Science Enabled by Specimen Data

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.

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.

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.

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.

Gillespie, L. J., P. C. Sokoloff, G. A. Levin, J. Doubt, and R. T. McMullin. 2024. Vascular plant, bryophyte, and lichen biodiversity of Agguttinni Territorial Park, Baffin Island, Nunavut, Canada: an annotated species checklist of a new Arctic protected area. Check List 20: 279–443.

Agguttinni Territorial Park is a large, newly established park on the east-central coast of Baffin Island in Nunavut, Canada. Previous knowledge of the plant and lichen biodiversity was limited and based mostly on collections made during the 1950 Baffin Island Expedition. We conducted a floristic inventory of the park in 2021 and re-examined previous collections. We recorded 141 species of vascular plants belonging to 25 families, 69 species of bryophytes in 27 families, and 93 species of lichens in 23 families. Most of the vascular plant and bryophyte species are new records for the park area, and some vascular plants, bryophytes, and lichens are newly reported for Baffin Island, Nunavut, or the Canadian Arctic or represent significant range extensions. Vascular plant species diversity varied greatly among localities, with inland valleys at the heads of fiords showing highest diversity and interior rocky barrens showing the lowest.

Rayos, A. L., M. A. M. Renner, and S. Y. W. Ho. 2024. The Neotropical endemic liverwort subfamily Micropterygioideae had circum‐Antarctic links to the rest of the Lepidoziaceae during the early Cretaceous. Ecology and Evolution 14.

Lepidoziaceae are the third‐largest family of liverworts, with about 860 species distributed on all continents. The evolutionary history of this family has not been satisfactorily resolved, with taxa such as Micropterygioideae yet to be included in phylogenetic analyses. We inferred a dated phylogeny of Lepidoziaceae using a data set consisting of 13 genetic markers, sampled from 147 species. Based on our phylogenetic estimate, we used statistical dispersal‐vicariance analysis to reconstruct the biogeographic history of the family. We inferred a crown age of 197 Ma (95% credible interval 157–240 Ma) for the family in the Australian region, with most major lineages also originating in the same region. Micropterygioideae are placed as the sister group to Lembidioideae, with these two lineages diverging from each other about 132 Ma in the South American–Australian region. With South America and Australia being connected through Antarctica at the time, our results suggest a circum‐Antarctic link between Micropterygioideae and the rest of the family. Crown Micropterygioideae were inferred to have arisen 45 Ma in South America before the continent separated from Antarctica. Extinction from southern temperate regions might explain the present‐day restriction of Micropterygioideae to the Neotropics. Our study reveals the influence of past geological events, such as continental drift, on the evolution and distribution of a widespread and diverse family of liverworts.

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.

Minghetti, E., P. M. Dellapé, M. Maestro, and S. I. Montemayor. 2024. Evaluating the climatic suitability of Engytatus passionarius Minghetti et al. (Heteroptera, Miridae) as a biological control agent of the invasive stinking passion flower Passiflora foetida L. in Australia through ecological niche models. Biological Control 191: 105461.

Passiflora foetida is a climbing vine, native to the Neotropical Region that is causing major economic and ecological damage in Australia, where it is rapidly spreading. Traditional control options, such as cutting, manual uprooting, and herbicide applications are only effective for local management. Currently, the plant bug Engytatus passionarius is the most promising biological control agent. Specificity tests performed in its native range in Argentina suggest it is highly specific to the plant, and it has not been observed in the field associated with other plants. As climate determines the establishment of insects, knowing if the environmental conditions suit their requirements is key to introducing a species in a region. Also, an overlap between the climatic niches of species is an indicator of similar requirements. To explore the possibilities of a successful establishment of E. passionarius in Australia, ecological niche models (ENM) were built for the plant bug and for the vine and their overlap was measured. The ENM projected to Australia recognized suitable environmental conditions for the establishment of E. passionarius in several regions where P. foetida is present, both for current and future scenarios. Moreover, the niche of the plant bug is almost completely overlapped with that of the vine. All the aforementioned evidence seems to indicate that E. passionarius has a good chance to become an effective biological control agent of P. foetida.

Finegan, B., D. Delgado, A. L. Hernández Gordillo, N. Zamora Villalobos, R. Núñez Florez, F. Díaz Santos, and S. Vílchez Mendoza. 2024. Multi-dimensional temperature sensitivity of protected tropical mountain rain forests. Frontiers in Forests and Global Change 6.

Introduction Tropical mountain rain forests (TMRF, natural forests at > 300 m asl) are globally important for biodiversity and ecosystem services and are believed to be highly vulnerable to climate change. But there are no specific approaches for rigorous assessment of their vulnerability at the landscape and local scales necessary for management for adaptation. We address the challenge of evaluating the ecological sensitivity to temperature of TMRF, applying a multidimensional approach in protected areas over a 440–2,950 m asl altitudinal gradient in Costa Rica, synthesizing results of a long-term research programme (2012-present). We evaluate the sensitivity to the current spatial temperature gradient of eleven ecosystem properties in three categories: forest composition and diversity, thermal characteristics of forest stands and forest structure and dynamics.MethodsData are from 29 to 32 plots of 50 m x 50 m (0.25 ha) distributed over the gradient, in which all trees, palms and tree ferns ≥ 10 dbh are identified to species and measured for recruitment, growth and mortality. An experimental study of leaf litter decomposition rates was carried out in twelve plots. Current and future (SSP 585, 2070) values of mean annual temperatures MAT were obtained from online climate surfaces. Thermal characteristics of forest stands were determined using MATs of species occurrences in GBIF and include a new index, the Community Thermal Capital Index (CTCI), calculated as CTI-MAT.ResultsWe classified degrees of sensitivity to temperature as very weak, weak, moderate or substantial. All eleven ecosystem properties are substantially sensitive, so changes in their values are expected under rising temperatures. Species density, the community temperature index CTI, tree recruitment and mortality rates and leaf litter decomposition rates are positively related to temperature, while the community weighted mean thermal niche breadth, the CTCI, net basal area increments, stand basal area and carbon in aboveground biomass are negatively related. Results point to zones of vulnerability in the protected areas.DiscussionIn montane forests, positive values of the CTCI–climate credit– robust basal area growth and very low mortality and leaf litter decomposition rates suggest healthy ecosystems and no risk of mountaintop extinction. Lowland forests may be vulnerable to degradation and biotic attrition, showing current basal area loss, high mortality and climate debts. National and local actors are participating in a process of adoption of the sensitivity analysis and recommendations regarding zones of vulnerability.

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.

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.

Rodríguez-Merino, A. 2023. Identifying and Managing Areas under Threat in the Iberian Peninsula: An Invasion Risk Atlas for Non-Native Aquatic Plant Species as a Potential Tool. Plants 12: 3069.

Predicting the likelihood that non-native species will be introduced into new areas remains one of conservation’s greatest challenges and, consequently, it is necessary to adopt adequate management measures to mitigate the effects of future biological invasions. At present, not much information is available on the areas in which non-native aquatic plant species could establish themselves in the Iberian Peninsula. Species distribution models were used to predict the potential invasion risk of (1) non-native aquatic plant species already established in the peninsula (32 species) and (2) those with the potential to invade the peninsula (40 species). The results revealed that the Iberian Peninsula contains a number of areas capable of hosting non-native aquatic plant species. Areas under anthropogenic pressure are at the greatest risk of invasion, and the variable most related to invasion risk is temperature. The results of this work were used to create the Invasion Risk Atlas for Alien Aquatic Plants in the Iberian Peninsula, a novel online resource that provides information about the potential distribution of non-native aquatic plant species. The atlas and this article are intended to serve as reference tools for the development of public policies, management regimes, and control strategies aimed at the prevention, mitigation, and eradication of non-native aquatic plant species.