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Science Enabled by Specimen Data

Rautela, K., A. Kumar, S. K. Rana, A. Jugran, and I. D. Bhatt. 2024. Distribution, Chemical Constituents and Biological Properties of Genus Malaxis. Chemistry & Biodiversity.

The genus Malaxis (family Orchidaceae), comprises nearly 183 species available across the globe. The plants of this genus have long been employed in traditional medical practices because of their numerous biological properties, like the treatment of infertility, hemostasis, burning sensation, bleeding diathesis, fever, diarrhea, dysentery, febrifuge, tuberculosis, etc. Various reports highlight their phytochemical composition and biological activities. However, there is a lack of systematic review on the distribution, phytochemistry, and biological properties of this genus. Hence, this study aims to conduct a thorough and critical review of Malaxis species, covering data published from 1965 to 2022 with nearly 90 articles. Also, it examines different bioactive compounds, their chemistry, and pharmacotherapeutics as well as their traditional uses. A total of 191 unique compounds, including the oil constituents were recorded from Malaxis species. The highest active ingredients were obtained from Malaxis acuminata (103) followed by Malaxis muscifera (50) and Malaxis rheedei (33). In conclusion, this review offers an overview of the current state of knowledge on Malaxis species and highlights prospects for future research projects on them. Additionally, it recommends the promotion of domestication studies for rare medicinal orchids like Malaxis and the prompt implementation of conservation measures.

Angulo, J. C., J. M. Burke, and F. A. Michelangeli. 2023. Characterizing the frequency, morphological gradient, and distribution of dioecy in Miconia (Melastomataceae). International Journal of Plant Sciences.

Dioecy has evolved many times independently within the angiosperms. The distribution, frequency of occurrence, and floral morphology of dioecious angiosperms constitute the foundations for comparative studies of dioecy, yet for many groups they are still poorly characterized. We assessed species of Miconia for the presence of dioecious reproductive system, characterized the floral morphology for staminate and pistillate flowers, and used herbarium records to analyze patterns of distribution and elevational range. We find that dioecious Miconia represent an uncommon case of mismatched stage of organ abortion between staminate and pistillate flowers, with functionally pistillate flower morphology largely consistent across species, and morphological expression in functionally staminate flowers varying from near absent to slight reductions in gynoecia. We identify 58 dioecious species and 15 putatively dioecious species within Miconia that are distributed primarily in montane habitats between 1000 m – 3500 m in the Andes, parts of Central America, and the Caribbean. Our results double the last known count of dioecy in Miconia and highlight the gradient of vestigial morphology in staminate flowers. Lastly, we provide discussion on the significance of dioecy in relation to floral development, pollination, and ecology in Miconia.

Finegan, B., D. Delgado, A. L. Hernández Gordillo, N. Zamora Villalobos, R. Núñez Florez, F. Díaz Santos, and S. Vílchez Mendoza. 2024. Multi-dimensional temperature sensitivity of protected tropical mountain rain forests. Frontiers in Forests and Global Change 6.

Introduction Tropical mountain rain forests (TMRF, natural forests at > 300 m asl) are globally important for biodiversity and ecosystem services and are believed to be highly vulnerable to climate change. But there are no specific approaches for rigorous assessment of their vulnerability at the landscape and local scales necessary for management for adaptation. We address the challenge of evaluating the ecological sensitivity to temperature of TMRF, applying a multidimensional approach in protected areas over a 440–2,950 m asl altitudinal gradient in Costa Rica, synthesizing results of a long-term research programme (2012-present). We evaluate the sensitivity to the current spatial temperature gradient of eleven ecosystem properties in three categories: forest composition and diversity, thermal characteristics of forest stands and forest structure and dynamics.MethodsData are from 29 to 32 plots of 50 m x 50 m (0.25 ha) distributed over the gradient, in which all trees, palms and tree ferns ≥ 10 dbh are identified to species and measured for recruitment, growth and mortality. An experimental study of leaf litter decomposition rates was carried out in twelve plots. Current and future (SSP 585, 2070) values of mean annual temperatures MAT were obtained from online climate surfaces. Thermal characteristics of forest stands were determined using MATs of species occurrences in GBIF and include a new index, the Community Thermal Capital Index (CTCI), calculated as CTI-MAT.ResultsWe classified degrees of sensitivity to temperature as very weak, weak, moderate or substantial. All eleven ecosystem properties are substantially sensitive, so changes in their values are expected under rising temperatures. Species density, the community temperature index CTI, tree recruitment and mortality rates and leaf litter decomposition rates are positively related to temperature, while the community weighted mean thermal niche breadth, the CTCI, net basal area increments, stand basal area and carbon in aboveground biomass are negatively related. Results point to zones of vulnerability in the protected areas.DiscussionIn montane forests, positive values of the CTCI–climate credit– robust basal area growth and very low mortality and leaf litter decomposition rates suggest healthy ecosystems and no risk of mountaintop extinction. Lowland forests may be vulnerable to degradation and biotic attrition, showing current basal area loss, high mortality and climate debts. National and local actors are participating in a process of adoption of the sensitivity analysis and recommendations regarding zones of vulnerability.

Thongsangtum, N., J. Huang, S.-F. Li, Y. Thasod, and T. Su. 2023. Calophyllum (Calophyllaceae) from late Oligocene–Early Miocene of Li Basin, northern Thailand and its biogeographic and paleoclimatic implications. Palaeoworld.

Fossils from tropical Asia, which are far from fully investigated, are important for understanding the evolution of plant diversity and the associated surrounding environment there. In this study, we report, as the first record in Thailand, the well-preserved leaf fossils of Calophyllum Linnaeus (Calophyllaceae) from the upper Oligocene–Lower Miocene lacustrine deposits in Li Basin, northern Thailand. The fossils were identified through detailed comparison with leaves of extant and fossil species. These leaf fossils are assigned to Calophyllum based on several key leaf characteristics such as oblanceolate or oblong in shape and parallel secondary veins, nearly perpendicular to the midvein, as well as secondary veins alternate, closely placed, craspedodromous, parallel, dense, and distinct on surface, forming marginal veins. Based on detailed morphological comparison, these fossil leaves are assigned to C. suraikholaensis Awasthi and Prasad, 1990 and Calophyllum sp. The discovery of Calophyllum indicates a montane subtropical to tropical climate in northern Thailand during the Oligocene–Miocene. Together with previous fossil records, these results suggest that this genus probably originated in India during the Paleogene, and spread from India to Indochina during the Neogene, leading to its modern distribution, which currently prefers tropical climates.

Freire-Fierro, A., F. Forest, D. S. Devey, J. F. B. Pastore, J. W. Horn, X.-J. Ge, Z. Wang, et al. 2023. Monnina (Polygalaceae), a New World monophyletic genus full of contrasts. Botanical Journal of the Linnean Society.

Endemic to the Neotropics, Monnina is the second largest genus of Polygalaceae, yet little is known about its phylogenetic history, biogeography, and morphological character evolution. To address these knowledge gaps, we conducted Bayesian and maximum likelihood (ML) analyses of nuclear ITS and plastid trnL–F regions to test the monophyly of Monnina s.l. We used this phylogenetic framework to (i) infer divergence time estimates of lineages within the genus and reconstruct their historical biogeography; (ii) reconstruct the evolution of morphological characters of putative ecological and evolutionary importance in Monnina; and (iii) test for correlations between our phylogenetic hypothesis and environmental data. Our results reveal that Monnina is monophyletic with an indehiscent, 1–2-seeded fruit as a synapomorphy for the genus. We identify six clades within Monnina based on our combined phylogenetic results: Clades A, B, and D are primarily distributed in southern and eastern South America, Clades C and E are primarily Central Andean, and Clade F is chiefly distributed in the Northern Andes and Central America. The ancestor of the Monnina stem lineage dispersed from Australia/Africa to South America during the late Eocene to early Oligocene. The divergences of major lineages within the genus began in the early Miocene. We inferred the most recent common ancestor of Monnina to be an herbaceous plant with one-seeded samaroid fruits. The origins of fleshy fruits and shrubby habits are phylogenetically correlated within Monnina, and their concerted convergent evolution may have promoted increased net diversification rates in the two most species-rich subclades of the genus.

Maurin, O., A. Anest, F. Forest, I. Turner, R. L. Barrett, R. C. Cowan, L. Wang, et al. 2023. Drift in the tropics: Phylogenetics and biogeographical patterns in Combretaceae. Global Ecology and Biogeography.

Aim The aim of this study was to further advance our understanding of the species-rich, and ecologically important angiosperm family Combretaceae to provide new insights into their evolutionary history. We assessed phylogenetic relationships in the family using target capture data and produced a dated phylogenetic tree to assess fruit dispersal modes and patterns of distribution. Location Tropical and subtropical regions. Time Period Cretaceous to present. Major Taxa Studied Family Combretaceae is a member of the rosid clade and comprises 10 genera and more than 500 species, predominantly assigned to genera Combretum and Terminalia, and occurring on all continents and in a wide range of ecosystems. Methods We use a target capture approach and the Angiosperms353 universal probes to reconstruct a robust dated phylogenetic tree for the family. This phylogenetic framework, combined with seed dispersal traits, biome data and biogeographic ranges, allows the reconstruction of the biogeographical history of the group. Results Ancestral range reconstructions suggest a Gondwanan origin (Africa/South America), with several intercontinental dispersals within the family and few transitions between biomes. Relative abundance of fruit dispersal types differed by both continent and biome. However, intercontinental colonizations were only significantly enhanced by water dispersal (drift fruit), and there was no evidence that seed dispersal modes influenced biome shifts. Main Conclusions Our analysis reveals a paradox as drift fruit greatly enhanced dispersal distances at intercontinental scale but did not affect the strong biome conservatism observed.

Hill, A., M. F. T. Jiménez, N. Chazot, C. Cássia‐Silva, S. Faurby, L. Herrera‐Alsina, and C. D. Bacon. 2023. Apparent effect of range size and fruit colour on palm diversification may be spurious. Journal of Biogeography.

Aim Fruit selection by animal dispersers with different mobility directly impacts plant geographical range size, which, in turn, may impact plant diversification. Here, we examine the interaction between fruit colour, range size and diversification rate in palms by testing two hypotheses: (1) species with fruit colours attractive to birds have larger range sizes due to high dispersal ability and (2) disperser mobility affects whether small or large range size has higher diversification, and intermediate range size is expected to lead to the highest diversification rate regardless of disperser. Location Global. Time Period Contemporary (or present). Major Taxa Studied Palms (Arecaceae). Methods Palm species were grouped based on likely animal disperser group for given fruit colours. Range sizes were estimated by constructing alpha convex hull polygons from distribution data. We examined disperser group, range size or an interaction of both as possible drivers of change in diversification rate over time in a likelihood dynamic model (Several Examined State-dependent Speciation and Extinction [SecSSE]). Models were fitted, rate estimates were retrieved and likelihoods were compared to those of appropriate null models. Results Species with fruit colours associated with mammal dispersal had larger ranges than those with colours associated with bird dispersal. The best fitting SecSSE models indicated that the examined traits were not the primary driver of the heterogeneity in diversification rates in the model. Extinction rate complexity had a marked impact on model performance and on diversification rates. Main Conclusions Two traits related to dispersal mobility, range size and fruit colour, were not identified as the main drivers of diversification in palms. Increased model extinction rate complexity led to better performing models, which indicates that net diversification should be estimated rather than speciation alone. However, increased complexity may lead to incorrect SecSSE model conclusions without careful consideration. Finally, we find palms with more mobile dispersers do not have larger range sizes, meaning other factors are more important determinants of range size.

Lima, V. P., R. A. Ferreira de Lima, F. Joner, L. D’Orangeville, N. Raes, I. Siddique, and H. ter Steege. 2023. Integrating climate change into agroforestry conservation: A case study on native plant species in the Brazilian Atlantic Forest. Journal of Applied Ecology.

Designing multispecies systems with suitable climatic affinity and identifying species' vulnerability under human‐driven climate change are current challenges to achieve successful adaptation of natural systems. To address this problem, we need to (1) identify groups of species with climatic similarity under climate scenarios and (2) identify areas with high conservation value under predicted climate change.To recognize species with similar climatic niche requirements that can be grouped for mixed cropping in Brazil, we employed ecological niche models (ENMs) and Spearman's ρ for overlap. We also used prioritization algorithms to map areas of high conservation value using two Shared Socioeconomic Pathways (SSP2‐4.5 and SSP5‐8.5) to assess mid‐term (2041–2060) and long‐term (2061–2080) climate change impacts.We identified 15 species groups with finer climatic affinities at different times depicted on hierarchical clustering dendrograms, which can be combined into agroecological agroforestry systems. Furthermore, we highlight the climatically suitable areas for these groups of species, thus providing an outlook of where different species will need to be planted over time to be conserved. In addition, we observed that climate change is predicted to modify the spatial association of these groups under different future climate scenarios, causing a mean negative change in species climatic similarity of 9.5% to 13.7% under SSP2‐4.5 scenario and 9.5% to 10.5% under SSP5‐8.5, for 2041–2060 and 2061–2080, respectively.Synthesis and applications. Our findings provide a framework for agroforestry conservation. The groups of species with finer climatic affinities identified and the climatically suitable areas can be combined into agroecological productive systems, and provide an outlook of where different species may be planted over time. In addition, the conservation priority zones displaying high climate stability for each species individually and all at once can be incorporated into Brazil's conservation plans by policymakers to prioritize specific sites. Lastly, we urge policymakers, conservation organizations and donors to promote interventions involving farmers and local communities, since the species' evaluated have proven to maintain landscapes with productive forest fragments and can be conserved in different Brazilian ecosystems.

Richard-Bollans, A., C. Aitken, A. Antonelli, C. Bitencourt, D. Goyder, E. Lucas, I. Ondo, et al. 2023. Machine learning enhances prediction of plants as potential sources of antimalarials. Frontiers in Plant Science 14.

Plants are a rich source of bioactive compounds and a number of plant-derived antiplasmodial compounds have been developed into pharmaceutical drugs for the prevention and treatment of malaria, a major public health challenge. However, identifying plants with antiplasmodial potential can be time-consuming and costly. One approach for selecting plants to investigate is based on ethnobotanical knowledge which, though having provided some major successes, is restricted to a relatively small group of plant species. Machine learning, incorporating ethnobotanical and plant trait data, provides a promising approach to improve the identification of antiplasmodial plants and accelerate the search for new plant-derived antiplasmodial compounds. In this paper we present a novel dataset on antiplasmodial activity for three flowering plant families – Apocynaceae, Loganiaceae and Rubiaceae (together comprising c. 21,100 species) – and demonstrate the ability of machine learning algorithms to predict the antiplasmodial potential of plant species. We evaluate the predictive capability of a variety of algorithms – Support Vector Machines, Logistic Regression, Gradient Boosted Trees and Bayesian Neural Networks – and compare these to two ethnobotanical selection approaches – based on usage as an antimalarial and general usage as a medicine. We evaluate the approaches using the given data and when the given samples are reweighted to correct for sampling biases. In both evaluation settings each of the machine learning models have a higher precision than the ethnobotanical approaches. In the bias-corrected scenario, the Support Vector classifier performs best – attaining a mean precision of 0.67 compared to the best performing ethnobotanical approach with a mean precision of 0.46. We also use the bias correction method and the Support Vector classifier to estimate the potential of plants to provide novel antiplasmodial compounds. We estimate that 7677 species in Apocynaceae, Loganiaceae and Rubiaceae warrant further investigation and that at least 1300 active antiplasmodial species are highly unlikely to be investigated by conventional approaches. While traditional and Indigenous knowledge remains vital to our understanding of people-plant relationships and an invaluable source of information, these results indicate a vast and relatively untapped source in the search for new plant-derived antiplasmodial compounds.

Robin-Champigneul, F., J. Gravendyck, H. Huang, A. Woutersen, D. Pocknall, N. Meijer, G. Dupont-Nivet, et al. 2023. Northward expansion of the southern-temperate podocarp forest during the Early Eocene Climatic Optimum: Palynological evidence from the NE Tibetan Plateau (China). Review of Palaeobotany and Palynology: 104914.

The debated vegetation response to climate change can be investigated through palynological fossil records from past extreme climate conditions. In this context, the early Eocene (53.3 to 41.2 million years ago (Ma)) is often referred to as a model for a greenhouse Earth. In the Xining Basin, situated on the North-eastern Tibetan Plateau (NETP), this time interval is represented by an extensive and well-dated sedimentary sequence of evaporites and red mudstones. Here we focus on the palynological record of the Early Eocene Climatic Optimum (EECO; 53.3 to 49.1 Ma) and study the fossil gymnosperm pollen composition in these sediments. In addition, we also investigate the nearest living relatives (NLR) or botanical affinity of these genera and the paleobiogeographic implications of their occurrence in the Eocene of the NETP. To reach our objective, we complemented transmitted light microscopy with laser scanning- and electron microscopy techniques, to produce high-resolution images, and illustrate the morphological variation within fossil and extant gymnosperm pollen. Furthermore, a morphometric analysis was carried out to investigate the infra- and intrageneric variation of these and related taxa. To place the data in context we produced paleobiogeographic maps for Phyllocladidites and for other Podocarpaceae, based on data from a global fossil pollen data base, and compare these with modern records from GBIF. We also assessed the climatic envelope of the NLR. Our analyses confirm the presence of Phyllocladidites (NLR Phyllocladus, Podocarpaceae) and Podocarpidites (NLR Podocarpus, Podocarpaceae) in the EECO deposits in the Xining Basin. In addition, a comparative study based on literature suggests that Parcisporites is likely a younger synonym of Phyllocladidites. Our findings further suggest that the Phyllocladidites specimens are derived from a lineage that was much more diverse than previously thought, and which had a much larger biogeographical distribution during the EECO than at present. Based on the climatic envelope of the NLR, we suggest that the paleoclimatic conditions in the Xining Basin were warmer and more humid during the EECO. We conclude that phylloclade-type conifers typical of the southern-temperate podocarp forests, had a northward geographical expansion during the EECO, followed by extirpation.