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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.

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.

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.

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. https://doi.org/10.1016/j.biocontrol.2024.105461

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.

Putra, A. R., K. A. Hodgins, and A. Fournier‐Level. 2023. Assessing the invasive potential of different source populations of ragweed (Ambrosia artemisiifolia L.) through genomically informed species distribution modelling. Evolutionary Applications. https://doi.org/10.1111/eva.13632

The genetic composition of founding populations is likely to play a key role in determining invasion success. Individual genotypes may differ in habitat preference and environmental tolerance, so their ability to colonize novel environments can be highly variable. Despite the importance of genetic variation on invasion success, its influence on the potential distribution of invaders is rarely investigated. Here, we integrate population genomics and ecological niche models (ENMs) into a single framework to predict the distribution of globally invasive common ragweed (Ambrosia artemisiifolia) in Australia. We identified three genetic clusters for ragweed and used these to construct cluster‐specific ENMs and characterize within‐species niche differentiation. The potential range of ragweed in Australia depended on the genetic composition and continent of origin of the introduced population. Invaders originating from warmer, wetter climates had a broader potential distribution than those from cooler, drier ones. By quantifying this change, we identified source populations most likely to expand the ragweed distribution. As prevention remains the most effective method of invasive species management, our work provides a valuable way of ranking the threat posed by different populations to better inform management decisions.

Rocha, J., P. J. Nunes, A. Pinto, L. Fenina, A. L. Afonso, A. R. Seixas, R. Cruz, et al. 2024. Ecological adaptation of Australian Myrtaceae through the leaf waxes analysis: Corymbia citriodora, Eucalyptus gunnii, and Eucalyptus globulus. Flora 310: 152435. https://doi.org/10.1016/j.flora.2023.152435

Seeking to get insight into the close relationship between plant waxes and the climatic conditions of plants’ original biomes, the leaves of three Myrtaceae from the eastern Australian-Tasmanian region (Corymbia citriodora (Hook.) K.D.Hill & L.A.S.Johnson (lemon-scented gum), Eucalyptus gunnii Hook. (cider gum), and Eucalyptus globulus Labill. (blue gum)) were selected. The present study relied on the analysis of juvenile leaf samples of the three species collected at the Botanical Garden of the University of Trás-os-Montes e Alto Douro (Portugal) during the driest and warmest period of the year (July), to ensure the same environmental conditions as the Australian species from December to February, for cider gum and blue gum, and from June to September, for lemon-scented gum. Both surfaces of the leaves of the three Myrtaceae species exhibit superhydrophobic behavior. They are covered with wax tubules, but these are thicker and the surface is smoother in the case of cider gum. From the chemical standpoint, the leaf waxes of the three species revealed a prevalence of β-diketones and sterols over alcohols, alkanes, and esters. The relative ketone/sterol concentration ratio demonstrated an environmental dynamic variation with climate, i.e., with the ombrothermic regimes. The highest concentration of β-diketone and the lowest concentration of sterols was observed for species from dryer conditions (lemon-scented gum), whereas the reverse trend was found for species from wetter conditions (cider gum and blue gum).The present work strongly suggests that the chemical composition of leaf waxes, rather than wettability, seems to be directly correlated with environmental variability at the species’ natural site. The methodology proposed here opens exciting new prospects for the investigation of the environmental dynamics of terrestrial plants.

McCulloch-Jones, E. J., T. Kraaij, N. Crouch, and K. T. Faulkner. 2023. Assessing the invasion risk of traded alien ferns using species distribution models. NeoBiota 87: 161–189. https://doi.org/10.3897/neobiota.87.101104

Risk analysis plays a crucial role in regulating and managing alien and invasive species but can be time-consuming and costly. Alternatively, combining invasion and impact history with species distribution models offers a cost-effective and time-efficient approach to assess invasion risk and identify species for which a comprehensive risk analysis should take precedence. We conducted such an assessment for six traded alien fern species, determining their invasion risk in countries where they are traded. Four of the species (Dicksonia antarctica, Dryopteris erythrosora, Lygodium japonicum, and Phlebodium aureum) showed limited global distributions, while Adiantum raddianum and Sphaeropteris cooperi had broader distributions. A. raddianum, however, was the only species found to pose a high invasion risk in two known trade countries – the USA and Australia – and requires a complete risk analysis to determine the appropriate regulatory responses. Dicksonia antarctica, Phlebodium aureum (for New Zealand), and Dryopteris erythrosora (for the USA) posed a medium risk of invasion due to the lack of evidence of impacts, and a complete risk analysis is thus deemed less crucial for these species in these countries. For other species, suitable environments were not predicted in the countries where they are traded, thus the risk of invasion is low, and a complete risk analysis is not required. For species in countries where suitable environments are predicted but no trade information or presence data are available, risk assessments are recommended to better determine the risk posed. Despite the relatively limited potential global distribution of the studied ferns relative to other major plant invaders (e.g., Pinus spp. and Acacia spp.), their history of invasion, documented impacts in pristine environments, and high propagule pressure from trade warrants concern, possibly necessitating legislative and regulatory measures in environmentally suitable regions.

Quillfeldt, P., Y. Bedolla-Guzmán, M. M. Libertelli, Y. Cherel, M. Massaro, and P. Bustamante. 2023. Mercury in Ten Storm-Petrel Populations from the Antarctic to the Subtropics. Archives of Environmental Contamination and Toxicology. https://doi.org/10.1007/s00244-023-01011-3

The oceans become increasingly contaminated as a result of global industrial production and consumer behaviour, and this affects wildlife in areas far removed from sources of pollution. Migratory seabirds such as storm-petrels may forage in areas with different contaminant levels throughout the annual cycle and may show a carry-over of mercury from the winter quarters to the breeding sites. In this study, we compared mercury levels among seven species of storm-petrels breeding on the Antarctic South Shetlands and subantarctic Kerguelen Islands, in temperate waters of the Chatham Islands, New Zealand, and in temperate waters of the Pacific off Mexico. We tested for differences in the level of contamination associated with breeding and inter-breeding distribution and trophic position. We collected inert body feathers and metabolically active blood samples in ten colonies, reflecting long-term (feathers) and short-term (blood) exposures during different periods ranging from early non-breeding (moult) to late breeding. Feathers represent mercury accumulated over the annual cycle between two successive moults. Mercury concentrations in feathers ranged over more than an order of magnitude among species, being lowest in subantarctic Grey-backed Storm-petrels (0.5 μg g −1 dw) and highest in subtropical Leach’s Storm-petrels (7.6 μg g −1 dw, i.e. posing a moderate toxicological risk). Among Antarctic Storm-petrels, Black-bellied Storm-petrels had threefold higher values than Wilson’s Storm-petrels, and in both species, birds from the South Shetlands (Antarctica) had threefold higher values than birds from Kerguelen (subantarctic Indian Ocean). Blood represents mercury taken up over several weeks, and showed similar trends, being lowest in Grey-backed Storm-petrels from Kerguelen (0.5 μg g −1 dw) and highest in Leach’s Storm-petrels (3.6 μg g −1 dw). Among Antarctic storm-petrels, species differences in the blood samples were similar to those in feathers, but site differences were less consistent. Over the breeding season, mercury decreased in blood samples of Antarctic Wilson’s Storm-petrels, but did not change in Wilson’s Storm-petrels from Kerguelen or in Antarctic Black-bellied Storm-petrels. In summary, we found that mercury concentrations in storm-petrels varied due to the distribution of species and differences in prey choice. Depending on prey choices, Antarctic storm-petrels can have similar mercury concentrations as temperate species. The lowest contamination was observed in subantarctic species and populations. The study shows how seabirds, which accumulate dietary pollutants in their tissues in the breeding and non-breeding seasons, can be used to survey marine pollution. Storm-petrels with their wide distributions and relatively low trophic levels may be especially useful, but more detailed knowledge on their prey choice and distributions is needed.

Huynh, S., A. Cloutier, G. Chen, D. T. C. Chan, D. K. Lam, K. P. Huyvaert, F. Sato, et al. 2023. Whole-genome analyses reveal past population fluctuations and low genetic diversities of the North Pacific albatrosses X. Zhou [ed.],. Molecular Biology and Evolution. https://doi.org/10.1093/molbev/msad155

Abstract Throughout the Plio-Pleistocene, climate change has impacted tropical marine ecosystems substantially, with even more severe impacts predicted in the Anthropocene. Although many studies have clarified demographic histories of seabirds in polar regions, the history of keystone seabirds of the tropics is unclear, despite the prominence of albatrosses (Diomedeidae, Procellariiformes) as the largest and most threatened group of oceanic seabirds. To understand the impact of climate change on tropical albatrosses, we investigated the evolutionary and demographic histories of all four North Pacific albatrosses and their prey using whole-genome analyses. We report a striking concordance in demographic histories among the four species, with a notable dip in effective population size at the beginning of the Pleistocene and a population expansion in the Last Glacial Period when sea levels were low, which resulted in increased potential coastal breeding sites. Abundance of the black-footed albatross dropped again during the Last Glacial Maximum, potentially linked to climate-driven loss of breeding sites and concordant genome-derived decreases in its major prey. We find very low genome-wide (π < 0.001) and adaptative genetic diversities across the albatrosses, with genes of the major histocompatibility complex close to monomorphic. We also identify recent selective sweeps at genes associated with hyperosmotic adaptation, longevity, and cognition and memory. Our study has shed light on the evolutionary and demographic histories of the largest tropical oceanic seabirds and provides evidence for their large population fluctuations and alarmingly low genetic diversities.

Hill, A., M. F. T. Jiménez, N. Chazot, C. Cássia‐Silva, S. Faurby, L. Herrera‐Alsina, and C. D. Bacon. 2023. Apparent effect of range size and fruit colour on palm diversification may be spurious. Journal of Biogeography. https://doi.org/10.1111/jbi.14683

Aim Fruit selection by animal dispersers with different mobility directly impacts plant geographical range size, which, in turn, may impact plant diversification. Here, we examine the interaction between fruit colour, range size and diversification rate in palms by testing two hypotheses: (1) species with fruit colours attractive to birds have larger range sizes due to high dispersal ability and (2) disperser mobility affects whether small or large range size has higher diversification, and intermediate range size is expected to lead to the highest diversification rate regardless of disperser. Location Global. Time Period Contemporary (or present). Major Taxa Studied Palms (Arecaceae). Methods Palm species were grouped based on likely animal disperser group for given fruit colours. Range sizes were estimated by constructing alpha convex hull polygons from distribution data. We examined disperser group, range size or an interaction of both as possible drivers of change in diversification rate over time in a likelihood dynamic model (Several Examined State-dependent Speciation and Extinction [SecSSE]). Models were fitted, rate estimates were retrieved and likelihoods were compared to those of appropriate null models. Results Species with fruit colours associated with mammal dispersal had larger ranges than those with colours associated with bird dispersal. The best fitting SecSSE models indicated that the examined traits were not the primary driver of the heterogeneity in diversification rates in the model. Extinction rate complexity had a marked impact on model performance and on diversification rates. Main Conclusions Two traits related to dispersal mobility, range size and fruit colour, were not identified as the main drivers of diversification in palms. Increased model extinction rate complexity led to better performing models, which indicates that net diversification should be estimated rather than speciation alone. However, increased complexity may lead to incorrect SecSSE model conclusions without careful consideration. Finally, we find palms with more mobile dispersers do not have larger range sizes, meaning other factors are more important determinants of range size.