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Science Enabled by Specimen Data

Estrada-Sánchez, I., A. Espejo-Serna, J. García-Cruz, and A. R. López-Ferrari. 2024. Richness, distribution, and endemism of neotropical subtribe Ponerinae (Orchidaceae, Epidendreae). Brazilian Journal of Botany 47: 501–517. https://doi.org/10.1007/s40415-024-01005-y

The subtribe Ponerinae (Orchidaceae) includes the genera Helleriella A. D. Hawkes, Isochilus R. Brown, Nemaconia Knowles & Westc., and Ponera Lindl. Most of its species are epiphytes and usually grow on trees of the genus Quercus L. in cloud forests and temperate coniferous and broad-leaved forests; some taxa are rarely lithophytes or less frequently terrestrial. The aim of this study was to estimate the distribution of the species of the subtribe Ponerinae using ecological niche models (ENM), determine areas with highest richness and endemism rates with the occurrence data and the models obtained, and determine if the areas with highest richness and endemism recognized in this work are located within any of the conservation areas (ANPs) and/or Regiones Terrestres Prioritarias (RTPs). We reviewed 1 044 herbarium specimens from ten institutional collections, corresponding to two species of Helleriella , eleven of Isochilus , six of Nemaconia , and two of Ponera , and a geographic and taxonomic database was generated. ENM were constructed with MaxEnt 3.3; and we determine areas with highest species richness and endemism with Biodiverse 4.3. Mexico is the richest country with 21 species, followed by Guatemala with nine. The more widely distributed species are: Isochilus linearis (Jacq.) R.Br, and Nemaconia striata (Lindl.) Van den Berg, Salazar & Soto Arenas; I . oaxacanus Salazar & Soto Arenas is endemic to Mexican state of Oaxaca and N . dressleriana (Soto Arenas) van den Berg, Salazar & Soto Arenas of Morelos. The cells with higher occurrence richness and occurrence weighted endemism were located in Chiapas Highlands, and the higher occurrence of corrected weighted endemism is located in Transmexican Volcanic Belt, considered the nucleus of the Mexican Transition Zone. On the other hand, the cells with greater ENM richness and ENM weighted endemism were located in Sierra Madre del Sur, and the higher ENM corrected weighted endemism in Sierra Madre Oriental. It is suggested to change the status of the regions Cañón del Zopilote and El Tlacuache from RTPs to ANPs.

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.

Reyna, P. B., S. Castillo, and M. C. de Aranzamendi. 2024. What if there is no further south to go: Assessing the vulnerability of Nacella species to climate change. Estuarine, Coastal and Shelf Science 301: 108735. https://doi.org/10.1016/j.ecss.2024.108735

In the current context of climate change, southern South America and the Southern Ocean are undergoing profound environmental transformations that impose challenges to marine species. Shifts in species distribution ranges will occur through expansions or contractions of the range edges. Invertebrates such as Nacella spp., that being template-cold water species, will be more vulnerable to increasing temperature and will therefore suffer range contraction as temperatures increase southward. To understand the future of this sensitive group of gastropods, the potential impact of future climate on the distribution ranges of six species of the genus Nacella was studied using ensemble ecological niche models and representative concentration pathway 8.5 scenarios for the years 2050 and 2100. The results indicate that all the species studied will undergo a shift in their distribution in response to the projected changes in climate with a decline in habitat suitability. Particularly, the species will lose suitable areas mainly in the northern edge of their current distribution. Nevertheless, the species may not change their distribution equally. Our study suggests that N. magellanica, N. clypeater, and N. concinna appear to exhibit vulnerability, albeit with potentially lesser impact. Nacella magellanica is the limpet that shows the least distribution change in 2100. Both species, N. clypeater and N. concinna, will move southward while the Antarctic species will expand their distribution to other Antarctic areas. The most significant impact is expected for three Magellanic species (N. deaurata, N. flammea, and N. mytilina), currently distributed across the southern tip of South America. With restricted geographical ranges, these species face increased vulnerability to habitat loss as they cannot migrate southward. This comprehensive analysis offers invaluable insights into how Nacella species could tackle the challenges of climate change. The emphasis on specific species' vulnerabilities and the differential impacts on their distribution enhances our understanding of the potential consequences of climate change in the studied region. Furthermore, it will aid in formulating effective conservation and management strategies to protect Antarctic and sub-Antarctic ecosystems.

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.

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. https://doi.org/10.1016/j.jaridenv.2024.105139

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.

Belotti López de Medina, C. R. 2024. Diet breadth and biodiversity in the pre-hispanic South-Central Andes (Western South America) during the Holocene: An exploratory analysis and review. The Holocene. https://doi.org/10.1177/09596836241231446

This paper presents an exploratory study on the taxonomic diversity of pre-Hispanic archaeofaunas in the South-Central Andes (SCA; western South America) from the Pleistocene-Holocene boundary to the Late-Holocene. The SCA is a complex of diverse environments and has undergone distinct climate events for the last 13,000 years, such as the occurrence of warmer and drier conditions in the Middle-Holocene. The South-Central Andean area was part of the larger Andes interaction area, which was a primary center for animal and plant domestication and the emergence of agro-pastoralist economies. Since subsistence was key to these processes, the SCA provides a relevant case study on the interactions among environment, foodways and sociocultural evolution. Taxonomic diversity was used here as a proxy for diet breadth. A total of 268 archaeofaunal assemblages were sampled from the zooarchaeological literature. Reviewed variables included the cultural chronology and spatial coordinates of the assemblages, as well as the presence and abundance of taxa at the family rank. Taxonomic diversity covered two dimensions: composition (families present in each assemblage) and structure (quantitative relationships among taxa), which was measured through richness (NTAXA), ubiquity and relative abundance (NISP based rank-order). Despite the uneven distribution of samples, the analyses revealed the following trends: (1) a moderate relationship between NTAXA and distance from coastline for most of the Holocene; (2) a potential decrease in assemblage richness for coastal ecoregions during the Late-Holocene; and (3) a generalized increase in the relative abundance of Camelidae.

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. https://doi.org/10.1038/s41477-024-01649-4

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.

Goldsmit, J., C. W. McKindsey, R. W. Schlegel, D. Deslauriers, and K. L. Howland. 2024. Predicted shifts in suitable habitat of interacting benthic species in a warmer and invaded Canadian Arctic. Elem Sci Anth 12. https://doi.org/10.1525/elementa.2023.00018

Climate change and related expanding shipping activity are predicted to increase the risk of aquatic invasive species arriving in the Arctic. The goal of this study was to predict the distribution of an interconnected set of native and non-native primary producers and primary and secondary consumers in this changing context. Groups of species were selected to represent a benthic coastal Arctic food web in Hudson Bay, including kelps and eelgrass as primary producers (Alaria esculenta, Agarum clathratum, Saccharina latissima, Laminaria solidungula, and Zostera marina), amphipods as primary consumers (Gammarus oceanicus and G. setosus), and fish as secondary consumers (sculpins Gymnacanthus tricuspis, Myoxocephalus scorpius, M. scorpioides, and M. quadricornis). Ensemble models were used to predict the distribution of these native and several analogue non-native species (species known to be invasive elsewhere that can be considered analogues to Hudson Bay species): Dumontia contorta, Undaria pinnatifida, Sargassum muticum, and Codium fragile (primary producers); Gammarus tigrinus (primary consumer); and Artediellus atlanticus and A. uncinatus (secondary consumers). Predicted habitat suitability of trophic groups and analogue non-native species were overlaid under current and future climate change scenarios to assess areas of change through time. The predicted direction of potential distribution shifts varies by species identity (species composition) but not trophic group. Overall trophic relationships and roles in the ecosystem are likely to be maintained over time because while some species are predicted to decrease their potential ranges (e.g., M. quadricornis), others in the same trophic groups are predicted to increase (e.g., M. scorpius). Overlap (or lack thereof) between native and analogue non-native species pairs are expected to vary through time enabling novel interactions (e.g., competition) in space and time. This approach will help to identify current and future high-risk areas for trophic level changes and interactions with invasive species in response to global warming.

Xiao, S., S. Li, J. Huang, X. Wang, M. Wu, R. Karim, W. Deng, and T. Su. 2024. Influence of climate factors on the global dynamic distribution of Tsuga (Pinaceae). Ecological Indicators 158: 111533. https://doi.org/10.1016/j.ecolind.2023.111533

Throughout the Quaternary period, climate change has significantly influenced plant distribution, particularly affecting species within the genus Tsuga (Endl.) Carrière. This climatic impact ultimately led to the extinction of all Tsuga species in Europe. Today, there are ten recognized species of Tsuga worldwide, one of listed as a vulnerable species and four as near-threatened species. The genus Tsuga exhibits a disjunctive distribution in East Asia (EA), eastern North America (ENA), and western North America (WNA). It is crucial to comprehend the mechanisms underlying these distributional changes and to identify key climate variables to develop effective conservation strategies for Tsuga under future climate scenarios. In this study, we applied the maximum entropy (MaxEnt) model by combining distribution data for Tsuga with abundant pollen fossil data. Our objective was to investigate the climate factors that shape the distribution of Tsuga, identify climate thresholds, and elucidate distribution dynamics in the context of significant climate changes over the past 1070 thousand years (ka). Our findings highlight the pivotal role of precipitation as the key climate factor affecting the distribution of Tsuga. Specifically, in EA, summer precipitation was the key driver, while in North America (NA), winter precipitation exerted greater importance. Moreover, we observed similarities in climatic requirements between Tsuga species in Europe and EA, and declines in summer precipitation and winter temperature were major factors contributing to the extinction of Tsuga species in Europe. Quaternary glacial and interglacial fluctuations exerted substantial impacts on Tsuga distribution dynamics. The disappearance of Tsuga species in the Korean Peninsula may have occurred during the LGM (Last Glacial Maximum). The potential suitable area for Tsuga species in EA expanded during the cold periods, while in NA, it contracted. In the future, climate change may result Tsuga distribution area contraction in both the EA and NA. Our study has identified distinct response patterns of Tsuga in various geographic regions to Quaternary climate change and offers corresponding suggestions for Tsuga conservation. In the future, it will be imperative to prioritize the conservation of natural Tsuga distributions in EA and NA, with a focus on the impacts of precipitation fluctuation on the dynamic distribution of this genus.

Liendo, D., J. A. Campos, and A. Gandarillas. 2023. Cortaderia selloana, an example of aggressive invaders that affect human health, yet to be included in binding international invasive catalogues. NeoBiota 89: 229–237. https://doi.org/10.3897/neobiota.89.110500

Invasive plant species can suppress local biodiversity, affect soil properties and modify the landscape. However, an additional concern of plant invasions that has been more disregarded is their impact on environmental human health. Here, we discuss the case of Cortaderia selloana (Schult. & Schult.f.) Asch. & Graebn, as an example of a worldwide invasive species with a strong environmental impact. We summarise the main facts regarding the C. selloana invasion, the recent clinical evidence of its impact on human health and the great potential expansion of the species in the context of climate change. C. selloana constitutes a clear example to boost demands from policy makers for urgent and efficient measures to control or eradicate invasive species, also in ruderal areas. This aggressive invader is still out of relevant binding international invasive species catalogues, including the European List of Invasive Alien Species of Union concern (Union list), and is still subjected to extensive trading in some European countries. Therefore, including C. selloana in the Union list becomes mandatory to impose full restrictions on keeping, importing, selling, breeding and cultivating the species.