Search Results (68)

To recast Theodosius Dobzhansky’s famous 1973 quote: ‘nothing in coral taxonomy makes sense except in light of reticulate evolution’. Coral species evolve through the continual intermixing of ancestral lineages forming a network of changing genetic interconnections rather than stable hierarchical trees. Most species are not discrete units but rather are components of continua with variable genetic, morphological, and geographic boundaries. Hybridisation and introgression are key processes maintaining reticulated networks, making polyphyletic species (those with mixed evolutionary origins) potentially the norm. This creates grey zones of speciation where taxonomic divisions are uncertain and gene flow is ongoing. With this understanding, we critically review: (1) Sources of information for taxonomic decisions, including biology, population dynamics and the need for comprehensive field and foundational molecular studies capturing environment-correlated and geographic variations; (2) Nomenclature (a human construct) and taxonomy (which endeavours to reflect nature’s organisation): (3) Synonymy, including serial errors stemming from historical publications; (4) Type specimens, their use and misuse as a basis for taxonomic decisions; (5) Genus and species level agreements and disagreements between morphological and molecular taxonomies; (6) Use of the terms ‘cryptic species’, ‘cryptic variant’ and ‘cryptic lineage’; (7) Taxonomic decisions based on inferences beyond the scope of individual studies, creating nomenclatural instability and concern, not least among those working to address the impacts of climate change. This review also provides context for an extensive array of Factsheets and linked documentation about each of the species included in CoralsOfTheWorld.org (2026 in prep.). Full article

Chengdu, China, is endowed with abundant ancient and famous trees as well as historical habitats, which are crucial for sustaining urban biodiversity and cultural continuity. This study focuses on the historical habitats along the Second Ring Road and develops a comprehensive evaluation system across five dimensions: ancient and famous trees, species diversity, historical habitat quality, historical habitat health, and historical-cultural value. Twelve representative historical habitats were analyzed using fishnet analysis, image segmentation, and plant diversity surveys to characterize biodiversity patterns and develop strategies for optimizing urban biodiversity conservation and sustainable habitat management. Results indicate: (1) significant variation among historical habitat types, with Huanhuaxi Park achieving the highest overall quality; (2) except in park habitats, comprehensive quality shows no significant correlation with the density of ancient and famous trees, while habitat size exerts a strong influence; (3) the evaluation index system still requires refinement. This research provides practical guidance for the conservation of ancient trees and the sustainable management of historical habitats. At the theoretical level, it underscores the relevance of an “ecology–society–culture” framework, revealing how historical habitats simultaneously sustain ecological functions, support social practices, and embody cultural expression. Overall, the study offers a new perspective for integrating urban biodiversity conservation with cultural heritage protection. Full article

The Collatz conjecture is a famous unsolved problem in mathematics, known for its deceptively simple rules that generate complex, unpredictable behaviour. It can be efficiently modelled using a Petri net that represents its inverse graph, where each place corresponds to an integer and each transition encodes an inverse rule. The net, constructed up to a bound n, reveals the tree-like structure of predecessors and highlights properties such as recurrence, reachability, and liveness. Token flows simulate possible trajectories towards 1. This formal approach enables the investigation of the problem through discrete event systems theory and opens perspectives for parametric or inductive extensions beyond the bounded domain. The model proposed provides a structured framework for visualising and analysing the inverse dynamics of the conjecture. Some key numerical results highlight the challenges of working within a finite domain: for $n_{max}=1000$, the constructed Petri net comprises 1000 places and 667 transitions, including 417 source nodes (no predecessors), 333 sink nodes (no successors), and 218 isolated orphans, i.e., nodes only reachable via $\mathrm{Div}2$ transitions with no incoming $3n+1$ edge. Full article

Tieguanyin tea, celebrated as one of China’s top ten famous teas, is highly regarded for its unique flavor and taste. However, recent intensification of global warming has escalated the occurrence of abiotic stresses, posing significant threats to the growth, development, yield, and quality of Tieguanyin tea plants. DOF (DNA-binding one zinc finger protein), a plant-specific transcription factor, plays a critical role in plant development and stress response. In this study, we identified and analyzed 58 CsDOF genes across the whole genome, which were found to be randomly and unevenly distributed across 15 chromosomes. A phylogenetic tree was constructed using DOF genes from Arabidopsis thaliana and Tieguanyin, categorizing these genes into 10 subgroups. Collinearity analysis revealed homologous gene pairs between CsDOF and OsDOF(19 pairs), StDOF (101 pairs), and ZmDOF (24 pairs). Cis-acting element analysis indicated that CsDOF genes contain elements related to both stress and hormone responses. Heat map analysis demonstrated that subfamily C2 predominantly regulates the growth and development of roots, stems, and leaves in Tieguanyin. Tertiary structure analysis of CsDOF proteins revealed diverse structures, underscoring the functional variability within the CsDOF gene family. Furthermore, qRT-PCR analysis was employed to assess the expression profiles of 13 CsDOF genes under high-temperature and drought conditions. Notably, CsDOF51 and CsDOF12 exhibited significant expression changes under drought and high-temperature stress, respectively, while CsDOF44 showed significant changes under both conditions. This study provides foundational knowledge of the CsDOF gene family and offers novel insights for enhancing the drought and heat tolerance of Tieguanyin tea. Full article

Constructing a scientific health risk assessment system for ancient trees is crucial for preserving cultural heritage and tree resources. As Fuzhou’s city tree, ancient banyan trees (Ficus microcarpa) with expansive canopies and aerial roots have shaped local ecology and history over millennia. However, urbanization-induced habitat loss and structural vulnerabilities (e.g., root damage and branch injuries) increasingly threaten their health. Current generic tree evaluation standards inadequately address banyan trees’ unique aerial root physiology. This study developed a tailored assessment model using 140 ancient banyan trees from Fuzhou’s urban core and Minhou County. The researchers analyzed 12 tree health indicators (crown, trunk, visible roots, etc.) and two environmental factors through structural equation modeling (SEM) and cluster analysis. Key findings: (1) The SEM demonstrated strong data fit (CMIN/DF = 1.575, RMSEA = 0.064, TLI = 0.927, and CFI = 0.945), validating model reliability. (2) Mechanical damage to the visible root system (weight = 0.135) most significantly impacted health, while canopy closure (0.036) and crown saturation (0.034) showed minimal effects. (3) The site environment strongly correlated with trunk and visible root system health but not crown conditions. (4) In total, 60.71% of the sampled trees were healthy/sub-healthy, while 39.29% exhibited poor health. This methodology provides a replicable framework for ancient tree conservation, emphasizing species-specific evaluation criteria and environmental management strategies. The weighted indicator system enables precise health diagnostics and prioritized protection measures for vulnerable heritage trees. Full article

This study examines the changes that have occurred in the specific and varietal composition of fruit trees in one of the world’s most famous agricultural areas, the Conca d’Oro, a plain surrounding Palermo (Sicily, Italy). Changes in specific and varietal composition over the centuries are the result of endogenous changes to the orchards (e.g., the spread of cultivation techniques such as irrigation or the introduction of new species and varieties), social and economic changes (e.g., the development of citrus farming in response to the demand from citrus markets). The disappearance of traditional germplasm is a complex phenomenon due to the changes occurring since the middle of the last century in the agricultural system. The more recent changes occur, unfortunately, mainly due to the expansion of the city, which has erased many orchards and vegetable gardens, but also due to the loss of the emotional, economic, and social value of orchards. The protection of this germplasm becomes indispensable in a period of climate change that, among other things, reduces the effectiveness of agrochemicals. Some germplasm protection and product enhancement initiatives are currently in place in this area and can be applied in other fruit-growing areas as well. Full article

The size of leaves and fruits is a crucial agronomic and economic trait for fruit trees. The ‘Bartlett’ pear is a famous cultivar with succulent and delicious fruit and is cultivated globally. ‘Xiang shuomi’ is a bud sport of the ‘Bartlett’ pear, discovered in our breeding work, and exhibits enlarged leaves and fruits. However, the specific regulatory mechanism of this superior agronomic trait is still elusive. In this study, comprehensive transcriptome and metabolome analyses were performed to explore the differences in gene expression and metabolite accumulation between these two pear cultivars. The transcriptome analysis showed a total of 1279 differentially expressed genes (DEGs), with the flavonoid biosynthetic process being the most significant enriched biological process. Metabolome data indicated the detection of 412 differentially abundant metabolites (DAMs), with the metabolites of flavonoid biosynthesis being enriched significantly. The integrative transcriptomic and metabolomics analysis further confirmed the pivotal role of the flavonoid biosynthetic process in distinguishing the two cultivars. Importantly, the genes that encoded enzymes related to flavonoid biosynthesis, including CHS, CHI, HCT, LAR and CYP75B1, increased their expressions in the ‘Xiang shuomi’ pear. Correspondingly, the metabolites galangin, chlorogenic acid, luteolin and catechin were found to accumulate in the ‘Xiang shuomi’ pear. Overall, this research identified key pathways and genes influencing the fruit and leaf size of pears, providing fundamental information for the high-yield breeding of fruit trees. Full article

Tieguanyin tea, a renowned oolong tea, is one of the ten most famous teas in China. The Squamosa Promoter Binding Protein (SBP)-box transcription factor family, widely present in plants, plays a crucial role in plant development, growth, and stress responses. In this study, we identify and analyze 22 CsSBP genes at the genome-wide level. These genes were distributed unevenly across 11 chromosomes. Using Arabidopsis thaliana and Solanum lycopersicum L. as model organisms, we constructed a phylogenetic tree to classify these genes into six distinct subfamilies. Collinearity analysis revealed 20 homologous gene pairs between AtSBP and CsSBP, 21 pairs between SiSBP and CsSBP, and 14 pairs between OsSBP and CsSBP. Cis-acting element analysis indicated that light-responsive elements were the most abundant among the CsSBP genes. Protein motif, domain, and gene architecture analyses demonstrated that members of the same subgroup shared similar exon–intron structures and motif arrangements. Furthermore, we evaluated the expression profiles of nine CsSBP genes under light, shade, and cold stress using qRT-PCR analysis. Notably, CsSBP1, CsSBP17, and CsSBP19 were significantly upregulated under all three stresses. This study provides fundamental insights into the CsSBP gene family and offers a novel perspective on the mechanisms of SBP transcription factor-mediated stress responses, as well as Tieguanyin tea’s adaptation to environmental variations. Full article

Planetary photogrammetry remains an important technical means of producing high-precision planetary maps. High-quality control networks are fundamental to successful bundle adjustment. However, current software tools used by the planetary mapping community to construct and edit control networks exhibit very low efficiency. Moreover, redundant and invalid control points in the control network can further increase the time required for the bundle adjustment process. Due to a lack of targeted algorithm optimization, existing software tools and methods are unable to meet the photogrammetric processing requirements of massive planetary remote sensing images. To address these issues, we first proposed an efficient control network construction framework based on approximate orthoimage matching and hash quick search. Next, to effectively reduce the redundant control points in the control network and decrease the computation time required for bundle adjustment, we then proposed a control network-thinning algorithm based on a K-D tree fast search. Finally, we developed an automatic detection method based on ray tracing for identifying invalid control points in the control network. To validate the proposed methods, we conducted photogrammetric processing experiments using both the Lunar Reconnaissance Orbiter (LRO) narrow-angle camera (NAC) images and the Origins Spectral Interpretation Resource Identification Security Regolith Explorer (OSIRIS-REx) PolyCam images; we then compared the results with those derived from the famous open-source planetary photogrammetric software, the United States Geological Survey (USGS) Integrated Software for Imagers and Spectrometers (ISIS) version 8.0.0. The experimental results demonstrate that the proposed methods significantly improve the efficiency and quality of constructing control networks for large-scale planetary images. For thousands of planetary images, we were able to speed up the generation and editing of the control network by more than two orders of magnitude. Full article

Pteroceltis tatarinowii Maxim is a famous paper-making tree endemic to China with a wide distribution. Leaves of this tree growing in different habitats show a certain plasticity, which is important for their ecological adaption. Here, the photosynthesis ability, hydraulic properties, and anatomy of P. tatarinowii leaves from a limestone forest (Langya Mountain) and a cultivated forest (Xiaoling Village) in Anhui province were compared. The results showed that leaves from Xiaoling Village had higher net photosynthesis rate and hydraulic conductivity, which were closely related to their higher vein density, stomatal density and palisade tissue thickness than leaves from Langya Mountain. However, lower leaf water potentials at turgor loss point and at 50% loss of conductivity, as well as a higher leaf hardness, for Langya Mountain leaves indicated their higher hydraulic safety and drought resistance than those of leaves from Xiaoling Village. This study reveals a hydraulic trade-off between efficiency and safety for P. tatarinowii leaves growing in distinct habitats. Further studies should include more habitats and different vegetation communities to clarify the ecological adaption so as to provide a scientific basis for the protection of this species. Full article

Stick and leaf insects are a group among the Insecta that are famous for their extraordinary mimicry ability. Since the establishment of the Phasmatodea, their internal classification has been constantly revised. Mitochondrial genes as molecular markers have been widely used for species classification, but the phylogenetic relationships within the Phasmatodea remain to be thoroughly discussed. In the present study, five mitogenomes of Phasmatodea ranging from 15,746 bp to 16,747 bp in length were sequenced. Bayesian inference (BI) and maximum likelihood (ML) analyses were carried out based on a 13 PCGs data matrix (nt123) and a combined matrix of 13 PCGs and two rRNA genes (nt123_rRNA). The present study supports the conclusion that Phylliidae was the basal group of Neophasmatodea and confirms the monophyly of Lonchodinae and Necrosciinae, but it shows that Lonchodidae was polyphyletic. A sister group of Bacillidae and Pseudophasmatidae was also recovered. The phylogenetic tree based on the nt_123 dataset showed higher node support values. The construction of a divergent time tree in this study supported the conclusion that extant Phasmatodea originated in the Jurassic (170 Mya) and most lineages diverged after the Cretaceous–Paleogene extinction event. To explore whether the mitochondrial genes of Phraortes liaoningensis collected from high latitudes where low temperatures occur for eight months of the year are under selection pressure, this study used the branch-site model and the branch model to analyze the selection pressure on the 13 mitochondria protein-coding genes (PCGs). We found that both ND2 and ND4L of Ph. liaoningensis exhibited positive selection sites using the branch-site model. This study shows that a low-temperature environment causes mitochondrial genes to be selected to meet the energy requirements for survival. Full article

The combinatorial problem in this paper is motivated by a variant of the famous traveling salesman problem where the salesman must return to the starting point after each delivery. The total length of a delivery route is related to a metric known as closeness centrality. The closeness centrality of a vertex v in a graph G was defined in 1950 by Bavelas to be $CC\left(v\right)={\displaystyle \frac{\left|V\right(G\left)\right|-1}{SD\left(v\right)}}$, where $SD\left(v\right)$ is the sum of the distances from v to each of the other vertices (which is one-half of the total distance in the delivery route). We provide a real-world example involving the Metro Atlanta Rapid Transit Authority rail network and identify stations whose $SD$ values are nearly identical, meaning they have a similar proximity to other stations in the network. We then consider theoretical aspects involving asymmetric trees. For integer values of k, we considered the asymmetric tree with paths of lengths $k,2k,\dots ,nk$ that are incident to a center vertex. We investigated trees with different values of k, and for $k=1$ and $k=2$, we established necessary and sufficient conditions for the existence of two vertices with identical $SD$ values, which has a surprising connection to the triangular numbers. Additionally, we investigated asymmetric trees with paths incident to two vertices and found a sufficient condition for vertices to have equal $SD$ values. This leads to new combinatorial proofs of identities arising from Pascal’s triangle. Full article

Ginkgo biloba is a famous economic tree. Ginkgo leaves have been utilized as raw materials for medicines and health products due to their rich active ingredient composition, especially flavonoids. Since the routine measurement of total flavones is time-consuming and destructive, rapid, non-destructive detection of total flavones in ginkgo leaves is of significant importance to producers and consumers. Hyperspectral imaging technology is a rapid and non-destructive technique for determining the total flavonoid content. In this study, we discuss five modeling methods, and three spectral preprocessing methods are discussed. Bayesian Ridge (BR) and multiplicative scatter correction (MCS) were selected as the best model and the best pretreatment method, respectively. The spectral prediction results based on the BR + MCS treatment were very accurate (R_Test² = 0.87; RMSE_Test = 1.03 mg/g), showing a high correlation with the analytical measurements. In addition, we also found that the more and deeper the leaf cracks, the higher the flavonoid content, which helps to evaluate leaf quality more quickly and easily. In short, hyperspectral imaging is an effective technique for rapid and accurate determination of total flavonoids in ginkgo leaves and has great potential for developing an online quality detection system for ginkgo leaves. Full article

Chimonanthus praecox, a member of the Calycanthaceae family, is a unique, traditional, and famous flowering economic tree species in China. Despite the existence of several varieties, only a few cultivars have been formally named. Currently, expression sequence tag–simple sequence repeat (EST-SSR) markers are extensively used to identify different species and varieties; a large number of microsatellites can be identified from transcriptome databases. A total of 162,638 unigenes were assembled using RNA-seq; 82,778 unigenes were annotated using the Nr, Nt, Swiss-Prot, Pfam, GO, KOG, and KEGG databases. In total, 13,556 SSR loci were detected from 11,691 unigenes, with trinucleotide repeat motifs being the most abundant among the six repeat motifs. To develop the markers, 64,440 pairs of SSR primers with polymorphism potential were designed, and 75 pairs of primers were randomly selected for amplification. Among these markers, seven pairs produced amplified fragments of the expected size with high polymorphism. Using these markers, 12 C. praecox varieties were clustered into two monophyletic clades. Microsatellites in the transcriptome of C. praecox exhibit rich types, strong specificity, and great polymorphism potential. These EST-SSR markers serve as molecular technical methods for identifying different varieties of C. praecox and facilitate the exploration of a large number of candidate genes associated with important traits. Full article

In 1924, exactly a century ago, the world-famous children’s author Alan Milne wrote this much-loved rhyme about the play activities of his young son: Where am I going? I don’t quite know. Down to the stream where the king-cups grow-Up on the hill where the pine-trees blow-Anywhere, anywhere. I don’t know…Where am I going? The high rooks call: “It’s awful fun to be born at all”. Where am I going? The ring-doves coo: “We do have beautiful things to do”. But in 2024, in much of the Western world, allowing a young child to wander in this manner would be seen by many as dangerous, reckless and negligent. For example, in 2019, Renee Umstattd Meyer and her colleagues found that a large proportion of children in the post-industrial world did not take the recommended amount of exercise in the outdoor environment, and even where spaces were specifically made available to them, parents feared that they would be infiltrated by crime and violence. This article considers the emergent effects of significant cultural change in children’s independent and collaborative free play opportunities. It draws on an ethological and biocultural perspective to argue why independent, active free play, particularly involving peer collaboration, is so important to human development. Full article