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Science Enabled by Specimen Data

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. https://doi.org/10.1111/jbi.14850

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. https://doi.org/10.1111/geb.13847

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.

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. https://doi.org/10.1093/botlinnean/boae007

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. https://doi.org/10.1093/evolut/qpae034

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.

Ramos, R. S., G. M. Via do Pico, M. Brea, and D. M. Kröhling. 2024. New fossil woods (upper Pleistocene) from the lower-middle Uruguay river basin (South America) reveal the past distribution of Aspidosperma (Apocynaceae). Quaternary International. https://doi.org/10.1016/j.quaint.2024.03.004

The present work describes the taxonomic and paleobiogeographic study of two fossil woods related to extant Aspidosperma. The silicified specimens come from the fossil localities of Santa Ana (30°54′S, 57°55′W) and Concordia (31°19′S, 57°59′W), Entre Ríos Province, Argentina, belonging to the El Palmar Formation (Late Pleistocene). This unit represents the sedimentary body of the upper fluvial terrace generated by the Uruguay River in its middle basin in eastern Argentina. The anatomical features that distinguish the woods are growth rings delimited by axial parenchyma and fibers, semi-ring to-diffuse-porous woods; mainly solitary vessels; simple perforation plates; alternate, bordered, and vestured intervessel pits; scarce paratracheal and diffuse apotracheal axial parenchyma; homocellular, and uniseriate to-triseriate rays; non-septate fibers. Climate reconstruction modelled at the regional scale (Ecological Niche Modeling) revealed variations in macroecological diversity patterns of the nearest living relatives (Aspidosperma australe and A. polyneuron) over the last ca. 130,000 years. Optically stimulated luminescence dating of sediments from the upper part of the El Palmar Formation in the type area reveals that the unit spans from the Last Interglacial period (warm substage, MIS marine isotope stage 5a), to the penultimate interglacial (MIS 7). This period was characterized by warmer and wetter conditions than those observed today. The eco-anatomical characteristics of the fossil record reflect this type of environment. The modern analogues of the fossils studied here are now part of the forests that integrate the Atlantic forest and Araucaria forest biogeographic provinces in South America.

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. https://doi.org/10.1111/nph.19601

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.

Noori, S., A. Hofmann, D. Rödder, M. Husemann, and H. Rajaei. 2024. A window to the future: effects of climate change on the distribution patterns of Iranian Zygaenidae and their host plants. Biodiversity and Conservation. https://doi.org/10.1007/s10531-023-02760-2

Climate change has been suggested as an important human-induced driver for the ongoing sixth mass extinction. As a common response to climate change, and particularly global warming, species move toward higher latitudes or shift uphill. Furthermore, rapid climate change impacts the biotic interactions of species, particularly in the case of Zygaenid moths which exhibit high specialization in both habitat and host plant preferences. Iranian Zygaenidae are relatively well-known and represent a unique fauna with a high endemism rate (46%) in the whole Palearctic; as such they are a good model group to study the impact of climate change on future distributions. In this study, we used species distribution models (SDMs) and ensembles of small models (ESMs) to investigate the impact of climate change on the future distribution of endemic and non-endemic species of zygaenids, as well as their larval host plants. Three different climate scenarios were applied to forecast the probable responses of the species to different climate change intensities. Our results suggest that the central and southern parts of the country will be impacted profoundly by climate change compared to the northern regions. Beyond this, most endemic species will experience an altitudinal shift from their current range, while non-endemic species may move towards higher latitudes. Considering that the regions with higher diversity of zygaenids are limited to mountainous areas, mainly within the Irano-Anatolian biodiversity hotspot, the identification of their local high diversity regions for conservation practices has a high priority.

SILVA, I. M. D., J. E. SERRÃO, M. M. D. SANTOS, R. S. D. SILVA, A. G. D. CARVALHO, E. M. PIRES, J. C. ZANUNCIO, and M. A. SOARES. 2023. Insecticidal plants as trade opportunities and use by small vegetable producers: an example using essential oils to control Diaphania hyalinata (Lepidoptera: Crambidae). Anais da Academia Brasileira de Ciências 95. https://doi.org/10.1590/0001-3765202320191305

Production and sale of botanical insecticides depend on knowing the potential opportunities for these products. Essential oils from plants secondary metabolism can control pests, especially in agricultural systems where synthetic insecticides are limited, as in organic agriculture. The objective of this study was to evaluate the toxicity of essential oils to Diaphania hyalinata (Lepidoptera: Crambidae) and to show regions with the potential to use Cinnamomum zeylanicum, Citrus sinensis, and Syzygium aromaticum in the formulation and commercialization of insecticides to control this insect. The C. zeylanicum oil was more toxic to larvae and pupae and the S. aromaticum to eggs of D. hyalinata. Essential oils are an alternative for the management of D. hyalinata. The production of pesticides from essential oils of C. zeylanicum, C. sinensis, and S. aromaticum to control D. hyalinata has high potential in America. Also, Asia, Africa, Europe, the Middle East, and Asia can extract these plants to formulate insecticide molecules for the America countries.

Angulo, J. C., J. M. Burke, and F. A. Michelangeli. 2023. Characterizing the frequency, morphological gradient, and distribution of dioecy in Miconia (Melastomataceae). International Journal of Plant Sciences. https://doi.org/10.1086/729063

Dioecy has evolved many times independently within the angiosperms. The distribution, frequency of occurrence, and floral morphology of dioecious angiosperms constitute the foundations for comparative studies of dioecy, yet for many groups they are still poorly characterized. We assessed species of Miconia for the presence of dioecious reproductive system, characterized the floral morphology for staminate and pistillate flowers, and used herbarium records to analyze patterns of distribution and elevational range. We find that dioecious Miconia represent an uncommon case of mismatched stage of organ abortion between staminate and pistillate flowers, with functionally pistillate flower morphology largely consistent across species, and morphological expression in functionally staminate flowers varying from near absent to slight reductions in gynoecia. We identify 58 dioecious species and 15 putatively dioecious species within Miconia that are distributed primarily in montane habitats between 1000 m – 3500 m in the Andes, parts of Central America, and the Caribbean. Our results double the last known count of dioecy in Miconia and highlight the gradient of vestigial morphology in staminate flowers. Lastly, we provide discussion on the significance of dioecy in relation to floral development, pollination, and ecology in Miconia.

Zhang, H., W. Guo, and W. Wang. 2023. The dimensionality reductions of environmental variables have a significant effect on the performance of species distribution models. Ecology and Evolution 13. https://doi.org/10.1002/ece3.10747

How to effectively obtain species‐related low‐dimensional data from massive environmental variables has become an urgent problem for species distribution models (SDMs). In this study, we will explore whether dimensionality reduction on environmental variables can improve the predictive performance of SDMs. We first used two linear (i.e., principal component analysis (PCA) and independent components analysis) and two nonlinear (i.e., kernel principal component analysis (KPCA) and uniform manifold approximation and projection) dimensionality reduction techniques (DRTs) to reduce the dimensionality of high‐dimensional environmental data. Then, we established five SDMs based on the environmental variables of dimensionality reduction for 23 real plant species and nine virtual species, and compared the predictive performance of those with the SDMs based on the selected environmental variables through Pearson's correlation coefficient (PCC). In addition, we studied the effects of DRTs, model complexity, and sample size on the predictive performance of SDMs. The predictive performance of SDMs under DRTs other than KPCA is better than using PCC. And the predictive performance of SDMs using linear DRTs is better than using nonlinear DRTs. In addition, using DRTs to deal with environmental variables has no less impact on the predictive performance of SDMs than model complexity and sample size. When the model complexity is at the complex level, PCA can improve the predictive performance of SDMs the most by 2.55% compared with PCC. At the middle level of sample size, the PCA improved the predictive performance of SDMs by 2.68% compared with the PCC. Our study demonstrates that DRTs have a significant effect on the predictive performance of SDMs. Specifically, linear DRTs, especially PCA, are more effective at improving model predictive performance under relatively complex model complexity or large sample sizes.