Science Enabled by Specimen Data

Campbell, L. C. E., E. T. Kiers, and G. Chomicki. 2022. The evolution of plant cultivation by ants. Trends in Plant Science. https://doi.org/10.1016/j.tplants.2022.09.005

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. 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.

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. https://doi.org/10.1111/jbi.14507

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.

Amaral, D. T., I. A. S. Bonatelli, M. Romeiro-Brito, E. M. Moraes, and F. F. Franco. 2022. Spatial patterns of evolutionary diversity in Cactaceae show low ecological representation within protected areas. Biological Conservation 273: 109677. https://doi.org/10.1016/j.biocon.2022.109677

Mapping biodiversity patterns across taxa and environments is crucial to address the evolutionary and ecological dimensions of species distribution, suggesting areas of particular importance for conservation purposes. Within Cactaceae, spatial diversity patterns are poorly explored, as are the abiotic factors that may predict these patterns. We gathered geographic and genetic data from 921 cactus species by exploring both the occurrence and genetic databases, which are tightly associated with drylands, to evaluate diversity patterns, such as phylogenetic diversity and endemism, paleo-, neo-, and superendemism, and the environmental predictor variables of such patterns in a global analysis. Hotspot areas of cacti diversity are scattered along the Neotropical and Nearctic regions, mainly in the desertic portion of Mesoamerica, Caribbean Island, and the dry diagonal of South America. The geomorphological features of these regions may create a complexity of areas that work as locally buffered zones over time, which triggers local events of diversification and speciation. Desert and dryland/dry forest areas comprise paleo- and superendemism and may act as both museums and cradles of species, displaying great importance for conservation. Past climates, topography, soil features, and solar irradiance seem to be the main predictors of distinct endemism types. The hotspot areas that encompass a major part of the endemism cells are outside or poorly covered by formal protection units. The current legally protected areas are not able to conserve the evolutionary diversity of cacti. Given the rapid anthropogenic disturbance, efforts must be reinforced to monitor biodiversity and the environment and to define/plan current and new protected areas.

Kapuka, A., L. Dobor, and T. Hlásny. 2022. Climate change threatens the distribution of major woody species and ecosystem services provision in southern Africa. Science of The Total Environment 850: 158006. https://doi.org/10.1016/j.scitotenv.2022.158006

In southern Africa, woody vegetation provides essential ecological, regulation, and cultural ecosystem services (ES), yet many species and ecosystems are increasingly threatened by climate change and land-use transformations. We investigated the effect of climate change on the distribution of eight species in 18 countries in southern Africa, covering 36 % of the continent. We proposed a loser/winner ranking of the species based on the changes in land climatic suitability within their historical distribution and future gains and losses of suitable areas. We interpreted these findings in terms of changes in key ES (timber, food, and energy) provision and identified hotspots of ES provision decline. We used species presence data from the Global Biodiversity Information Facility, climatic data from the AfriClim dataset, and the MaxEnt algorithm to project the changes in species-specific land climatic suitability.Among the eight investigated species, the baseline suitability range of Mopane (Colophosperm mopane) was least affected by climate change. At the same time, the area of its future distribution was projected to double, rendering it a regional winner. Another two species, manketti (Schinziophyton rautanenii) and leadwood (Combretum imberbe) showed high future gains too; however, the impact on their baseline suitability range differed between the climatic scenarios. The baseline range of African rosewood (Guibourtia coleosperma) declined entirely, and the future gains were negligible, rendering the species a regional loser. The effect of climate change was particularly severe on timber-producing species (four out of eight species), while species providing food (four species) and energy (four species) were affected less. Our projections portrayed distinct hotspot and coldspot areas, where climatic suitability for multiple species was concurrently projected to decline or persist. This assessment can inform spatially targeted adaptation and conservation actions and strategies, which are currently lacking in many African regions.

Boeschoten, L. E., U. Sass-Klaassen, M. Vlam, R. N. J. Comans, G. F. Koopmans, B. R. V. Meyer-Sand, S. N. Tassiamba, et al. 2022. Clay and soil organic matter drive wood multi-elemental composition of a tropical tree species: Implications for timber tracing. Science of The Total Environment 849: 157877. https://doi.org/10.1016/j.scitotenv.2022.157877

Forensic methods to independently trace timber origin are essential to combat illegal timber trade. Tracing product origin by analysing their multi-element composition has been successfully applied in several commodities, but its potential for timber is not yet known. To evaluate this potential the drivers of wood multi-elemental composition need to be studied. Here we report on the first study relating wood multi-elemental composition of forest trees to soil chemical and physical properties.We studied the reactive soil element pools and the multi-elemental composition in sapwood and heartwood for 37 Azobé (Lophira alata) trees at two forest sites in Cameroon. A total of 46 elements were measured using ICP-MS. We also measured three potential drivers of soil and wood elemental composition: clay content, soil organic matter and pH. We tested associations between soil and wood using multiple regressions and multivariate analyses (Mantel test, db-RDA). Finally, we performed a Random Forest analysis of heartwood elemental composition to check site assignment accuracy.We found elemental compositions of soil, sapwood and heartwood to be significantly associated. Soil clay content and organic matter positively influenced individual element concentrations (for 13 and 9 elements out of 46 respectively) as well as the multi-elemental composition in wood. However, associations between wood and topsoil elemental concentrations were only significant for one element. We found close associations between element concentrations and composition in sapwood and heartwood. Lastly, the Random Forest assignment success was 97.3 %.Our findings indicate that wood elemental composition is associated with that in the topsoil and its variation is related to soil clay and organic matter content. These associations suggests that the multi-elemental composition of wood can yield chemical fingerprints obtained from sites that differ in soil properties. This finding in addition to the high assignment accuracy shows potential of multi-element analysis for tracing wood origin.

Führding‐Potschkat, P., H. Kreft, and S. M. Ickert‐Bond. 2022. Influence of different data cleaning solutions of point‐occurrence records on downstream macroecological diversity models. Ecology and Evolution 12. https://doi.org/10.1002/ece3.9168

Digital point‐occurrence records from the Global Biodiversity Information Facility (GBIF) and other data providers enable a wide range of research in macroecology and biogeography. However, data errors may hamper immediate use. Manual data cleaning is time‐consuming and often unfeasible, given that the databases may contain thousands or millions of records. Automated data cleaning pipelines are therefore of high importance. Taking North American Ephedra as a model, we examined how different data cleaning pipelines (using, e.g., the GBIF web application, and four different R packages) affect downstream species distribution models (SDMs). We also assessed how data differed from expert data. From 13,889 North American Ephedra observations in GBIF, the pipelines removed 31.7% to 62.7% false positives, invalid coordinates, and duplicates, leading to datasets between 9484 (GBIF application) and 5196 records (manual‐guided filtering). The expert data consisted of 704 records, comparable to data from field studies. Although differences in the absolute numbers of records were relatively large, species richness models based on stacked SDMs (S‐SDM) from pipeline and expert data were strongly correlated (mean Pearson's r across the pipelines: .9986, vs. the expert data: .9173). Our results suggest that all R package‐based pipelines reliably identified invalid coordinates. In contrast, the GBIF‐filtered data still contained both spatial and taxonomic errors. Major drawbacks emerge from the fact that no pipeline fully discovered misidentified specimens without the assistance of taxonomic expert knowledge. We conclude that application‐filtered GBIF data will still need additional review to achieve higher spatial data quality. Achieving high‐quality taxonomic data will require extra effort, probably by thoroughly analyzing the data for misidentified taxa, supported by experts.

Zhao, J., X. Yu, W. J. Kress, Y. Wang, Y. Xia, and Q. Li. 2022. Historical biogeography of the gingers and its implications for shifts in tropical rain forest habitats. Journal of Biogeography 49: 1339–1351. https://doi.org/10.1111/jbi.14386

Aim The relationships between biome shifts and global environmental changes in temperate zone habitats have been extensively explored; yet, the historical dynamics of taxa found in the tropical rain forest (TRF) remain poorly known. This study aims to reconstruct the relationships between tropical rain forest shifts and global environmental changes through the patterns of historical biogeography of a pantropical family of monocots, the Zingiberaceae. Location Global. Taxon Zingiberaceae. Methods We sampled DNA sequences (nrITS, trnK, trnL-trnF and psbA-trnH) from GenBank for 77% of the genera, including 30% of species, in the Zingiberaceae. Global fossil records of the Zingiberaceae were collected from literatures. Rates of speciation, extinction and diversification were estimated based on phylogenetic data and fossil records through methods implemented in BAMM. Ancestral ranges were estimated using single-tree BioGeoBEARS and multiple-trees BioGeoBEARS in RASP. Dispersal rate through time and dispersal rate among regions were calculated in R based on the result of ancestral estimation. Results The common ancestor of the Zingiberaceae likely originated in northern Africa during the mid-Cretaceous, with later dispersal to the Asian tropics. Indo-Burma, rather than Malesia, was likely a provenance of the common ancestor of Alpinioideae–Zingiberoideae. Several abrupt shifts of evolutionary rates from the Palaeocene were synchronized with sudden global environmental changes. Main conclusions Integrating phylogenetic patterns with fossil records suggests that the Zingiberaceae dispersed to Asia through drift of the Indian Plate from Africa in the late Palaeocene. Formation of island chains, land corridors and warming temperatures facilitated the emigration of the Zingiberaceae to a broad distribution across the tropics. Moreover, dramatic fluctuations of the speciation rate of Zingiberoideae appear to have been synchronized with global climate fluctuations. In general, the evolutionary history of the Zingiberaceae broadens our understanding of the association between TRF shifts in distribution and past global environmental changes, especially the origin of TRF in Southeast Asia.

Catarino, S., D. Goyder, I. Darbyshire, E. Costa, R. Figueira, M. C. Duarte, and M. M. Romeiras. 2022. Species Diversity and Endemicity in the Angolan Leguminosae Flora. Frontiers in Ecology and Evolution 10. https://doi.org/10.3389/fevo.2022.871261

Angola has a great diversity of species and ecosystems and a high level of endemism. However, knowledge of the native flora remains very incomplete and outdated. Leguminosae is the largest family in the country, including many species which are of local or more regional economic importance. Based on an extensive review of bibliographic sources, natural history collections, and online databases, the checklist of Angolan Leguminosae plants was updated, including data on their native distribution, conservation status, and principal uses. The endemic taxa were the subject of additional investigation, including the main habitat, the number of collections preserved in herbaria, and the locality of the first collection. We identified 953 Leguminosae taxa occurring in Angola, of which 165 are endemic to the country. Among the 180 genera found, Crotalaria (136) and Indigofera (96) have the highest number of taxa. Almost half of the studied species have important applications, mainly in traditional medicine (385), forage (267), timber (188), and food (120). Nevertheless, only 27.7% have been assessed according to the IUCN Red List and 10 species are classified as threatened. Thirty-three endemics are known only from the type specimen, revealing the lack of knowledge on these species and the need for further field research. More than 30 type specimens were collected in the Serra da Chela, which highlights the importance of this region for biodiversity conservation.