Biology subjects

Malhi, Y.

Publications and source records attributed to Malhi, Y..

17 recordsLinked to original sources

bioRxiv2025

Diagnosing linearity along the carbon cascade in terrestrial biosphere models

Elevated carbon dioxide (eCO2) fertilises photosynthesis, driving an increase in terrestrial gross primary production (GPP). However, it is unclear how effectively increased GPP propagates along the "carbon (C) cascade" to increase net primary production (NPP) and vegetation C stocks (Cveg) in different plant compartments. Vegetation models simulate divergent C cycle projections and have been criticised for being overly photosynthesis-driven (source-driven), neglecting processes that lead to non-linear behaviour in response to the GPP increase, which may attenuate (or amplify) changes in NPP and vegetation C stocks. Here, we introduce an analytical framework to diagnose linearity (L) of the land C cycle as the ratio of relative changes in linked fluxes and pools and apply it to outputs from 16 models of the TRENDY v11 ensemble. We found widely varying patterns in L across models and for the different links. Six models showed a clear dominance of larger relative changes in NPP than in GPP in global simulations (LNPP:GPP >1 for >60% of gridcells), indicating increased carbon use efficiency under eCO2. Only three models had LNPP:GPP < 1 for >60% of gridcells. Four models showed a clear dominance of larger relative changes in steady-state Cveg than in NPP, while five models showed an opposite pattern - in both cases with a large spread of LCveg*:NPP across gridcells within models. Three models showed a larger relative increase in root C than in Cveg, while two models showed a clear dominance of the opposite pattern. Widely differing distributions of L across models and links reveal a strong influence of alternative process representations (nonlinear behaviour) in individual models. However, for all links, L deviations from 1 were roughly balanced across the model ensemble, leading to an overall linear behaviour of terrestrial C cycle representations.

ecology↗

bioRxiv2025

An AI-based and coding-free protocol for forests Leaf Area Index (LAI) calculation

O_LISeasonal and spatial variations in leaf area index (LAI) are challenging to detect in tropical forests due to dynamic lighting conditions and the subtle differences in the variation. Many existing LAI software tools offer one-click processing of all images through auto-threshold segmentation (e.g., HemispheR, HemiPy and Hemisfer), but they produce results with large discrepancies. Some software (e.g. CAN-EYE) requires manual tuning of each image, making large-scale analysis impractical. C_LIO_LIWe analysed 19,000 images from four tropical forest subtypes and found that using coding-free AI software to process hemispherical images can significantly improve the consistency of leaf-sky segmentation, thereby enhancing LAI outcomes. C_LIO_LIThe results show that replacing the auto-threshold with AI substantially reduced inter-software disagreement and delineated correct seasonal and spatial patterns. CAN-EYE was able to identify seasonal patterns but produced less accurate results than the CAN-EYE-AI integrated approach due to subjective user bias. C_LIO_LIThe high consistency achieved through AI integration enables reliable cross-site and cross-operator comparisons. As users can customise the AI model according to local images and combine the AI model with other LAI software, our integrated, affordable, and coding-free method offers wide applicability and high consistency of LAI measurements, facilitating the advancement of tropical forest monitoring and research. C_LI Data/Code for peer review statementOne of the key features of this method is coding-free. The method is explained in Protocolv20251118.docx. We have uploaded R codes for drawing figures in a zip pack. These codes and the protocol will be deposited in the Zenodo (or figshare) database under accession link [TBC]. Since Zenodo allows authors to archive updated versions after publication, we may update the protocol by uploading a revised version to Zenodo. Please check the Zenodo archive for any new versions. In the protocol, we note that users can use Image_conversion_20220407.m and lets_change_values.R instead of the Renormalise function of ilastik to modify values in the classification output images. These codes are not essential for users following our protocol, but could be useful for integrating ilastik with other LAI software not covered in this paper. Additionally, the protocol mentions that Gather_LAI_fapar_from_caneye.R can be used to consolidate output Excel files, eliminating the need to manually open each file. Field measurements of LAI and GCC are available on request.

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

Higher functional resilience of temperate forests at intermediate latitudes of a large latitudinal gradient in South America

Accurately mapping and assessing plant functional composition across space and time is pivotal for understanding environmental change impacts on the biodiversity and functioning of forests. Here, we test the capabilities of a combination of in-situ and remote sensing approaches to deliver accurate estimates of the functional composition of temperate forest ecosystems considering leaf and stem morphological, nutrient, hydraulic, and photosynthetic traits. We identify hydrological stress, soil, and topography as key drivers of plant functional traits. Further, hydrological stress and soil are key determinants of functional dispersion and redundancy in temperate forests distributed across a large latitudinal (30{degrees}S to 53{degrees}S) gradient in Chile. Functional dispersion peaks across Mediterranean forests, woodlands, and scrub, occupying between 30{degrees}S to 35{degrees}S. Conversely, functional redundancy peaks between 42{degrees}S and 53{degrees}S, corresponding to Magellanic subpolar forests. Although functional dispersion and redundancy peak at different latitudes corresponding to distinct forest types; they are both high at latitudes between 35{degrees}S and 42{degrees}S, coinciding with Valdivian temperate rainforests. Our results highlight areas in temperate forests in South America where both tree functional dispersion and redundancy are high, and hence could potentially be more resilient to environmental changes.

ecology↗

bioRxiv2024

Tree Surface Area Allometry

Utilizing terrestrial laser scanning (TLS) and three-dimensional modeling, this study quantitatively assessed the woody surface areas of 2161 trees across ecosystems encompassing both tropical and temperate forests. TLS enables precise measurement of tree structures at unprecedented scales. This research builds on theoretical scaling relationships with empirical data, significantly refining our understanding of tree woody surface area. Key findings indicate that direct measurements diverge from theoretical predictions, particularly in the finer branch structures, suggesting modifications to existing allometric models might be necessary. This integration of direct measurements with TLS not only challenges established theories but also enhances our capability to accurately model tree surface area, which is key for understanding forest carbon dynamics and metabolic scaling in ecological systems.

ecology↗

bioRxiv2024

Why models underestimate tropical forest productivity: a case study in West Africa

Tropical forests dominate terrestrial photosynthesis, yet there are major contradictions in our understanding due to a lack of field studies, especially outside the tropical Americas. A recent field study indicated that West African forests have among the highest forests gross primary productivity (GPP) yet observed, contradicting models that rank them lower than Amazonian forests. Here, we explore possible reasons for this data-model mismatch. We found the in situ GPP measurements higher than multiple global GPP products at the studied sites in Ghana. The underestimation of GPP by models largely disappears when a standard photosynthesis model is informed by local field-measured values of (a) fractional absorbed photosynthetic radiation (fAPAR), and (b) photosynthetic traits. Satellites systematically underestimate fAPAR in the tropics due to cloud contamination issues. The study highlights the potential widespread underestimation of tropical forests GPP and carbon cycling and hints at the ways forward for model and input data improvement. Related manuscriptThe recent field study mentioned above is a manuscript currently accepted by Nature Communications (manuscript id NCOMMS-23-37419), which is available as a preprint https://www.researchsquare.com/article/rs-3136892/v1 Codes and data availabilityAll data and codes underlying the study are currently shared via Github (link here) which will be made available through Zenodo upon acceptance.

ecology↗

bioRxiv2023

Contrasting carbon cycle along tropical forest aridity gradients in W Africa and Amazonia

2Tropical forests cover large areas of equatorial Africa and play a significant role in the global carbon cycle. However, there has been a lack of in-situ measurements to understand the forests gross and net primary productivity (GPP and NPP) and their allocation. Here we present the first detailed field assessment of the carbon budget of multiple forest sites in Africa, by monitoring 14 one-hectare plots along an aridity gradient in Ghana. When compared with an equivalent aridity gradient in Amazonia using the same measurement protocol, the studied West African forests generally had higher GPP and NPP and lower carbon use efficiency (CUE). The West African aridity gradient consistently shows the highest NPP, CUE, GPP, and autotrophic respiration at a medium-aridity site, Bobiri. Notably, NPP and GPP of the site are the highest yet reported anywhere in the tropics using similar methods. Widely used data products (MODIS and FLUXCOM) substantially underestimate productivity when compared to in situ measurements, in Amazonia and especially in Africa. Our analysis suggests that the high productivity of the African forests is linked to their large GPP allocation to canopy and semi-deciduous characteristics, which may be a result of a seasonal climate coupled with high soil fertility.

ecology↗

bioRxiv2023

Major axes of variation in tree demography across global forests

The future trajectory of global forests is closely intertwined with tree demography, and a major fundamental goal in ecology is to understand the key mechanisms governing spatial-temporal patterns in tree population dynamics. While historical research has made substantial progress in identifying the mechanisms individually, their relative importance among forests remains unclear mainly due to practical limitations. One approach is to group mechanisms according to their shared effects on the variability of tree vital rates and to quantify patterns therein. We developed a conceptual and statistical framework (variance partitioning of Bayesian multilevel models) that attributes the variability in tree growth, mortality, and recruitment to variation in species, space, and time, and their interactions, categories we refer to as organising principles (OPs). We applied the framework to data from 21 forest plots covering more than 2.9 million trees of approximately 6,500 species. We found that differences among species, the species OP, proved a major source of variability in tree vital rates, explaining 28-33% of demographic variance alone, and in interaction with space 14-17%, totalling 40-43%. The average variability among species declined with species richness across forests, indicating that diverse forests featured smaller interspecific differences in vital rates supporting the theory that the range of vital rates is similar across global forests. Decomposing the variance in vital rates into the proposed OPs showed that taxonomy is crucial to predicting and understanding tree demography on large forest plots. A focus on how variance is organized in forests can facilitate the construction of more targeted models with clearer expectations of which covariates might drive a vital rate. This study therefore highlights the most promising avenues for future research, both in terms of understanding the relative contributions of groups of mechanisms to forest demography and diversity, and for improving projections of forest ecosystems.

ecology↗

bioRxiv2023

Photosynthetic and water transport strategies of plants along a tropical forest aridity gradient: a test of optimality theory

(1) The research conducted, including the rationaleThe direct effect of aridity on photosynthetic and water-transport strategies is not easy to discern in global analyses because of large-scale correlations between precipitation and temperature. We analyze tree traits collected along an aridity gradient in Ghana, West Africa that shows little temperature variation, in an attempt to disentangle thermal and hydraulic influences on plant traits. (2) MethodsPredictions derived from optimality theory on the variation of key plant traits along the aridity gradient are tested with field measurements. (3) resultsMost photosynthetic traits show trends consistent with optimality-theory predictions, including higher photosynthetic capacity in the drier sites, and an association of higher photosynthetic capacity with greater respiration rates and greater water transport. Hydraulic traits show less consistency with theory or global-scale pattern, especially predictions based on xylem efficiency-safety tradeoff. Nonetheless, the link between photosynthesis and water transport still holds: species (predominantly deciduous species found in drier sites) with both higher sapwood-to-leaf area ratio (AS/AL) and potential hydraulic conductivity (Kp), implying higher transpiration, tend to have both higher photosynthetic capacity and lower leaf-internal CO2. (4) ConclusionsThese results indicate that aridity is an independent driver of spatial patterns of photosynthetic traits, while plants show a diversity of water-transport strategies along the aridity gradient. Plain language summaryAlong an aridity gradient in Ghana, West-Africa, we used optimality theory to explain that aridity is an important driver of photosynthetic traits, independent of temperature. Toward drier sites, plants have higher photosynthetic capacities per leaf area but have fewer leaves. We also explain how plants arrange water transportation to support quicker photosynthesis at drier sites. However, plants at the drier sites seem to have diverse combinations of hydraulic traits to satisfy the need for photosynthesis. We reported surprising data-theory inconsistency for some hydraulic traits along the aridity gradient where further research is needed.

ecology↗

bioRxiv2022

Logging alters tropical forest structure, while conversion reduces biodiversity and functioning

The impacts of degradation and deforestation on tropical forests are poorly understood, particularly at landscape scales. We present an extensive ecosystem analysis of the impacts of logging and conversion of tropical forest to oil palm from a large-scale study in Borneo, synthesizing responses from 82 variables categorized into four ecological levels spanning a broad suite of ecosystem properties: 1) structure and environment, 2) species traits, 3) biodiversity, and 4) ecosystem functions. Responses were highly heterogeneous and often complex and non-linear. Variables that were directly impacted by the physical process of timber extraction, such as soil structure, were sensitive to even moderate amounts of logging, whereas measures of biodiversity and ecosystem functioning were generally resilient to logging but more affected by conversion to oil palm plantation. One-Sentence SummaryLogging tropical forest mostly impacts structure while biodiversity and functions are more vulnerable to habitat conversion.

ecology↗

bioRxiv2022

TLS2trees: a scalable tree segmentation pipeline for TLS data

Above Ground Biomass (AGB) is an important metric used to quantify the mass of carbon stored in terrestrial ecosystems. For forests, this is routinely estimated at the plot scale (typically [≥]1 ha) using inventory measurements and allometry. In recent years, Terrestrial Laser Scanning (TLS) has appeared as a disruptive technology that can generate a more accurate assessment of tree and plot scale AGB; however, operationalising TLS methods has had to overcome a number of challenges. One such challenge is the segmentation of individual trees from plot level point clouds that are required to estimate woody volume, this is often done manually (e.g. with interactive point cloud editing software) and can be very time consuming. Here we present TLS2trees, an automated processing pipeline and set of Python command line tools that aims to redress this processing bottleneck. TLS2trees consists of existing and new methods and is specifically designed to be horizontally scalable. The processing pipeline is demonstrated across 10 plots of 7 forest types; from open savanna to dense tropical rainforest, where a total of 10,557 trees are segmented. TLS2trees segmented trees are compared to 1,281 manually segmented trees. Results indicate that TLS2trees performs well, particularly for larger trees (i.e. the cohort of largest trees that comprise 50% of total plot volume), where plot-wise tree volume bias is {+/-}0.4 m3 and %RMSE is ~60%. To facilitate improvements to the presented methods as well as modification for other laser scanning modes (e.g. mobile and UAV laser scanning), TLS2trees is a free and open-source software (FOSS).

ecology↗

bioRxiv2021

Tropical tree growth sensitivity to climate is driven by species intrinsic growth rate and leaf traits

A better understanding of how climate affects growth in tree species is essential for improved predictions of forest dynamics under climate change. Long-term climate averages (mean climate) and short-term deviations from these averages (anomalies) both influence tree growth, but the rarity of long-term data integrating climatic gradients with tree censuses has so far limited our understanding of their respective role, especially in tropical systems. Here, we combined 49 years of growth data for 509 tree species across 23 tropical rainforest plots along a climatic gradient to examine how tree growth responds to both climate means and anomalies, and how species functional traits mediate these tree growth responses to climate. We showed that short-term, anomalous increases in atmospheric evaporative demand and solar radiation consistently reduced tree growth. Drier forests and fast-growing species were more sensitive to water stress anomalies. In addition, species traits related to water use and photosynthesis partly explained differences in growth sensitivity to both long-term and short-term climate variations. Our study demonstrates that both climate means and anomalies shape tree growth in tropical forests, and that species traits can be leveraged to understand these demographic responses to climate change, offering a promising way forward to forecast tropical forest dynamics under different climate trajectories.

ecology↗

bioRxiv2021

Does insect herbivory suppress ecosystem productivity? Evidence from a temperate woodland

Our current understanding of the relationship between insect herbivory and ecosystem productivity is limited. Previous studies have typically quantified only leaf area loss, or have been conducted during outbreak years. These set-ups often ignore the physiological changes taking place in the remaining plant tissue after insect attack, or may not represent typical, non-outbreak herbivore densities. Here, we estimate the amount of carbon lost to insect herbivory in a temperate deciduous woodland both through leaf area loss and, notably, through changes in leaf gas exchange in non-consumed leaves under non-outbreak densities of insects. We calculate how net primary productivity changes with decreasing and increasing levels of herbivory, and estimate what proportion of the carbon involved in the leaf area loss is transferred further in the food web. We estimate that the net primary productivity of an oak stand under ambient levels of herbivory is 54 - 69% lower than that of a completely intact stand. The effect of herbivory quantified only as leaf area loss (0.1 Mg C ha-1 yr-1) is considerably smaller than when the effects of herbivory on leaf physiology are included (8.5 Mg C ha-1 yr-1). We propose that the effect of herbivory on primary productivity is non-linear and mainly determined by changes in leaf gas exchange. We call for replicated studies in other systems to validate the relationship between insect herbivory and ecosystem productivity described here.

ecology↗

bioRxiv2020

The evolutionary assembly of forest communities along environmental gradients: recent diversification or sorting of pre-adapted clades?

O_LIBiogeographic events occurring in the deep past can contribute to the structure of modern ecological communities. However, little is known about how the emergence of environmental gradients shape the evolution of species that underlie community assembly. In this study, we address how the creation of novel environments lead to community assembly via two non-mutually exclusive processes: 1) the immigration and ecological sorting of pre-adapted clades (ISPC), and 2) recent adaptive diversification (RAD). We study these processes in the context of the elevational gradient created by the uplift of the Central Andes. C_LIO_LIWe develop a novel approach and method based on the decomposition of species turnover into within- and among-clade components, where clades correspond to lineages that originated before mountain uplift. Effects of ISPC and RAD can be inferred from how components of turnover change with elevation. We test our approach using data from over 500 Andean forest plots. C_LIO_LIWe found that species turnover between communities at different elevations is dominated by the replacement of clades that originated before the uplift of the Central Andes. C_LIO_LIOur results suggest that immigration and sorting of clades pre-adapted to montane habitats is the primary mechanism shaping communities across elevations. C_LI

ecology↗

bioRxiv2020

Automated and accurate segmentation of leaf venation networks via deep learning

O_LILeaf vein network geometry can predict levels of resource transport, defence, and mechanical support that operate at different spatial scales. However, it is challenging to quantify network architecture across scales, due to the difficulties both in segmenting networks from images, and in extracting multi-scale statistics from subsequent network graph representations. C_LIO_LIHere we develop deep learning algorithms using convolutional neural networks (CNNs) to automatically segment leaf vein networks. Thirty-eight CNNs were trained on subsets of manually-defined ground-truth regions from >700 leaves representing 50 southeast Asian plant families. Ensembles of 6 independently trained CNNs were used to segment networks from larger leaf regions (~100 mm2). Segmented networks were analysed using hierarchical loop decomposition to extract a range of statistics describing scale transitions in vein and areole geometry. C_LIO_LIThe CNN approach gave a precision-recall harmonic mean of 94.5% {+/-} 6%, outperforming other current network extraction methods, and accurately described the widths, angles, and connectivity of veins. Multi-scale statistics then enabled identification of previously-undescribed variation in network architecture across species. C_LIO_LIWe provide a LeafVeinCNN software package to enable multi-scale quantification of leaf vein networks, facilitating comparison across species and exploration of the functional significance of different leaf vein architectures. C_LI

plant biology↗

bioRxiv2020

Only 40% of the world's forests are in good health

Many global environmental agendas, including halting biodiversity loss, reversing land degradation, and limiting climate change, depend upon retaining forests with high ecological integrity, yet the scale and degree of forest modification remains poorly quantified and mapped. By integrating data on observed and inferred human pressures and an index of lost connectivity, we generate the first globally-consistent, continuous index of forest condition as determined by degree of anthropogenic modification. Globally, only 17.4 million km2 of forest (40.5%) have high landscape level integrity (mostly found in Canada, Russia, the Amazon, Central Africa and New Guinea) and only 27% of this area is found in nationally-designated protected areas. Of the forest in protected areas, only 56% has high landscape level integrity. Ambitious policies that prioritize the retention of forest integrity, especially in the most intact areas, are now urgently needed alongside current efforts aimed at halting deforestation and restoring the integrity of forests globally.

ecology↗

bioRxiv2019

THE INFLUENCE OF ECOSYSTEM AND PHYLOGENY ON TROPICAL TREE CROWN SIZE AND SHAPE

1The sizes and shapes of tree crowns are of fundamental importance in ecology, yet understanding the forces that determine them remains elusive. A cardinal question facing ecologists is the degree to which general and non-specific versus ecological and context-dependent processes are responsible for shaping tree crowns. Here, we test this question for the first time across diverse tropical ecosystems. Using trees from 20 plots varying in elevation, precipitation, and ecosystem type (savanna-forest transitions) across the paleo- and neo-tropics, we test the relationship between crown dimensions and tree size. By analyzing these scaling relationships across environmental gradients, biogeographic regions, and phylogenetic distance, we extend Metabolic Scaling Theory (MST) predictions to include how local selective pressures shape variation in crown dimensions. Across all sites, we find strong agreement between mean trends and MST predictions for the scaling of crown size and shape, but large variation around the mean. While MST explained approximately half of the observed variation in tree crown dimensions, we find that local, ecosystem, and phylogenetic predictors account for the half of the residual variation. Crown scaling does not change significantly across regions, but does change across ecosystem types, where savanna tree crowns grow more quickly with tree size than forest tree crowns. Crowns of legumes were wider and larger than those of other taxa. Thus, while MST can accurately describe the central tendency of tree crown size, local ecological conditions and evolutionary history appear to modify the scaling of crown shape. Importantly, our extension of MST incorporating these differences accounts for the mechanisms driving variation in the scaling of crown dimensions across the tropics. These results are critical when scaling the function of individual trees to larger spatial scales or incorporating the size and shape of tree crowns in global biogeochemical models.

ecology↗