Biology subjects

Pimiento, C.

Publications and source records attributed to Pimiento, C..

8 recordsLinked to original sources

bioRxiv2026

Temporal resolution reshapes dynamics of inferred community structure and extinction selectivity across the Permian-Triassic mass extinction

The Permian-Triassic mass extinction fundamentally restructured ecosystems, yet it remains unresolved whether ecological collapse unfolded gradually or in discrete steps, and how extinction selectivity varied with environmental change. Here, we analyse marine food webs from Meishan (China) at high temporal resolution. We show that trophic structure destabilised prior to peak biodiversity loss, followed by a structural tipping point during the extinction interval when the community became less robust to secondary extinctions. Extinction selectivity shifted substantially across the study interval. During the extinction interval, extinction was concentrated at lower trophic levels, propagating upwards from benthic herbivores to higher-level consumers. Although coarse resolution preserves temporal trends in trophic structure and extinction selectivity, it obscures abrupt transitions, sequential extinction dynamics, and critical shifts in ecological organisation. We demonstrate that temporal resolution governs inference of extinction dynamics, with important implications for reconstructing past ecological crises and interpreting ecosystem responses to rapid environmental change.

paleontology↗

bioRxiv2026

Robust evidence for modest diversity loss across the K/Pg in neoselachians: Response to Guinot et al.

We reconstructed the neoselachian diversity over the past 145 million years using new occurrence dataset and DeepDive1-3. We recovered a small decline through the K/Pg following a steady increase during the Cretaceous, and a prolonged, substantial decline towards the present following a mid-Eocene peak2. Guinot et al. argue that our conclusions are compromised by problems in the underlying data and by the way extinction magnitude across the K/Pg was quantified. They cast doubt particularly on the pattern across the K/Pg, which they consider to be at odds with all previous analyses. They raise no issue with the Cretaceous trend, even though it was recovered with the same dataset and methods. We audited the alleged data issues reported in Guinot et al. and found that they mostly reflect operational choices (see Supplementary Information). However, we applied their data treatment and ran sensitivity tests to evaluate how this approach affects our results, specifically around the K/Pg. None of our tests recovered a diversity collapse for neoselachians during this interval. As such, we demonstrate that our findings are robust and consistent across different data treatments.

paleontology↗

bioRxiv2026

No global collapse of food webs across the Permian-Triassic Mass Extinction

The Permian-Triassic mass extinction (PTME), the Earths most severe biotic crisis associated with extreme environmental perturbations, eliminated >80% of marine species1. However, whether it triggered a globally pervasive top-down collapse of marine food webs, and whether recovery proceeded through bottom-up reassembly, remain unresolved2-4. Here we reconstruct spatially explicit metacommunity food webs from seven regions spanning equatorial to high latitudes to test how extinction dynamics and ecosystem reorganization varied geographically. By integrating estimates of community structure and species interactions, we provide direct inference on trophic disruption across the PTME. Despite catastrophic species loss and flattening of the latitudinal diversity gradient5, trophic collapse was not globally uniform, and higher trophic levels were not globally truncated. Instead, extinction selectivity was spatially heterogenous and tracked environmental severity. Benthic, low-motility herbivores with limited respiratory capacity were disproportionately lost, consistent with intensified warming, deoxygenation and disruption of primary productivity under elevated pCO2. Mid-to high-latitude communities became top-heavy and structurally complex, whereas tropical systems remained bottom-heavy and less robust to secondary extinction. These results demonstrate that trophic disruption and recovery were geographically structured, mediated by environmental forcing, species traits and pre-extinction food-web architecture, with implications for predicting marine ecosystem responses to ongoing climate change.

paleontology↗

bioRxiv2025

Integrating functional and phylogenetic perspectives reveals new priorities for bird and mammal conservation

Finite resources dictate that conservation biologists must prioritise some species over others. Conservation metrics, such as EDGE (Evolutionarily Distinct and Globally Endangered; EDGE1) and FUSE (Functionally Unique, Specialised and Endangered), make prioritisation based on species evolutionary or functional distinctiveness, respectively, and degree of threat. EDGE is in part based on the rationale that the evolutionary distinctiveness it captures serves to maximise biodiversity in form and function. However, doubts exist as to whether or not evolutionary distinctiveness truly serves as a proxy for functional distinctiveness, and, therefore, if the prominent use of EDGE lists by conservation practitioners adequately protects functional distinctiveness. To address this, we conducted a direct global comparison of EDGE against FUSE. Unlike EDGE, FUSE directly measures and prioritises functional distinctiveness. Here, we compare EDGE and FUSE scores for two well-studied groups: mammals (n = 5319 species) and birds (n = 7932 species). These groups are central to global conservation and, until now, have not been assessed under FUSE. We find that species rankings under EDGE and FUSE differ significantly, highlighting that these two metrics capture distinct, complementary aspects of biodiversity. This suggests that conservation strategies based solely on EDGE may overlook species with critical functional roles. Rather than assuming alignment between evolutionary and functional distinctiveness, we propose integrating both within a single measure, leveraging the strengths and benefits of each. To this end, we present a new conservation metric - EFUSE (Evolutionarily and Functionally Unique, Specialised, and Endangered) - which incorporates both evolutionary and functional distinctiveness into a single measure. EFUSE ensures that important components of biodiversity, which relate to ecosystem functioning, natures future contributions to people, and the intrinsic value of species, are adequately maximised in conservation decision-making.

ecology↗

bioRxiv2025

Global gaps and priorities for shark and ray conservation: Integrating threat, function, and evolutionary distinctiveness

Elasmobranchs (sharks, rays, and skates) face unprecedented extinction risk, with over one-third of species threatened primarily by overfishing. While marine protected areas (MPAs) are essential tools to help safeguard marine ecosystems and the species that inhabit them, we lack a comprehensive understanding of how well elasmobranchs are protected globally. Here, we (1) evaluate the current level of protection for elasmobranchs, (2) employ CAPTAIN reinforcement learning algorithm to identify areas that optimise conservation based on species level of threat and their functional and evolutionary distinctiveness, and (3) examine conservation conflicts and opportunities by identifying areas where conservation priorities overlap with high and low fishing pressures. Our analysis revealed severe protection deficits, with elasmobranchs having on average only 3% of their range covered by no-take MPAs and 64% of species under-represented relative to random expectations. Areas that optimise conservation priorities consistently converged in Australian, Southeast Asia, the Indian Ocean, Atlantic Africa, European Atlantic coasts, the Caribbean, and South American Atlantic regions. However, areas of highest conservation priority often coincided with intensive fishing, particularly in East Asian seas, highlighting conservation conflicts requiring strategic management. Our results provide actionable insights for policymakers to optimise conservation strategies and maximise biodiversity retention. TeaserReinforcement learning identifies priority areas to expand ocean protection for unique and irreplaceable elasmobranchs.

ecology↗

bioRxiv2025

FINS - A global occurrence dataset of fossil neoselachians from the Cretaceous to the Quaternary

MotivationModern sharks, rays and skates (Neoselachii) are a diverse, globally distributed, and ecologically important group. They possess a rich, geologically extensive, and well-documented fossil record that provides a powerful basis for studying their macroevolution, paleoecology and biogeography. However, addressing paleobiological questions require quantifying the fossil record trough occurrences, i.e., records of the presence of a taxon at a unique location in space and time. Although the Paleobiology Database (PBDB) offers an invaluable source of fossil occurrences, it still does not provide a complete compilation of neoselachian data. To facilitate exploring questions in quantitative paleobiology, here we present the Fossil Neoselachian (FINS) dataset--a comprehensive, systematically curated global synthesis of fossil occurrences spanning the past 145 million years. Main types of variables containedFINS consists of fossil occurrences, each linked to a collection (location where fossils were reported from) and a source (citation of the publications from which data was obtained). Occurrence data mostly consists of taxonomic variables (e.g., classification, names and ranks), status (extinct/extant) and abundance. Collection data provide geographic (e.g., country, ocean and paleo-coordinates) and geological (e.g., formation and age) variables. All data was subjected to a meticulous curation process, which is described through taxonomic and age validation variables. Spatial location and grainGlobal, with fossil occurrences recovered from all continents. Time period and grainFrom the Cretaceous to the Quaternary (145 - 0 Ma), with temporal resolution generally corresponding to geological stages or epochs. Major taxa and level of measurementNeoselachians (superorders: Selachimorpha and Batoidea). FINS comprises 30,100 occurrences from 5,972 collections and 1,990 publications. It consists of 1,606 species, 512 genera, 88 families and 14 orders. Over 70% of occurrences are identified at the species level. Overall, FINS effectively doubles the number of neoselachian records previously available in the PBDB and substantially expands their geographic coverage, particularly in the Global South. Software formatThe dataset is provided an .xlsx spreadsheet with four tabs - Collections, Occurrences, References_Literature and References_PBDB.

paleontology↗

bioRxiv2023

Benchmarking imputation methods for discrete biological data

Trait datasets are at the basis of a large share of ecology and evolutionary research, being used to infer ancestral morphologies, to quantify species extinction risks, or to evaluate the functional diversity of biological communities. These datasets, however, are often plagued by missing data, for instance due to incomplete sampling limited data and resource availabilities. Several imputation methods exist to predict missing values and have been successfully evaluated and used to fill the gaps in datasets of quantitative traits. Here we explore the performance of different imputation methods on discrete biological traits i.e. qualitative or categorical traits such as diet or habitat. We develop a bioinformatics pipeline to impute trait data combining phylogenetic, machine learning, and deep learning methods while integrating a simulation framework to evaluate their performance on synthetic datasets. Using this pipeline we run a wide range of simulations under different missing rates, mechanisms, and biases and different evolutionary models. Our results indicate that a new ensemble approach, where we combined the imputation results of a selection of imputation methods provides the most robust and accurate prediction of missing discrete traits. We apply our pipeline to an incomplete trait dataset of 1015 elasmobranch species (including sharks and rays) and found a high imputation accuracy of the predictions based on an expert-based assessment of the missing traits. Our bioinformatic pipeline, implemented in an open-source R package, facilitates the application and comparison of multiple imputation methods to make robust predictions of missing trait values in biological datasets.

bioinformatics↗

bioRxiv2020

Functionally unique, specialised, and endangered (FUSE) species: towards integrated metrics for the conservation prioritisation toolbox

Identifying species with disproportionate contributions to biodiversity can lead to effective conservation prioritisation. Despite well-established methods for identifying endangered species adding inordinately to evolutionary diversity, in this context functional diversity has been overlooked. Here, we compare different metrics designed to identify threatened species that contribute strongly to functional diversity. We use the diverse and threatened global marine megafauna as a case study. We found that functional contributions of species are not fully captured in a single metric. Although we found a very strong correlation between functional specialisation and distinctiveness, functional uniqueness was only moderately correlated with the other two metrics and identified a different set of top-10 species. These functional contributions were then integrated and combined with extinction risk to identify species that are both important contributors to functional diversity and endangered. For instance, the top-10 Functionally Unique Specialized and Endangered (FUSE) species contains three critically endangered, five endangered and two vulnerable species which - despite comprising only 3% of species - are among the top 10% most functionally unique and hold 15% of the global functional richness. The FUSE index was remarkably robust to different mathematical formulations. Combining one or more facets of a species contribution to functional diversity with endangerment, such as with the FUSE index, adds to the toolbox for conservation prioritisation. Nevertheless, we discuss how these new tools must be handled with care alongside other metrics and information.

ecology↗