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Buffan L, Condamine FL, Stutz NS, Pujos F, Antoine PO, Marivaux L. The fate of South America's endemic mammalian fauna in response to the most dramatic Cenozoic climate disruption. Proc Natl Acad Sci U S A 2025; 122:e2419520122. [PMID: 40324071 PMCID: PMC12107189 DOI: 10.1073/pnas.2419520122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2024] [Accepted: 03/30/2025] [Indexed: 05/07/2025] Open
Abstract
Around 34 Mya, the Eocene-Oligocene transition (EOT) marked the most dramatic global climatic cooling of the Cenozoic. On a planetary scale, paleontological evidence suggests that this transition was associated with major faunal turnovers, sometimes even regarded as a mass extinction crisis. In South America, there is no consensus on the response of the endemic mammals to this transition. Here, using a vetted fossil dataset and cutting-edge Bayesian methods, we analyzed the dynamics of South American mammal (SAM) diversification and their possible drivers across latitude (tropical vs. extratropical), taxonomic groups, and trophic guilds throughout the Eocene-Oligocene (ca. 56 to 23 Ma). Our results did not evidence any mass extinction among SAM at the EOT. Instead, they experienced a gradual and long-term diversity decline from the middle Eocene to the early Oligocene, followed by a sudden waxing-and-waning diversity associated with a large taxonomic-but not ecological-turnover. Tropical and extratropical lineages have had very distinct macroevolutionary histories. No effective change in the pace at which tropical lineages diversify was found, thus favoring the tropical stability hypothesis proposed by Wallace. Diversity-dependent effects, temperature, and Andean uplift were recovered as probable drivers of SAM diversification across the period. Contrasting evidence casts doubt on the common hypothesis primarily linking Oligocene faunal changes to grassland expansion. Our findings illustrate the uniqueness of the deep-time interplay between endemic SAM and their physical environment in a context of climatic shift, highlighting the need to consider regional idiosyncrasies for understanding the coevolution of life and climate.
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Affiliation(s)
- Lucas Buffan
- Équipes Paléontologie − Phylogénie Évolution Moléculaire, Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier cedex 534095, France
| | - Fabien L. Condamine
- Équipes Paléontologie − Phylogénie Évolution Moléculaire, Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier cedex 534095, France
| | - Narla S. Stutz
- Équipes Paléontologie − Phylogénie Évolution Moléculaire, Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier cedex 534095, France
| | - François Pujos
- Instituto Argentino de Nivología, Glaciología y Ciencias Ambientales, Centro Científico Tecnológico–Consejo Nacional de Investigaciones Científicas y Técnicas–Mendoza, Parque General San Martín, Mendoza5500, Argentina
| | - Pierre-Olivier Antoine
- Équipes Paléontologie − Phylogénie Évolution Moléculaire, Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier cedex 534095, France
| | - Laurent Marivaux
- Équipes Paléontologie − Phylogénie Évolution Moléculaire, Institut des Sciences de l’Évolution de Montpellier, Université de Montpellier, CNRS, Institut de Recherche pour le Développement, Montpellier cedex 534095, France
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2
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Mondanaro A, Girardi G, Castiglione S, Timmermann A, Zeller E, Venugopal T, Serio C, Melchionna M, Esposito A, Di Febbraro M, Raia P. EutherianCoP. An integrated biotic and climate database for conservation paleobiology based on eutherian mammals. Sci Data 2025; 12:6. [PMID: 39805871 PMCID: PMC11729879 DOI: 10.1038/s41597-024-04181-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2024] [Accepted: 11/28/2024] [Indexed: 01/16/2025] Open
Abstract
We present a new database, EutherianCoP, of fossil mammals which lived globally from the Late Pleistocene to the Holocene. The database includes 13,972 fossil occurrences of 786 extant or recently extinct placental mammal species, plus 155,198 current occurrences for those of them which survived to the present. The occurrences are correlated with radiometric age information. For all species, we provide 32 different traits, inclusive of taxonomic, phenotypic, life history, biogeographic and phylogenetic information. Differently from any other compilation, the occurrences are complemented with estimates of past climatic conditions, including site-interpolated monthly and annual precipitation and temperature, leaf area index, megabiome type and net primary productivity, which are derived from transient paleo model simulations conducted with the Community Earth System Model 1.2 and the BIOME4 vegetation model. All data are further downloadable for further investigation.
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Affiliation(s)
- Alessandro Mondanaro
- Department of Earth Science, University of Florence, via G. La Pira 4, 50121, Florence, Italy.
| | - Giorgia Girardi
- DiSTAR, University of Naples "Federico II", 80126, via Vicinale Cupa Cintia 26, Naples, Italy
| | - Silvia Castiglione
- DiSTAR, University of Naples "Federico II", 80126, via Vicinale Cupa Cintia 26, Naples, Italy
| | - Axel Timmermann
- IBS Center for Climate Physics, 46241, Busan, South Korea
- Pusan National University, 46241, Busan, South Korea
| | - Elke Zeller
- IBS Center for Climate Physics, 46241, Busan, South Korea
- Pusan National University, 46241, Busan, South Korea
| | - Thushara Venugopal
- IBS Center for Climate Physics, 46241, Busan, South Korea
- Pusan National University, 46241, Busan, South Korea
| | - Carmela Serio
- DiSTAR, University of Naples "Federico II", 80126, via Vicinale Cupa Cintia 26, Naples, Italy
| | - Marina Melchionna
- DiSTAR, University of Naples "Federico II", 80126, via Vicinale Cupa Cintia 26, Naples, Italy
| | - Antonella Esposito
- DiSTAR, University of Naples "Federico II", 80126, via Vicinale Cupa Cintia 26, Naples, Italy
| | - Mirko Di Febbraro
- EnviXLab, Department of Biosciences and Territory, University of Molise, 86090, Pesche (Isernia), Italy
| | - Pasquale Raia
- DiSTAR, University of Naples "Federico II", 80126, via Vicinale Cupa Cintia 26, Naples, Italy.
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3
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Silvestro D, Latrille T, Salamin N. Toward a Semi-Supervised Learning Approach to Phylogenetic Estimation. Syst Biol 2024; 73:789-806. [PMID: 38916476 PMCID: PMC11639169 DOI: 10.1093/sysbio/syae029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Revised: 05/21/2024] [Accepted: 06/24/2024] [Indexed: 06/26/2024] Open
Abstract
Models have always been central to inferring molecular evolution and to reconstructing phylogenetic trees. Their use typically involves the development of a mechanistic framework reflecting our understanding of the underlying biological processes, such as nucleotide substitutions, and the estimation of model parameters by maximum likelihood or Bayesian inference. However, deriving and optimizing the likelihood of the data is not always possible under complex evolutionary scenarios or even tractable for large datasets, often leading to unrealistic simplifying assumptions in the fitted models. To overcome this issue, we coupled stochastic simulations of genome evolution with a new supervised deep-learning model to infer key parameters of molecular evolution. Our model is designed to directly analyze multiple sequence alignments and estimate per-site evolutionary rates and divergence without requiring a known phylogenetic tree. The accuracy of our predictions matched that of likelihood-based phylogenetic inference when rate heterogeneity followed a simple gamma distribution, but it strongly exceeded it under more complex patterns of rate variation, such as codon models. Our approach is highly scalable and can be efficiently applied to genomic data, as we showed on a dataset of 26 million nucleotides from the clownfish clade. Our simulations also showed that the integration of per-site rates obtained by deep learning within a Bayesian framework led to significantly more accurate phylogenetic inference, particularly with respect to the estimated branch lengths. We thus propose that future advancements in phylogenetic analysis will benefit from a semi-supervised learning approach that combines deep-learning estimation of substitution rates, which allows for more flexible models of rate variation, and probabilistic inference of the phylogenetic tree, which guarantees interpretability and a rigorous assessment of statistical support.
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Affiliation(s)
- Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Thibault Latrille
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Nicolas Salamin
- Department of Computational Biology, University of Lausanne, 1015 Lausanne, Switzerland
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4
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Del Cid CC, Hauffe T, Carrillo JD, May MR, Warnock RCM, Silvestro D. Challenges in estimating species' age from phylogenetic trees. GLOBAL ECOLOGY AND BIOGEOGRAPHY : A JOURNAL OF MACROECOLOGY 2024; 33:e13890. [PMID: 39830735 PMCID: PMC11741515 DOI: 10.1111/geb.13890] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Accepted: 06/23/2024] [Indexed: 01/22/2025]
Abstract
Aim Species age, the elapsed time since origination, can give insight into how species longevity might influence eco-evolutionary dynamics, which has been hypothesized to influence extinction risk. Traditionally, species' ages have been estimated from fossil records. However, numerous studies have recently used the branch lengths of time-calibrated phylogenies as estimates of the ages of extant species. This approach poses problems because phylogenetic trees only contain direct information about species identity at the tips and not along the branches. Here, we show that incomplete taxon sampling, extinction, and different assumptions about speciation modes can significantly alter the relationship between true species age and phylogenetic branch lengths, leading to high error rates. We found that these biases can lead to erroneous interpretations of eco-evolutionary patterns derived from comparing phylogenetic age and other traits, such as extinction risk. Innovation For bifurcating speciation, the default assumption in most analyses of species age, we propose a probabilistic approach based on the properties of a birth-death process to improve the estimation of species ages. Our approach can reduce the error by one order of magnitude under cases of high extinction and a high percentage of unsampled extant species. Main conclusion Our results call for caution in interpreting the relationship between phylogenetic ages and eco-evolutionary traits, as this can lead to biased and erroneous conclusions. We show that, under the assumption of bifurcating speciation, we can obtain unbiased approximations of species age by combining information from branch lengths with the expectations of a birth-death process.
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Affiliation(s)
- Carlos Calderón Del Cid
- Laboratório de Ecologia Espacial, Instituto de Biologia, Universidade Federal da Bahia, CEP 40170-110, Salvador, Bahia, Brazil
- Department of Biology, University of Fribourg, Switzerland and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Torsten Hauffe
- Department of Biology, University of Fribourg, Switzerland and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Juan D Carrillo
- Department of Biology, University of Fribourg, Switzerland and Swiss Institute of Bioinformatics, Fribourg, Switzerland
| | - Michael R May
- Department of Evolution and Ecology, University of California Davis, Davis, CA USA, 94709
| | - Rachel C M Warnock
- GeoZentrum Nordbayern, Friedrich-Alexander Universität Erlangen-Nürnberg, Loewenichstrasse 28, 91054, Erlangen, Germany
| | - Daniele Silvestro
- Department of Biology, University of Fribourg, Switzerland and Swiss Institute of Bioinformatics, Fribourg, Switzerland
- Department of Biological and Environmental Sciences and Gothenburg Global Biodiversity Centre, University of Gothenburg, Sweden
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5
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Hauffe T, Cantalapiedra JL, Silvestro D. Trait-mediated speciation and human-driven extinctions in proboscideans revealed by unsupervised Bayesian neural networks. SCIENCE ADVANCES 2024; 10:eadl2643. [PMID: 39047110 PMCID: PMC11268411 DOI: 10.1126/sciadv.adl2643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2023] [Accepted: 06/21/2024] [Indexed: 07/27/2024]
Abstract
Species life-history traits, paleoenvironment, and biotic interactions likely influence speciation and extinction rates, affecting species richness over time. Birth-death models inferring the impact of these factors typically assume monotonic relationships between single predictors and rates, limiting our ability to assess more complex effects and their relative importance and interaction. We introduce a Bayesian birth-death model using unsupervised neural networks to explore multifactorial and nonlinear effects on speciation and extinction rates using fossil data. It infers lineage- and time-specific rates and disentangles predictor effects and importance through explainable artificial intelligence techniques. Analysis of the proboscidean fossil record revealed speciation rates shaped by dietary flexibility and biogeographic events. The emergence of modern humans escalated extinction rates, causing recent diversity decline, while regional climate had a lesser impact. Our model paves the way for an improved understanding of the intricate dynamics shaping clade diversification.
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Affiliation(s)
- Torsten Hauffe
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
| | - Juan L. Cantalapiedra
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
- GloCEE Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, Universidad de Alcalá, 28801 Alcalá de Henares, Spain
- Museum für Naturkunde, Leibniz Institute for Evolution and Biodiversity Science, Invalidenstraße 43, 10115 Berlin, Germany
| | - Daniele Silvestro
- Department of Biology, University of Fribourg and Swiss Institute of Bioinformatics, 1700 Fribourg, Switzerland
- Department of Biological and Environmental Sciences, Gothenburg Global Biodiversity Centre, University of Gothenburg, 40530 Gothenburg, Sweden
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6
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Nascimento JCS, Blanco F, Domingo MS, Cantalapiedra JL, Pires MM. The reorganization of predator-prey networks over 20 million years explains extinction patterns of mammalian carnivores. Ecol Lett 2024; 27:e14448. [PMID: 38814285 DOI: 10.1111/ele.14448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 05/09/2024] [Accepted: 05/10/2024] [Indexed: 05/31/2024]
Abstract
Linking the species interactions occurring at the scale of local communities to their potential impact at evolutionary timescales is challenging. Here, we used the high-resolution fossil record of mammals from the Iberian Peninsula to reconstruct a timeseries of trophic networks spanning more than 20 million years and asked whether predator-prey interactions affected regional extinction patterns. We found that, despite small changes in species richness, trophic networks showed long-term trends, gradually losing interactions and becoming sparser towards the present. This restructuring of the ecological networks was driven by the loss of medium-sized herbivores, which reduced prey availability for predators. The decrease in prey availability was associated with predator longevity, such that predators with less available prey had greater extinction risk. These results not only reveal long-term trends in network structure but suggest that prey species richness in ecological communities may shape large scale patterns of extinction and persistence among predators.
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Affiliation(s)
- João C S Nascimento
- Programa de Pós-Graduação em Ecologia, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
| | - Fernando Blanco
- Department of Biological and Environmental Sciences, University of Gothenburg, Gothenburg, Sweden
- Gothenburg Global Biodiversity Centre, Gothenburg, Sweden
- Museum für Naturkunde, Berlin, Germany
| | - M Soledad Domingo
- Departamento de Geodinámica, Estratigrafía y Paleontología, Facultad de Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Juan L Cantalapiedra
- Museum für Naturkunde, Berlin, Germany
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales (CSIC), Madrid, Spain
- GloCEE Global Change Ecology and Evolution Research Group, Departamento de Ciencias de la Vida, University of Alcalá, Madrid, Spain
| | - Mathias M Pires
- Departamento de Biologia Animal, Instituto de Biologia, Universidade Estadual de Campinas, Campinas, São Paulo, Brazil
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7
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Cooper RB, Flannery-Sutherland JT, Silvestro D. DeepDive: estimating global biodiversity patterns through time using deep learning. Nat Commun 2024; 15:4199. [PMID: 38760390 PMCID: PMC11101433 DOI: 10.1038/s41467-024-48434-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 04/30/2024] [Indexed: 05/19/2024] Open
Abstract
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.
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Affiliation(s)
- Rebecca B Cooper
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland.
| | | | - Daniele Silvestro
- Department of Biology, University of Fribourg, 1700, Fribourg, Switzerland.
- Swiss Institute of Bioinformatics, 1700, Fribourg, Switzerland.
- Department of Biological and Environmental Sciences, Global Gothenburg Biodiversity Centre, University of Gothenburg, Gothenburg, 413 19, Sweden.
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8
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Guinot G, Condamine FL. Global impact and selectivity of the Cretaceous-Paleogene mass extinction among sharks, skates, and rays. Science 2023; 379:802-806. [PMID: 36821692 DOI: 10.1126/science.abn2080] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
The Cretaceous-Paleogene event was the last mass extinction event, yet its impact and long-term effects on species-level marine vertebrate diversity remain largely uncharacterized. We quantified elasmobranch (sharks, skates, and rays) speciation, extinction, and ecological change resulting from the end-Cretaceous event using >3200 fossil occurrences and 675 species spanning the Late Cretaceous-Paleocene interval at global scale. Elasmobranchs declined by >62% at the Cretaceous-Paleogene boundary and did not fully recover in the Paleocene. The end-Cretaceous event triggered a heterogeneous pattern of extinction, with rays and durophagous species reaching the highest levels of extinction (>72%) and sharks and nondurophagous species being less affected. Taxa with large geographic ranges and/or those restricted to high-latitude settings show higher survival. The Cretaceous-Paleogene event drastically altered the evolutionary history of marine ecosystems.
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Affiliation(s)
- Guillaume Guinot
- Institut des Sciences de l'Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, France
| | - Fabien L Condamine
- Institut des Sciences de l'Évolution de Montpellier, Université de Montpellier, CNRS, IRD, EPHE, Place Eugène Bataillon, 34095 Montpellier, France
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9
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Darroch SAF, Saupe EE, Casey MM, Jorge MLSP. Integrating geographic ranges across temporal scales. Trends Ecol Evol 2022; 37:851-860. [PMID: 35691773 DOI: 10.1016/j.tree.2022.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/10/2022] [Accepted: 05/16/2022] [Indexed: 11/16/2022]
Abstract
Geographic ranges are a fundamental unit of biogeography and macroecology. Increasingly, paleontologists and ecologists alike are reconstructing geographic ranges of species from fossils, in order to understand the long-term processes governing biogeographic and macroevolutionary patterns. As these reconstructions have become increasingly common, uncertainty has arisen over the equivalency of paleo-ranges and modern ranges. Here, we argue geographic ranges are time-averaged at all temporal scales, and reflect the biotic and abiotic processes operating across the equivalent range of time and space scales. This conceptual framework integrates the study of geographic ranges reconstructed using modern and ancient data, and highlights the potential for ranges to illuminate processes responsible for diversity patterns over intervals spanning days to tens of millions of years of Earth history.
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Affiliation(s)
- Simon A F Darroch
- Department of Earth and Environmental Sciences, Vanderbilt University, 5726 Stevenson Center, Nashville, TN 37240, USA; Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN 37235, USA; Senckenberg Museum of Natural History, Frankfurt 60325, Germany.
| | - Erin E Saupe
- University of Oxford, Department of Earth Sciences, South Parks Road, Oxford, OX1 3AN, UK
| | - Michelle M Casey
- Towson University, Department of Physics, Astronomy and Geosciences, 8000 York Road, Towson, MD 21252, USA
| | - Maria L S P Jorge
- Department of Earth and Environmental Sciences, Vanderbilt University, 5726 Stevenson Center, Nashville, TN 37240, USA
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10
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Freestone AL, Torchin ME, Jurgens LJ, Bonfim M, López DP, Repetto MF, Schlöder C, Sewall BJ, Ruiz GM. Stronger predation intensity and impact on prey communities in the tropics. Ecology 2021; 102:e03428. [PMID: 34105781 DOI: 10.1002/ecy.3428] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 12/21/2020] [Accepted: 02/05/2021] [Indexed: 11/06/2022]
Abstract
The hypothesis that biotic interactions strengthen toward lower latitudes provides a framework for linking community-scale processes with the macroecological scales that define our biosphere. Despite the importance of this hypothesis for understanding community assembly and ecosystem functioning, the extent to which interaction strength varies across latitude and the effects of this variation on natural communities remain unresolved. Predation in particular is central to ecological and evolutionary dynamics across the globe, yet very few studies explore both community-scale causes and outcomes of predation across latitude. Here we expand beyond prior studies to examine two important components of predation strength: intensity of predation (including multiple dimensions of the predator guild) and impact on prey community biomass and structure, providing one of the most comprehensive examinations of predator-prey interactions across latitude. Using standardized experiments, we tested the hypothesis that predation intensity and impact on prey communities were stronger at lower latitudes. We further assessed prey recruitment to evaluate the potential for this process to mediate predation effects. We used sessile marine invertebrate communities and their fish predators in nearshore environments as a model system, with experiments conducted at 12 sites in four regions spanning the tropics to the subarctic. Our results show clear support for an increase in both predation intensity and impact at lower relative to higher latitudes. The predator guild was more diverse at low latitudes, with higher predation rates, longer interaction durations, and larger predator body sizes, suggesting stronger predation intensity in the tropics. Predation also reduced prey biomass and altered prey composition at low latitudes, with no effects at high latitudes. Although recruitment rates were up to three orders of magnitude higher in the tropics than the subarctic, prey replacement through this process was insufficient to dampen completely the strong impacts of predators in the tropics. Our study provides a novel perspective on the biotic interaction hypothesis, suggesting that multiple components of the predator community likely contribute to predation intensity at low latitudes, with important consequences for the structure of prey communities.
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Affiliation(s)
- Amy L Freestone
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA.,Smithsonian Environmental Research Center, Edgewater, Maryland, 21037-0028, USA.,Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama
| | - Mark E Torchin
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama
| | - Laura J Jurgens
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA.,Smithsonian Environmental Research Center, Edgewater, Maryland, 21037-0028, USA.,Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama
| | - Mariana Bonfim
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Diana P López
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Michele F Repetto
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Carmen Schlöder
- Smithsonian Tropical Research Institute, Apartado, 0843-03092, Balboa, Ancon, Panama
| | - Brent J Sewall
- Department of Biology, Temple University, Philadelphia, Pennsylvania, 19122, USA
| | - Gregory M Ruiz
- Smithsonian Environmental Research Center, Edgewater, Maryland, 21037-0028, USA
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11
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Hagen O, Flück B, Fopp F, Cabral JS, Hartig F, Pontarp M, Rangel TF, Pellissier L. gen3sis: A general engine for eco-evolutionary simulations of the processes that shape Earth's biodiversity. PLoS Biol 2021; 19:e3001340. [PMID: 34252071 PMCID: PMC8384074 DOI: 10.1371/journal.pbio.3001340] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 07/22/2021] [Accepted: 06/23/2021] [Indexed: 11/21/2022] Open
Abstract
Understanding the origins of biodiversity has been an aspiration since the days of early naturalists. The immense complexity of ecological, evolutionary, and spatial processes, however, has made this goal elusive to this day. Computer models serve progress in many scientific fields, but in the fields of macroecology and macroevolution, eco-evolutionary models are comparatively less developed. We present a general, spatially explicit, eco-evolutionary engine with a modular implementation that enables the modeling of multiple macroecological and macroevolutionary processes and feedbacks across representative spatiotemporally dynamic landscapes. Modeled processes can include species' abiotic tolerances, biotic interactions, dispersal, speciation, and evolution of ecological traits. Commonly observed biodiversity patterns, such as α, β, and γ diversity, species ranges, ecological traits, and phylogenies, emerge as simulations proceed. As an illustration, we examine alternative hypotheses expected to have shaped the latitudinal diversity gradient (LDG) during the Earth's Cenozoic era. Our exploratory simulations simultaneously produce multiple realistic biodiversity patterns, such as the LDG, current species richness, and range size frequencies, as well as phylogenetic metrics. The model engine is open source and available as an R package, enabling future exploration of various landscapes and biological processes, while outputs can be linked with a variety of empirical biodiversity patterns. This work represents a key toward a numeric, interdisciplinary, and mechanistic understanding of the physical and biological processes that shape Earth's biodiversity.
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Affiliation(s)
- Oskar Hagen
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Benjamin Flück
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Fabian Fopp
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
| | - Juliano S. Cabral
- Ecosystem Modeling, Center for Computational and Theoretical Biology,
University of Würzburg, Würzburg, Germany
| | - Florian Hartig
- Theoretical Ecology, University of Regensburg, Regensburg,
Germany
| | | | - Thiago F. Rangel
- Department of Ecology, Institute of Biological Sciences, Federal
University of Goiás, Goiânia, Brazil
| | - Loïc Pellissier
- Landscape Ecology, Institute of Terrestrial Ecosystems, Department of
Environmental Systems Science, ETH Zürich, Zürich, Switzerland
- Land Change Science Research Unit, Swiss Federal Institute for Forest,
Snow and Landscape Research, WSL, Birmensdorf, Switzerland
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12
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Januario M, Quental TB. Re-evaluation of the "law of constant extinction" for ruminants at different taxonomical scales. Evolution 2021; 75:656-671. [PMID: 33486771 DOI: 10.1111/evo.14177] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Revised: 12/15/2020] [Accepted: 12/27/2020] [Indexed: 11/27/2022]
Abstract
The "law of constant extinction," proposed by Van Valen, states that long and short-lived taxa have equal chances of going extinct. This pattern of age-independent extinction was originally inferred using the fossil record of several different taxa and relied on survivorship curves built from the literal reading of the fossil record. Van Valen's seminal work was mostly done at higher taxonomic levels, hence its prevalence at the species level could not be directly inferred. The surprisingly few subsequent studies done at the species level have challenged the prevalence of age-independent extinction, but those have, for the most part, failed to explicitly incorporate inherent biases of the fossil record. Using a recent Bayesian framework that accounts for several of those biases, including the fact that very short-living lineages might never make to the record itself, we showed that Ruminantia species present age-dependent extinction, where extinction probability decreases with species age. An analysis at the genus level suggested age-independent extinction but further examination suggested that the pattern might be more complex than previously reported by Van Valen. Our results indicate that different taxonomic levels may present different extinction regimes, which could justify the development of new macroevolutionary theory and methods.
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Affiliation(s)
- Matheus Januario
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Tiago B Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
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13
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Fraser D, Soul LC, Tóth AB, Balk MA, Eronen JT, Pineda-Munoz S, Shupinski AB, Villaseñor A, Barr WA, Behrensmeyer AK, Du A, Faith JT, Gotelli NJ, Graves GR, Jukar AM, Looy CV, Miller JH, Potts R, Lyons SK. Investigating Biotic Interactions in Deep Time. Trends Ecol Evol 2020; 36:61-75. [PMID: 33067015 DOI: 10.1016/j.tree.2020.09.001] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/16/2022]
Abstract
Recent renewed interest in using fossil data to understand how biotic interactions have shaped the evolution of life is challenging the widely held assumption that long-term climate changes are the primary drivers of biodiversity change. New approaches go beyond traditional richness and co-occurrence studies to explicitly model biotic interactions using data on fossil and modern biodiversity. Important developments in three primary areas of research include analysis of (i) macroevolutionary rates, (ii) the impacts of and recovery from extinction events, and (iii) how humans (Homo sapiens) affected interactions among non-human species. We present multiple lines of evidence for an important and measurable role of biotic interactions in shaping the evolution of communities and lineages on long timescales.
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Affiliation(s)
- Danielle Fraser
- Palaeobiology, Canadian Museum of Nature, Ottawa, ON, Canada; Biology and Earth Sciences, Carleton University, Ottawa, ON, Canada; Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA.
| | - Laura C Soul
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Anikó B Tóth
- Centre for Ecosystem Science, School of Biological, Earth and Environmental Sciences, UNSW, Sydney, NSW, Australia
| | - Meghan A Balk
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Jussi T Eronen
- Ecosystems and Environment Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland; Helsinki Institute of Sustainability Science, Faculty of Biological and Environmental Sciences, Ecosystems and Environment Research Programme, University of Helsinki, Helsinki, Finland; BIOS research Unit, Helsinki, Finland
| | - Silvia Pineda-Munoz
- Department of Earth and Atmospheric Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | | | - Amelia Villaseñor
- Department of Anthropology, University of Arkansas, Fayetteville, AR, USA
| | - W Andrew Barr
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA; Center for the Advanced Study of Human Paleobiology, Department of Anthropology, The George Washington University, Washington, DC, USA
| | - Anna K Behrensmeyer
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Andrew Du
- Department of Anthropology and Geography, Colorado State University, Fort Collins, CO, USA
| | - J Tyler Faith
- Natural History Museum of Utah, University of Utah, Salt Lake City, UT,USA; Department of Anthropology, University of Utah, Salt Lake City, UT, USA
| | | | - Gary R Graves
- Department of Vertebrate Zoology, National Museum of Natural History, Smithsonian Institution, Washington, DC, USA; Center for Macroecology, Evolution and Climate, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Advait M Jukar
- Department of Paleobiology and Evolution of Terrestrial Ecosystems Program, Smithsonian Institution, National Museum of Natural History, Washington, DC , USA
| | - Cindy V Looy
- Department of Integrative Biology, Museum of Paleontology, University and Jepson Herbaria, University of California-Berkeley, Berkeley, CA , USA
| | - Joshua H Miller
- Department of Geology, University of Cincinnati, Cincinnati, OH, USA
| | - Richard Potts
- Human Origins Program, National Museum of Natural History, Smithsonian Institution, Washington, DC , USA
| | - S Kathleen Lyons
- School of Biological Sciences, University of Nebraska-Lincoln, Lincoln, NE, USA
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14
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Past Extinctions of Homo Species Coincided with Increased Vulnerability to Climatic Change. ACTA ACUST UNITED AC 2020. [DOI: 10.1016/j.oneear.2020.09.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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15
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Andermann T, Faurby S, Turvey ST, Antonelli A, Silvestro D. The past and future human impact on mammalian diversity. SCIENCE ADVANCES 2020; 6:6/36/eabb2313. [PMID: 32917612 PMCID: PMC7473673 DOI: 10.1126/sciadv.abb2313] [Citation(s) in RCA: 50] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 07/16/2020] [Indexed: 05/18/2023]
Abstract
To understand the current biodiversity crisis, it is crucial to determine how humans have affected biodiversity in the past. However, the extent of human involvement in species extinctions from the Late Pleistocene onward remains contentious. Here, we apply Bayesian models to the fossil record to estimate how mammalian extinction rates have changed over the past 126,000 years, inferring specific times of rate increases. We specifically test the hypothesis of human-caused extinctions by using posterior predictive methods. We find that human population size is able to predict past extinctions with 96% accuracy. Predictors based on past climate, in contrast, perform no better than expected by chance, suggesting that climate had a negligible impact on global mammal extinctions. Based on current trends, we predict for the near future a rate escalation of unprecedented magnitude. Our results provide a comprehensive assessment of the human impact on past and predicted future extinctions of mammals.
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Affiliation(s)
- Tobias Andermann
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden.
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Søren Faurby
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
| | - Samuel T Turvey
- Institute of Zoology, Zoological Society of London, London, UK
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Royal Botanic Gardens, Kew, Richmond, UK
| | - Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Göteborg, Sweden
- Gothenburg Global Biodiversity Centre, Göteborg, Sweden
- Department of Biology, University of Fribourg, Fribourg, Switzerland
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