Science Enabled by Specimen Data
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. https://doi.org/10.1111/jbi.14683
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.
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. https://doi.org/10.3389/fpls.2023.1173328
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.
Obiakara, M. C., O. S. Olubode, and K. S. Chukwuka. 2023. Climate change and the potential distribution of the invasive shrub, Leucaena leucocephala (Lam.) De Wit in Africa. Tropical Ecology. https://doi.org/10.1007/s42965-023-00294-w
Leucaena leucocephala , previously known as ‘miracle tree’ because of its numerous agroforestry uses has become a serious invasive species in tropical regions. Despite the risks associated with the spread of L. leucocephala , changes in its distribution with respect to climate are poorly understood, particularly in Africa where it has been widely introduced in more than 30 countries. To provide first-line information for the management of L. leucocephala , we examined its potential distribution in Africa using ecological niche modelling. We identified bioclimatic variables that determine the global distribution of L. leucocephala , and calibrated niche models using MaxEnt and species occurrences recorded between 1973 and 2013. The potential distribution of this species was estimated from model projections in Africa based on current and future climatic conditions. We tested the hypothesis of niche conservatism for L. leucocephala by comparing its climatic niche in Africa to that of its native range. Under current conditions, L. leucocephala is constrained between 30° S and 20° N in Africa, with the broadest distribution in East Africa. High rainfall areas in Central Africa with no known records of this species hitherto, were found to be highly suitable for its establishment. We predicted a significant decrement in the extent of areas at risk of invasion by L. Leucocephala under changing climates in Africa. Our results revealed that the study species occupies a similar but non-identical climatic niche in Africa in relation to its native niche. Climate change is likely to impede the spread of L. leucocephala in Africa.
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. https://doi.org/10.1007/s11258-023-01302-8
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. https://doi.org/10.1016/j.gloplacha.2023.104073
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.
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. https://doi.org/10.17129/botsci.2754
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. https://doi.org/10.1111/1365-2435.14215
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.
Williams, C. J. R., D. J. Lunt, U. Salzmann, T. Reichgelt, G. N. Inglis, D. R. Greenwood, W. Chan, et al. 2022. African Hydroclimate During the Early Eocene From the DeepMIP Simulations. Paleoceanography and Paleoclimatology 37. https://doi.org/10.1029/2022pa004419
The early Eocene (∼56‐48 million years ago) is characterised by high CO2 estimates (1200‐2500 ppmv) and elevated global temperatures (∼10 to 16°C higher than modern). However, the response of the hydrological cycle during the early Eocene is poorly constrained, especially in regions with sparse data coverage (e.g. Africa). Here we present a study of African hydroclimate during the early Eocene, as simulated by an ensemble of state‐of‐the‐art climate models in the Deep‐time Model Intercomparison Project (DeepMIP). A comparison between the DeepMIP pre‐industrial simulations and modern observations suggests that model biases are model‐ and geographically dependent, however these biases are reduced in the model ensemble mean. A comparison between the Eocene simulations and the pre‐industrial suggests that there is no obvious wetting or drying trend as the CO2 increases. The results suggest that changes to the land sea mask (relative to modern) in the models may be responsible for the simulated increases in precipitation to the north of Eocene Africa. There is an increase in precipitation over equatorial and West Africa and associated drying over northern Africa as CO2 rises. There are also important dynamical changes, with evidence that anticyclonic low‐level circulation is replaced by increased south‐westerly flow at high CO2 levels. Lastly, a model‐data comparison using newly‐compiled quantitative climate estimates from palaeobotanical proxy data suggests a marginally better fit with the reconstructions at lower levels of CO2.
Reichgelt, T., D. R. Greenwood, S. Steinig, J. G. Conran, D. K. Hutchinson, D. J. Lunt, L. J. Scriven, and J. Zhu. 2022. Plant Proxy Evidence for High Rainfall and Productivity in the Eocene of Australia. Paleoceanography and Paleoclimatology 37. https://doi.org/10.1029/2022pa004418
During the early to middle Eocene, a mid‐to‐high latitudinal position and enhanced hydrological cycle in Australia would have contributed to a wetter and “greener” Australian continent where today arid to semi‐arid climates dominate. Here, we revisit 12 southern Australian plant megafossil sites from the early to middle Eocene to generate temperature, precipitation and seasonality paleoclimate estimates, net primary productivity (NPP) and vegetation type, based on paleobotanical proxies and compare to early Eocene global climate models. Temperature reconstructions are uniformly subtropical (mean annual, summer, and winter mean temperatures 19–21 °C, 25–27 °C and 14–16 °C, respectively), indicating that southern Australia was ∼5 °C warmer than today, despite a >20° poleward shift from its modern geographic location. Precipitation was less homogeneous than temperature, with mean annual precipitation of ∼60 cm over inland sites and >100 cm over coastal sites. Precipitation may have been seasonal with the driest month receiving 2–7× less than mean monthly precipitation. Proxy‐model comparison is favorable with an 1680 ppm CO2 concentration. However, individual proxy reconstructions can disagree with models as well as with each other. In particular, seasonality reconstructions have systemic offsets. NPP estimates were higher than modern, implying a more homogenously “green” southern Australia in the early to middle Eocene, when this part of Australia was at 48–64 °S, and larger carbon fluxes to and from the Australian biosphere. The most similar modern vegetation type is modern‐day eastern Australian subtropical forest, although distance from coast and latitude may have led to vegetation heterogeneity.
Sluiter, I. R. K., G. R. Holdgate, T. Reichgelt, D. R. Greenwood, A. P. Kershaw, and N. L. Schultz. 2022. A new perspective on Late Eocene and Oligocene vegetation and paleoclimates of South-eastern Australia. Palaeogeography, Palaeoclimatology, Palaeoecology 596: 110985. https://doi.org/10.1016/j.palaeo.2022.110985
We present a composite terrestrial pollen record of latest Eocene through Oligocene (35.5–23 Ma) vegetation and climate change from the Gippsland Basin of south-eastern Australia. Climates were overwhelmingly mesothermic through this time period, with mean annual temperature (MAT) varying between 13 and 18 °C, with an average of 16 °C. We provide evidence to support a cooling trend through the Eocene–Oligocene Transition (EOT), but also identify three subsequent warming cycles through the Oligocene, leading to more seasonal climates at the termination of the Epoch. One of the warming episodes in the Early Oligocene appears to have also occurred at two other southern hemisphere sites at the Drake Passage as well as off eastern Tasmania, based on recent research. Similarities with sea surface temperature records from modern high southern latitudes which also record similar cycles of warming and cooling, are presented and discussed. Annual precipitation varied between 1200 and 1700 mm/yr, with an average of 1470 mm/yr through the sequence. Notwithstanding the extinction of Nothofagus sg. Brassospora from Australia and some now microthermic humid restricted Podocarpaceae conifer taxa, the rainforest vegetation of lowland south-eastern Australia is reconstructed to have been similar to present day Australian Evergreen Notophyll Vine Forests existing under the sub-tropical Köppen-Geiger climate class Cfa (humid subtropical) for most of the sequence. Short periods of cooler climates, such as occurred through the EOT when MAT was ~ 13 °C, may have supported vegetation similar to modern day Evergreen Microphyll Fern Forest. Of potentially greater significance, however, was a warm period in the Early to early Late Oligocene (32–26 Ma) when MAT was 17–18 °C, accompanied by small but important increases in Araucariaceae pollen. At this time, Araucarian Notophyll/Microphyll Vine Forest likely occurred regionally.