Science Enabled by Specimen Data

Bugado, R. E., N. Shrestha, R. A. Magri, J. Prado, and J. C. Lopes. 2025. Vanishing ecosystems: The looming threat of climate change on an iconic genus Vellozia in the Brazilian campos rupestres. Global Ecology and Conservation 58: e03439. https://doi.org/10.1016/j.gecco.2025.e03439

Climate change poses a significant threat to biodiversity and habitats worldwide, with mountainous regions and endemic species particularly vulnerable. One such ecosystem is the campos rupestres, a mountainous environment in the highlands of central-eastern Brazil, characterized by high species richness and endemism. Among this ecosystem's most diverse and abundant endemic genera is Vellozia (Velloziaceae), comprising 127 species. Using species distribution modeling, we assessed how climate change will likely affect suitable habitats for the genus. Additionally, we conducted IUCN extinction risk assessments and applied the EDGE2 method, incorporating a phylogenetic framework to identify species that should be prioritized for conservation. Our findings indicate that, on average, each species of Vellozia is expected to lose 84.26 % of its suitable habitat by 2060, with 13 species projected to lose 100 % of their habitat. Over half of the genus is projected to lose over 92 % of its suitable habitat. The species richness and endemism of Vellozia in the campos rupestres will diminish substantially in both geographic extent and species count. This decline is particularly concerning given that nearly half of the genus is microendemic, with 16 species occurring entirely outside protected areas. These findings highlight the potential for climate change to drastically reduce the habitat size and species richness of Vellozia and overall biodiversity within the campos rupestres ecosystem.

Hagelstam-Renshaw, C., J. J. Ringelberg, C. Sinou, W. Cardinal-McTeague, and A. Bruneau. 2024. Biome evolution in subfamily Cercidoideae (Leguminosae): a tropical arborescent clade with a relictual depauperate temperate lineage. Brazilian Journal of Botany 48. https://doi.org/10.1007/s40415-024-01058-z

Some plant lineages remain within the same biome over time (biome conservatism), whereas others seem to adapt more easily to new biomes. The c. 398 species (14 genera) of subfamily Cercidoideae (Leguminosae or Fabaceae) are found in many biomes around the world, particularly in the tropical regions of South America, Asia and Africa, and display a variety of growth forms (small trees, shrubs, lianas and herbaceous perennials). Species distribution maps derived from cleaned occurrence records were compiled and compared with existing biome maps and with the literature to assign species to biomes. Rainforest (144 species), succulent (44 species), savanna (36 species), and temperate (10 species) biomes were found to be important in describing the global distribution of Cercidoideae, with many species occurring in more than one biome. Two phylogenetically isolated species-poor temperate ( Cercis ) and succulent ( Adenolobus ) biome lineages are sister to two broadly distributed species-rich tropical clades. Ancestral state reconstructions on a time-calibrated phylogeny suggest biome shifts occurred throughout the evolutionary history of the subfamily, with shifts between the succulent and rainforest biomes, from the rainforest to savanna, from the succulent to savanna biome, and one early occurring shift into (or from) the temperate biome. Of the 26 inferred shifts in biome, three are closely associated with a shift from the ancestral tree/shrub growth form to a liana or herbaceous perennial habit. Only three of the 13 inferred transcontinental dispersal events are associated with biome shifts. Overall, we find that biome shifts tend to occur within the same continent and that dispersals to new continents tend to occur within the same biome, but that nonetheless the biome-conserved and biogeographically structured Cercidoideae have been able to adapt to different environments through time.

Streiff, S. J. R., E. O. Ravomanana, M. Rakotoarinivo, M. Pignal, E. P. Pimparé, R. H. J. Erkens, and T. L. P. Couvreur. 2024. High-quality herbarium-label transcription by citizen scientists improves taxonomic and spatial representation of the tropical plant family Annonaceae. Adansonia 46. https://doi.org/10.5252/adansonia2024v46a18

Herbarium specimens provide an important and central resource for biodiversity research. Making these records digitally available to end-users represents numerous challenges, in particular, transcribing metadata associated with specimen labels. In this study, we used the citizen science initiative ‘Les Herbonautes’ and the Récolnat network to transcribe specific data from all herbarium specimen labels stored at the Muséum national d’Histoire naturelle in Paris of the large tropical plant family Annonaceae. We compared this database with publicly available global biodiversity repository data and expert checklists. We investigated spatial and taxonomic advances in data availability at the global and country scales. A total of 20 738 specimens were transcribed over the course of more than two years contributing to and significantly extending the previously available specimen and species data for Annonaceae worldwide. We show that several regions, mainly in Africa and South East Asia not covered by online global datasets, are uniquely available in the P herbarium, probably linked to past history of the museum’s botanical exploration. While acknowledging the challenges faced during the transcription of historic specimens by citizen scientists, this study highlights the positive impact of adding records to global datasets both in space and time. This is illustrative for researchers, collection managers, policy makers as well as funders. These datasets will be valuable for numerous future studies in biodiversity research, including ecology, evolution, conservation and climate change science.

Camarena-Yupanqui, R. C., E. Orellana-Mendoza, R. M. Bernaola-Paucar, F. N. Ames-Martínez, H. Loardo-Tovar, and H. R. Quispe-Melgar. 2024. Seedling Production of Retrophyllum rospigliosii in Nurseries and Potential Reforestation Areas Using Modeling Techniques. Forests 15: 2179. https://doi.org/10.3390/f15122179

The success of reforestation and restoration projects depends on several factors, with proper seedling management and the selection of an appropriate planting area being crucial. In Peru, the populations of Retrophyllum rospigliosii (Pilg.) C.N.Page (Ulcumano) have been decreasing due to intensive logging of one of the most valuable woods in South America’s tropical forests. There are few studies that unify the production of plants through seeds in nurseries and the identification of suitable areas to place the plants produced. Our study has two components. The first aimed to optimize the plant production process through an experiment that evaluated the effects of three doses of controlled-release fertilizer (CRF) (4.2, 8.4, and 12.6 g/L) and two container sizes (115 and 180 cc) on the morphological quality of seedlings in the nursery. The second component involved identifying potential reforestation areas using ecological niche modeling, based on climatic and edaphic variables. The results indicated that the 4.2 g/L CRF treatment for both container sizes had a significant positive effect on seedling growth. The average germination rate was 85% at 120 days. At six months after seedling transplantation, treatments of 4.2 g/L CRF in 115 cc and 180 cc containers were shown to have the best positive effect on morphological variables of seedlings, with a root collar diameter of 3.76 mm and a height of 13.25 cm. Regarding the potential niche models, an area of 6321.97 km2 with ideal conditions for reforestation with R. rospigliosii was estimated, with the departments of Huánuco, Pasco, Junín, and Cusco showing the highest potential. Based on this, it is estimated that over three million plants are needed for large-scale reforestation projects. Integrating silvicultural studies with niche models is a valuable tool for supporting reforestation and ecosystem restoration projects.

Kessous, I. M., H. Farooq, W. Testo, M. F. T. Jiménez, B. Neves, A. R. Pinto, F. Salgueiro, et al. 2024. New insights into the classification, diversification, and evolutionary dynamics of bromeliads. Botanical Journal of the Linnean Society. https://doi.org/10.1093/botlinnean/boae074

Abstract The Neotropics have been host to a myriad of geological and climatic events that have shaped the biodiversity present in the region. Bromeliaceae forms one of the most prominent components of the Neotropical flora, being considered the largest group nearly exclusive to the Americas, with almost 4000 species divided into eight subfamilies. Here, we utilize a new time-calibrated molecular phylogeny including 1268 bromeliad taxa and integrate habitat and morphological data to answer the following questions: (i) Are bromeliad subfamilies monophyletic, and did Neogene and Quaternary events in South America coincide with their divergence? (ii) Did naked seeds of berry-fruited species, epiphytic growth, and climatic factors increase bromeliad diversification? Our analysis reconstructed a new topology concerning some recently diverged lineages, with the genus Bromelia emerging as the sister group of a clade including all remaining Bromelioideae lineages + Puyoideae. Miocene events possibly triggered the diversification of bromeliads after a long period of stasis during the Palaeogene. We hypothesize that the morphological shift between Bromelia and Bromelioideae (except Bromelia) is related to the colonization of a new high-elevation environment by Puyoideae in the Andes. Additionally, our results show that naked seeds and the epiphytic growth form positively influence diversification rate, while precipitation, temperature, and elevation have a negative influence. We emphasize the importance of considering a variety of morphological and ecological features to enhance our understanding of bromeliad evolution.

Magri, R. A., F. Luebert, A. Cabral, S. Alcantara, L. G. Lohmann, J. Prado, and J. C. Lopes. 2024. Historical biogeography of Vellozia (Velloziaceae) reveals range expansion in South American mountaintops after climatic cooling events and increased diversification rates after the occupation of Southern Espinhaço Province. Botanical Journal of the Linnean Society. https://doi.org/10.1093/botlinnean/boae072

The campos rupestres and the Brazilian Atlantic Forest Inselbergs (BAFI) are highly diverse vegetation types that grow on mountaintops of eastern Brazil and show outstanding levels of endemism. The plant family Velloziaceae is an iconic element of these vegetations, with the genus Vellozia, being exceptionally abundant in both these vegetations. In this study, we use Vellozia as a model to address three main questions: (i) What was the distribution of Vellozia’s most recent common ancestor? (ii) Did the range expansions of Vellozia occur during periods characterized by global cooling? (iii) When did Vellozia colonize the different South American highlands they occupy nowadays? To address these questions, we reconstructed the phylogeny of Vellozia using sequences of four molecular markers analysed using Bayesian and maximum likelihood inferences. We used the resulting phylogeny to reconstruct the ancestral distribution of Vellozia using the DEC model. Our findings indicate that Vellozia originated and subsequently diversified in the Oligocene, when the genus was broadly distributed through the Andes, BAFI, Cerrado, Caatinga, and the Chapada Diamantina, suggesting that the Cerrado may acted as a corridor between the Andes and eastern mountaintop vegetations. Vellozia subsequently occupied the southern Espinhaço during the Early Miocene, which was followed by increased diversification rates and several range expansions, especially after the Middle-Miocene Climatic Optimum, when cooler and drier periods allowed the expansion of open environments and the retraction of forests, allowing Vellozia to expand their distribution. These results highlight the unique evolutionary history of Vellozia and the importance of climatic cooling for the expansion of the genus.

Bradshaw, C. D., D. L. Hemming, T. Mona, W. Thurston, M. K. Seier, D. P. Hodson, J. W. Smith, et al. 2024. Transmission pathways for the stem rust pathogen into Central and East Asia and the role of the alternate host, barberry. Environmental Research Letters 19: 114097. https://doi.org/10.1088/1748-9326/ad7ee3

Abstract After many decades of effective control of stem rust caused by the Puccinia graminis f.sp. tritici, (hereafter Pgt) the reported emergence of race TTKSK/Ug99 of Pgt in Uganda reignited concerns about epidemics worldwide because ∼90% of world wheat cultivars had no resistance to the new race. Since it was initially detected in Uganda in 1998, Ug99 variants have now been identified in thirteen countries in Africa and the Middle East. Stem rust has been a major problem in the past, and concern is increasing about the risk of return to Central and East Asia. Whilst control programs in North America and Europe relied on the use of resistant cultivars in combination with eradication of barberry (Berberis spp.), the alternate host required for the stem rust pathogen to complete its full lifecycle, the focus in East Asia was principally on the use of resistant wheat cultivars. Here, we investigate potential airborne transmission pathways for stem rust outbreaks in the Middle East to reach East Asia using an integrated modelling framework combining estimates of fungal spore deposition from an atmospheric dispersion model, environmental suitability for spore germination, and crop calendar information. We consider the role of mountain ranges in restricting transmission pathways, and we incorporate a representation of a generic barberry species into the lifecycle. We find viable transmission pathways to East Asia from the Middle East to the north via Central Asia and to the south via South Asia and that an initial infection in the Middle East could persist in East Asia for up to three years due to the presence of the alternate host. Our results indicate the need for further assessment of barberry species distributions in East Asia and appropriate methods for targeted surveillance and mitigation strategies should stem rust incidence increase in the Middle East region.

Morales-Rozo, C., I. S. Acuña-Rodríguez, J. C. Benavides, V. J. Rincón-Parra, and M. Diazgranados. 2024. Prioritization of important plant areas for conservation of frailejones (Espeletiinae, Asteraceae) in the Northern Andes. Biodiversity and Conservation 33: 4073–4098. https://doi.org/10.1007/s10531-024-02939-1

The tropical Andes region harbors areas that are highly significant for biodiversity at both global and local scales. However, despite the severe conservation threats that this region has to confront, conservation initiatives are limited, by funding and because of the need for more information to decide which areas are priorities for conservation. Identifying Important Plant Areas (IPAs) offers a valuable methodology for establishing conservation priorities, a particularly complex task in a mega-biodiverse region such as the northern Andean tropics. Due to its iconic recognition and conservation value, this study focused on the Espeletiinae subtribe (Asteraceae) as a model group; hence, the distribution data for 138 species was compiled from 5560 georeferenced records. Using the IPA methodology, we divided the study area, this is, the distribution area of the subtribe in the Andean tropics, into 220 Units of Analysis (UA) represented by 10 × 10 km plots. Refined species’ distribution areas, incorporating richness, threatened species, and ecosystem-based richness distributions, were analyzed using newly generated maps to evaluate the conservation value of each UA. Our analysis identified 176 UAs with some level of relevance using sub-criterion cA1 (with 59 species) and 51 UAs using sub-criterion cB (with 76 species). Integrating both criteria, we classified 11 UAs as high-priority, 62 as medium-priority, and 147 as low-priority, highlighting the IPAs that require focused conservation efforts. Two identified high-priority IPAs are located in Venezuela and nine in Colombia, predominantly associated with the Eastern Cordillera. These areas concentrate between 7 and 12 species. They are mainly linked to the páramo complexes of Colombia and the Sierra Nevada in Venezuela, primarily within Cool Temperate Moist Grassland ecosystems on mountains. Our results provide a spatial planning procedure and analytical tool for decision-makers to guide conservation management and actions across northern Andes.

Shirey, V., and J. Rabinovich. 2024. Climate change-induced degradation of expert range maps drawn for kissing bugs (Hemiptera: Reduviidae) and long-standing current and future sampling gaps across the Americas. Memórias do Instituto Oswaldo Cruz 119. https://doi.org/10.1590/0074-02760230100

BACKGROUND Kissing bugs are the vectors of Trypanosoma cruzi, the etiological agent of Chagas disease (CD). Despite their epidemiological relevance, kissing bug species are under sampled in terms of their diversity and it is unclear what biases exist in available kissing bug data. Under climate change, range maps for kissing bugs may become less accurate as species shift their ranges to track climatic tolerance. OBJECTIVES Quantify inventory completeness in available kissing bug data. Assess how well range maps are at conveying information about current distributions and potential future distributions subject to shift under climate change. Intersect forecasted changes in kissing bug distributions with contemporary sampling gaps to identify regions for future sampling of the group. Identify whether a phylogenetic signal is present in expert range knowledge as more closely related species may be similarly well or lesser understood. METHODS We used species distribution models (SDM), specifically constructed from Bayesian additive regression trees, with Bioclim variables, to forecast kissing bug distributions into 2100 and intersect these with current sampling gaps to identify priority regions for sampling. Expert range maps were assessed by the agreement between the expert map and SDM generated occurrence probability. We used classical hypothesis testing methods as well as tests of phylogenetic signal to meet our objectives. FINDINGS Expert range maps vary in their quality of depicting current kissing bug distributions. Most expert range maps decline in their ability to convey information about kissing bug occurrence over time, especially in under sampled areas. We found limited evidence for a phylogenetic signal in expert range map performance. MAIN CONCLUSIONS Expert range maps are not a perfect account of species distributions and may degrade in their ability to accurately convey distribution knowledge under future climates. We identify regions where future sampling of kissing bugs will be crucial for completing biodiversity inventories.

Frateles, L. E. F., G. R. G. Tavares, G. Nakamura, N. J. da Silva, L. C. Terribile, and J. A. F. Diniz‐Filho. 2024. The Interaction Between the Linnean and Darwinian Shortfalls Affects Our Understanding of the Evolutionary Dynamics Driving Diversity Patterns of New World Coralsnakes. Journal of Biogeography. https://doi.org/10.1111/jbi.15014

Aim In this study, we sought to understand how the Linnean shortfall (i.e., the lack of knowledge about species taxonomy) interacts with the Darwinian shortfall (i.e., the lack of knowledge about phylogenetic relationships among species), which potentially jeopardises geographical patterns in estimates of speciation rates.LocationNew World.TaxonCoralsnakes (Serpentes: Elapidae).MethodsWe created an index of taxonomic uncertainty (ITU) that measures the likelihood of current species being split after undergoing future taxonomic revisions. The ITU was used in simulations where species with higher taxonomic uncertainty had a higher likelihood of having their phylogenetic branches split, generating new hypothetical species along their geographic ranges. We estimated the speciation rates before and after the split of taxonomically uncertain species.ResultsWe found that a high number of coralsnake species display substantial taxonomic uncertainty, positively correlated with the latitude of the species' geographical range centroid. The estimated speciation rates based on currently available data have a weak relationship with latitude. However, after incorporating taxonomic uncertainty into the phylogeny, we detect a higher positive correlation between speciation rate and latitude.Main ConclusionsThe observed change in speciation rates following the incorporation of taxonomic uncertainty highlights how such uncertainty can undermine the empirical evaluation of geographical patterns in speciation rates, revealing an interaction between the latitudinal taxonomic gradient and the latitudinal diversity gradient. Given that taxonomic changes can alter the number of species recognised as valid over time, our study highlights the need to incorporate taxonomic uncertainty into macroecological and macroevolutionary studies, enhancing the robustness of patterns inferred from these data.