Evaluating the predicted extinction risk of living amphibian species with the fossil record

DeepDive: estimating global biodiversity patterns through time using deep learning

Understanding how biodiversity has changed through time is a central goal of evolutionary biology. However, estimates of past biodiversity are challenged by the inherent incompleteness of the fossil record, even when state-of-the-art statistical methods are applied to adjust estimates while correcting for sampling biases. Here we develop an approach based on stochastic simulations of biodiversity and a deep learning model to infer richness at global or regional scales through time while incorporating spatial, temporal and taxonomic sampling variation. Our method outperforms alternative approaches across simulated datasets, especially at large spatial scales, providing robust palaeodiversity estimates under a wide range of preservation scenarios. We apply our method on two empirical datasets of different taxonomic and temporal scope: the Permian-Triassic record of marine animals and the Cenozoic evolution of proboscideans. Our estimates provide a revised quantitative assessment of two mass extinctions in the marine record and reveal rapid diversification of proboscideans following their expansion out of Africa and a >70% diversity drop in the Pleistocene.

The radiation continuum and the evolution of frog diversity

Most of life's vast diversity of species and phenotypes is often attributed to adaptive radiation. Yet its contribution to species and phenotypic diversity of a major group has not been examined. Two key questions remain unresolved. First, what proportion of clades show macroevolutionary dynamics similar to adaptive radiations? Second, what proportion of overall species richness and phenotypic diversity do these adaptive-radiation-like clades contain? We address these questions with phylogenetic and morphological data for 1226 frog species across 43 families (which represent >99% of all species). Less than half of frog families resembled adaptive radiations (with rapid diversification and morphological evolution). Yet, these adaptive-radiation-like clades encompassed ~75% of both morphological and species diversity, despite rapid rates in other clades (e.g., non-adaptive radiations). Overall, we support the importance of adaptive-radiation-like evolution for explaining diversity patterns and provide a framework for characterizing macroevolutionary dynamics and diversity patterns in other groups.

Ongoing declines for the world's amphibians in the face of emerging threats

Systematic assessments of species extinction risk at regular intervals are necessary for informing conservation action1,2. Ongoing developments in taxonomy, threatening processes and research further underscore the need for reassessment3,4. Here we report the findings of the second Global Amphibian Assessment, evaluating 8,011 species for the International Union for Conservation of Nature Red List of Threatened Species. We find that amphibians are the most threatened vertebrate class (40.7% of species are globally threatened). The updated Red List Index shows that the status of amphibians is deteriorating globally, particularly for salamanders and in the Neotropics. Disease and habitat loss drove 91% of status deteriorations between 1980 and 2004. Ongoing and projected climate change effects are now of increasing concern, driving 39% of status deteriorations since 2004, followed by habitat loss (37%). Although signs of species recoveries incentivize immediate conservation action, scaled-up investment is urgently needed to reverse the current trends.

How predictable are mass extinction events?

Many modern extinction drivers are shared with past mass extinction events, such as rapid climate warming, habitat loss, pollution and invasive species. This commonality presents a key question: can the extinction risk of species during past mass extinction events inform our predictions for a modern biodiversity crisis? To investigate if it is possible to establish which species were more likely to go extinct during mass extinctions, we applied a functional trait-based model of extinction risk using a machine learning algorithm to datasets of marine fossils for the end-Permian, end-Triassic and end-Cretaceous mass extinctions. Extinction selectivity was inferred across each individual mass extinction event, before testing whether the selectivity patterns obtained could be used to 'predict' the extinction selectivity exhibited during the other mass extinctions. Our analyses show that, despite some similarities in extinction selectivity patterns between ancient crises, the selectivity of mass extinction events is inconsistent, which leads to a poor predictive performance. This lack of predictability is attributed to evolution in marine ecosystems, particularly during the Mesozoic Marine Revolution, associated with shifts in community structure alongside coincident Earth system changes. Our results suggest that past extinctions are unlikely to be informative for predicting extinction risk during a projected mass extinction.

Integrating deep-time palaeontology in conservation prioritisation

Halting biodiversity loss under growing anthropogenic pressure is arguably the greatest environmental challenge we face. Given that not all species are equally threatened and that resources are always limited, establishing robust prioritisation schemes is critical for implementing effective conservation actions. To this end, the International Union for Conservation of Nature (IUCN) Red List of Threatened Species has become a widely used source of information on species’ extinction risk. Various metrics have been proposed that combine IUCN status with different aspects of biodiversity to identify conservation priorities. However, current strategies do not take full advantage of palaeontological data, with conservation palaeobiology often focussing on the near-time fossil record (the last 2 million years). Here, we make a case for the value of the deep-time (over 2 million years ago), as it can offer tangible parallels with today’s biodiversity crisis and inform on the intrinsic traits that make species prone to extinction. As such, palaeontological data holds great predictive power, which could be harnessed to flag species likely to be threatened but that are currently too poorly known to be identified as such. Finally, we identify key IUCN-based prioritisation metrics and outline opportunities for integrating palaeontological data to validate their implementation. Although the human signal of the current extinction crisis makes direct comparisons with the geological past challenging, the deep-time fossil record has more to offer to conservation than is currently recognised.

Clarifying the relationship between body size and extinction risk in amphibians by complete mapping of model space

In vertebrates, large body size is often a key diagnostic feature of species threatened with extinction. However, in amphibians the link between body size and extinction risk is highly uncertain, with previous studies suggesting positive, negative, u-shaped, or no relationship. Part of the reason for this uncertainty is 'researcher degrees of freedom': the subjectivity and selectivity in choices associated with specifying and fitting models. Here, I clarify the size-threat association in amphibians using Specification Curve Analysis, an analytical approach from the social sciences that attempts to minimize this problem by complete mapping of model space. I find strong support for prevailing negative associations between body size and threat status, the opposite of patterns typical in other vertebrates. This pattern is largely explained by smaller species having smaller geographic ranges, but smaller amphibian species also appear to lack some of the life-history advantages (e.g. higher reproductive output) that are often assumed to 'protect' small species in other taxa. These results highlight the need for a renewed conservation focus on the smallest species of the world's most threatened class of vertebrates, as aquatic habitats become increasingly degraded by human activity.

Two-hundred million years of anuran body-size evolution in relation to geography, ecology and life history

Surprisingly, little is known about body-size evolution within the most diverse amphibian order, anurans (frogs and toads), despite known effects of body size on the physiological, ecological and life-history traits of animals more generally. Here, we examined anuran body-size evolution among 2,434 species with over 200 million years of shared evolutionary history. We found clade-specific evolutionary shifts to new body-size optima along with numerous independent transitions to gigantic and miniature body sizes, despite the upper limits of anuran body size remaining quite consistent throughout the fossil record. We found a weak, positive correlation between a species' body size and maximum latitude and elevation, including a dearth of small species at higher elevations and broader latitudinal and elevational ranges in larger anurans. Although we found modest differences in mean anuran body size among microhabitats, there was extensive overlap in the range of body sizes across microhabitats. Finally, we found that larger anurans are more likely to consume vertebrate prey than smaller anurans are and that species with a free-swimming larval phase during development are larger on average than those in which development into a froglet occurs within the egg. Overall, anuran body size does not conform to geographic and ecological patterns observed in other tetrapods but is perhaps more notable for variation in body size within geographic regions, ecologies and life histories. Here, we document this variation and propose target clades for detailed studies aimed at disentangling how and why variation in body size was generated and is maintained in anurans.

Conservation palaeobiology and the shape of things to come

Conservation decision-making is a forward-looking process that involves choices among alternative images of how the future will unfold. Scenarios, easily understood as stories about plausible futures, are emerging as a powerful approach used by the conservation community to define a range of socio-ecological futures when standard, predictive modelling approaches to decision-making are inappropriate, providing a framework for making robust decisions under uncertainties. Conservation palaeobiologists can help the conservation community imagine the future. The utility of the past centres on orienting us to the present-grounding the future in the realm of what is plausible-by providing context against which to think about future scenarios, which may help stakeholders and decision-makers to develop a new mental map of a conservation problem, inspiring our intentions and moving us purposefully toward a desirable tomorrow. This article is part of a discussion meeting issue 'The past is a foreign country: how much can the fossil record actually inform conservation?'