The ecology of plant extinctions

Barratt C.D., Onstein R.E., Pinsky M.L., Steinfartz S., Kühl H.S., Forester B.R., Razgour O.

Abstract Global change is impacting biodiversity across all habitats on earth. New selection pressures from changing climatic conditions and other anthropogenic activities are creating heterogeneous ecological and evolutionary responses across many species' geographic ranges. Yet we currently lack standardised and reproducible tools to effectively predict the resulting patterns in species vulnerability to declines or range changes. We developed an informatic toolbox that integrates ecological, environmental and genomic data and analyses (environmental dissimilarity, species distribution models, landscape connectivity, neutral and adaptive genetic diversity, genotype‐environment associations and genomic offset) to estimate population vulnerability. In our toolbox, functions and data structures are coded in a standardised way so that it is applicable to any species or geographic region where appropriate data are available, for example individual or population sampling and genomic datasets (e.g. RAD‐seq, ddRAD‐seq, whole genome sequencing data) representing environmental variation across the species geographic range. To demonstrate multi‐species applicability, we apply our toolbox to three georeferenced genomic datasets for co‐occurring East African spiny reed frogs (Afrixalus fornasini, A. delicatus and A. sylvaticus) to predict their population vulnerability, as well as demonstrating that range loss projections based on adaptive variation can be accurately reproduced from a previous study using data for two European bat species (Myotis escalerai and M. crypticus). Our framework sets the stage for large scale, multi‐species genomic datasets to be leveraged in a novel climate change vulnerability framework to quantify intraspecific differences in genetic diversity, local adaptation, range shifts and population vulnerability based on exposure, sensitivity and landscape barriers.

Fisher D.O., Humphreys A.M.

Christenhusz M.J., Govaerts R.

Abstract Species go extinct each day, most without notice. The current human-induced extinction rate is up to 700 times higher than the background rate. Extinctions are not different for plants, animals, or fungi, although botanical and invertebrate extinctions are much more poorly documented than those of charismatic vertebrates. In a recent book on extinct plants (Christenhusz & Govaerts, 2023), an overview of botanical extinctions since 1753 was presented, listing which species became extinct and the probable reason for their extinction. As most have a date when they were last documented, a timeline of extinction can also be compiled based on these data. This timeline shows an increase from 1890 to 1940, but a decline in new recorded extinctions after the 1980s, which is likely a result of taxonomic impediment. Extinction rates before 1800 are impacted by the lack of data (here named Berkeley extinction). It can be concluded that extinction is highest in biodiversity-rich areas with high human influence (extinction hotspots). Two new combinations and a new name are proposed here, showing the importance of taxonomy to conservation. Although anthropogenic plant extinction is a global phenomenon, areas of particular concern are the Hawaiian Islands, southern Africa, Australia, the Indian Subcontinent, Southeast Asia, and Brazil. Extinctions have been mainly caused by land clearing for agriculture and urbanization, invasive feral animals, mining, river dams, diseases, and poaching. We predict that the unusual weather patterns associated with rapid climate change may result in more plant extinctions. Reintroduction, even if a species persists in cultivation, is not always possible due to lack of suitable remaining habitat where threats are decreased or removed. Successful reintroduction cannot be guaranteed. It is costly and usually dependent on short-term funding, after which these efforts may be in vain. Protection of species in their natural habitat is much more cost-effective in the long term. Sometimes, rescued plants should be introduced in similar habitats outside their natural range where the threats are absent. This follows the programmes of assisted migration for climate change mitigation, but this can also be assisted introduction to prevent extinction. Protection of critically endangered species that have naturalized outside their native range should also be considered.

Sun W., Ma Y., Corlett R.T.

Conservation programs for plant species with extremely small populations (PSESP) have been successfully implemented for several decades in China. Here we highlight how their inclusion in several national conservation policies helps meet targets of the Kunming–Montreal Global Biodiversity Framework (KMGBF) and show how lessons from these programs can be applied more widely.

Hollenbeck E.C., Sax D.F.

AbstractClimate change is conjectured to endanger tropical species, particularly in biodiverse montane regions, but accurate estimates of extinction risk are limited by a lack of empirical data demonstrating tropical species’ sensitivity to climate. To fill this gap, studies could match high-quality distribution data with multi-year transplant experiments. Here, we conduct field surveys of epiphyte distributions on three mountains in Central America and perform reciprocal transplant experiments on one mountain across sites that varied in elevation, temperature and aridity. We find that most species are unable to survive outside of their narrow elevational distributions. Additionally, our findings suggest starkly different outcomes from temperature conditions expected by 2100 under different climate change scenarios. Under temperatures associated with low-emission scenarios, most tropical montane epiphyte species will survive, but under emission scenarios that are moderately high, 5-36% of our study species may go extinct and 10-55% of populations may be lost. Using a test of tropical species’ climate tolerances from a large field experiment, paired with detailed species distribution data across multiple mountains, our work strengthens earlier conjecture about risks of wide-spread extinctions from climate change in tropical montane ecosystems.

Naughtin S.R., Castilla A.R., Smith A.B., Strand A.E., Dawson A., Hoban S., Abhainn E.A., Romero‐Severson J., Robinson J.D.

Climate change poses a threat to biodiversity, and it is unclear whether species can adapt to or tolerate new conditions, or migrate to areas with suitable habitats. Reconstructions of range shifts that occurred in response to environmental changes since the last glacial maximum (LGM) from species distribution models (SDMs) can provide useful data to inform conservation efforts. However, different SDM algorithms and climate reconstructions often produce contrasting patterns, and validation methods typically focus on accuracy in recreating current distributions, limiting their relevance for assessing predictions to the past or future. We modeled historically suitable habitat for the threatened North American tree green ash Fraxinus pennsylvanica using 24 SDMs built using two climate models, three calibration regions, and four modeling algorithms. We evaluated the SDMs using contemporary data with spatial block cross‐validation and compared the relative support for alternative models using a novel integrative method based on coupled demographic‐genetic simulations. We simulated genomic datasets using habitat suitability of each of the 24 SDMs in a spatially‐explicit model. Approximate Bayesian computation (ABC) was then used to evaluate the support for alternative SDMs through comparisons to an empirical population genomic dataset. Models had very similar performance when assessed with contemporary occurrences using spatial cross‐validation, but ABC model selection analyses consistently supported SDMs based on the CCSM climate model, an intermediate calibration extent, and the generalized linear modeling algorithm. Finally, we projected the future range of green ash under four climate change scenarios. Future projections using the SDMs selected via ABC suggest only minor shifts in suitable habitat for this species, while some of those that were rejected predicted dramatic changes. Our results highlight the different inferences that may result from the application of alternative distribution modeling algorithms and provide a novel approach for selecting among a set of competing SDMs with independent data.

Rose M.B., Velazco S.J., Regan H.M., Flint A.L., Flint L.E., Thorne J.H., Franklin J.

AbstractAimVariation in spatial predictions of species' ranges made by various models has been recognized as a significant source of uncertainty for modelling species distributions. Consensus approaches that combine the results of multiple models have been employed to reduce the uncertainty introduced by different algorithms. We evaluate how estimates of habitat suitability, projected using species distribution models (SDMs), varied among different consensus methods relative to the variation introduced by different global climate models (GCMs) and representative concentration pathways (RCPs) used for projection.LocationCalifornia Floristic Province (California, US portion).MethodsWe modelled the current and future potential distributions of 82 terrestrial plant species, developing model predictions under different combinations of GCMs, RCPs, time periods, dispersal assumptions and SDM consensus methods commonly used to combine different species distribution modelling algorithms. We assessed how each of these factors contributed to the variability in future predictions of species habitat suitability change and aggregate measures of proportional change in species richness. We also related variability in species‐level habitat change to species' attributes.ResultsAssuming full dispersal capacity, the variability between habitat predictions made by different consensus methods was higher than the variability introduced by different RCPs and GCMs. The relationships between species' attributes and variability in future habitat predictions depended on the source of uncertainty and dispersal assumptions. However, species with small ranges or low prevalence tended to be associated with high variability in range change forecasts.Main ConclusionsOur results support exploring multiple consensus approaches when considering changes in habitat suitability outside of species' current distributions, especially when projecting species with low prevalence and small range sizes, as these species tend to be of the greatest conservation concern yet produce highly variable model outputs. Differences in vulnerability between diverging greenhouse gas concentration scenarios are most readily observed for end‐of‐century time periods and within species' currently occupied habitats (no dispersal).

Chardon N.I., McBurnie L., Goodwin K.J., Pradhan K., Hille Ris Lambers J., Angert A.L.

Climate change is causing geographic range shifts globally, and understanding the factors that influence species' range expansions is crucial for predicting future biodiversity changes. A common, yet untested, assumption in forecasting approaches is that species will shift beyond current range edges into new habitats as they become macroclimatically suitable, even though microhabitat variability could have overriding effects on local population dynamics. We aim to better understand the role of microhabitat in range shifts in plants through its impacts on establishment by 1) examining microhabitat variability along large macroclimatic (i.e. elevational) gradients, 2) testing which of these microhabitat variables explain plant recruitment and seedling survival, and 3) predicting microhabitat suitability beyond species range limits. We transplanted seeds of 25 common tree, shrub, forb and graminoid species across and beyond their current elevational ranges in the Washington Cascade Range, USA, along a large elevational gradient spanning a broad range of macroclimates. Over five years, we recorded recruitment, survival, and microhabitat (i.e. high resolution soil, air and light) characteristics rarely measured in biogeographic studies. We asked whether microhabitat variables correlate with elevation, which variables drive species establishment, and whether microhabitat variables important for establishment are already suitable beyond leading range limits. We found that only 30% of microhabitat parameters covaried with elevation. We further observed extremely low recruitment and moderate seedling survival, and these were generally only weakly explained by microhabitat. Moreover, species and life stages responded in contrasting ways to soil biota, soil moisture, temperature, and snow duration. Microhabitat suitability predictions suggest that distribution shifts are likely to be species‐specific, as different species have different suitability and availability of microhabitat beyond their present ranges, thus calling into question low‐resolution macroclimatic projections that will miss such complexities. We encourage further research on species responses to microhabitat and including microhabitat in range shift forecasts.

Chevalier M., Broennimann O., Guisan A.

The ability of climatic niche models to predict species extinction risks can be hampered if niches are incompletely quantified. This can occur when niches are estimated considering only currently available climatic conditions, disregarding the fact that climate change can open up portions of the fundamental niche that are currently inaccessible to species. Using a new metric, we estimate the prevalence of potential situations of fundamental niche truncation by measuring whether current ecological niche limits are contiguous to the boundaries of currently available climatic conditions for 24,944 species at the global scale in both terrestrial and marine realms and including animals and plants. We show that 12,172 (~49%) species are showing niche contiguity, particularly those inhabiting tropical ecosystems and the marine realm. Using niche expansion scenarios, we find that 86% of species showing niche contiguity could have a fundamental niche potentially expanding beyond current climatic limits, resulting in lower—yet still alarming—rates of predicted biodiversity loss, particularly within the tropics. Caution is therefore advised when forecasting future distributions of species presenting niche contiguity, particularly towards climatic limits that are predicted to expand in the future. Niche contiguity occurs when only current climatic conditions are used to estimate the niche of a species, ignoring potential niche expansion under climate change. An assessment of 24,944 species shows that nearly half exhibit niche contiguity, which can lead to overestimates of biodiversity loss under climate change.

Auffret A.G., Nenzén H., Polaina E.

AbstractAimTo evaluate the performance of species distribution models in predicting observed colonisations, persistences and extirpations in response to changes in climate and land use over a multi‐decadal period.LocationSweden.MethodsWe use historical (early 20th century) land use and climate data to build species distribution models for 84 plant species across three provinces of Sweden. Model performance was then evaluated internally using a subset of the historical data for cross‐validation, as well as by using the models to project occurrences to the modern day and validating them with observed occurrences from 1990 to 2020. We then analysed predicted and observed occurrences in the modern period in terms of persistence, extirpation (local extinction) and colonisation in relation to species' habitat and climate associations.ResultsWe found overall high agreement between evaluation methods, although internal evaluation gave consistently higher values for model performance (using true skill statistic, TSS). Overall, extirpations were worst predicted, with on average fewer than one‐third of each species' extirpations being foreseen by the models. Colonisations were better predicted, while persistences were relatively well‐predicted. Predictive accuracy of colonisations was higher for species with relatively warmer temperature associations (climate‐driven expansion), while extirpations were better predicted in cool‐related species (retractions at cool edges). Colonisations of forest‐associated species were more common than predicted (underpredicted), despite widespread patterns of afforestation. Assessing grid‐cell level turnover, we found that in grid cells that experienced the largest changes in terms of climate and land use, predicted extirpations were less likely to have happened.Main ConclusionsWe found that commonly applied modelling approaches have limited ability to predict observed changes in species occurrences, especially extirpations. This suggests that we should take predictions of future biodiversity loss very seriously. However, the ability for species to (at least temporarily) persist in unsuitable conditions could be an opportunity for biodiversity conservation.

Peng S., Ramirez‐Parada T.H., Mazer S.J., Record S., Park I., Ellison A.M., Davis C.C.

Summary Anthropogenetic climate change has caused range shifts among many species. Species distribution models (SDMs) are used to predict how species ranges may change in the future. However, most SDMs rarely consider how climate‐sensitive traits, such as phenology, which affect individuals' demography and fitness, may influence species' ranges. Using > 120 000 herbarium specimens representing 360 plant species distributed across the eastern United States, we developed a novel ‘phenology‐informed’ SDM that integrates phenological responses to changing climates. We compared the ranges of each species forecast by the phenology‐informed SDM with those from conventional SDMs. We further validated the modeling approach using hindcasting. When examining the range changes of all species, our phenology‐informed SDMs forecast less species loss and turnover under climate change than conventional SDMs. These results suggest that dynamic phenological responses of species may help them adjust their ecological niches and persist in their habitats as the climate changes. Plant phenology can modulate species' responses to climate change, mitigating its negative effects on species persistence. Further application of our framework will contribute to a generalized understanding of how traits affect species distributions along environmental gradients and facilitate the use of trait‐based SDMs across spatial and taxonomic scales.

Svenning J., Lemoine R.T., Bergman J., Buitenwerf R., Le Roux E., Lundgren E., Mungi N., Pedersen R.Ø.

Bachman S.P., Brown M.J., Leão T.C., Nic Lughadha E., Walker B.E.

Summary More than 70% of all vascular plants lack conservation status assessments. We aimed to address this shortfall in knowledge of species extinction risk by using the World Checklist of Vascular Plants to generate the first comprehensive set of predictions for a large clade: angiosperms (flowering plants, c. 330 000 species). We used Bayesian Additive Regression Trees (BART) to predict the extinction risk of all angiosperms using predictors relating to range size, human footprint, climate, and evolutionary history and applied a novel approach to estimate uncertainty of individual species‐level predictions. From our model predictions, we estimate 45.1% of angiosperm species are potentially threatened with a lower bound of 44.5% and upper bound of 45.7%. Our species‐level predictions, with associated uncertainty estimates, do not replace full global, or regional Red List assessments, but can be used to prioritise predicted threatened species for full Red List assessment and fast‐track predicted non‐threatened species for Least Concern assessments. Our predictions and uncertainty estimates can also guide fieldwork, inform systematic conservation planning and support global plant conservation efforts and targets.

Ortega M.A., Cayuela L., Griffith D.M., Camacho A., Coronado I.M., del Castillo R.F., Figueroa-Rangel B.L., Fonseca W., Garibaldi C., Kelly D.L., Letcher S.G., Meave J.A., Merino-Martín L., Meza V.H., Ochoa-Gaona S., et. al.

Global biodiversity is negatively affected by anthropogenic climate change. As species distributions shift due to increasing temperatures and precipitation fluctuations, many species face the risk of extinction. In this study, we explore the expected trend for plant species distributions in Central America and southern Mexico under two alternative Representative Concentration Pathways (RCPs) portraying moderate (RCP4.5) and severe (RCP8.5) increases in greenhouse gas emissions, combined with two species dispersal assumptions (limited and unlimited), for the 2061–2080 climate forecast. Using an ensemble approach employing three techniques to generate species distribution models, we classified 1924 plant species from the region’s (sub)tropical forests according to IUCN Red List categories. To infer the spatial and taxonomic distribution of species’ vulnerability under each scenario, we calculated the proportion of species in a threat category (Vulnerable, Endangered, Critically Endangered) at a pixel resolution of 30 arc seconds and by family. Our results show a high proportion (58–67%) of threatened species among the four experimental scenarios, with the highest proportion under RCP8.5 and limited dispersal. Threatened species were concentrated in montane areas and avoided lowland areas where conditions are likely to be increasingly inhospitable. Annual precipitation and diurnal temperature range were the main drivers of species’ relative vulnerability. Our approach identifies strategic montane areas and taxa of conservation concern that merit urgent inclusion in management plans to improve climatic resilience in the Mesoamerican biodiversity hotspot. Such information is necessary to develop policies that prioritize vulnerable elements and mitigate threats to biodiversity under climate change.

Bureš P., Elliott T.L., Veselý P., Šmarda P., Forest F., Leitch I.J., Nic Lughadha E., Soto Gomez M., Pironon S., Brown M.J., Šmerda J., Zedek F.

Summary Angiosperms, which inhabit diverse environments across all continents, exhibit significant variation in genome sizes, making them an excellent model system for examining hypotheses about the global distribution of genome size. These include the previously proposed large genome constraint, mutational hazard, polyploidy‐mediated, and climate‐mediated hypotheses. We compiled the largest genome size dataset to date, encompassing 16 017 (> 5% of known) angiosperm species, and analyzed genome size distribution using a comprehensive geographic distribution dataset for all angiosperms. We observed that angiosperms with large range sizes generally had small genomes, supporting the large genome constraint hypothesis. Climate was shown to exert a strong influence on genome size distribution along the global latitudinal gradient, while the frequency of polyploidy and the type of growth form had negligible effects. In contrast to the unimodal patterns along the global latitudinal gradient shown by plant size traits and polyploid proportions, the increase in angiosperm genome size from the equator to 40–50°N/S is probably mediated by different (mostly climatic) mechanisms than the decrease in genome sizes observed from 40 to 50°N northward. Our analysis suggests that the global distribution of genome sizes in angiosperms is mainly shaped by climatically mediated purifying selection, genetic drift, relaxed selection, and environmental filtering.

Orihuela‐Rivero R., Morente‐López J., Reyes‐Betancort J.A., Schaefer H., Valido A., Menezes de Sequeira M., Romeiras M.M., Góis‐Marques C.A., Salas‐Pascual M., Vanderpoorten A., Fernández‐Palacios J.M., Patiño J.

ABSTRACTWhether species extinctions have accelerated during the Anthropocene and the extent to which certain species are more susceptible to extinction due to their ecological preferences and intrinsic biological traits are among the most pressing questions in conservation biology. Assessing extinction rates is, however, challenging, as best exemplified by the phenomenon of ‘dark extinctions’: the loss of species that disappear before they are even formally described. These issues are particularly problematic in oceanic islands, where species exhibit high rates of endemism and unique biological traits but are also among the most vulnerable to extinction. Here, we document plant species extinctions since Linnaeus' Species Plantarum in Macaronesia, a biogeographic region comprised of five hyperdiverse oceanic archipelagos, and identify the key drivers behind these extinctions. We compiled 168 records covering 126 taxa, identifying 13 global and 155 local extinction events. Significantly higher extinction rates were observed compared to the expected global background rate. We uncovered differentiated extinction patterns along altitudinal gradients, highlighting a recent coastal hotspot linked to socioeconomic changes in Macaronesian archipelagos from the 1960s onwards. Key factors influencing extinction patterns include island age, elevation, introduced herbivorous mammals, and human population size. Trait‐based analyses across the floras of the Azores and Canary Islands revealed that endemicity, pollination by vertebrates, nitrogen‐fixing capacity, woodiness, and zoochory consistently tended to increase extinction risk. Our findings emphasize the critical role of geography and biological traits, alongside anthropogenic impacts, in shaping extinction dynamics on oceanic islands. Enhancing our knowledge of life‐history traits within island floras is crucial for accurately predicting and mitigating future extinction risks, underscoring the urgent need for comprehensive biodiversity assessments in island ecosystems.