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Onoda, Y.

Publications and source records attributed to Onoda, Y..

11 recordsLinked to original sources

MillionTrees: A global benchmark for tree detection across geography, sensor, and annotation geometry

Airborne tree monitoring using remotely sensed data, combined with the growth of computer vision models for object detection and segmentation, can facilitate broad scale assessment of tree health, ecology and ecosystem function. However, datasets for airborne tree detection have been largely limited to a single geography, resolution, or annotation approach, making it difficult to develop general models and benchmark their utility for broad applications. We compile existing and newly published annotation datasets to create a comprehensive dataset for training and evaluating airborne tree detection in RGB imagery. The MillionTrees dataset has over a million individual trees from a broad range of forest types, tree species, and geographic locations. In addition, it has six million weakly supervised annotations from a range of sources including airborne LiDAR and photogrammetry, arborist surveys, and simulated landscapes. An evaluation standard is provided to facilitate rapid model development. We benchmark several existing tree detection algorithms and demonstrate that while current open-source models do not generalize across the diverse datasets in the benchmark, training on MillionTrees improves both within-domain and out-of-domain performance. Held-out validation datasets using ground truth derived from terrestrial LiDAR paired with overhead RGB show that overfitting to test data is common and hyperparameter tuning is an underappreciated challenge towards a global zero shot tree detection method. We discuss the limitations of the currently available data for airborne RGB tree detection, how to create more robust evaluation data and the need for better understanding of the uncertainty and utility of tree detection from airborne remote sensing.

ecology↗

Crown-based growth strategies explain the distribution and co-occurrence of tree functional groups along environmental gradients

Elucidating interspecific variation in growth strategies across environments is critical for understanding tree diversity and distribution. However, a systematic analysis across diverse forests remains scarce due to limited large-tree crown measurements. We analysed 3,814 trees from 107 canopy species in 23 natural forests using forest census data and unmanned aerial vehicle. Relative growth rate (growth rate/biomass) was decomposed into growing space efficiency (growth rate/crown area) and crown area ratio (crown area/biomass). Relative growth rates were similar among functional groups (deciduous broadleaf, evergreen broadleaf, evergreen conifer), but their underlying components differed. Deciduous trees exhibited 34-43% higher crown area ratio but 24-27% lower growing space efficiency than evergreen broadleaf and conifer trees. Across environments, growing space efficiency correlated positively with mean annual temperature, likely from extended growing seasons while crown area ratio correlated negatively, particularly in deciduous species. Snow loading limited crown area ratio in evergreen species, while deciduous achieved higher values through avoiding snow loads. Correlation between crown area ratio and specific leaf area indicated a coordinated strategy between crowns and leaves. Different functional groups achieve comparable growth efficiency either through crown expansion or biomass production, explaining their distinct distribution as well as co-occurrence across broad environments.

ecology↗

Molecular evolutionary evidence for coexistence within oak hybrid zones.

Resource allocation trade-offs in seedlings have been widely proposed to facilitate the coexistence of tree species; however, whether selection can maintain the underlying genetic variation under gene flow remains insufficiently investigated. Using a natural hybrid zone between two East Asian oaks, we evaluated whether loci associated with allocation trade-offs showed signatures of selection despite hybridisation. Acorns collected across the zone were cultivated in a common garden, where we quantified 25 seedling growth and functional traits, and analysed whole-genome variation. We identified trade-offs between leaf function and plant architecture. Trait-associated genomic regions demonstrated strong inter-chromosomal linkage disequilibrium in the hybrids, consistent with genetic coupling, and exhibited elevated interspecific differentiation and more pronounced genetic clines. These results indicate that multilocus selection counteracts gene flow through the development of genetic coupling, thereby maintaining resource allocation trade-offs that may contribute to tree coexistence.

evolutionary biology↗

Thermophilization, climatic debt, and consequent declines in primary productivity

Species have optimal environmental conditions, and ongoing climate warming is reshaping community composition. In particular, many ecosystems exhibit thermophilization, a shift toward species adapted to warmer conditions. However, this process is often slower in forests, leading to a mismatch between community composition and ambient temperature, referred to as climatic debt. Despite increasing attention, its effects on forest productivity remain unclear. Quantifying tree community responses to warming is therefore essential for predicting future forest dynamics and informing biodiversity conservation. In this study, we analyzed natural forests across Japan using data from the 3rd and 4th National Forest Inventory periods (2009-2018). We first assessed compositional consistency between survey periods using the Bray-Curtis index and excluded plots with high dissimilarity ([≥] 0.8). Species-specific thermal optima were estimated using species distribution models and used to calculate the Community Temperature Index (CTI). Thermophilization was quantified as the temporal change in CTI, while climatic debt was defined as the difference between CTI and mean annual temperature. We then examined the relationship between climatic debt and changes in aboveground biomass, used as a proxy for productivity, using linear mixed-effects models. We found a mean thermophilization rate of 0.005 {degrees}C yr-{superscript 1}. Despite this shift, climatic debt increased at an average rate of -0.022 {degrees}C yr-{superscript 1}, indicating a growing mismatch between climate warming and community thermal composition. Although thermophilization showed no statistically significant association with stand structure, it tended to vary with the proportion of small-diameter trees, suggesting the influence of multiple interacting drivers. Importantly, increasing climatic debt was significantly associated with declines in forest primary productivity, even after accounting for stand structure and regional variation. These results demonstrate that delayed thermal adjustment of tree communities can constrain forest productivity under ongoing climate warming, highlighting the importance of evaluating community-level thermal responses for sustaining forest ecosystem functioning.

ecology↗

LeafContourEFD: a reproducible workflow for elliptic Fourier analysis with orientation normalization and lateral asymmetry

PremiseElliptic Fourier analysis is widely used to quantify leaf shape variation, but inconsistent normalization and orientation alignment can introduce biologically irrelevant variation. In addition, a reproducible workflow from raw images to normalized elliptic Fourier descriptors (EFDs) is still lacking. Methods and ResultsWe developed LeafContourEFD, a GUI application for reproducible leaf morphometrics. It integrates image segmentation, contour extraction, EFD calculation, and an extended normalization framework, termed oriented true EFD normalization, based on a user-defined biological reference axis. Analyses of Quercus serrata, Q. crispula, and Triadica sebifera showed that existing normalization methods can introduce orientation-related variance when the first-harmonic major axis does not match the leaf base-to-tip axis. In contrast, oriented true normalization removed these artifacts, yielding clearer shape transitions along principal components allowing shape variation among leaves to be captured while preserving biologically meaningful lateral asymmetry. ConclusionsLeafContourEFD improves interpretability and reproducibility in outline-based morphometrics and provides transparent outputs and metadata for data sharing and cross-study comparisons.

plant biology↗

Impact of Low-Dose Narrowband UV Radiation on Skin Tissue and Mast Cells in a Canine Model

Narrowband ultraviolet radiation (NB-UVR) therapy is widely utilized in dermatology worldwide. While the immunosuppressive effects of ultraviolet radiation are well-documented, its non-inflammatory effects remain poorly understood. This study evaluated the effects of sub-minimal erythema dose (MED) narrowband ultraviolet radiation using a canine model. The effects of narrowband-ultraviolet B (310 nm) and A2 wavelengths (320 and 330 nm) were compared. Initially, we demonstrated the therapeutic potential of NB-UVR in dogs with spontaneous atopic dermatitis (n = 6, p < 0.05). Following 300 mJ/cm{superscript 2} sub-MED ultraviolet radiation exposure, intradermal skin testing, skin mast cell counts, and RNA sequencing analysis were conducted. Additionally, cell viability (WST assay) and apoptosis (DAPI staining) were assessed in vitro using a canine mast cell line. Ultraviolet radiation exposure significantly reduced intradermal skin test scores across all wavelengths and decreased skin mast cell counts at 310 nm (n = 3, p < 0.05). In vitro, cell viability was significantly reduced at 310 and 320 nm (p < 0.05), and 310 nm irradiation specifically increased apoptotic cell numbers (p < 0.05). RNA sequencing identified 71 differentially expressed genes at 320 nm, with enrichment analysis highlighting muscle cell components and functions, potentially associated with arrector pili muscle activity. These findings suggest that 310 nm irradiation induces apoptosis, while 320 nm elicits non-inflammatory modulatory effects, highlighting distinct wavelength-specific therapeutic mechanisms of narrowband ultraviolet radiation.

immunology↗

Disentangling leaf structural and material properties in relation to their anatomical and chemical compositional traits in oaks (Quercus L.)

The existence of sclerophyllous plants has been considered an adaptive strategy against different environmental stresses. As it literally means "hard-leaved", it is essential to quantify the leaf mechanical properties to understand sclerophylly. However, the relative importance of each leaf trait on mechanical properties is not yet well established. The genus Quercus is an excellent system to shed light on this since it minimizes phylogenetic variation while having a wide variation in sclerophylly. Thus, leaf anatomical traits and cell wall composition were measured, analyzing their relationship with LMA and leaf mechanical properties in a set of 25 oak species. Outer wall contributed strongly to leaf mechanical strength. Moreover, cellulose plays a critical role in increasing leaf strength and toughness. The PCA plot based on leaf trait values clearly separated Quercus species into two groups corresponding to evergreen and deciduous species. Sclerophyllous Quercus species are tougher and stronger due to their thicker epidermis outer wall and/or higher cellulose concentration. Furthermore, section Ilex species share common traits regardless of they occupy quite different climates. In addition, evergreen species living in Mediterranean-type climates share common leaf traits irrespective of their different phylogenetic origin.

plant biology↗

Quaternary climate change explains global patterns of tree beta-diversity

Both historical and contemporary environmental conditions determine present biodiversity patterns, but their relative importance is not well understood. One way to disentangle their relative effects is to assess how different dimensions of beta-diversity relate to past climatic changes, i.e., taxonomic, phylogenetic and functional compositional dissimilarity, and their components generated by replacement of species, lineages and traits (turnover) and richness changes (nestedness). Here, we quantify global patterns of each of these aspects of beta-diversity among neighboring sites for angiosperm trees using the most extensive global database of tree species-distributions (43,635 species). We found that temperature change since the Last Glacial Maximum (LGM) was the major influence on both turnover and nestedness components of beta-diversity, with a negative correlation to turnover and a positive correlation to nestedness. Moreover, phylogenetic and functional nestedness was higher than expected from taxonomic beta-diversity in regions that experienced large temperature changes since the LGM. This pattern reflects relatively greater losses of phylogenetic and functional diversity in species-poor assemblages, possibly caused by phylogenetically and functionally selective species extinction and recolonization during glacial-interglacial oscillations. Our results send a strong warning that rapid anthropogenic climate change is likely to result in a long-lasting phylogenetic and functional compositional simplification, potentially impairing forest ecosystem functioning.

ecology↗

Paleoclimate and current climate collectively shape the phylogenetic and functional diversity of trees worldwide

Trees are of vital importance for ecosystem functioning and services at local to global scales, yet we still lack a detailed overview of the global patterns of tree diversity and the underlying drivers, particularly the imprint of paleoclimate. Here, we present the high-resolution (110 km) worldwide mapping of tree species richness, functional and phylogenetic diversities based on [~]7 million quality-assessed occurrences for 46,752 tree species (80.5% of the estimated total number of tree species), and subsequent assessments of the influence of paleo-climate legacies on these patterns. All three tree diversity dimensions exhibited the expected latitudinal decline. Contemporary climate emerged as the strongest driver of all diversity patterns, with Pleistocene and deeper-time (>107 years) paleoclimate as important co-determinants, and, notably, with past cold and drought stress being linked to reduced current diversity. These findings demonstrate that tree diversity is affected by paleoclimate millions of years back in time and highlight the potential for tree diversity losses from future climate change.

ecology↗

Half of the world's tree biodiversity is unprotected and is increasingly threatened by human activities

Although trees are key to ecosystem functioning, many forests and tree species across the globe face strong threats. Preserving areas of high biodiversity is a core priority for conservation; however, different dimensions of biodiversity and varied conservation targets make it difficult to respond effectively to this challenge. Here, we (i) identify priority areas for global tree conservation using comprehensive coverage of tree diversity based on taxonomy, phylogeny, and functional traits; and (ii) compare these findings to existing protected areas and global biodiversity conservation frameworks. We find that ca. 51% of the top-priority areas for tree biodiversity are located in current protected areas. The remaining half top-priority areas are subject to moderate to high human pressures, indicating conservation actions are needed to mitigate these human impacts. Our findings emphasize the effectiveness of using tree conservation priority areas for future global conservation planning.

ecology↗

Does the leaf economic spectrum hold within plant functional types? A Bayesian multivariate trait meta-analysis

We investigated whether global leaf economic relationships are also present within plant functional types (PFTs), and the extent to which this hierarchical structure can be used to constrain trait estimates. We developed a hierarchical multivariate Bayesian model that assumes separate means and covariance structures within and across PFTs and fit this model to seven leaf traits from the TRY database related to leaf morphology, biochemistry, and photosynthetic metabolism. Trait correlations were generally consistent in direction within and across PFTs, and consistent with predictions of the leaf economic spectrum. However, correlation strength varied substantially across PFTs indicating that leaf economic relationships within PFTs are often confounded by the unique physiology of certain plant types or environmental conditions in certain biomes. Leveraging covariance in multivariate models reduced uncertainties in mean trait estimates, particularly for undersampled trait-PFT combinations. However, additional constraint from the across-PFT hierarchy was limited.\n\nData accessibilityThe R code and ancillary data for running these analyses is publicly available online via the Open Science Framework at https://osf.io/w8y73/. The TRY data request used for this analysis has been archived at http://try-db.org, and can be retrieved by providing the TRY data request ID (#1584). Alternatively, the exact preformatted data used in this analysis are available on request to Alexey Shiklomanov (alexey.shiklomanov@pnnl.gov).

ecology↗