Science Enabled by Specimen Data

Calvente, A., A. P. Alves da Silva, D. Edler, F. A. Carvalho, M. R. Fantinati, A. Zizka, and A. Antonelli. 2023. Spiny but photogenic: amateur sightings complement herbarium specimens to reveal the bioregions of cacti. American Journal of Botany.

Premise: Cacti are characteristic elements of the Neotropical flora and of major interest for biogeographic, evolutionary, and ecological studies. Here we test global biogeographic boundaries for Neotropical Cactaceae using specimen‐based occurrences coupled with data from visual observations, as a means to tackle the known collection biases in the family.MethodsSpecies richness and record density were assessed for preserved specimens and human observations and a bioregional scheme tailored to Cactaceae was produced using the interactive web application Infomap Bioregions based on data from 261,272 point records cleaned through automated and manual steps.Key ResultsWe find that areas in Mexico and southwestern USA, Eastern Brazil and along the Andean region have the greatest density of records and the highest species richness. Human observations complement information from preserved specimens substantially, especially along the Andes. We propose 24 cacti bioregions, among which the most species‐rich are: northern Mexico/southwestern USA, central Mexico, southern central Mexico, Central America, Mexican Pacific coast, central and southern Andes, northwestern Mexico/extreme southwestern USA, southwestern Bolivia, northeastern Brazil, Mexico/Baja California.ConclusionsThe bioregionalization proposed shows biogeographical boundaries specific to cacti, and can thereby aid further evolutionary, biogeographic, and ecological studies by providing a validated framework for further analyses. This classification builds upon, and is distinctive from, other expert‐derived regionalization schemes for other taxa. Our results showcase how observation data, including citizen‐science records, can complement traditional specimen‐based data for biogeographic research, particularly for taxa with specific specimen collection and preservation challenges and those that are threatened or internationally protected.This article is protected by copyright. All rights reserved.

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.

The objective of this work is to study the ethno botanical importance of Anogeissus leiocarpa and the potential impacts of climate and global changes on the spatial distribution of the species in order to contribute to its conservation and sustainable use. One hundred and eighty-nine (189) peoples were surveyed in the ten phytodistricts of Benin. Occurrences of Anogeissus leiocarpa downloaded from the Global Biodiversity Information Facility (GBIF) website (; dl.qgwnvf) was supplemented with those collected in the field to model the spatial distribution and the ecological niche of the species. Environmental climatic data were downloaded from Worldclim and Africlim website at the resolution of 2.5 minutes; non-climatic environmental data as soil, population and distance to dwellings (Settlement) were respectively downloaded from ISRIC and SEDAC website at the same resolution. The results of five modeling algorithms were compared: Maxent, BRT, RF, GLM, and GAM. From the main results, Anogeissus leiocarpa is well known and variously used by the surveyed population. Three categories of use were named: wood use (64 %), medicinal use (35 %) and spiritual or medico-magical use (1 %). The most named parts of the plants are the trunk and the leaves. Seven (7) forms of usage were named: service wood, decoction, timber, fuelwood, power, toothpick and trituration. Maxent and BRT algorithms have shown the best performance to predict suitable areas of Anogeissus leiocarpa (compared to RF, GLM and GAM) and were therefore combined to define conservation strategies for the species. Globally, there is an extension of the new suitable areas of the species. The suitable areas of the species are seldom threatened by climate change in Africa and Benin. Also, the protected areas of Benin will remain effective for the conservation of the species in the present and in the future.

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.

Telford, E. M., N. Stevens, G. F. Midgley, and C. E. R. Lehmann. 2023. Nodulation alleviates the stress of lower water availability in Vachellia sieberiana. Plant Ecology.

The genus Vachellia (Fabaceae) has a pan-tropical distribution and numerous Vachellia species are currently observed to be expanding their indigenous ranges and/or are invasive. Most Vachellia species have the capacity to enhance nitrogen uptake via an N 2 -fixing rhizobial mutualism that manifests in specialized root nodule structures enabling the catalysis of atmospheric N 2 into a plant useable form. Improved understanding of nodulation may provide new insight to the changing patterns of ecological success of Vachellia species. Here, we investigated how the seedling growth, allometry and nodulation of two common Vachellia species, the arid Vachellia erioloba and the mesic Vachellia sieberiana , responded to varied levels of water availability. Seedlings were grown at 4%, 8% and 16% soil moisture content (SMC) for four months. The seedling growth and allometry of V. erioloba was unresponsive to changing water availability, and no nodulation was observed. The allometry of V. sieberiana was responsive to changing water availability and nodulation was observed; with the highest nodule biomass and growth rate recorded at 4% SMC. These patterns suggest that V. erioloba does not require the rhizobial mutualism, possibly due to lower competitive interactions between woody plants and grass in the arid savanna. Whereas, due to the competitive vegetation interactions typical in the mesic savanna, N 2 - fixation via nodule development could provide V. sieberiana a competitive advantage over grass not only in limited N conditions, but also during periods of lower water availability.

Reichgelt, T., A. Baumgartner, R. Feng, and D. A. Willard. 2023. Poleward amplification, seasonal rainfall and forest heterogeneity in the Miocene of the eastern USA. Global and Planetary Change 222: 104073.

Paleoclimate reconstructions can provide a window into the environmental conditions in Earth history when atmospheric carbon dioxide concentrations were higher than today. In the eastern USA, paleoclimate reconstructions are sparse, because terrestrial sedimentary deposits are rare. Despite this, the eastern USA has the largest population and population density in North America, and understanding the effects of current and future climate change is of vital importance. Here, we provide terrestrial paleoclimate reconstructions of the eastern USA from Miocene fossil floras. Additionally, we compare proxy paleoclimate reconstructions from the warmest period in the Miocene, the Miocene Climatic Optimum (MCO), to those of an MCO Earth System Model. Reconstructed Miocene temperatures and precipitation north of 35°N are higher than modern. In contrast, south of 35°N, temperatures and precipitation are similar to today, suggesting a poleward amplification effect in eastern North America. Reconstructed Miocene rainfall seasonality was predominantly higher than modern, regardless of latitude, indicating greater variability in intra-annual moisture transport. Reconstructed climates are almost uniformly in the temperate seasonal forest biome, but heterogeneity of specific forest types is evident. Reconstructed Miocene terrestrial temperatures from the eastern USA are lower than modeled temperatures and coeval Atlantic sea surface temperatures. However, reconstructed rainfall is consistent with modeled rainfall. Our results show that during the Miocene, climate was most different from modern in the northeastern states, and may suggest a drastic reduction in the meridional temperature gradient along the North American east coast compared to today.

Campbell, L. C. E., E. T. Kiers, and G. Chomicki. 2022. The evolution of plant cultivation by ants. Trends in Plant Science.

Outside humans, true agriculture was previously thought to be restricted to social insects farming fungus. However, obligate farming of plants by ants was recently discovered in Fiji, prompting a re-examination of plant cultivation by ants. Here, we generate a database of plant cultivation by ants, identify three main types, and show that these interactions evolved primarily for shelter rather than food. We find that plant cultivation evolved at least 65 times independently for crops (~200 plant species), and 15 times in farmer lineages (~37 ant taxa) in the Neotropics and Asia/Australasia. Because of their high evolutionary replication, and variation in partner dependence, these systems are powerful models to unveil the steps in the evolution and ecology of insect agriculture.

Hinojosa-Espinosa, O., D. Potter, M. Ishiki, E. Ortiz, and J. L. Villaseñor. 2021. Dichrocephala integrifolia (Astereae, Asteraceae), a new exotic genus and species for Mexico and second record for the New World. Botanical Sciences 99: 708–716.

Background: Dichrocephala is an Old-World genus of the tribe Astereae within the family Asteraceae. One species, D . integrifolia , has been recently reported as introduced in the New World from a pair of collections from Guatemala. During field work in the state of Chiapas in southern Mexico, the species was found and collected. This is the first record of both the genus and species in Mexico and the second record for these taxa in the Americas.
 Question: Can D . integrifolia occur in more areas in the New World besides those known from Guatemala and Chiapas?
 Studied species: Dichrocephala integrifolia 
 Study site and dates: Mexico, Central America, and the Caribbean.
 Methods: An ecological niche model was made and it was projected into the New World.
 Results: The ecological niche model predicts the records of D. integrifolia in the New World in addition to other ecologically suitable areas, mostly in pine-oak forests in Mexico and Central America and zones with humid mountain and pine forest in the Caribbean. Moreover, a morphological description and illustrations of the species are provided to help with its identification.
 Conclusions: It is desirable to avoid the further spreading of D . integrifolia in the New World. Although this species is not considered as invasive, it seems to have a high dispersal potential and the ecological niche modelling indicates larger regions in the Americas that might be affected.

Ripley, B. S., S. L. Raubenheimer, L. Perumal, M. Anderson, E. Mostert, B. S. Kgope, G. F. Midgley, and K. J. Simpson. 2022. CO 2 ‐fertilisation enhances resilience to browsing in the recruitment phase of an encroaching savanna tree. Functional Ecology.

CO2‐fertilisation is implicated in the widespread and significant woody encroachment of savannas due to CO2‐stimulated increases in belowground reserves that enhance sapling regrowth after fire. However, the effect of CO2 concentration ([CO2]) on tree responses to the other major disturbance in savannas, herbivory, is poorly understood. Herbivory‐responses cannot be predicted from fire‐responses, as herbivore effects occur earlier during establishment and are moderated by plant palatability and defence rather than belowground carbon accumulation.

Matvijev, K., S. Dellicour, E. Kaymak, and O. J. Hardy. 2022. Spatially explicit phylogeographical reconstruction sheds light on the history of the forest cover in the Congo Basin. Journal of Biogeography.

Aim The impact of Pleistocene climatic oscillations on the biodiversity of African tropical rain forests remains poorly understood, and the Congo Basin is particularly understudied. We aim to elucidate how Pleistocene climatic oscillations shaped lowland tropical rain forests by investigating the intraspecific diversity and evolutionary history of a widespread tree species. Location Guineo-Congolian rain forest, Central Africa. Taxon Staudtia kamerunensis Warb. (Myristicaceae). Methods We used genome skimming combined with maximum likelihood and Bayesian inference to infer the plastid phylogeny. We estimated the time of speciation and differentiation, genetic diversity, and we employed a continuous phylogeographical approach to infer the dispersal history of its plastid lineages. Results We sequenced an average of 5,827,783 reads per sample, and the reconstructed reference plastome had a mean depth of 73.3. We identified five plastid lineages that diverged during the Early or Middle Pleistocene and are parapatric, suggesting past population fragmentation. Four lineages are endemic to Lower Guinea, and one spans the Congo Basin. We found contrasting patterns of expansion in the two regions, with a rapid and recent range expansion of the Congolian lineage in the last 200,000 years, while the spread of the Lower Guinean lineages was substantially slower. Main conclusion The contrasting demographic histories between eastern and western lineages, associated with contrasted levels of plant species richness and rates of endemism, suggest that forest cover was more stable in Lower Guinea during the Late Pleistocene than in Congolia, where the biodiversity might have been eroded before the forest re-expanded in the Congo basin. This study illustrates how a continuous phylogeographical inference approach, mostly applied so far for inferring the spread of fast-evolving pathogens over months or years, can provide new insights to reconstruct the dispersal history of tropical tree species over thousands or millions of years.