[This corrects the article DOI: 10.3389/fpls.2020.582422.].
Plants accumulate a vast array of secondary metabolites, which constitute a natural resource for pharmaceuticals. Oldenlandia corymbosa belongs to the Rubiaceae family, and has been used in traditional medicine to treat different diseases, including cancer. However, the active metabolites of the plant, their biosynthetic pathway and mode of action in cancer are unknown. To fill these gaps, we exposed this plant to eight different stress conditions and combined different omics data capturing gene expression, metabolic profiles and anti‐cancer activity. Our results show that O. corymbosa extracts are active against breast cancer cell lines and that ursolic acid is responsible for this activity. Moreover, we assembled a high‐quality genome and uncovered two genes involved in the biosynthesis of ursolic acid. Finally, we also revealed that ursolic acid causes mitotic catastrophe in cancer cells and identified three high‐confidence protein binding targets by Cellular Thermal Shift Assay (CETSA) and reverse docking. Altogether, these results constitute a valuable resource to further characterize the biosynthesis of active metabolites in the Oldenlandia group, while the mode of action of ursolic acid will allow us to further develop this valuable compound. This article is protected by copyright. All rights reserved.
Syzygium is a large genus (1200–1500 species) of Old World tropical trees, currently divided into five subgenera containing widely different numbers of species. Syzygium subgenus Perikion was defined by the presence of fibre bundles in the hypanthium wall, although until now this feature has not been investigated or images published. Furthermore, discovery of fibre bundles in certain species outside Syzygium subgenus Perikion calls for reassessment of the subgenus. In this paper, a morphological analysis is presented for all species previously associated with Syzygium subgenus Perikion or known to have fibre bundles. Results indicate the need for description of a new subgenus, Syzygium subgenus Oborapi, characterized by a distinctly goblet-shaped calyx, presence of fibre bundles in the hypanthium/mesocarp, prominent black lenticels on the abaxial leaf surface, ascending ovule orientation and species diversity centred on the Sunda Shelf. Fibre bundles are photographed and documented for the first time from a range of species and at different magnifications. A preliminary list of species is presented for Syzygium subgenus Perikion and Syzygium subgenus Oborapi, with recommendations for further investigation.
Re‐establishing extirpated wildlife—or “rewilding”—is touted as a way to restore biodiversity and ecosystem processes, but we lack real‐world examples of this process, particularly in Southeast Asia. Here, we use a decade of aggregated camera trap data, N‐mixture occupancy models, and input from local wildlife experts to describe the unassisted recolonization of two native large herbivores in Singapore. Sambar deer (Rusa unicolor) escaped from captivity (in private or public zoos) in the 1970s and contemporary camera trap data show they have only colonized nearby forest fragments and their abundance remains low. Wild pigs (Sus scrofa), in contrast, naturally recolonized by swimming from Malaysia in the 1990s and have rapidly expanded their range and abundance across Singapore. While wild pigs have not recolonized all viable green spaces yet, their trajectory indicates they soon will. We also note that a third ungulate, the muntjac deer (Muntiacus muntjak), was captured in camera trapping in 2014 and 2015 but was never recorded afterward despite increased sampling effort, and thus we do not focus on their presumably unsuccessful recolonization. The divergent rewilding trajectories between sambar deer and wild pigs suggest different conservation outcomes and management requirements. Sambar deer may restore lost plant–animal interactions such as herbivory and seed dispersal without requiring significant management. Wild pigs, in contrast, have reached high numbers rapidly and may require active management to avoid hyperabundance and negative ecological impacts in regions, such as Singapore that lack both hunting and large predators.
Decomposition and fire are major carbon pathways in many ecosystems, yet potential linkages between these processes are poorly understood. We test whether variability in decomposability and flammability across species are related to each other and to key plant functional traits in tropical swamp forests, where habitat degradation is elevating decomposition and fire regimes. Using senesced and fresh leaves of 22 swamp tree species in Singapore, we conducted an in situ decomposition experiment and a laboratory flammability experiment. We analysed 16 leaf physical and biochemical traits as predictors of decomposability and components of flammability: combustibility, ignitability, and sustainability. Decomposability and flammability were largely decoupled across species, despite some shared predictive traits such as specific leaf area. Physical traits predicted that thicker leaves with a smaller specific leaf area and volume decomposed faster, while various cation concentrations predicted flammability components, particularly ignitability. We show that flammability and decomposability of swamp forest leaves are decoupled because flammability is mostly driven by biochemical traits, while decomposition is driven by physical traits. Our approach identifies species that are slow to decompose and burn (e.g., Calophyllum tetrapterum and Xanthophyllum flavescens) which could be planted to mitigate carbon losses in tropical swamp reforestation.
Invasive plants are a growing ecological problem worldwide, but biases and patterns within invasive plant research may affect our understanding of invasive plant ecology. In this study, we analyzed 458 invasive plant papers sampled from the two journals dedicated entirely to the field of invasion biology, i.e., Biological Invasions and Neobiota. From these papers, we collected information on geographic coverage, climate, habitat, taxonomic coverage, plant functional type, and research topic to examine trends across a 21‐year time period from 1999 to 2020. Our analysis found that invasive plant research was consistently biased toward temperate grassland and forest ecosystems particularly within the Americas, Europe, and Australia, and toward smaller, herbaceous invasive plant species (i.e., forbs, grasses, and shrubs), with an increase in interest in invasive nitrogen‐fixing legumes over time. Our analysis also identified “hot” research topics in invasive plant research at specific time periods, such as a peak in the use of genetic analysis methods in 2014–2015 and a more recent focus on plant physiological and functional traits. While current models, concepts, and understanding of plant invasion ecology are still driven by such biases, this has been partially offset by recent increased research in understudied systems, as well as increasing awareness that plant invasion is heavily affected by their growth types, physiological traits, and soil interactions. As the field of invasion biology becomes ever increasingly important over time, focusing invasive plant research on understudied ecosystems and plant groups will allow us to develop a more holistic understanding of the ecology of invasive plants. In particular, given the outsized importance of the tropics to global biodiversity, the threats they face, and the dearth of studies, it is of critical importance that more invasive plant research is conducted within the tropics to develop a more globally representative understanding of invasive plant ecology. We analyzed 458 invasive plant papers sampled from two journals of invasion biology, Biological Invasions and Neobiota, across the past two decades. The analysis identified several trends and biases in invasion plant, and these findings help identify critically understudied areas of invasion plant biology worldwide, in particular within tropical ecosystems.
In the present paper we publish eight new species from New Guinea, H. domaensis , H. gauttierensis , H. liddleana , H. lucida , H. paradisea , H. pulleana , H. tarikuensis , and H. unirana , and one subspecies, H. krusenstierniana subsp. laticorolla . Five taxa were first diagnosed based on specimens at the Leiden herbarium, one species is only known from a collection at Edinburgh and Lae herbaria, while three are based on recently collected specimens. Hoya leucantha , originally described from a specimen in bud, has been identified among herbarium specimens and was also recently recollected. It is therefore fully described and illustrated for the first time.
Landscape visual quality (LVQ) relates to a landscape’s spatial, functional and visual structure at a given time, which can affect the senses and experience of the person using or viewing the landscape. A holistic LVQ assessment can be undertaken by using two complementary approaches. The first uses visual quality assessment tools to measure a person’s perceptive responses to landscapes; the second, the focus of our study, is based on the quantitative assessment of the physical attributes of landscapes. The physical attributes of landscapes refer to their spatial configuration and composition, and have conventionally been characterised using 2D or 2.5D metrics. The use of 3D attributes is an emerging field, but there is scant information on the range of 3D metrics that can describe the physical attributes of landscapes and which relate to the perception of landscape quality. This study develops 3D spatial metrics to describe landscapes' structures and spatial characteristics grounded on landscape visualization theory. These metrics are derived from point clouds and describe 3D attributes of volume and area, landscape diversity, shape, connectivity, colour, topography, and openness. The effectiveness of the 3D spatial metrics to quantify LVQ was verified using a set of urban landscapes in the high-rise, compact environment of our study sites. The results show that 3D spatial metrics can successfully detect the differences among landscapes in the dimensions of naturalness, complexity, coherence and visual scale. For example, landscapes with a random distribution and irregular shapes had high values in horizontal, vertical, and distance diversity (HVDD) and the shape index, respectively, indicating their high spatial and shape diversities. Our study highlights the potential of using 3D spatial metrics derived from point clouds for a more holistic and objective LVQ assessment.
Perceptions of, and attitudes toward, wildlife are influenced by exposure to, and direct experiences with, nature. Butterflies are a conspicuous and ubiquitous component of urban nature across megacities that are highly urbanized with little opportunity for human–nature interactions. We evaluated public familiarity with, perceptions of and attitudes toward butterflies across nine megacities in East and Southeast Asia through face-to-face interviews with 1774 urban park users. A total of 79% of respondents had seen butterflies in their cities mostly in urban parks, indicating widespread familiarity with butterflies. Those who had seen butterflies also had higher perceptions of butterflies, whereas greater than 50% of respondents had positive attitudes toward butterflies. Frequent visits to natural places in urban neighbourhoods was associated with (i) sightings of caterpillars, indicating increased familiarity with urban wildlife, and (ii) increased connectedness to nature. We found two significant positive relationships: (i) between connectedness to nature and attitudes toward butterflies and (ii) between connectedness to nature and perceptions of butterflies, firmly linking parks users' thoughts and feelings about butterflies with their view of nature. This suggests that butterflies in urban parks can play a key role in building connectedness to nature and consequently pro-environmental behaviours and support for wildlife conservation among urban residents.
The Annonaceae family contains important tropical crops, but the number of species used commercially is limited, and development of other promising species for cultivation is hindered by a lack of genomic resources to support the building of breeding programmes. The family is part of the magnoliids, an ancient lineage of angiosperms for which evolutionary relationships with other major clades have remained unclear. To provide novel resources to both plant breeders and evolutionary research, we described the chromosome-level genome assembly of the soursop (Annona muricata L.), using DNA data generated with PacBio and Illumina short-read technology, in combination with 10XGenomics, BioNano data, and Hi-C sequencing. To disentangle key angiosperm relationships, we reconstructed phylogenomic trees comparing a wider sampling of available angiosperm genomes and reveal that the soursop represents a genomic mosaic supporting different evolutionary histories, with scaffolds almost exclusively supporting singular topologies. However, coalescent methods and a majority of genes support magnoliids as sister to monocots and eudicots, where previously published whole genome-based studies remained inconclusive. The soursop genome highlights the need for more early diverging angiosperm genomes and critical assessment of the suitability of such genomes for inferring evolutionary history. The soursop is the first genome assembled in Annonaceae and supports further studies of floral evolution in magnoliids, whilst providing an essential resource for delineating relationships of major lineages at the base of the angiosperms. Both genome-assisted improvement in promising Annonaceae fruit crops and conservation efforts will be strengthened by the availability of the soursop genome. The genome assembly as a community resource will further strengthen the role of Annonaceae as a model group for research on the ecology, evolution, and domestication potential of tropical species in pomology and agroforestry.
Background and Aims A targeted enrichment NGS approach was used to construct the phylogeny of Amomum Roxb. (Zingiberaceae). Phylogenies based on hundreds of nuclear genes, the whole plastome and the rDNA cistron were compared with an ITS-based phylogeny. Trends in genome size (GS) evolution were examined, chromosomes were counted and the geographical distribution of phylogenetic lineages was evaluated. Methods In total, 92 accessions of 54 species were analysed. ITS was obtained for 79 accessions, 37 accessions were processed with Hyb-Seq and sequences from 449 nuclear genes, the whole cpDNA, and the rDNA cistron were analysed using concatenation, coalescence and supertree approaches. The evolution of absolute GS was analysed in a phylogenetic and geographical context. The chromosome numbers of 11 accessions were counted. Key Results Four groups were recognised in all datasets though their mutual relationships differ among datasets. While group A (A. subulatum and A. petaloideum) is basal to the remaining groups in the nuclear gene phylogeny, in the cpDNA topology it is sister to group B (A. repoeense and related species) and, in the ITS topology, it is sister to group D (the Elettariopsis lineage). The former Elettariopsis makes a monophyletic group. There is an increasing trend in GS during evolution. The largest GS values were found in group D in two tetraploid taxa, A. cinnamomeum and A. aff. biphyllum (both 2n = 96 chromosomes). The rest varied in GS (2C = 3.54–8.78 pg) with a constant chromosome number 2n = 48. There is a weak connection between phylogeny, GS and geography in Amomum. Conclusions Amomum consists of four groups, and the former Elettariopsis is monophyletic. Species in this group have the largest GS. Two polyploids were found and GS greatly varied in the rest of Amomum.
The monocot family Costaceae Nakai consists of seven genera but their mutual relationships have not been satisfactorily resolved in previous studies employing classical molecular markers. Phylogenomic analyses of 365 nuclear genes and nearly-complete plastome data provides almost fully resolved insights into their diversification. Paracostus is identified as sister to all other taxa, followed by several very short branches leading to discrete lineages, suggesting an ancient rapid radiation of these early lineages and leaving the exact relationships among them unresolved. Relationships among Chamaecostus, Dimerocostus and Monocostus confirmed earlier findings that these genera form a monophyletic group. The Afro-American Costus is also monophyletic. By contrast, Tapeinochilos appeared as a well-supported crown lineage of Cheilocostus rendering it paraphyletic. As these two genera differ morphologically from one another owing to a shift from insect- to bird-pollination, we propose to keep both names. The divergence time within Costaceae was estimated using penalized likelihood utilizing two fossils within Zingiberales, †Spirematospermum chandlerae and †Ensete oregonense, indicated a relatively recent diversification of Costaceae, between 18–9 Mya. Based on these data, the current pantropical distribution of the family is hypothesized to be the result of several long-distance intercontinental dispersal events, which do not correlate with global geoclimatic changes.
Background Urban agriculture is potentially an important piece of the food security puzzle for a rapidly growing urban world population. Community gardening is also promoted as a safe and viable form of exercise for aging populations in crowded settings where opportunities to participate in other action activities may be limited. Knowledge of potential site-specific health risks to environmental contaminants is important in dialogues promoting urban farming. Methods We assess the pseudo-total concentrations of selected potentially toxic elements (PTEs) in the soils of community gardens, public parks, and woodlands in the tropical urban island nation of Singapore. We compare concentrations of cadmium, copper, lead, and zinc with amalgamated risk guidelines to form a baseline understanding of the level of contamination in these spaces. We also perform providence tracking with lead isotopes to identify potential sources of contaminants. Results All pseudo-total concentrations of Cd, Cu, Pb, and Zn in the soil were below threshold concentrations considered to represent substantial risk. Further, PTE concentrations in gardens were largely equivalent to those found in community parks and woodlands, but the geographical distribution varied. Provenance tracking with Pb isotopes indicated Pb in gardens was both anthropogenic and natural, but spatially variable. The lack of strong spatial clustering of areas with the highest PTE concentrations was inconsistent with a common point source of contamination. However, the correlation between Cu and Zn suggest a common source for these elements, such as road/trafficking or atmospheric deposition. Conclusion We find limited risk of urban gardeners to exposure to Cd, Cu, Pb, and Zn—elements that are commonly abundant in urban settings with dense transportation networks and substantial industrial activities. The low levels of PTEs are encouraging for the promotion of urban farming for food production and leisure in this dense urban setting. However, as concentrations were low, we did not assess bioavailability and bioaccessibility of the PTEs. These assessments would need to be determined in cases of with higher levels of contamination to provide a more thorough consideration of actual human risk.
Species radiations, despite immense phenotypic variation, can be difficult to resolve phylogenetically when genetic change poorly matches the rapidity of diversification. Genomic potential furnished by palaeopolyploidy, and relative roles for adaptation, random drift and hybridisation in the apportionment of genetic variation, remain poorly understood factors. Here, we study these aspects in a model radiation, Syzygium, the most species-rich tree genus worldwide. Genomes of 182 distinct species and 58 unidentified taxa are compared against a chromosome-level reference genome of the sea apple, Syzygium grande. We show that while Syzygium shares an ancient genome doubling event with other Myrtales, little evidence exists for recent polyploidy events. Phylogenomics confirms that Syzygium originated in Australia-New Guinea and diversified in multiple migrations, eastward to the Pacific and westward to India and Africa, in bursts of speciation visible as poorly resolved branches on phylogenies. Furthermore, some sublineages demonstrate genomic clines that recapitulate cladogenetic events, suggesting that stepwise geographic speciation, a neutral process, has been important in Syzygium diversification.
Carbon and nitrogen losses from degraded wetlands and methane emissions from flooded wetlands are both important sources of greenhouse gas emissions. However, the net-exchange dependence on hydrothermal conditions and wetland integrity remains unclear. Using a global-scale in situ database on net greenhouse gas exchanges, we show diverse hydrology-influenced emission patterns in CO2, CH4 and N2O. We find that total CO2-equivalent emissions from wetlands are kept to a minimum when the water table is near the surface. By contrast, greenhouse gas exchange rates peak in flooded and drained conditions. By extrapolating the current trajectory of degradation, we estimate that between 2021 and 2100, wetlands could result in greenhouse gas emissions equivalent to around 408 gigatons of CO2. However, rewetting wetlands could reduce these emissions such that the radiative forcing caused by CH4 and N2O is fully compensated by CO2 uptake. As wetland greenhouse gas budgets are highly sensitive to changes in wetland area, the resulting impact on climate from wetlands will depend on the balance between future degradation and restoration.
As a precursor to the Dipterocarpaceae account for the Flora of Singapore, the following 31 names are lectotypified: Anisoptera laevis Ridl., A. megistocarpa Slooten, Balanocarpus heimii King, B. wrayi King, Dipterocarpus cornutus Dyer, D. elongatus Korth., D. kunstleri King, D. penangianus Foxw., D. skinneri var. hirtus Ridl., D. sublamellatus Foxw., Hopea ferruginea Parijs, H. globosa Brandis, H. gratissima Wall. ex Kurz, H. griffithii Kurz, H. lowii Dyer ex Brandis, H. mengarawan Miq., H. sangal Korth., Retinodendron pauciflorum Korth., Shorea bracteolata Dyer, Shorea gibbosa Brandis, Shorea macroptera Dyer, Shorea ochrophloia Strugnell ex Symington, Shorea parvifolia Dyer, Shorea pauciflora King, Shorea platycarpa F.Heim, Shorea rigida Brandis, Shorea sericea Dyer, Sunaptea odorata Griff., Vatica ovalis Korth., V. ridleyana Brandis and V. wallichii Dyer.
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