Science Enabled by Specimen Data

Zhao, Y., G. A. O’Neill, N. C. Coops, and T. Wang. 2024. Predicting the site productivity of forest tree species using climate niche models. Forest Ecology and Management 562: 121936.

Species occurrence-based climate niche models (CNMs) serve as valuable tools for predicting the future ranges of species’ suitable habitats, aiding the development of climate change adaptation strategies. However, these models do not address an essential aspect - productivity, which holds economic significance for timber production and ecological importance for carbon sequestration and ecosystem services. In this study, we investigated the potential to extend the CNMs to predict species productivity under various climate conditions. Lodgepole pine (Pinus contorta Dougl. ex Loud.) and Douglas-fir (Pseudotsuga menziesii Franco.) were selected as our model species due to their comprehensive range-wide occurrence data and measurement of site productivity. To achieve this, we compared and optimized the performance of four individual modeling algorithms (Random Forest (RF), Maxent, Generalized Boosted Models (GBM), and Generalized Additive Model (GAM)) in reflecting site productivity by evaluating the effect of spatial filtering, and the ratio of presence to absence (p/a ratio) observations. Additionally, we applied a binning process to capture the overarching trend of climatic effects while minimizing the impact of other factors. We observed consistency in optimal performance across both species when using the unfiltered data and a 1:1.5 p/a ratio, which could potentially be extended to other species. Among the modeling algorithms explored, we selected the ensemble model combining RF and Maxent as the final model to predict the range-wide site productivity for both species. The predicted range-wide site productivity was validated with an independent dataset for each species and yielded promising results (R2 above 0.7), affirming our model’s credibility. Our model introduced an innovative approach for predicting species productivity with high accuracy using only species occurrence data, and significantly advanced the application of CNMs. It provided crucial tools and insights for evaluating climate change's impact on productivity and holds a better potential for informed forest management and conservation decisions.

Köhler, M., M. Romeiro‐Brito, and M. Telhe. 2024. The Cerrado through cacti. Journal of Biogeography.

Cerrado is a large and heterogeneous ecoregion in the Neotropics marked by the fire‐prone savanna vegetation, to which succulent lineages are usually not associated due to this adverse condition. However, recent studies have highlighted the importance of Cerrado as an ancestral range for the origin, dispersal and in situ diversification of remarkable lineages of South American cacti. In this perspective, we explore the implications of these occurrences in the Cerrado, shedding light on a frequently overlooked aspect of this ecoregion—the role of scattered rocky outcrop habitats acting as micro‐refuges for fire‐sensitive lineages. We show that most cacti occurrences are associated with patches of rock outcrops across the Cerrado. In contrast, when terricolous, a few disparate and not closely related species can develop underground structures or present a specialized habit that facilitates their presence as a putative response to fire—reinforcing the evolutionary lability of fire adaptation in Cerrado lineages. Despite some notable endemisms, several occurrences are from species with core distributions in adjacent ecoregions (e.g. Caatinga and Chaco), demonstrating the permeability of Cerrado, which can act concomitantly as a biogeographical barrier (especially due to its fire‐prone habitats) and as a corridor for biota interchange. Finally, we stress that Cerrado heterogeneity, often leading to different circumscriptions, is a relevant issue when studying and characterizing Neotropical biota, which must be further explored and considered to assess the evolutionary assembly of the biomes involved.

Owen, E., M. Zuliani, M. Goldgisser, and C. Lortie. 2024. The importance of native shrubs on the distribution and diversity of reptiles and amphibians in the central drylands of Southwestern USA. Biodiversity and Conservation 33: 2131–2151.

Conservation and management of drylands is a global challenge. Key attributes of these ecosystems, such as dominant vegetation including shrubs, can provide a crucial mechanism to inform conservation strategies. The shrub species Ephedra californica and Larrea tridentata are common native shrub species within the deserts of California and frequently benefit other plant and animal species. Here, we tested the hypothesis that shrubs support reptile and amphibian communities through relative increases in available habitat, estimated through increasing shrub densities at the site level. Reported occurrence data from the Global Biodiversity Information Facility (GBIF) and high-resolution satellite images were used to test for local-to-regional patterns in reptile and amphibian distribution and diversity by shrub densities at sites. At 43 distinct sites, the relationship between shrub density and reported reptile and amphibian communities was also tested. A total of 71 reptile and amphibian species were reported regionally. Increases in shrub density across sites positively influenced the relative abundance and richness of reptiles and amphibians observed. Moreover, increasing shrub density also had a positive influence on species evenness. Aridity differences between sites did not significantly influence the relationship between shrub density and reptiles and amphibians suggesting that the relationship was robust. This study highlights the importance of foundational shrub species in supporting reptile and amphibian communities in arid and semi-arid regions. Large-scale patterns of biodiversity in deserts can be supported by positive plant-animal interactions including small islands of fertility and resources for animals in the context of a warming climate.

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.

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.

Zachos, L. G., and A. Ziegler. 2024. Selective concentration of iron, titanium, and zirconium substrate minerals within Gregory’s diverticulum, an organ unique to derived sand dollars (Echinoidea: Scutelliformes). PeerJ 12: e17178.

Gregory’s diverticulum, a digestive tract structure unique to a derived group of sand dollars (Echinoidea: Scutelliformes), is filled with sand grains obtained from the substrate the animals inhabit. The simple methods of shining a bright light through a specimen or testing response to a magnet can reveal the presence of a mineral-filled diverticulum. Heavy minerals with a specific gravity of >2.9 g/cm3 are selectively concentrated inside the organ, usually at concentrations one order of magnitude, or more, greater than found in the substrate. Analyses of diverticulum content for thirteen species from nine genera, using optical mineralogy, powder X-ray diffraction, scanning electron microscopy and energy dispersive X-ray spectroscopy, as well as micro-computed tomography shows the preference for selection of five major heavy minerals: magnetite (Fe3O4), hematite (Fe2O3), ilmenite (FeTiO3), rutile (TiO2), and zircon (ZrSiO4). Minor amounts of heavy or marginally heavy amphibole, pyroxene and garnet mineral grains may also be incorporated. In general, the animals exhibit a preference for mineral grains with a specific gravity of >4.0 g/cm3, although the choice is opportunistic and the actual mix of mineral species depends on the mineral composition of the substrate. The animals also select for grain size, with mineral grains generally in the range of 50 to 150 μm, and do not appear to alter this preference during ontogeny. A comparison of analytical methods demonstrates that X-ray attenuation measured using micro-computed tomography is a reliable non-destructive method for heavy mineral quantification when supported by associated analyses of mineral grains extracted destructively from specimens or from substrate collected together with the specimens. Commonalities in the electro-chemical surface properties of the ingested minerals suggest that such characteristics play an important role in the selection process.

Silveira, P., F. G. de Sousa, P. Böning, N. M. Maciel, J. Stropp, and S. Lötters. 2024. Do aposematic species have larger range sizes? A case study with neotropical poison frogs. Journal of Biogeography.

AbstractAimAposematic animals, i.e., those that are defended and warn potential predators through signals, are suggested to have resource‐gathering advantages against non‐aposematic ones. We here explore this in a biogeographic framework expecting that aposematic species are better dispersers, which translates into larger geographic range size.LocationSouth America.TaxonPoison frogs (Amphibia; Aromobatidae and Dendrobatidae).MethodsWe use 43 toxic and 26 non‐toxic poison frog species from the lowlands only as representatives of aposematic and non‐aposematic study organisms, respectively. Realised and potential geographic ranges are calculated using minimum convex polygon and species distribution modelling methods, respectively. Accounting for species body size and phylogeny, we test if both range and aposematism are correlated using linear mixed‐effects models.ResultsAposematic and non‐aposematic species neither differ in realised nor in potential geographic range size. There was no effect on body size.Main ConclusionsThe role of aposematism is not yet as clear as suggested and determinants of poison frog range sizes are multifaceted. A more integrative approach is needed using the information on behaviour, predation risk, and reproductive biology to assess the role of aposematism on observed species distributions. Such data are not yet available for most species, neither poison frogs nor other aposematic animals.

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.

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.

Souto, C. P., L. P. Zalazar, M. Tadey, and A. C. Premoli. 2024. Modeling past, present and future: Species-specific responses to climate changes in three shrub congeners from south American drylands. Journal of Arid Environments 221: 105139.

Drylands cover ca. 40% of the land global surface and deliver significant ecosystem services. These regions are the most sensitive, prone to suffer the effects of climate and distribution changes, so estimates on projected range shifts are crucial to complement traditional approaches to biodiversity conservation and sustainability. Shrubs of the Monte Desert dominate the largest temperate dryland in South America. Our goal is to assess the spatial distribution and niche overlap of three native shrubs (Larrea cuneifolia (LC), L. divaricata (LD), and L. nitida (LN)), under present climate conditions, to retrodict their potential past distribution, and anticipate their predicted range under future climate scenarios. We used ecological niche modeling that were projected to the past (LGM and Mid Holocene) and future (2050 and 2070) under two scenarios of greenhouse gas emissions and two model of global circulation. All species have high niche overlap (67–89%), but showed species-specific responses, highlighting the need to develop mitigation measures particularly for LD and LN in the face of climate change and land use pressures. Global South deserts are being highly degraded and information on future potential ranges of endemic species can support the development of sustainable conservation and management plans.

Anest, A., Y. Bouchenak-Khelladi, T. Charles-Dominique, F. Forest, Y. Caraglio, G. P. Hempson, O. Maurin, and K. W. Tomlinson. 2024. Blocking then stinging as a case of two-step evolution of defensive cage architectures in herbivore-driven ecosystems. Nature Plants.

Dense branching and spines are common features of plant species in ecosystems with high mammalian herbivory pressure. While dense branching and spines can inhibit herbivory independently, when combined, they form a powerful defensive cage architecture. However, how cage architecture evolved under mammalian pressure has remained unexplored. Here we show how dense branching and spines emerged during the age of mammalian radiation in the Combretaceae family and diversified in herbivore-driven ecosystems in the tropics. Phylogenetic comparative methods revealed that modern plant architectural strategies defending against large mammals evolved via a stepwise process. First, dense branching emerged under intermediate herbivory pressure, followed by the acquisition of spines that supported higher speciation rates under high herbivory pressure. Our study highlights the adaptive value of dense branching as part of a herbivore defence strategy and identifies large mammal herbivory as a major selective force shaping the whole plant architecture of woody plants. This study explores the evolution of two traits, branching density and spine presence, in the globally distributed plant family Combretaceae. These traits were found to have appeared in a two-step process in response to mammalian herbivory pressure, revealing the importance of large mammals in the evolution of plant architecture diversity.

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.

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.