2#E emerged in Brittany, the countrys most pig-dense region, and rapidly became the most frequently detected swIAV genotype across France. This drastic change in the swIAV lineages proportions at a national scale was unprecedented, making H1avN2#E a unique case for understanding swIAV evolution and spreading patterns. Phylogenetic analyses suggested an introduction of the H1avN2#E genotype from a restricted source, likely originating from Denmark. It spread rapidly with low genetic diversity at the start of the epizootic in 2020, showing increasing diversification in 2021 and 2022, and exhibiting reassortments with other enzootic genotypes. Amino acid sequence alignments of H1avN2#E antigenic sites revealed major mutations and deletions compared to vaccine 1C strain (HA-1C.2.2) and previously predominant H1avN1 strains (HA-1C.2.1). Antigenic cartography confirmed significant antigenic distances between H1avN2#E and other 1C strains, suggesting the new genotype escaped from the swine population preexisting immunity. Epidemiologically, the H1avN2#E virus exhibited epizootic hallmarks with more severe clinical outcomes compared to H1avN1 viruses. These factors likely contributed to the spread of H1avN2#E within the pig population. The rapid rise of H1avN2#E highlighted the dynamic nature of swIAV genetic and antigenic diversity, underscoring the importance of adapted surveillance programs to support risk assessment in the event of new outbreaks. This also demonstrate the need to strengthen biosecurity measures when receiving pigs in a herd and to limit trading of swIAV-excreting live swine between European countries.

evolutionary biology↗

bioRxiv2024

Harnessing temporal and spectral dimensionality to map and identify species of individual trees in diverse tropical forests

Species-level canopy maps underpin tropical forest biodiversity monitoring, conservation planning, and carbon accounting, yet high species richness and structural complexity make remote classification challenging. Here we evaluate how far a two-step mapping approach can be taken, and where it breaks down, in hyperdiverse moist forest at the Paracou Field Station, French Guiana. First, we delineate individual tree crowns from ten repeat uncrewed aerial vehicle (UAV) RGB surveys with Mask R-CNN, fusing predictions across dates by temporal consensus: mean segmentation F1 rose from 0.68 (single date) to 0.78 (ten dates), covering approximately 86% of test-region canopy area. Second, we classify each crown from a single airborne hyperspectral acquisition (416-2500 nm, 1 m) using machine learning classifiers trained and tested on 3,186 field-verified crowns spanning 169 species. Linear Discriminant Analysis performed best (weighted F1 = 0.75), outperforming more flexible models, but unevenly: across repeated cross-validation (20 x 5-fold), on average 50 species (95% CI: 41-63) attained F1 [≥] 0.7 in a given fold and only 15 did so reliably, with many rare species unclassifiable (macro-average F1 = 0.48). Combining both steps, we estimate approximately 70% of the landscapes canopy area was correctly mapped to species. Band-importance and ablation analyses identified the far-red edge (748-775 nm) as the most informative spectral region. These results advance on studies limited to 20 or fewer species and set out spectral-resolution and training-data requirements for airborne and forthcoming spaceborne imaging spectrometers, while showing that accuracy remains strongly conditioned by training-data availability and the single-site, single-acquisition design.

ecology↗