Tree Shape Research Articles

Genome-wide identification, expression analysis, and abiotic stress response of the CBL and CIPK gene families in Artocarpus nanchuanensis

Artocarpus nanchuanensis, the northernmost species in the jackfruit genus, has great economic and horticultural value due to its nutritious fruit and beautiful tree shape. Calcineurin B-like proteins (CBLs) act as plant-specific Ca2+ sensors and participate in regulating plant responses to various abiotic stresses by interacting with CBL-interacting protein kinases (CIPKs). However, the characteristics and functions of the CBL and CIPK genes in A. nanchuanensis are still unclear. Here, we identified 14 CBL and 33 CIPK genes from the A. nanchuanensis genome, and based on phylogenetic analysis, they were divided into 4 and 7 clades, respectively. Gene structure and motif analysis indicated that the AnCBL and AnCIPK genes were relatively conserved. Colinear analysis showed that segmental duplication contributed to the expansion of the AnCBL and AnCIPK gene families. Expression analysis showed that AnCBL and AnCIPK genes were widely expressed in various tissues of A. nanchuanensis and exhibited tissue-specific expression. In addition, three genes (AnCBL6, AnCIPK7/8) may play important roles in response to salt, cold, and drought stresses. In summary, this study lays an important foundation for the improvement of stress resistance in A. nanchuanensis and provides new insight for the functional research on CBL and CIPK gene families.

Recovering the Shape of an Equilateral Quantum Tree by Two Spectra

Recovering the Shape of an Equilateral Quantum Tree by Two Spectra

Distributions of 4-subtree patterns for uniform random unrooted phylogenetic trees

Tree shape statistics based on peripheral structures have been utilized to study evolutionary mechanisms and inference methods. Partially motivated by a recent study by Pouryahya and Sankoff on modeling the accumulation of subgenomes in the evolution of polyploids, we present the distribution of subtree patterns with four or fewer leaves for the unrooted Proportional to Distinguishable Arrangements (PDA) model. We derive a recursive formula for computing the joint distributions, as well as a Strong Law of Large Numbers and a Central Limit Theorem for the joint distributions. This enables us to confirm several conjectures proposed by Pouryahya and Sankoff, as well as provide some theoretical insights into their observations. Based on their empirical datasets, we demonstrate that the statistical test based on the joint distribution could be more sensitive than those based on one individual subtree pattern to detect the existence of evolutionary forces such as whole genome duplication.

Mixing with native broadleaf trees modified soil microbial communities of Cunninghamia lanceolata monocultures in South China.

Mixing with different broadleaf trees into the monocultures of Cunninghamia lanceolata is widely adopted as an efficient transformation of the pure C. lanceolata forest. However, it is unclear how native broad-leaved trees influence the belowground ecological environment of the pure C. lanceolata culture plantation in nutrient-poor soil of South China. Herein, we aimed to investigate how a long-time mixing with native broadleaf trees shape soil microbial community of the pure C. lanceolata forest across different soil depth (0-20 cm and 20-40 cm) and to clarify relationships between the modified soil microbial community and those affected soil chemical properties. Using high-throughput sequencing technology, microbial compositions from the mixed C. lanceolata-broadleaf forest and the pure C. lanceolata forest were analyzed. Network analysis was utilized to investigate correlations among microorganisms, and network robustness was assessed by calculating network natural connectivity. Results demonstrated that the content of soil microbial biomass carbon and nitrogen, total phosphorus and pH in mixed forest stand were significantly higher than those in pure forest stand, except for available phosphorus in topsoil (0-20 cm). Simultaneously, the mixed C. lanceolata-broadleaf forest has a more homogeneous bacterial and fungal communities across different soil depth compared with the pure C. lanceolata forest, wherein the mixed forest recruited more diverse bacterial community in subsoil (20-40 cm) and reduced the diversity of fungal community in topsoil. Meanwhile, the mixed forest showed higher bacterial community stability while the pure forest showed higher fungal community stability. Moreover, bacterial communities showed significant correlations with various soil chemical indicators, whereas fungal communities exhibited correlations with only TP and pH. Therefore, the mixed C. lanceolata-broadleaf forest rely on their recruiting bacterial community to enhance and maintain the higher nutrient status of soil while the pure C. lanceolata forest rely on some specific fungi to satisfy their phosphorus requirement for survive strategy.

The challenge of noise pollution in high-density urban areas: Relationship between 2D/3D urban morphology and noise perception

Urban morphology is closely intertwined with people's perception of noise, understanding their relationship is crucial for resident health. Previous studies have primarily focused on actual environmental noise, neglecting variations in how people perceive noise in different urban environments. More study is needed to elucidate how noise perception varies across different types of noise and urban areas. This study, based on noise complaint data, quantifies the perceived noise environment in New York City. It establishes a framework for urban morphology measurement from both 2D and 3D perspectives and employs regression models to explore the correlation between urban morphology and the perception of distinct noise types, as well as regional disparities in noise perception. Findings indicate that:(1) Three-dimensional urban morphology indices, such as tree shape, Google view images (GVI) building index, provide a better explanation of noise perception than 2D indices. (2) The impact of urban morphology on the noise perception exhibits significant regional variations. In densely populated Manhattan, diverse building morphology can better enhance the quality of the perceived acoustic environment. However, this conclusion does not hold true in other regions. (3) Urban morphology also has distinct effects on different types of noise complaints. For instance, residential complaints are most strongly correlated with building height compared with other complaint types. Last, by considering the collaborative effects of various variables, specific recommendations are proposed for local areas with similar impact profiles. This study can serve as a reference for the construction of noise-friendly high-density cities and the promotion of sustainable urban health.

Estimating aboveground volume of diverse urban tree species: Developing allometric equations for higher taxonomic levels

Allometric equations are essential for quantifying carbon storage in trees; however, owing to the high species diversity in urban green spaces, the development of allometric equations for all urban tree species is not feasible. In this study, we estimated the aboveground volume of urban trees and determined the fitness of several allometric equations. We compared the equations for different taxonomic levels, i.e., division, family, and species. A field survey was conducted across three types of urban green spaces (street trees, parks, and residential gardens) in three cities (Seoul, Goyang, and Wonju) in South Korea. We estimated the aboveground volumes of 1080 trees from their diameter measurements using a laser dendrometer, carried out at successive points from the ground to the top of the trees. Various tree size metrics, such as the diameter at breast height (DBH), height, and/or crown diameter, were applied as independent variable(s) in the equations. For gymnosperm trees, the allometric equations for higher taxonomic levels (RMSE: 0.011 m3) yielded goodness-of-fits similar to those at the species level (RMSE: 0.009 m3). For angiosperm trees, the family-level allometric equations satisfactorily covered the inter-species heterogeneity of tree shape, whereas the division-level allometric equations did not. The scaling exponent coefficients of allometric equations for each family (b = 1.65−2.69) linearly increased with an increasing mean height-to-DBH ratio. Although the allometric equations based on crown diameter were more unstable than those based on the DBH, integrating the height variable into the equations could ensure the feasibility of the allometric equations based on crown diameter. Our study facilitates the development of nationally specific emission factors for settlement areas and suggests the applicability of generalized or crown-based allometric equations for urban trees.

Climate anomalies and neighbourhood crowding interact in shaping tree growth in old‐growth and selectively logged tropical forests

Abstract Climate extremes and biotic interactions at the neighbourhood scale affect tropical forest dynamics with long‐term consequences for biodiversity, global carbon cycling and climate change mitigation. However, forest disturbance may change crowding intensity, and thus the relative contribution of climate extremes and neighbourhood interactions on tree growth, thereby influencing tropical forest resistance and resilience to climate change. Here, we aim to evaluate the separate and interactive effects of climate and neighbours on tree growth in old‐growth and disturbed tropical forests. We used 30 years of growth measurements for over 300 tropical tree species from 15 forest plots in French Guiana to investigate the separate and interactive effects of climate anomalies (in solar radiation, maximum temperature, vapour pressure deficit and climatic water deficit) and neighbourhood crowding on individual tree growth. Contrasting old‐growth and selectively logged forests, we also examined how disturbance history affects tree growth sensitivity to climate and neighbours. Finally, for the most abundant 100 species, we evaluated the role of 12 functional traits pertaining to water relations, light and carbon use in mediating tree growth sensitivity to climate anomalies, neighbourhood crowding and their interactions. Climate anomalies tied to heat and drought stress and neighbourhood crowding independently reduced tree growth, and showed positive interactive effects which attenuated their separate effects on tree growth. Their separate and interactive effects were stronger in disturbed than undisturbed forests. Fast‐growing species (i.e. higher intrinsic growth rates) were more abundant in disturbed forests and more sensitive to climate anomalies and neighbourhood crowding. Traits related to water relations, light and carbon use captured species sensitivities to different climate anomalies and neighbourhood crowding levels but were weak predictors of their interactions. Synthesis: Our results demonstrate that climate anomalies and neighbourhood crowding can interact to shape tropical tree growth, suggesting that considering the biotic context may improve predictions of tropical forest dynamics facing altered climate regimes. Furthermore, species traits can capture tree growth sensitivity to the separate effects of climate and neighbours, suggesting that better representing leading functional dimensions in tropical tree strategies offers a promising way towards a better understanding of the underlying ecological mechanisms that govern tropical forest dynamics.

Complete chloroplast genome of the Malus baccata var. gracilis provides insights into the evolution and phylogeny of Malus species.

Malus baccata (L.) var. gracilis (Rehd.) has high ornamental value and breeding significance, andcomparative chloroplast genome analysis was applied to facilitate genetic breeding for desired traits andresistance and provide insight into the phylogeny of this genus. Using data from whole-genomesequencing, a tetrameric chloroplast genome with a length of 159,992 bp and a total GC content of36.56% was constructed. The M. baccata var. gracilis chloroplast genome consists of a large single-copy sequence (88,100 bp), a short single-copy region (19,186 bp), and two inverted repeat regions, IRa(26,353 bp) and IRb (26,353 bp). This chloroplast genome contains 112 annotated genes, including 79protein-coding genes (nine multicopy), 29 tRNA genes (eight multicopy), and four rRNA genes (allmulticopy). Calculating the relative synonymous codon usage revealed a total of 32 high-frequencycodons, and the codons exhibited a biased usage pattern towards A/U as the ending nucleotide.Interspecific sequence comparison and boundary analysis revealed significant sequence variation in thevast single-copy region, as well as generally similar expansion and contraction of the SSC and IRregions for 10 analyzed Malus species. M. baccata var. gracilis and Malus hupehensis were groupedtogether into one branch based on phylogenetic analysis of chloroplast genome sequences. Thechloroplast genome of Malus species provides an important foundation for species identification, geneticdiversity analysis, and Malus chloroplast genetic engineering. Additionally, the results can facilitate theuse of pendant traits to improve apple tree shape.

Recovering the shape of an equilateral quantum tree with the Dirichlet conditions at the pendant vertices

We consider two spectral problems on an equilateral rooted tree with the standard (continuity and Kirchhoff's type) conditions at the interior vertices (except of the root if it is interior) and Dirichlet conditions at the pendant vertices (except of the root if it is pendant). For the first (Neumann) problem we impose the standard conditions (if the root is an interior vertex) or Neumann condition (if the root is a pendant vertex) at the root, while for the second (Dirichlet) problem we impose the Dirichlet condition at the root. We show that for caterpillar trees the spectra of the Neumann problem and of the Dirichlet problem uniquely determine the shape of the tree. Also, we present an example of co-spectral snowflake graphs.

Design and Development of a Biomimetic Solar Tree for Sustainable Cogeneration: An Energy and Exergy Assessment

Solar energy is becoming an increasingly popular and important source of renewable energy. Solar trees have emerged as a novel and innovative approach to harvesting solar energy. Solar trees are artificial structures that mimic the shape and function of trees, with branches or leaves that contain photovoltaic cells to convert sunlight into electricity. The solar tree generates both electrical and thermal energy from solar radiation. The present study tested the thermal (module temperature, heat loss coefficient), electrical (power output), and operating parameters of a solar tree at Universiti Malaysia Pahang, Pekan, Malaysia, on a typical sunny day. First-law analysis and second-law analysis were carried out to determine exergy losses during the photovoltaic conversion process of solar trees. The data obtained from the experiment is utilized to determine the energy and exergy efficiencies of the solar tree. The energy efficiency ranges from 16.8% to 8.3% throughout the day, displaying some variability. However, as for the exergy efficiency of the photovoltaic solar tree under consideration, it is observed to be lower, ranging from 16.1% to 6.6% for electricity generation. It is observed that the exergy losses increased with increasing module temperature and a drop in exergy efficiency.

Ecosystem engineering: Rufous-bellied woodpecker Dendrocopos hyperythrus (Vigors, 1831) modifying tree shapes of Himalayan broadleaved forests

The study, conducted from 2005 to 2018, encompassed twelve sites in Nepal, including both protected and non-protected areas. The primary focus of the observations was on tree species, their shapes, structures, and their interactions with the rufous-bellied woodpecker. The rufous-bellied woodpecker in Nepal's Himalayas predominantly utilized specific tree species, notably oak (Quercus semecarpifolia and Q. glauca), birch (Betula utilis), Himalayan holly (Ilex dyperina), and maple (Acer species). These trees displayed a remarkable diversity in girth sizes, ranging from 0.5 meters to almost 2.5 meters, with tree heights varying from 5 to 30 meters. Among these, Quercus semecarpifolia was the preferred choice. Notably, rufous-bellied woodpeckers exhibited a distinctive behavior of drilling numerous small holes around tree trunks, often forming ring-like structures. These "sap-wells" were meticulously created by drilling dense rows of small holes encircling the tree trunks and served as the primary food source for the woodpeckers. They attracted a wide array of insects and offered a valuable source of protein. This continuous interaction between the woodpeckers and the trees resulted in unique modifications to the trunks of old-growth forest trees. Over time, the trees developed swollen trunks, and some trunks even displayed bending and deformations due to the woodpecker’s sap-well chiselling activities. Furthermore, the study observed several other bird species benefiting from these sap-wells created by the rufous-bellied woodpeckers. This observation underscores the broader ecological significance of these structures, benefiting a diverse range of species within the ecosystem. In essence, this study sheds light on the rufous-bellied woodpecker's role as an "ecosystem engineer" and an indicator of forest health in the temperate Himalayas, emphasizing its critical ecological importance.

Carbon Stock Environment of Mapping Vegetation in UMMAT Education Forest West Rinjani

Indonesia is a country that has a role as carbon sink which is very influential on climate change in the Southeast Asian region, on the island of Lombok there are clusters that stretch forest hills from West Rinjani to East Rinjani. This Forest Protected or Educational Forest which has been controlled has an area of ​​more than 90 hectares with based on Minister Environment and forest Republic Indonesia SK 405/MENLHK/Setjen/PLA.0/6/2016 in couple years ago are diversity of flora and several types of plants and trees. Land fires or forest areas in Mount Rinjani National Park on the eve of the 78th Indonesian independence along the Aik Berik hiking trail were caused by humans or due to negligence. The community thinks about the condition, the destruction as well as the benefits of Protected Forest/Edu Forest, residents have perceptions about carbon storage and the benefits of Protected forest as a carbon store as well as people’s perceptions about climate change that is happening. The Data was obtained systematically have marked 9 plots divers growth stage 20x20 m for tree shape, 10x10m for poles, 5x5m for saplings, 2x2m for seedlings, 1x1m for wet grass. The form of balance and harmony that is still protected by Muslims the bond between human and Allah, and their environment. The Universe of God’s gave gift to manage and maintain it, so that it remains sustainable and good. In the Al-Qur’an it is explicitly stated that all forms of damage that exist on this earth are the result of human activities in interacting with their environment. That the universe was created by Allah as a form of His love for humans. Allah created and this nature for the benefit of humans. Nature is made a verse or a sign of the existence and omnipotence of Allah. Realizing that the universe is God’s creation, then taking care of the earth and preserving it is part of the consequences of this monotheistic belief. The primary data used is hill mapping, settlements and watershed observations of perceptions about carbon storage to vegetation, while the purpose of the activity or research is to carry out an analysis of identifying community perceptions of carbon storage and forest vegetation in Batu Bolong Village.

How Trees Shape Urban Spaces: Multiplicity and Differentiation of the Urban Forest Viewed from a Visual-Spatial Perspective

Abstract Background The field of urban forestry encompasses many dimensions, of which that of visual-spatial perception, addressing the spatial relationship between city and trees, has received little attention. Analyzing the urban forest from a visual-spatial perspective is needed to understand relationships between different components as well as site-specific qualities. Methods Tree configurations describe the relationship between form and space, determined by the relative disposition of the trees which result from an interaction between design and the development over time. Based on field observations, with the city of Delft in the Netherlands as a case study, 35 generic tree configuration types have been defined. With this “vocabulary,” specific tree configurations and their relations are researched, describing the urban forest from an eye-level perspective as an essential level on which the spatiality of the urban forest can be understood. Results Unraveling the urban forest components by comparing two emblematic ensembles of tree configurations allows an understanding of their heterogeneity as well as their coherence and dynamics. Conclusions The relationship of the tree vocabulary with the specific location exposes their role as an ordering structure and a carrier of the identity of Delft, and their differentiation and site-specific qualities, revealing a composition of wooded areas each with their own characteristics, shows both urban and forested areas as equivalent components of an urban forest mosaic. This differentiation can be used as a tool for strengthening relations between the different components as well as diversity and heterogeneity in urban forests.

On recovering the shape of a quantum tree from the spectrum of the Dirichlet boundary problem

Spectral problems are considered generated by the Sturm-Liouville equation on equilateral trees with the Dirichlet boundary conditions at the pendant vertices and continuity and Kirchhoff's conditions at the interior vertices. It is proved that there are no co-spectral (i.e., having the same spectrum of such problem) among equilateral trees of $\leq 8$ vertices. All co-spectral trees of $9$ vertices are presented.

Research on the Growth Characteristics of the Electrical Tree at Polyethylene/Silicone Rubber Composite Interface Under Power Frequency Voltage

During operation, the composite interface of the cable joint will experience a tangential electric field. When the composite interface has insulation defects, it is easy to experience interface discharge. Electrical tree is a phenomenon of electrical degradation and it’s a precursor of polymer breakdown. It is observed in the laboratory that under the power frequency voltage, the electrical tree will initiate at the composite interface, and the tree growth will finally lead to the interface breakdown. This paper investigates the development of an electrical tree at the composite interface of polyethylene/silicone rubber under power frequency voltage through microscopic observation. The results show that the air gap of the interface is the weak position of insulation, and the electrical tree will be initiated from the triple junction of the air gap and the impacted area of the two materials. The increase in voltage amplitude will speed up the initiation. High amplitudes also promote the electrical tree. The electrical tree shape will be changed from a branch structure at low voltage to a single branch structure at high voltage. The study on the electrical tree at the interface provides a visual display of the degradation process of the material before the breakdown at the composite interface.

Potassium deficiency diagnosis method of apple leaves based on MLR-LDA-SVM

IntroductionAt present, machine learning and image processing technology are widely used in plant disease diagnosis. In order to address the challenges of subjectivity, cost, and timeliness associated with traditional methods of diagnosing potassium deficiency in apple tree leaves. MethodsThe study proposes a model that utilizes image processing technology and machine learning techniques to enhance the accuracy of detection during each growth period. Leaf images were collected at different growth stages and processed through denoising and segmentation. Color and shape features of the leaves were extracted and a multiple regression analysis model was used to screen for key features. Linear discriminant analysis was then employed to optimize the data and obtain the optimal shape and color feature factors of apple tree leaves during each growth period. Various machine-learning methods, including SVM, DT, and KNN, were used for the diagnosis of potassium deficiency. ResultsThe MLR-LDA-SVM model was found to be the optimal model based on comprehensive evaluation indicators. Field experiments were conducted to verify the accuracy of the diagnostic model, achieving high diagnostic accuracy during different growth periods. DiscussionThe model can accurately diagnose whether potassium deficiency exists in apple tree leaves during each growth period. This provides theoretical guidance for intelligent and precise water and fertilizer management in orchards.

Classification of tree forms in aerial LiDAR point clouds using CNN for 3D tree modelling

ABSTRACT Three-dimensional models of trees that correspond to the real-world forms of the trees on the ground are used in urban planning, solar power estimation, and other disciplines. Previous studies have focused on generating 3D tree models from high-density point cloud data such as Terrestrial Laser Scanning (TLS) data, which is expensive and limited to small spatial extents. However, there has been limited exploration of inexpensive solutions to model trees over large spatial extents. The goal of this study is to use widely available discrete return Airborne Laser Scanning (ALS) data along with field-captured tree photographs and Google Street View (GSV) images to develop 3D equivalents of trees over larger spatial extents. To this end, we designed a process to assign representative 3D models for individual trees in discrete return ALS point clouds. This study demonstrates the use of a Convolutional Neural Network (CNN) model and 3D models generated with Structure from Motion (SfM) for the realistic modelling of deciduous non-overlapping trees from discrete return ALS data. We classified and labelled the crown shapes of deciduous trees in a study area into four classes based on GSV images of trees. We delineated and segmented non-overlapping deciduous trees from ALS data and reduced them to 2D images using voxel point counts. Next, we trained a CNN architecture to match the 2D images to the corresponding classes observed from GSV images. For each class, we created a representative 3D tree model using field-captured circumnavigational photos of trees and SfM. To demonstrate 3D visualization using the 3D tree models, we created a 3D visualization of the trees surrounding a parking lot. The trained CNN model from this study can be used to classify non-overlapping deciduous trees from discrete return ALS data and subsequently visualize near-realistic 3D tree models of trees.

Configuration of the Tree Shape in a Bi-axis Apple Orchard using ‘Fuji’/M.9 Grafted Plants – Tree Growth and Productivity during Early Years According to the Planting Distance

Configuration of the Tree Shape in a Bi-axis Apple Orchard using ‘Fuji’/M.9 Grafted Plants – Tree Growth and Productivity during Early Years According to the Planting Distance

Stem shape and structural complexity change in beech forests along a management gradient

For about half a century, attempts have been made to manage forests as close to nature as possible. This management targeted the creation of structures that resemble those found in primary forests. Laser scanning provides the opportunity to quantify such structural “naturalness” and allows to evaluate which management practices come closest to forest structures found in primary forests. In this paper, European beech (Fagus sylvatica L.) forests with different management intensity were compared to primary forests in terms of their structural complexity and the shape of tree stems. For this purpose, data from mobile and terrestrial laser scans (MLS and TLS) of managed forests, of forests whose management has been abandoned, and of primary forests was used. We found that management intensity influenced the distribution of plant material in the forest stand and thus the structural complexity on stand level. Also, management affected the shape of the stems. Here, it is important to consider the management history of the forest stands and the forest development phase in which management was abandoned. The stem shapes of trees in primary forests were significantly different (larger stem diameters and longer branch free boles) from those of the other investigated forests. Nevertheless, our results showed that it is possible to achieve old-growth-like structures such as high standing volumes, a multi layered canopy, high number of large trees and high variation in tree size and age through targeted silvicultural treatments in order to accelerate the close-to-nature development of forests. The present study illustrates the possibility of using mobile and terrestrial laser scanning to objectively compare and evaluate the structural effects of different silvicultural concepts.

Chemical screening of inhibitors specific for MdDOX-Co that cause an apple columnar tree-shape.

MdDOX-Co, the ectopic expression of which is considered to cause the apple columnar tree shape, belongs to the 2-oxoglutarate-dependent dioxygenase (2ODD) family. It adds a hydroxyl group to position 12 of gibberellins (GAs). However, the 2ODD enzymes related to GA biosynthesis and catabolism are phylogenetically distinct from MdDOX-Co. Thus, it is possible that substrates other than GAs exist in MdDOX-Co. To identify the previously unidentified substrate(s) of MdDOX-Co, we searched for MdDOX-Co-specific inhibitors. Chemical screening using gas chromatography-mass spectrometry was performed to investigate the effects of 2400 compounds that inhibited the catalytic reaction of MdDOX-Co, but not the catabolic reaction of GA 2-oxidase, an enzyme involved in GA catabolism. By applying two positive compounds in Arabidopsis, a chemical 3-((2-chloro-6-fluorobenzyl)thio)-5,7-dimethyl-5H-pyrazolo[3,4-e][1,4,2]dithiazine-1,1-dioxide designated as TPDD that did not inhibit GA biosynthesis was selected. The structure-activity relationships among the TPDD analogs were also obtained.