Science Enabled by Specimen Data

Bürger, M., and J. Chory. 2024. A potential role of heat‐moisture couplings in the range expansion of Striga asiatica. Ecology and Evolution 14.

Parasitic weeds in the genera Orobanche, Phelipanche (broomrapes) and Striga (witchweeds) have a devastating impact on food security across much of Africa, Asia and the Mediterranean Basin. Yet, how climatic factors might affect the range expansion of these weeds in the context of global environmental change remains unexplored. We examined satellite‐based environmental variables such as surface temperature, root zone soil moisture, and elevation, in relation to parasitic weed distribution and environmental conditions over time, in combination with observational data from the Global Biodiversity Information Facility (GBIF). Our analysis reveals contrasting environmental and altitude preferences in the genera Striga and Orobanche. Asiatic witchweed (Striga asiatica), which infests corn, rice, sorghum, and sugar cane crops, appears to be expanding its range in high elevation habitats. It also shows a significant association with heat‐moisture coupling events, the frequency of which is rising in such environments. These results point to geographical shifts in distribution and abundance in parasitic weeds due to climate change.

Köhler, M., M. Romeiro‐Brito, and M. Telhe. 2024. The Cerrado through cacti. Journal of Biogeography.

Cerrado is a large and heterogeneous ecoregion in the Neotropics marked by the fire‐prone savanna vegetation, to which succulent lineages are usually not associated due to this adverse condition. However, recent studies have highlighted the importance of Cerrado as an ancestral range for the origin, dispersal and in situ diversification of remarkable lineages of South American cacti. In this perspective, we explore the implications of these occurrences in the Cerrado, shedding light on a frequently overlooked aspect of this ecoregion—the role of scattered rocky outcrop habitats acting as micro‐refuges for fire‐sensitive lineages. We show that most cacti occurrences are associated with patches of rock outcrops across the Cerrado. In contrast, when terricolous, a few disparate and not closely related species can develop underground structures or present a specialized habit that facilitates their presence as a putative response to fire—reinforcing the evolutionary lability of fire adaptation in Cerrado lineages. Despite some notable endemisms, several occurrences are from species with core distributions in adjacent ecoregions (e.g. Caatinga and Chaco), demonstrating the permeability of Cerrado, which can act concomitantly as a biogeographical barrier (especially due to its fire‐prone habitats) and as a corridor for biota interchange. Finally, we stress that Cerrado heterogeneity, often leading to different circumscriptions, is a relevant issue when studying and characterizing Neotropical biota, which must be further explored and considered to assess the evolutionary assembly of the biomes involved.

Dantas, V. L., L. C. S. Oliveira, C. R. Marcati, and J. Sonsin‐Oliveira. 2024. Coordination of bark and wood traits underlies forest‐to‐savanna evolutionary transitions. Journal of Biogeography.

Aim To test the hypothesis that adaptive shifts leading to the assembly of tropical savannas involved coordination between bark and wood traits and to understand the underlying mechanisms.LocationTropical South America.TaxonAngiosperms (woody).MethodsWe compiled data on three bark traits (total, inner and outer relative bark thickness), wood density, maximum height, five secondary xylem traits and on species' habitat information (light environment, climate, soil and fire history) for Neotropical savanna, forest and generalist species (biome groups). We tested for pairwise and multivariate associations among traits across species and if biome group and habitat conditions explained species positions along the resulting strategy axes.ResultsTraits covaried along four different axes. The first axis was consistent with a trade‐off between fire (thick barks) and shade tolerance (low bark to diameter ratio, high vessel density) and contributed to differentiate the three biome groups according to the preference for shaded environments. Forest species also differed from savanna and generalist species in a separate axis by being more resource acquisitive. Maximum height and wood density did not strongly trade‐off with bark thickness, although maximum height was negatively covaried with relative outer bark thickness. Preference for shaded conditions was the main driver of variation in the two principal strategy axes, but temperature, fire and soil sand content also explained differences in plant stature between savanna and generalist species.Main ConclusionsAllocation to bark is constrained by trade‐offs with wood, opposing shade‐tolerant and acquisitive forest species to fire‐resistant and conservative savanna species. Rather than a single strategy axis, three axes are necessary to understand the functional differences among savanna, forest and generalist species. Because two of these axes are controlled by light availability, the associated traits tend to covary in space and time, but not across species.

Serra‐Diaz, J. M., J. Borderieux, B. Maitner, C. C. F. Boonman, D. Park, W. Guo, A. Callebaut, et al. 2024. occTest: An integrated approach for quality control of species occurrence data. Global Ecology and Biogeography.

Aim Species occurrence data are valuable information that enables one to estimate geographical distributions, characterize niches and their evolution, and guide spatial conservation planning. Rapid increases in species occurrence data stem from increasing digitization and aggregation efforts, and citizen science initiatives. However, persistent quality issues in occurrence data can impact the accuracy of scientific findings, underscoring the importance of filtering erroneous occurrence records in biodiversity analyses.InnovationWe introduce an R package, occTest, that synthesizes a growing open‐source ecosystem of biodiversity cleaning workflows to prepare occurrence data for different modelling applications. It offers a structured set of algorithms to identify potential problems with species occurrence records by employing a hierarchical organization of multiple tests. The workflow has a hierarchical structure organized in testPhases (i.e. cleaning vs. testing) that encompass different testBlocks grouping different testTypes (e.g. environmental outlier detection), which may use different testMethods (e.g. Rosner test, jacknife,etc.). Four different testBlocks characterize potential problems in geographic, environmental, human influence and temporal dimensions. Filtering and plotting functions are incorporated to facilitate the interpretation of tests. We provide examples with different data sources, with default and user‐defined parameters. Compared to other available tools and workflows, occTest offers a comprehensive suite of integrated tests, and allows multiple methods associated with each test to explore consensus among data cleaning methods. It uniquely incorporates both coordinate accuracy analysis and environmental analysis of occurrence records. Furthermore, it provides a hierarchical structure to incorporate future tests yet to be developed.Main conclusionsoccTest will help users understand the quality and quantity of data available before the start of data analysis, while also enabling users to filter data using either predefined rules or custom‐built rules. As a result, occTest can better assess each record's appropriateness for its intended application.

Renjana, E., E. R. Firdiana, M. H. Angio, L. W. Ningrum, I. Q. Lailaty, A. Rahadiantoro, I. Martiansyah, et al. 2024. Spatial habitat suitability prediction of essential oil wild plants on Indonesia’s degraded lands. PeerJ 12: e17210.

Background Essential oils are natural products of aromatic plants with numerous uses. Essential oils have been traded worldwide and utilized in various industries. Indonesia is the sixth largest essential oil producing country, but land degradation is a risk to the continuing extraction and utilization of natural products. Production of essential oil plants on degraded lands is a potential strategy to mitigate this risk. This study aimed to identify degraded lands in Indonesia that could be suitable habitats for five wild native essential oil producing plants, namely Acronychia pedunculata (L.) Miq., Baeckea frutescens L., Cynometra cauliflora L., Magnolia montana (Blume) Figlar, and Magnolia sumatrana var. glauca (Blume) Figlar & Noot using various species distribution models. Methods The habitat suitability of these species was predicted by comparing ten species distribution models, including Bioclim, classification and regression trees (CART), flexible discriminant analysis (FDA), Maxlike, boosted regression trees (BRT), multivariate adaptive regression splines (MARS), generalized linear models (GLM), Ranger, support vector machine (SVM), and Random Forests (RF). Bioclimatic, topographic and soil variables were used as the predictors of the model habitat suitability. The models were evaluated according to their AUC and TSS metrics. Model selection was based on ranking performance. The total suitable area for five native essential oil producing plants in Indonesia’s degraded lands was derived by overlaying the models with degraded land locations. Results The habitat suitability model for these species was well predicted with an AUC value >0.8 and a TSS value >0.7. The most important predictor variables affecting the habitat suitability of these species are mean temperature of wettest quarter, precipitation seasonality, precipitation of warmest quarter, precipitation of coldest quarter, cation exchange capacity, nitrogen, sand, and soil organic carbon. C. cauliflora has the largest predicted suitable area, followed by M. montana, B. frutescens, M. sumatrana var. glauca, and A. pedunculata. The overlapping area between predictive habitat suitability and degraded lands indicates that the majority of degraded lands in Indonesia’s forest areas are suitable for those species. Conclusion The degraded lands predicted as suitable habitats for five native essential oil producing plants were widely spread throughout Indonesia, mostly in its main islands. These findings can be used by the Indonesian Government for evaluating policies for degraded land utilization and restorations that can enhance the lands’ productivity.

Ferreira, G. E., J. L. Clark, L. Clavijo, A. Zuluaga, A. Chautems, M. J. G. Hopkins, A. O. Araujo, and M. Perret. 2024. Phylogenetics, character evolution, and historical biogeography of the Neotropical genus Besleria (Gesneriaceae). Botanical Journal of the Linnean Society.

Besleria, a genus of perennial herbs, shrubs, or small trees growing in the understorey of rainforests, is one of the largest genera of neotropical Gesneriaceae, with over 165 species. Despite the ecological importance and ubiquity of Besleria in rainforest ecosystems, taxonomic and evolutionary studies of Besleria are limited. Here, we generated a phylogenetic analysis of Besleria using four nuclear and chloroplast DNA regions (ITS, matK, rps16, and trnL-trnF) covering more than 50% of the recognized species, along with two secondary calibration points to infer divergence times. Our results support the monophyly of Besleria and allowed us to revise the infrageneric classification and biogeographical history of the genus. We identified five major clades that do not correspond to sections or subsections in previous classifications. These clades are well circumscribed geographically but remain difficult to characterize using previously hypothesized morphological characters. Biogeographical reconstructions indicate an origin in the northern Andes during the Middle Miocene (ca. 15 Mya). The current distribution patterns of this plant group have been significantly shaped by geological and climatic events, particularly Andean uplift and the formation of the Panama Isthmus.

Ramírez-Barahona, S. 2024. Incorporating fossils into the joint inference of phylogeny and biogeography of the tree fern order Cyatheales R. Warnock, and M. Zelditch [eds.],. Evolution.

Present-day geographic and phylogenetic patterns often reflect the geological and climatic history of the planet. Neontological distribution data are often sufficient to unravel a lineage’s biogeographic history, yet ancestral range inferences can be at odds with fossil evidence. Here, I use the fossilized birth–death process and the dispersal–extinction cladogenesis model to jointly infer the dated phylogeny and range evolution of the tree fern order Cyatheales. I use data for 101 fossil and 442 extant tree ferns to reconstruct the biogeographic history of the group over the last 220 million years. Fossil-aware reconstructions evince a prolonged occupancy of Laurasia over the Triassic–Cretaceous by Cyathealean tree ferns, which is evident in the fossil record but hidden from analyses relying on neontological data alone. Nonetheless, fossil-aware reconstructions are affected by uncertainty in fossils’ phylogenetic placement, taphonomic biases, and specimen sampling and are sensitive to interpretation of paleodistributions and how these are scored. The present results highlight the need and challenges of incorporating fossils into joint inferences of phylogeny and biogeography to improve the reliability of ancestral geographic range estimation.

Anest, A., Y. Bouchenak-Khelladi, T. Charles-Dominique, F. Forest, Y. Caraglio, G. P. Hempson, O. Maurin, and K. W. Tomlinson. 2024. Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems. Nature Plants.

Dense branching and spines are common features of plant species in ecosystems with high mammalian herbivory pressure. While dense branching and spines can inhibit herbivory independently, when combined, they form a powerful defensive cage architecture. However, how cage architecture evolved under mammalian pressure has remained unexplored. Here we show how dense branching and spines emerged during the age of mammalian radiation in the Combretaceae family and diversified in herbivore-driven ecosystems in the tropics. Phylogenetic comparative methods revealed that modern plant architectural strategies defending against large mammals evolved via a stepwise process. First, dense branching emerged under intermediate herbivory pressure, followed by the acquisition of spines that supported higher speciation rates under high herbivory pressure. Our study highlights the adaptive value of dense branching as part of a herbivore defence strategy and identifies large mammal herbivory as a major selective force shaping the whole plant architecture of woody plants. This study explores the evolution of two traits, branching density and spine presence, in the globally distributed plant family Combretaceae. These traits were found to have appeared in a two-step process in response to mammalian herbivory pressure, revealing the importance of large mammals in the evolution of plant architecture diversity.

Prochazka, L. S., S. Alcantara, J. G. Rando, T. Vasconcelos, R. C. Pizzardo, and A. Nogueira. 2024. Resource availability and disturbance frequency shape evolution of plant life forms in Neotropical habitats. New Phytologist.

Organisms use diverse strategies to thrive in varying habitats. While life history theory partly explains these relationships, the combined impact of resource availability and disturbance frequency on life form strategy evolution has received limited attention.We use Chamaecrista species, a legume plant lineage with a high diversity of plant life forms in the Neotropics, and employ ecological niche modeling and comparative phylogenetic methods to examine the correlated evolution of plant life forms and environmental niches.Chamaephytes and phanerophytes have optima in environments characterized by moderate water and nutrient availability coupled with infrequent fire disturbances. By contrast, annual plants thrive in environments with scarce water and nutrients, alongside frequent fire disturbances. Similarly, geophyte species also show increased resistance to frequent fire disturbances, although they thrive in resource‐rich environments.Our findings shed light on the evolution of plant strategies along environmental gradients, highlighting that annuals and geophytes respond differently to high incidences of fire disturbances, with one enduring it as seeds in a resource‐limited habitat and the other relying on reserves and root resprouting systems in resource‐abundant habitats. Furthermore, it deepens our understanding of how organisms evolve associated with their habitats, emphasizing a constraint posed by low‐resource and high‐disturbance environments.

Short, A. W., J. S. V. Sebastian, J. Huang, G. Wang, M. Dassanayake, P. M. Finnegan, J. D. Parker, et al. 2024. Comparative transcriptomics of the chilling stress response in two Asian mangrove species Bruguiera gymnorhiza and Rhizophora apiculata. Tree Physiology.

Abstract Low temperatures largely determine the geographic limits of plant species by reducing survival and growth. Interspecific differences in the geographic distribution of mangrove species have been associated with cold tolerance, with exclusively tropical species being highly cold-sensitive and subtropical species being relatively cold-tolerant. To identify species-specific adaptations to low temperatures, we compared the chilling stress response of two widespread Indo-West Pacific mangrove species from Rhizophoraceae with differing latitudinal range limits—Bruguiera gymnorhiza (subtropical range limit) and Rhizophora apiculata (tropical range limit). For both species, we measured the maximum photochemical efficiency of photosystem II (Fv/Fm) as a proxy for the physiological condition of the plants and examined gene expression profiles during chilling at 15 °C and 5 °C. At 15 °C, B. gymnorhiza maintained a significantly higher Fv/Fm than R. apiculata. However, at 5 °C, both species displayed equivalent Fv/Fm values. Thus, species-specific differences in chilling tolerance were only found at 15 °C, and both species were sensitive to chilling at 5 °C. At 15 °C, B. gymnorhiza down-regulated genes related to the light reactions of photosynthesis and up-regulated a gene involved in cyclic electron flow regulation, while R. apiculata down-regulated more RuBisCo related genes. At 5 °C, both species repressed genes related to CO2 assimilation. The down-regulation of genes related to light absorption and up-regulation of genes related to cyclic electron flow regulation are photoprotective mechanisms that likely contributed to the greater PSII photochecmical efficiency of B. gymnorhiza at 15 °C. The results of this study provide evidence that the distributional range limits and potentially the expansion rates of plant species are associated with differences in the regulation of photosynthesis and photoprotective mechanisms under low temperatures.