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Bradshaw CJA, Saltré F, Crabtree SA, Reepmeyer C, Moutsiou T. Small populations of Palaeolithic humans in Cyprus hunted endemic megafauna to extinction. Proc Biol Sci 2024; 291:20240967. [PMID: 39288802 DOI: 10.1098/rspb.2024.0967] [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: 02/06/2024] [Revised: 07/26/2024] [Accepted: 08/19/2024] [Indexed: 09/19/2024] Open
Abstract
The hypothesized main drivers of megafauna extinctions in the late Quaternary have wavered between over-exploitation by humans and environmental change, with recent investigations demonstrating more nuanced synergies between these drivers depending on taxon, spatial scale, and region. However, most studies still rely on comparing archaeologically based chronologies of timing of initial human arrival into naïve ecosystems and palaeontologically inferred dates of megafauna extinctions. Conclusions arising from comparing chronologies also depend on the reliability of dated evidence, dating uncertainties, and correcting for the low probability of preservation (Signor-Lipps effect). While some models have been developed to test the susceptibility of megafauna to theoretical offtake rates, none has explicitly linked human energetic needs, prey choice, and hunting efficiency to examine the plausibility of human-driven extinctions. Using the island of Cyprus in the terminal Pleistocene as an ideal test case because of its late human settlement (~14.2-13.2 ka), small area (~11 000 km2), and low megafauna diversity (2 species), we developed stochastic models of megafauna population dynamics, with offtake dictated by human energetic requirements, prey choice, and hunting-efficiency functions to test whether the human population at the end of the Pleistocene could have caused the extinction of dwarf hippopotamus (Phanourios minor) and dwarf elephants (Palaeoloxodon cypriotes). Our models reveal not only that the estimated human population sizes (n = 3000-7000) in Late Pleistocene Cyprus could have easily driven both species to extinction within < 1000 years, the model predictions match the observed, Signor-Lipps-corrected chronological sequence of megafauna extinctions inferred from the palaeontological record (P. minor at ~12-11.1 ka, followed by P. cypriotes at ~10.3-9.1 ka).
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Affiliation(s)
- Corey J A Bradshaw
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100 , Adelaide, South Australia 5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage , Wollongong, New South Wales, Australia
| | - Frédérik Saltré
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, GPO Box 2100 , Adelaide, South Australia 5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage , Wollongong, New South Wales, Australia
| | - Stefani A Crabtree
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage , Wollongong, New South Wales, Australia
- Department of Environment and Society, Utah State University, 5200 Old Main Hill , Logan, UT 84322, USA
- The Santa Fe Institute, 1399 Hyde Park Road , Santa Fe, NM 87501, USA
| | - Christian Reepmeyer
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage , Wollongong, New South Wales, Australia
- Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Dürenstr. 35-37 , Bonn 53173, Germany
- College of Arts, Society and Education, James Cook University Cairns, Nguma-bada campus, GPO Box 6811 Cairns , Queensland 4870, Australia
| | - Theodora Moutsiou
- Archaeological Research Unit, University of Cyprus, 12 Gladstone Street , Nicosia 1095, Cyprus
- College of Arts, Society and Education, James Cook University Cairns , Cairns, Queensland 4870, Australia
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2
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Hagen ER. A critique of Thompson and Ramírez-Barahona (2023) or: how I learned to stop worrying and love the fossil record. Biol Lett 2024; 20:20240039. [PMID: 39192834 DOI: 10.1098/rsbl.2024.0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 03/12/2024] [Accepted: 05/02/2024] [Indexed: 08/29/2024] Open
Abstract
A recent study published in Biology Letters by Thompson and Ramírez-Barahona (2023) argued that, according to analyses of diversification on two massive molecular phylogenies comprising thousands of species, there is no evidence that angiosperms (i.e. flowering plants) were affected by the Cretaceous-Paleogene mass extinction. Here, I critique these conclusions from both methodological and philosophical perspectives. I demonstrate that the methods used in their study possess statistical limitations that strongly reduce the power to detect a true mass extinction event using data similar to those analysed by Thompson and Ramírez-Barahona (2023). Additionally, I use their study as a springboard to examine the relationship between phylogenetic and fossil evidence in diversification studies.
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Affiliation(s)
- Eric Robert Hagen
- Department of Ecology & Evolutionary Biology, University of Toronto , Toronto, Ontario, Canada M5S 3B2
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3
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Bradshaw CJA, Reepmeyer C, Saltré F, Agapiou A, Kassianidou V, Demesticha S, Zomeni Z, Polidorou M, Moutsiou T. Demographic models predict end-Pleistocene arrival and rapid expansion of pre-agropastoralist humans in Cyprus. Proc Natl Acad Sci U S A 2024; 121:e2318293121. [PMID: 38753504 PMCID: PMC11126943 DOI: 10.1073/pnas.2318293121] [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: 10/19/2023] [Accepted: 04/09/2024] [Indexed: 05/18/2024] Open
Abstract
The antiquity of human dispersal into Mediterranean islands and ensuing coastal adaptation have remained largely unexplored due to the prevailing assumption that the sea was a barrier to movement and that islands were hostile environments to early hunter-gatherers [J. F. Cherry, T. P. Leppard, J. Isl. Coast. Archaeol. 13, 191-205 (2018), 10.1080/15564894.2016.1276489]. Using the latest archaeological data, hindcasted climate projections, and age-structured demographic models, we demonstrate evidence for early arrival (14,257 to 13,182 calendar years ago) to Cyprus and predicted that large groups of people (~1,000 to 1,375) arrived in 2 to 3 main events occurring within <100 y to ensure low extinction risk. These results indicate that the postglacial settlement of Cyprus involved only a few large-scale, organized events requiring advanced watercraft technology. Our spatially debiased and Signor-Lipps-corrected estimates indicate rapid settlement of the island within <200 y, and expansion to a median of 4,000 to 5,000 people (0.36 to 0.46 km-2) in <11 human generations (<300 y). Our results do not support the hypothesis of inaccessible and inhospitable islands in the Mediterranean for pre-agropastoralists, agreeing with analogous conclusions for other parts of the world [M. I. Bird et al., Sci. Rep. 9, 8220 (2019), 10.1038/s41598-019-42946-9]. Our results also highlight the need to revisit these questions in the Mediterranean and test their validity with new technologies, field methods, and data. By applying stochastic models to the Mediterranean region, we can place Cyprus and large islands in general as attractive and favorable destinations for paleolithic peoples.
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Affiliation(s)
- Corey J. A. Bradshaw
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, SA5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW2522, Australia
| | - Christian Reepmeyer
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW2522, Australia
- Commission for Archaeology of Non-European Cultures, German Archaeological Institute, Bonn53173, Germany
- College of Arts, Society and Education, James Cook University Cairns, Cairns, QLD4870, Australia
| | - Frédérik Saltré
- Global Ecology | Partuyarta Ngadluku Wardli Kuu, College of Science and Engineering, Flinders University, Adelaide, SA5001, Australia
- Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, Wollongong, NSW2522, Australia
| | - Athos Agapiou
- Cyprus University of Technology, Lemesos3036, Cyprus
| | | | - Stella Demesticha
- Archaeological Research Unit, University of Cyprus, Nicosia1095, Cyprus
| | - Zomenia Zomeni
- Geological Survey Department, Ministry of Agriculture, Rural Development and the Environment of the Republic of Cyprus, Nicosia1301, Cyprus
| | | | - Theodora Moutsiou
- College of Arts, Society and Education, James Cook University Cairns, Cairns, QLD4870, Australia
- Archaeological Research Unit, University of Cyprus, Nicosia1095, Cyprus
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4
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Shang H. Probing long-lived radioactive isotopes on the double-logarithmic Segrè chart. Front Chem 2024; 12:1057928. [PMID: 38410817 PMCID: PMC10894952 DOI: 10.3389/fchem.2024.1057928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 01/09/2024] [Indexed: 02/28/2024] Open
Abstract
Isotopes have been widely applied in a variety of scientific subjects; many aspects of isotopes, however, remain not well understood. In this study, I investigate the relation between the number of neutrons (N) and the number of protons (Z) in stable isotopes of non-radioactive elements and long-lived isotopes of radioactive elements at the double-linear scale (conventional Segrè chart) and the double-logarithmic scale. Statistical analyses show that N is a power-law function of Z for these isotopes: N = 0.73 × Z 1.16. This power-law relation provides better predictions for the numbers of neutrons in stable isotopes of non-radioactive elements and long-lived isotopes of radioactive elements than the linear relation on the conventional Segrè chart. The power-law pattern reveled here offers empirical guidance for probing long-lived isotopes of unknown radioactive elements.
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Affiliation(s)
- Haitao Shang
- Institute of Ecology and Evolution, University of Oregon, Eugene, OR, United States
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5
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Singh A, Chhimpa R, Yadav AC. Fitness fluctuations in the Bak-Sneppen model. Phys Rev E 2023; 108:044109. [PMID: 37978651 DOI: 10.1103/physreve.108.044109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2023] [Accepted: 09/15/2023] [Indexed: 11/19/2023]
Abstract
We study the one-dimensional Bak-Sneppen model for the evolution of species in an ecosystem. Of particular interest are the temporal fluctuations in fitness variables. We numerically compute the power spectral density and apply the finite-size scaling method to get data collapse. A clear signature of 1/f^{α} noise with α≈1.2 (long-time correlations) emerges for both local and global (or average) fitness noises. The limiting value of the spectral exponent, 0 or 2, corresponds to no interaction or a random neighbor version of the model, respectively. The local power spectra are spatially uncorrelated and also show an additional scaling, ∼1/L, in the frequency regime L^{-λ}≪f≪1/2, where L is the linear extent of the system.
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Affiliation(s)
- Abha Singh
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Rahul Chhimpa
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
| | - Avinash Chand Yadav
- Department of Physics, Institute of Science, Banaras Hindu University, Varanasi 221 005, India
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6
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Sudakow I, Myers C, Petrovskii SV, Sumrall CD, Witts J. Mathematical modeling is an efficient research tool to address challenges in mass extinction research: Reply to comments on "Knowledge gaps and missing links in understanding mass extinctions: Can mathematical modeling help?". Phys Life Rev 2023; 46:5-7. [PMID: 37244153 DOI: 10.1016/j.plrev.2023.05.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 05/07/2023] [Indexed: 05/29/2023]
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7
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Monarrez PM, Heim NA, Payne JL. Reduced strength and increased variability of extinction selectivity during mass extinctions. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230795. [PMID: 37771968 PMCID: PMC10523066 DOI: 10.1098/rsos.230795] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Accepted: 08/29/2023] [Indexed: 09/30/2023]
Abstract
Two of the traits most often observed to correlate with extinction risk in marine animals are geographical range and body size. However, the relative effects of these two traits on extinction risk have not been investigated systematically for either background times or during mass extinctions. To close this knowledge gap, we measure and compare extinction selectivity of geographical range and body size of genera within five classes of benthic marine animals across the Phanerozoic using capture-mark-recapture models. During background intervals, narrow geographical range is strongly associated with greater extinction probability, whereas smaller body size is more weakly associated with greater extinction probability. During mass extinctions, the association between geographical range and extinction probability is reduced in every class and fully eliminated in some, whereas the association between body size and extinction probability varies in strength and direction across classes. While geographical range is universally the stronger predictor of survival during background intervals, variation among classes during mass extinction suggests a fundamental shift in extinction processes during these global catastrophes.
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Affiliation(s)
- Pedro M. Monarrez
- Department of Earth and Planetary Sciences, Stanford University, Stanford, CA 94305, USA
| | - Noel A. Heim
- Department of Earth and Climate Sciences, Tufts University, Medford, MA 02155, USA
| | - Jonathan L. Payne
- Department of Earth and Planetary Sciences, Stanford University, Stanford, CA 94305, USA
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8
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Boulila S, Peters SE, Müller RD, Haq BU, Hara N. Earth's interior dynamics drive marine fossil diversity cycles of tens of millions of years. Proc Natl Acad Sci U S A 2023; 120:e2221149120. [PMID: 37428908 PMCID: PMC10629558 DOI: 10.1073/pnas.2221149120] [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: 12/13/2022] [Accepted: 05/24/2023] [Indexed: 07/12/2023] Open
Abstract
The fossil record reveals that biotic diversity has fluctuated quasi-cyclically through geological time. However, the causal mechanisms of biotic diversity cycles remain unexplained. Here, we highlight a common, correlatable 36 ± 1 Myr (million years) cycle in the diversity of marine genera as well as in tectonic, sea-level, and macrostratigraphic data over the past 250 Myr of Earth history. The prominence of the 36 ± 1 Myr cycle in tectonic data favors a common-cause mechanism, wherein geological forcing mechanisms drive patterns in both biological diversity and the preserved rock record. In particular, our results suggest that a 36 ± 1 Myr tectono-eustatically driven sea-level cycle may originate from the interaction between the convecting mantle and subducting slabs, thereby pacing mantle-lithospheric deep-water recycling. The 36 ± 1 Myr tectono-eustatic driver of biodiversity is likely related to cyclic continental inundations, with expanding and contracting ecological niches on shelves and in epeiric seas.
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Affiliation(s)
- Slah Boulila
- Sorbonne Université, CNRS, Institut des Sciences de la Terre Paris, ParisF-75005, France
- Astronomie et Systèmes Dynamiques/Institut de Mécanique Céleste et de Calcul des Ephémérides, CNRS-UMR8028, Observatoire de Paris, Paris Sciences & Lettres University, Sorbonne Université, Paris75014, France
| | - Shanan E. Peters
- Department of Geoscience, University of Madison, Madison, WI53706
| | - R. Dietmar Müller
- EarthByte Group, School of Geosciences, University of Sydney, Sydney, NSW2006, Australia
| | - Bilal U. Haq
- Sorbonne Université, CNRS, Institut des Sciences de la Terre Paris, ParisF-75005, France
- Smithsonian Institution, Washington,DC20024
| | - Nathan Hara
- Département d’astronomie, Université de Genève, Genève1290, Switzerland
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9
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Fiorentino G, Lattke J, Troya A, Sosiak C, Dong M, Barden P. Deep time extinction of largest insular ant predators and the first fossil Neoponera (Formicidae: Ponerinae) from Miocene age Dominican amber. BMC Biol 2023; 21:26. [PMID: 36750946 PMCID: PMC9906935 DOI: 10.1186/s12915-022-01488-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 11/30/2022] [Indexed: 02/09/2023] Open
Abstract
BACKGROUND Ponerine ants are almost exclusively predatory and comprise many of the largest known ant species. Within this clade, the genus Neoponera is among the most conspicuous Neotropical predators. We describe the first fossil member of this lineage: a worker preserved in Miocene-age Dominican amber from Hispaniola. RESULTS Neoponera vejestoria sp. nov. demonstrates a clear case of local extinction-there are no known extant Neoponera species in the Greater Antilles. The species is attributable to an extant and well-defined species group in the genus, which suggests the group is older than previously estimated. Through CT scan reconstruction and linear morphometrics, we reconstruct the morphospace of extant and fossil ants to evaluate the history and evolution of predatory taxa in this island system. CONCLUSIONS The fossil attests to a shift in insular ecological community structure since the Miocene. The largest predatory taxa have undergone extinction on the island, but their extant relatives persist throughout the Neotropics. Neoponera vejestoria sp. nov. is larger than all other predatory ant workers known from Hispaniola, extant or extinct. Our results empirically demonstrate the loss of a functional niche associated with body size, which is a trait long hypothesized to be related to extinction risk.
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Affiliation(s)
- Gianpiero Fiorentino
- Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, USA.
| | - John Lattke
- grid.20736.300000 0001 1941 472XDepartamento de Zoologia, Universidade Federal Do Paraná, Curitiba, Brazil
| | - Adrian Troya
- grid.440857.a0000 0004 0485 2489Departamento de Biología, Escuela Politécnica Nacional, Quito, Ecuador
| | - Christine Sosiak
- grid.260896.30000 0001 2166 4955Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, USA
| | - Minsoo Dong
- grid.412010.60000 0001 0707 9039Applied Biology Program, Division of Bio-Resource Sciences, Kangwon National University, Chuncheon, South Korea
| | - Phillip Barden
- grid.260896.30000 0001 2166 4955Federated Department of Biological Sciences, New Jersey Institute of Technology, Newark, USA ,grid.241963.b0000 0001 2152 1081Division of Invertebrate Zoology, American Museum of Natural History, New York City, USA
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10
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Solé R, Levin S. Ecological complexity and the biosphere: the next 30 years. Philos Trans R Soc Lond B Biol Sci 2022; 377:20210376. [PMID: 35757877 PMCID: PMC9234814 DOI: 10.1098/rstb.2021.0376] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Global warming, habitat loss and overexploitation of limited resources are leading to alarming biodiversity declines. Ecosystems are complex adaptive systems that display multiple alternative states and can shift from one to another in abrupt ways. Some of these tipping points have been identified and predicted by mathematical and computational models. Moreover, multiple scales are involved and potential mitigation or intervention scenarios are tied to particular levels of complexity, from cells to human–environment coupled systems. In dealing with a biosphere where humans are part of a complex, endangered ecological network, novel theoretical and engineering approaches need to be considered. At the centre of most research efforts is biodiversity, which is essential to maintain community resilience and ecosystem services. What can be done to mitigate, counterbalance or prevent tipping points? Using a 30-year window, we explore recent approaches to sense, preserve and restore ecosystem resilience as well as a number of proposed interventions (from afforestation to bioengineering) directed to mitigate or reverse ecosystem collapse. The year 2050 is taken as a representative future horizon that combines a time scale where deep ecological changes will occur and proposed solutions might be effective. This article is part of the theme issue ‘Ecological complexity and the biosphere: the next 30 years’.
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Affiliation(s)
- Ricard Solé
- ICREA-Complex Systems Lab, Universitat Pompeu Fabra, Dr Aiguader 80, Barcelona 08003, Spain.,Institut de Biologia Evolutiva, CSIC-UPF, Pg Maritim de la Barceloneta 37, Barcelona 08003, Spain.,Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Simon Levin
- Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA.,Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA
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11
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Knowledge Gaps and Missing Links in Understanding Mass Extinctions: Can Mathematical Modeling Help? Phys Life Rev 2022; 41:22-57. [DOI: 10.1016/j.plrev.2022.04.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 04/11/2022] [Indexed: 11/20/2022]
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12
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During MAD, Smit J, Voeten DFAE, Berruyer C, Tafforeau P, Sanchez S, Stein KHW, Verdegaal-Warmerdam SJA, van der Lubbe JHJL. The Mesozoic terminated in boreal spring. Nature 2022; 603:91-94. [PMID: 35197634 PMCID: PMC8891016 DOI: 10.1038/s41586-022-04446-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2021] [Accepted: 01/19/2022] [Indexed: 12/26/2022]
Abstract
The Cretaceous-Palaeogene mass extinction around 66 million years ago was triggered by the Chicxulub asteroid impact on the present-day Yucatán Peninsula1,2. This event caused the highly selective extinction that eliminated about 76% of species3,4, including all non-avian dinosaurs, pterosaurs, ammonites, rudists and most marine reptiles. The timing of the impact and its aftermath have been studied mainly on millennial timescales, leaving the season of the impact unconstrained. Here, by studying fishes that died on the day the Mesozoic era ended, we demonstrate that the impact that caused the Cretaceous-Palaeogene mass extinction took place during boreal spring. Osteohistology together with stable isotope records of exceptionally preserved perichondral and dermal bones in acipenseriform fishes from the Tanis impact-induced seiche deposits5 reveal annual cyclicity across the final years of the Cretaceous period. Annual life cycles, including seasonal timing and duration of reproduction, feeding, hibernation and aestivation, vary strongly across latest Cretaceous biotic clades. We postulate that the timing of the Chicxulub impact in boreal spring and austral autumn was a major influence on selective biotic survival across the Cretaceous-Palaeogene boundary.
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Affiliation(s)
- Melanie A D During
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands. .,Subdepartment of Evolution and Development, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
| | - Jan Smit
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands
| | - Dennis F A E Voeten
- Subdepartment of Evolution and Development, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,European Synchrotron Radiation Facility, Grenoble, France
| | | | - Paul Tafforeau
- European Synchrotron Radiation Facility, Grenoble, France
| | - Sophie Sanchez
- Subdepartment of Evolution and Development, Department of Organismal Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.,European Synchrotron Radiation Facility, Grenoble, France
| | - Koen H W Stein
- Royal Belgian Institute of Natural Sciences, Directorate 'Earth and History of Life', Brussels, Belgium.,Earth System Science-AMGC, Vrije Universiteit Brussel, Brussels, Belgium
| | | | - Jeroen H J L van der Lubbe
- Department of Earth Sciences, Faculty of Science, Vrije Universiteit Amsterdam, Amsterdam, the Netherlands.,School of Earth and Environmental Sciences, Cardiff University, Cardiff, UK
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13
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Greenberg DA, Pyron RA, Johnson LGW, Upham NS, Jetz W, Mooers AØ. Evolutionary legacies in contemporary tetrapod imperilment. Ecol Lett 2021; 24:2464-2476. [PMID: 34510687 PMCID: PMC9048422 DOI: 10.1111/ele.13868] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/12/2021] [Accepted: 07/29/2021] [Indexed: 12/13/2022]
Abstract
The Tree of Life will be irrevocably reshaped as anthropogenic extinctions continue to unfold. Theory suggests that lineage evolutionary dynamics, such as age since origination, historical extinction filters and speciation rates, have influenced ancient extinction patterns - but whether these factors also contribute to modern extinction risk is largely unknown. We examine evolutionary legacies in contemporary extinction risk for over 4000 genera, representing ~30,000 species, from the major tetrapod groups: amphibians, birds, turtles and crocodiles, squamate reptiles and mammals. We find consistent support for the hypothesis that extinction risk is elevated in lineages with higher recent speciation rates. We subsequently test, and find modest support for, a primary mechanism driving this pattern: that rapidly diversifying clades predominantly comprise range-restricted, and extinction-prone, species. These evolutionary patterns in current imperilment may have important consequences for how we manage the erosion of biological diversity across the Tree of Life.
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Affiliation(s)
- Dan A. Greenberg
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - R. Alexander Pyron
- Department of Biological Sciences, George Washington University, Washington, District of Columbia, USA
| | - Liam G. W. Johnson
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Nathan S. Upham
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
- School of Life Sciences, Arizona State University, Tempe, Arizona, USA
| | - Walter Jetz
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, Connecticut, USA
- Center for Biodiversity and Global Change, Yale University, New Haven, Connecticut, USA
| | - Arne Ø. Mooers
- Department of Biological Sciences, Simon Fraser University, Burnaby, British Columbia, Canada
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14
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Monarrez PM, Heim NA, Payne JL. Mass extinctions alter extinction and origination dynamics with respect to body size. Proc Biol Sci 2021; 288:20211681. [PMID: 34610766 PMCID: PMC8493190 DOI: 10.1098/rspb.2021.1681] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2021] [Accepted: 09/14/2021] [Indexed: 11/12/2022] Open
Abstract
Whether mass extinctions and their associated recoveries represent an intensification of background extinction and origination dynamics versus a separate macroevolutionary regime remains a central debate in evolutionary biology. The previous focus has been on extinction, but origination dynamics may be equally or more important for long-term evolutionary outcomes. The evolution of animal body size is an ideal process to test for differences in macroevolutionary regimes, as body size is easily determined, comparable across distantly related taxa and scales with organismal traits. Here, we test for shifts in selectivity between background intervals and the 'Big Five' mass extinction events using capture-mark-recapture models. Our body-size data cover 10 203 fossil marine animal genera spanning 10 Linnaean classes with occurrences ranging from Early Ordovician to Late Pleistocene (485-1 Ma). Most classes exhibit differences in both origination and extinction selectivity between background intervals and mass extinctions, with the direction of selectivity varying among classes and overall exhibiting stronger selectivity during origination after mass extinction than extinction during the mass extinction. Thus, not only do mass extinction events shift the marine biosphere into a new macroevolutionary regime, the dynamics of recovery from mass extinction also appear to play an underappreciated role in shaping the biosphere in their aftermath.
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Affiliation(s)
- Pedro M. Monarrez
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
| | - Noel A. Heim
- Department of Earth and Ocean Sciences, Tufts University, Medford, MA 02155, USA
| | - Jonathan L. Payne
- Department of Geological Sciences, Stanford University, Stanford, CA 94305, USA
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15
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Pontes-Nogueira M, Martins M, Alencar LRV, Sawaya RJ. The role of vicariance and dispersal on the temporal range dynamics of forest vipers in the Neotropical region. PLoS One 2021; 16:e0257519. [PMID: 34534245 PMCID: PMC8448354 DOI: 10.1371/journal.pone.0257519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Accepted: 09/06/2021] [Indexed: 11/23/2022] Open
Abstract
The emergence of the diagonal of open/dry vegetations, including Chaco, Cerrado and Caatinga, is suggested to have acted as a dispersal barrier for terrestrial organisms by fragmenting a single large forest that existed in South America into the present Atlantic and Amazon forests. Here we tested the hypothesis that the expansion of the South American diagonal of open/dry landscapes acted as a vicariant process for forest lanceheads of the genus Bothrops, by analyzing the temporal range dynamics of those snakes. We estimated ancestral geographic ranges of the focal lancehead clade and its sister clade using a Bayesian dated phylogeny and the BioGeoBEARS package. We compared nine Maximum Likelihood models to infer ancestral range probabilities and their related biogeographic processes. The best fitting models (DECTS and DIVALIKETS) recovered the ancestor of our focal clade in the Amazon biogeographic region of northwestern South America. Vicariant processes in two different subclades resulted in disjunct geographic distributions in the Amazon and the Atlantic Forest. Dispersal processes must have occurred mostly within the Amazon and the Atlantic Forest and not between them. Our results suggest the fragmentation of a single ancient large forest into the Atlantic and Amazon forests acting as a driver of vicariant processes for the snake lineage studied, highlighting the importance of the diagonal of open/dry landscapes in shaping distribution patterns of terrestrial biota in South America.
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Affiliation(s)
| | - Marcio Martins
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, São Paulo, Brazil
| | - Laura R. V. Alencar
- Department of Biological Sciences, Clemson University, Clemson, South Carolina, United States of America
| | - Ricardo J. Sawaya
- Centro de Ciências Naturais e Humanas, Universidade Federal do ABC, São Bernardo do Campo, Brazil
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16
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Neidhöfer C. On the Evolution of the Biological Framework for Insight. PHILOSOPHIES 2021; 6:43. [DOI: 10.3390/philosophies6020043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The details of abiogenesis, to date, remain a matter of debate and constitute a key mystery in science and philosophy. The prevailing scientific hypothesis implies an evolutionary process of increasing complexity on Earth starting from (self-) replicating polymers. Defining the cut-off point where life begins is another moot point beyond the scope of this article. We will instead walk through the known evolutionary steps that led from these first exceptional polymers to the vast network of living biomatter that spans our world today, focusing in particular on perception, from simple biological feedback mechanisms to the complexity that allows for abstract thought. We will then project from the well-known to the unknown to gain a glimpse into what the universe aims to accomplish with living matter, just to find that if the universe had ever planned to be comprehended, evolution still has a long way to go.
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17
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Sidorova A, Tverdislov V, Levashova N, Garaeva A. A model of autowave self-organization as a hierarchy of active media in the biological evolution. Biosystems 2020; 198:104234. [PMID: 32889101 DOI: 10.1016/j.biosystems.2020.104234] [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: 06/22/2020] [Revised: 08/23/2020] [Accepted: 08/24/2020] [Indexed: 11/28/2022]
Abstract
Within the framework of the active media concept, we develop a biophysical model of autowave self-organization which is treated as a hierarchy of active media in the evolution of the biosphere. We also propose a mathematical model of the autowave process of speciation in a flow of mutations for the three main taxonometric groups (prokaryotes, unicellular and multicellular eukaryotes) with a naturally determined lower boundary of living matter (the appearance of prokaryotes) and an open upper boundary for the formation of new species. It is shown that the fluctuation-bifurcation description of the evolution for the formation of new taxonometric groups as a trajectory of transformation of small fluctuations into giant ones adequately reflects the process of self-organization during the formation of taxa. The major concepts of biological evolution, conditions of hierarchy formation as a fundamental manifestation of self-organization and complexity in the evolution of biological systems are considered.
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Affiliation(s)
- Alla Sidorova
- Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Vsevolod Tverdislov
- Head of the Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Natalia Levashova
- Department of Mathematics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
| | - Anastasia Garaeva
- Postgraduate Student of the Department of Biophysics, Faculty of Physics, Lomonosov Moscow State University, Moscow, 119991, Russia.
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18
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Sheppard C, Sheppard A, Fenner D. Coral mass mortalities in the Chagos Archipelago over 40 years: Regional species and assemblage extinctions and indications of positive feedbacks. MARINE POLLUTION BULLETIN 2020; 154:111075. [PMID: 32319906 DOI: 10.1016/j.marpolbul.2020.111075] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/12/2020] [Accepted: 03/13/2020] [Indexed: 05/24/2023]
Abstract
The global decline of reef corals has been driven largely by several marine heatwaves. This has greatly reduced coral cover but has reduced coral diversity also. While there is a lack of data in most locations to detect coral species losses, reefs of the Chagos Archipelago, central Indian Ocean, have long term monitoring data extending back to the late 1970s. Severe declines in cover have occurred since the 1970s, with regional extinctions of some species and key species assemblages. There is a severe decline in coral settlement, along with a substantial loss of habitat quality which has reduced the habitat available for settlement. This is a clear precursor to positive feedback. Regional species extinctions here occur mainly when total coral cover is <10% of pre-warming levels. Climate models predict more frequent and more severe marine heatwaves, and even if this ecosystem recovers it will contain fewer species.
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Affiliation(s)
- Charles Sheppard
- School of Life Sciences, University of Warwick, CV4 7AL, UK; School of Ocean Sciences, Bangor University, LL57 2DG, UK.
| | - Anne Sheppard
- School of Life Sciences, University of Warwick, CV4 7AL, UK; School of Ocean Sciences, Bangor University, LL57 2DG, UK
| | - Douglas Fenner
- NOAA Contractor and Consultant, Pago Pago, AS 96799, USA
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19
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Schubel JR, Thompson K. Farming the Sea: The Only Way to Meet Humanity's Future Food Needs. GEOHEALTH 2019; 3:238-244. [PMID: 32159044 PMCID: PMC7007165 DOI: 10.1029/2019gh000204] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 08/15/2019] [Accepted: 08/19/2019] [Indexed: 05/29/2023]
Abstract
A major change began 10,000-12,000 years ago when humans began to practice agriculture. A series of "green revolutions" enabled the human population to explode, but these advancements have dramatically changed the planet. The United Nations predicts that we will need to produce 50% more food by 2050 to feed another 2.5 billion people, but this will be challenging with tighter land and water resources and a changing climate. Responsible marine aquaculture can complement responsible land-based agriculture and aquaculture and well-managed fisheries to increase the global supply of nutritious food.
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20
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Interplay of spatial dynamics and local adaptation shapes species lifetime distributions and species–area relationships. THEOR ECOL-NETH 2019. [DOI: 10.1007/s12080-019-0410-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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21
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Nawrot R, Scarponi D, Azzarone M, Dexter TA, Kusnerik KM, Wittmer JM, Amorosi A, Kowalewski M. Stratigraphic signatures of mass extinctions: ecological and sedimentary determinants. Proc Biol Sci 2018; 285:rspb.2018.1191. [PMID: 30209225 PMCID: PMC6158527 DOI: 10.1098/rspb.2018.1191] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 08/21/2018] [Indexed: 11/24/2022] Open
Abstract
Stratigraphic patterns of last occurrences (LOs) of fossil taxa potentially fingerprint mass extinctions and delineate rates and geometries of those events. Although empirical studies of mass extinctions recognize that random sampling causes LOs to occur earlier than the time of extinction (Signor–Lipps effect), sequence stratigraphic controls on the position of LOs are rarely considered. By tracing stratigraphic ranges of extant mollusc species preserved in the Holocene succession of the Po coastal plain (Italy), we demonstrated that, if mass extinction took place today, complex but entirely false extinction patterns would be recorded regionally due to shifts in local community composition and non-random variation in the abundance of skeletal remains, both controlled by relative sea-level changes. Consequently, rather than following an apparent gradual pattern expected from the Signor–Lipps effect, LOs concentrated within intervals of stratigraphic condensation and strong facies shifts mimicking sudden extinction pulses. Methods assuming uniform recovery potential of fossils falsely supported stepwise extinction patterns among studied species and systematically underestimated their stratigraphic ranges. Such effects of stratigraphic architecture, co-produced by ecological, sedimentary and taphonomic processes, can easily confound interpretations of the timing, duration and selectivity of mass extinction events. Our results highlight the necessity of accounting for palaeoenvironmental and sequence stratigraphic context when inferring extinction dynamics from the fossil record.
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Affiliation(s)
- Rafał Nawrot
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Daniele Scarponi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Via Zamboni 67, 40126 Bologna, Italy
| | - Michele Azzarone
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Via Zamboni 67, 40126 Bologna, Italy
| | - Troy A Dexter
- Gerace Research Centre, University of the Bahamas, San Salvador, Bahamas
| | - Kristopher M Kusnerik
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
| | - Jacalyn M Wittmer
- Department of Geological Sciences, State University of New York at Geneseo, One College Circle, Geneseo, NY 14454, USA
| | - Alessandro Amorosi
- Dipartimento di Scienze Biologiche, Geologiche e Ambientali, University of Bologna, Via Zamboni 67, 40126 Bologna, Italy
| | - Michał Kowalewski
- Florida Museum of Natural History, University of Florida, 1659 Museum Road, Gainesville, FL 32611, USA
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22
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Burin G, Alencar LRV, Chang J, Alfaro ME, Quental TB. How Well Can We Estimate Diversity Dynamics for Clades in Diversity Decline? Syst Biol 2018; 68:47-62. [DOI: 10.1093/sysbio/syy037] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 05/09/2018] [Indexed: 01/13/2023] Open
Affiliation(s)
- Gustavo Burin
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Laura R V Alencar
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
| | - Jonathan Chang
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Michael E Alfaro
- Department of Ecology and Evolutionary Biology, University of California, 610 Young Drive South, Los Angeles, CA 90095, USA
| | - Tiago B Quental
- Departamento de Ecologia, Instituto de Biociências, Universidade de São Paulo, Rua do Matão, Travessa 14, São Paulo - SP 05508-900, Brazil
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23
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Brook BW, Alroy J. Pattern, process, inference and prediction in extinction biology. Biol Lett 2017; 13:rsbl.2016.0828. [PMID: 28077688 DOI: 10.1098/rsbl.2016.0828] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2016] [Accepted: 12/08/2016] [Indexed: 11/12/2022] Open
Abstract
Extinction is a key feature of the evolutionary history of life, and assessments of extinction risk are essential for the effective protection of biodiversity. The goal in assembling this special issue of Biology Letters was to highlight problems and questions at the research frontier of extinction biology, with an emphasis on recent developments in the methodology of inferring the patterns and processes of extinction from a background of often noisy and sparse data. In selecting topics, we sought to illustrate how extinction is not simply a self-evident phenomenon, but the subject of a dynamic and quantitatively rigorous field of natural science, with practical applications to conservation.
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Affiliation(s)
- Barry W Brook
- School of Biological Sciences, University of Tasmania, Private Bag 55, Hobart 7001, Australia
| | - John Alroy
- Department of Biological Sciences, Macquarie University, New South Wales 2109, Australia
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24
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25
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Rothman DH. Thresholds of catastrophe in the Earth system. SCIENCE ADVANCES 2017; 3:e1700906. [PMID: 28948221 PMCID: PMC5606709 DOI: 10.1126/sciadv.1700906] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/24/2017] [Indexed: 05/23/2023]
Abstract
The history of the Earth system is a story of change. Some changes are gradual and benign, but others, especially those associated with catastrophic mass extinction, are relatively abrupt and destructive. What sets one group apart from the other? Here, I hypothesize that perturbations of Earth's carbon cycle lead to mass extinction if they exceed either a critical rate at long time scales or a critical size at short time scales. By analyzing 31 carbon isotopic events during the past 542 million years, I identify the critical rate with a limit imposed by mass conservation. Identification of the crossover time scale separating fast from slow events then yields the critical size. The modern critical size for the marine carbon cycle is roughly similar to the mass of carbon that human activities will likely have added to the oceans by the year 2100.
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Affiliation(s)
- Daniel H Rothman
- Lorenz Center, Department of Earth, Atmospheric, and Planetary Sciences, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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26
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The Invertebrate Invasion and Evolution of Mesozoic Soil Ecosystems: The Ichnofossil Record of Ecological Innovations. ACTA ACUST UNITED AC 2017. [DOI: 10.1017/s1089332600000747] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Mesozoic soil ecosystems are intriguing because they are the products of many unique factors and events in geologic history. One of the most notable events that likely shaped Mesozoic soil ecosystems was the Permo-Triassic extinction. At that time, estimates of 20% of plant species, 50% of tetrapod genera, roughly 60% of insect families, and approximately 91 to 97% of shallow marine life became extinct (e.g., Padian and Clemens, 1985; Raup, 1986; Niklas et al., 1980; Wing and Sues, 1992; Labandeira and Sepkoski, 1993; and references therein). Over the span of the next 180 million years the supercontinent Pangea disassembled and the continents moved toward the configuration we see today (Scotese and Golonka, 1992); the Pangean mega-monsoonal climate pattern deteriorated into more zonal climates through to the Cretaceous (e.g., Parrish et al., 1982; Dubiel et al., 1991; Parrish, 1993); sea-level rose and flooded continental interiors, reaching its second greatest maximum since the Ordovician (e.g., Haq et al., 1987, 1988); and several major evolutionary episodes occurred, including the evolution and diversification of the angiosperms, mammals, birds, and many of the neopteran insects (Lillegraven et al., 1979; Carpenter and Burham, 1985; Friis et al., 1987; Wing and Sues, 1992; Labandeira and Sepkoski, 1993).
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27
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Abstract
G. Udny Yule (1924) was perhaps the first to examine the subject of rates of taxonomic evolution mathematically, but George Gaylord Simpson was the first to examine the subject from within the confines of the so-called Modern Synthesis of Biology (Simpson, 1944). In that sense, therefore, Simpson's can be regarded as the first modern study of rates of taxonomic evolution. Although he is almost universally regarded as the catalyst behind the current interest in taxonomic evolutionary rates, it is a remarkable fact that Simpson's aims were almost entirely different from those of current workers. In a very important sense, Simpson's taxonomic rates of evolution were not taxonomic at all, but were morphological, or even more to the point, genetic.
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28
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Sneppen K. Models of life: epigenetics, diversity and cycles. REPORTS ON PROGRESS IN PHYSICS. PHYSICAL SOCIETY (GREAT BRITAIN) 2017; 80:042601. [PMID: 28106010 DOI: 10.1088/1361-6633/aa5aeb] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
This review emphasizes aspects of biology that can be understood through repeated applications of simple causal rules. The selected topics include perspectives on gene regulation, phage lambda development, epigenetics, microbial ecology, as well as model approaches to diversity and to punctuated equilibrium in evolution. Two outstanding features are repeatedly described. One is the minimal number of rules to sustain specific states of complex systems for a long time. The other is the collapse of such states and the subsequent dynamical cycle of situations that restitute the system to a potentially new metastable state.
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Affiliation(s)
- Kim Sneppen
- Center for Models of Life, Niels Bohr Institute, Blegdamsvej 17, 2100 Copenhagen, Denmark
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29
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Silvestro D, Zizka A, Bacon CD, Cascales-Miñana B, Salamin N, Antonelli A. Fossil biogeography: a new model to infer dispersal, extinction and sampling from palaeontological data. Philos Trans R Soc Lond B Biol Sci 2016; 371:20150225. [PMID: 26977065 PMCID: PMC4810818 DOI: 10.1098/rstb.2015.0225] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Methods in historical biogeography have revolutionized our ability to infer the evolution of ancestral geographical ranges from phylogenies of extant taxa, the rates of dispersals, and biotic connectivity among areas. However, extant taxa are likely to provide limited and potentially biased information about past biogeographic processes, due to extinction, asymmetrical dispersals and variable connectivity among areas. Fossil data hold considerable information about past distribution of lineages, but suffer from largely incomplete sampling. Here we present a new dispersal–extinction–sampling (DES) model, which estimates biogeographic parameters using fossil occurrences instead of phylogenetic trees. The model estimates dispersal and extinction rates while explicitly accounting for the incompleteness of the fossil record. Rates can vary between areas and through time, thus providing the opportunity to assess complex scenarios of biogeographic evolution. We implement the DES model in a Bayesian framework and demonstrate through simulations that it can accurately infer all the relevant parameters. We demonstrate the use of our model by analysing the Cenozoic fossil record of land plants and inferring dispersal and extinction rates across Eurasia and North America. Our results show that biogeographic range evolution is not a time-homogeneous process, as assumed in most phylogenetic analyses, but varies through time and between areas. In our empirical assessment, this is shown by the striking predominance of plant dispersals from Eurasia into North America during the Eocene climatic cooling, followed by a shift in the opposite direction, and finally, a balance in biotic interchange since the middle Miocene. We conclude by discussing the potential of fossil-based analyses to test biogeographic hypotheses and improve phylogenetic methods in historical biogeography.
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Affiliation(s)
- Daniele Silvestro
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Alexander Zizka
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden
| | - Christine D Bacon
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden
| | | | - Nicolas Salamin
- Department of Ecology and Evolution, University of Lausanne, 1015 Lausanne, Switzerland Swiss Institute of Bioinformatics, Quartier Sorge, 1015 Lausanne, Switzerland
| | - Alexandre Antonelli
- Department of Biological and Environmental Sciences, University of Gothenburg, Carl Skottsbergs gata 22B, Gothenburg 413 19, Sweden Gothenburg Botanical Garden, Carl Skottsbergs gata 22A, Gothenburg 413 19, Sweden
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30
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Diversification in vipers: Phylogenetic relationships, time of divergence and shifts in speciation rates. Mol Phylogenet Evol 2016; 105:50-62. [DOI: 10.1016/j.ympev.2016.07.029] [Citation(s) in RCA: 133] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 04/01/2016] [Accepted: 07/28/2016] [Indexed: 11/17/2022]
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31
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Bairey E, Kelsic ED, Kishony R. High-order species interactions shape ecosystem diversity. Nat Commun 2016; 7:12285. [PMID: 27481625 PMCID: PMC4974637 DOI: 10.1038/ncomms12285] [Citation(s) in RCA: 174] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2016] [Accepted: 06/20/2016] [Indexed: 02/02/2023] Open
Abstract
Classical theory shows that large communities are destabilized by random interactions among species pairs, creating an upper bound on ecosystem diversity. However, species interactions often occur in high-order combinations, whereby the interaction between two species is modulated by one or more other species. Here, by simulating the dynamics of communities with random interactions, we find that the classical relationship between diversity and stability is inverted for high-order interactions. More specifically, while a community becomes more sensitive to pairwise interactions as its number of species increases, its sensitivity to three-way interactions remains unchanged, and its sensitivity to four-way interactions actually decreases. Therefore, while pairwise interactions lead to sensitivity to the addition of species, four-way interactions lead to sensitivity to species removal, and their combination creates both a lower and an upper bound on the number of species. These findings highlight the importance of high-order species interactions in determining the diversity of natural ecosystems.
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Affiliation(s)
- Eyal Bairey
- Department of Physics, Technion—Israel Institute of Technology, Haifa 3200003, Israel
| | - Eric D. Kelsic
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Roy Kishony
- Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
- Department of Biology and Department of Computer Science, Technion—Israel Institute of Technology, Haifa 3200003, Israel
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32
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Reconsidering the Loss of Evolutionary History: How Does Non-random Extinction Prune the Tree-of-Life? BIODIVERSITY CONSERVATION AND PHYLOGENETIC SYSTEMATICS 2016. [DOI: 10.1007/978-3-319-22461-9_4] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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33
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David M. Raup, 1933–2015. Proc Natl Acad Sci U S A 2015; 112:15002-3. [DOI: 10.1073/pnas.1521181112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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34
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Liow LH, Reitan T, Harnik PG. Ecological interactions on macroevolutionary time scales: clams and brachiopods are more than ships that pass in the night. Ecol Lett 2015; 18:1030-9. [PMID: 26293753 DOI: 10.1111/ele.12485] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2015] [Revised: 04/28/2015] [Accepted: 07/02/2015] [Indexed: 11/28/2022]
Abstract
Competition among organisms has ecological and evolutionary consequences. However, whether the consequences of competition are manifested and measureable on macroevolutionary time scales is equivocal. Marine bivalves and brachiopods have overlapping niches such that competition for food and space may occur. Moreover, there is a long-standing debate over whether bivalves outcompeted brachiopods evolutionarily, because brachiopod diversity declined through time while bivalve diversity increased. To answer this question, we estimate the origination and extinction dynamics of fossil marine bivalve and brachiopod genera from the Ordovician through to the Recent while simultaneously accounting for incomplete sampling. Then, using stochastic differential equations, we assess statistical relationships among diversification and sampling dynamics of brachiopods and bivalves and five paleoenvironmental proxies. None of these potential environmental drivers had any detectable influence on brachiopod or bivalve diversification. In contrast, elevated bivalve extinction rates causally increased brachiopod origination rates, suggesting that bivalves have suppressed brachiopod evolution.
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Affiliation(s)
- Lee Hsiang Liow
- Department of Biosciences, Centre for Evolutionary and Ecological Synthesis, University of Oslo, PO Box 1066, Blindern, Oslo, 0316, Norway
| | - Trond Reitan
- Department of Biosciences, Centre for Evolutionary and Ecological Synthesis, University of Oslo, PO Box 1066, Blindern, Oslo, 0316, Norway
| | - Paul G Harnik
- Department of Earth and Environment, Franklin and Marshall College, Lancaster, PA, USA
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Abstract
Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing evolvability. In particular, if extinction events extinguish indiscriminately many ways of life, indirectly they may select for the ability to expand rapidly through vacated niches. Lineages with such an ability are more likely to persist through multiple extinctions. Lending computational support for this hypothesis, this paper shows how increased evolvability will result from simulated extinction events in two computational models of evolved behavior. The conclusion is that although they are destructive in the short term, extinction events may make evolution more prolific in the long term.
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36
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Evolutionary food web model based on body masses gives realistic networks with permanent species turnover. Sci Rep 2015; 5:10955. [PMID: 26042870 PMCID: PMC4455292 DOI: 10.1038/srep10955] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/12/2015] [Indexed: 11/09/2022] Open
Abstract
The networks of predator-prey interactions in ecological systems are remarkably complex, but nevertheless surprisingly stable in terms of long term persistence of the system as a whole. In order to understand the mechanism driving the complexity and stability of such food webs, we developed an eco-evolutionary model in which new species emerge as modifications of existing ones and dynamic ecological interactions determine which species are viable. The food-web structure thereby emerges from the dynamical interplay between speciation and trophic interactions. The proposed model is less abstract than earlier evolutionary food web models in the sense that all three evolving traits have a clear biological meaning, namely the average body mass of the individuals, the preferred prey body mass, and the width of their potential prey body mass spectrum. We observed networks with a wide range of sizes and structures and high similarity to natural food webs. The model networks exhibit a continuous species turnover, but massive extinction waves that affect more than 50% of the network are not observed.
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Whelan NV, Kocot KM, Halanych KM. Employing Phylogenomics to Resolve the Relationships among Cnidarians, Ctenophores, Sponges, Placozoans, and Bilaterians. Integr Comp Biol 2015; 55:1084-95. [PMID: 25972566 DOI: 10.1093/icb/icv037] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Despite an explosion in the amount of sequence data, phylogenomics has failed to settle controversy regarding some critical nodes on the animal tree of life. Understanding relationships among Bilateria, Ctenophora, Cnidaria, Placozoa, and Porifera is essential for studying how complex traits such as neurons, muscles, and gastrulation have evolved. Recent studies have cast doubt on the historical viewpoint that sponges are sister to all other animal lineages with recent studies recovering ctenophores as sister. However, the ctenophore-sister hypothesis has been criticized as unrealistic and caused by systematic error. We review past phylogenomic studies and potential causes of systematic error in an effort to identify areas that can be improved in future studies. Increased sampling of taxa, less missing data, and a priori removal of sequences and taxa that may cause systematic error in phylogenomic inference will likely be the most fruitful areas of focus when assembling future datasets. Ultimately, we foresee metazoan relationships being resolved with higher support in the near future, and we caution against dismissing novel hypotheses merely because they conflict with historical viewpoints of animal evolution.
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Affiliation(s)
- Nathan V Whelan
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA;
| | - Kevin M Kocot
- School of Biological Sciences, The University of Queensland, 325 Goddard Building, St Lucia, QLD 4101, Australia
| | - Kenneth M Halanych
- *Department of Biological Sciences, Molette Biology Laboratory for Environmental and Climate Change Studies, Auburn University, 101 Life Sciences Building, Auburn, AL 36849, USA
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Walther V, Hiley CT, Shibata D, Swanton C, Turner PE, Maley CC. Can oncology recapitulate paleontology? Lessons from species extinctions. Nat Rev Clin Oncol 2015; 12:273-85. [PMID: 25687908 PMCID: PMC4569005 DOI: 10.1038/nrclinonc.2015.12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Although we can treat cancers with cytotoxic chemotherapies, target them with molecules that inhibit oncogenic drivers, and induce substantial cell death with radiation, local and metastatic tumours recur, resulting in extensive morbidity and mortality. Indeed, driving a tumour to extinction is difficult. Geographically dispersed species of organisms are perhaps equally resistant to extinction, but >99.9% of species that have ever existed on this planet have become extinct. By contrast, we are nowhere near that level of success in cancer therapy. The phenomena are broadly analogous--in both cases, a genetically diverse population mutates and evolves through natural selection. The goal of cancer therapy is to cause cancer cell population extinction, or at least to limit any further increase in population size, to prevent the tumour burden from overwhelming the patient. However, despite available treatments, complete responses are rare, and partial responses are limited in duration. Many patients eventually relapse with tumours that evolve from cells that survive therapy. Similarly, species are remarkably resilient to environmental change. Paleontology can show us the conditions that lead to extinction and the characteristics of species that make them resistant to extinction. These lessons could be translated to improve cancer therapy and prognosis.
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Affiliation(s)
- Viola Walther
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Crispin T Hiley
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Darryl Shibata
- Department of Pathology, USC Keck School of Medicine, Hoffman Medical Research Center 211, 2011 Zonal Avenue, Los Angeles, CA 90089-9092, USA
| | - Charles Swanton
- Translational Cancer Therapeutics Laboratory, Cancer Research UK London Research Institute, 44 Lincoln's Inn Fields, London WC2A 3LY, UK
| | - Paul E Turner
- Department of Ecology and Evolutionary Biology, Yale University, 165 Prospect Street, New Haven, CT 06511, USA
| | - Carlo C Maley
- Center for Evolution and Cancer, Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, 2340 Sutter Street, San Francisco, CA 94143, USA
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Beaulieu JM, O'Meara BC. Extinction can be estimated from moderately sized molecular phylogenies. Evolution 2015; 69:1036-43. [PMID: 25639334 DOI: 10.1111/evo.12614] [Citation(s) in RCA: 81] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2014] [Accepted: 01/03/2015] [Indexed: 11/27/2022]
Abstract
Hundreds of studies have been dedicated to estimating speciation and extinction from phylogenies of extant species. Although it has long been known that estimates of extinction rates using trees of extant organisms are often uncertain, an influential paper by Rabosky (2010) suggested that when birth rates vary continuously across the tree, estimates of the extinction fraction (i.e., extinction rate/speciation rate) will appear strongly bimodal, with a peak suggesting no extinction and a peak implying speciation and extinction rates are approaching equality. On the basis of these results, and the realistic nature of this form of rate variation, it is now generally assumed by many practitioners that extinction cannot be understood from molecular phylogenies alone. Here, we reevaluated and extended the analyses of Rabosky (2010) and come to the opposite conclusion-namely, that it is possible to estimate extinction from molecular phylogenies, even with model violations due to heritable variation in diversification rate. Note that while it may be tempting to interpret our study as advocating the application of simple birth-death models, our goal here is to show how a particular model violation does not necessitate the abandonment of an entire field: use prudent caution, but do not abandon all hope.
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Affiliation(s)
- Jeremy M Beaulieu
- National Institute for Biological and Mathematical Synthesis, University of Tennessee, Knoxville, Tennessee, 37996.
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Eiserhardt WL, Borchsenius F, Plum CM, Ordonez A, Svenning JC. Climate-driven extinctions shape the phylogenetic structure of temperate tree floras. Ecol Lett 2015; 18:263-72. [PMID: 25604755 DOI: 10.1111/ele.12409] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 12/04/2014] [Accepted: 12/15/2014] [Indexed: 11/26/2022]
Abstract
When taxa go extinct, unique evolutionary history is lost. If extinction is selective, and the intrinsic vulnerabilities of taxa show phylogenetic signal, more evolutionary history may be lost than expected under random extinction. Under what conditions this occurs is insufficiently known. We show that late Cenozoic climate change induced phylogenetically selective regional extinction of northern temperate trees because of phylogenetic signal in cold tolerance, leading to significantly and substantially larger than random losses of phylogenetic diversity (PD). The surviving floras in regions that experienced stronger extinction are phylogenetically more clustered, indicating that non-random losses of PD are of increasing concern with increasing extinction severity. Using simulations, we show that a simple threshold model of survival given a physiological trait with phylogenetic signal reproduces our findings. Our results send a strong warning that we may expect future assemblages to be phylogenetically and possibly functionally depauperate if anthropogenic climate change affects taxa similarly.
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Affiliation(s)
- Wolf L Eiserhardt
- Section for Ecoinformatics & Biodiversity, Department of Bioscience, Aarhus University, Ny Munkegade 114, DK-8000, Aarhus C, Denmark; Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AE, UK
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41
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Rees T. Taxamatch, an algorithm for near ('fuzzy') matching of scientific names in taxonomic databases. PLoS One 2014; 9:e107510. [PMID: 25247892 PMCID: PMC4172526 DOI: 10.1371/journal.pone.0107510] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Accepted: 08/20/2014] [Indexed: 11/19/2022] Open
Abstract
Misspellings of organism scientific names create barriers to optimal storage and organization of biological data, reconciliation of data stored under different spelling variants of the same name, and appropriate responses from user queries to taxonomic data systems. This study presents an analysis of the nature of the problem from first principles, reviews some available algorithmic approaches, and describes Taxamatch, an improved name matching solution for this information domain. Taxamatch employs a custom Modified Damerau-Levenshtein Distance algorithm in tandem with a phonetic algorithm, together with a rule-based approach incorporating a suite of heuristic filters, to produce improved levels of recall, precision and execution time over the existing dynamic programming algorithms n-grams (as bigrams and trigrams) and standard edit distance. Although entirely phonetic methods are faster than Taxamatch, they are inferior in the area of recall since many real-world errors are non-phonetic in nature. Excellent performance of Taxamatch (as recall, precision and execution time) is demonstrated against a reference database of over 465,000 genus names and 1.6 million species names, as well as against a range of error types as present at both genus and species levels in three sets of sample data for species and four for genera alone. An ancillary authority matching component is included which can be used both for misspelled names and for otherwise matching names where the associated cited authorities are not identical.
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Affiliation(s)
- Tony Rees
- CSIRO Oceans and Atmosphere Flagship, Hobart, Tasmania, Australia
- * E-mail:
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Saakian DB, Ghazaryan MH, Hu CK. Punctuated equilibrium and shock waves in molecular models of biological evolution. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2014; 90:022712. [PMID: 25215763 DOI: 10.1103/physreve.90.022712] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2013] [Indexed: 06/03/2023]
Abstract
We consider the dynamics in infinite population evolution models with a general symmetric fitness landscape. We find shock waves, i.e., discontinuous transitions in the mean fitness, in evolution dynamics even with smooth fitness landscapes, which means that the search for the optimal evolution trajectory is more complicated. These shock waves appear in the case of positive epistasis and can be used to represent punctuated equilibria in biological evolution during long geological time scales. We find exact analytical solutions for discontinuous dynamics at the large-genome-length limit and derive optimal mutation rates for a fixed fitness landscape to send the population from the initial configuration to some final configuration in the fastest way.
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Affiliation(s)
- David B Saakian
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan; Yerevan Physics Institute, Alikhanian Brothers Str. 2, Yerevan 375036, Armenia; and National Center for Theoretical Sciences: Physics Division, National Taiwan University, Taipei 10617, Taiwan
| | | | - Chin-Kun Hu
- Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan
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Quantitative Trait Loci Mapping Problem: An Extinction-Based Multi-Objective Evolutionary Algorithm Approach. ALGORITHMS 2013. [DOI: 10.3390/a6030546] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Affiliation(s)
- Tiago B. Quental
- Universidade de São Paulo (USP), Departamento de Ecologia, São Paulo, SP, Brazil
| | - Charles R. Marshall
- University of California Museum of Paleontology, 1101 Valley Life Sciences Building, University of California Berkeley, Berkeley, CA 94720–4780, USA
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46
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A molecular phylogeny of Asian barbets: Speciation and extinction in the tropics. Mol Phylogenet Evol 2013; 68:1-13. [DOI: 10.1016/j.ympev.2013.03.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2012] [Revised: 03/01/2013] [Accepted: 03/06/2013] [Indexed: 11/18/2022]
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Guo H, Lee TH, Wang X, Paterson AH. Function relaxation followed by diversifying selection after whole-genome duplication in flowering plants. PLANT PHYSIOLOGY 2013; 162:769-78. [PMID: 23580595 PMCID: PMC3668069 DOI: 10.1104/pp.112.213447] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2012] [Accepted: 04/09/2013] [Indexed: 05/20/2023]
Abstract
Episodes of whole-genome duplication (WGD) followed by gene loss dominate the evolutionary history of flowering plants. Despite the importance of understanding gene evolution following WGD, little is known about the evolutionary dynamics of this process. In this study, we analyzed duplicated genes from three WGD events in the Arabidopsis (Arabidopsis thaliana) lineage using multiple data types. Most duplicated genes that have survived from the most recent WGD (α) are under purifying selection in modern Arabidopsis populations. Using the number of identified protein-protein interactions as a proxy for functional divergence, approximately 92.7% of α-duplicated genes were diverged in function from one another in modern Arabidopsis populations, indicating that their preservation is no longer explicable by dosage balance. Dosage-balanced retention declines with antiquity of duplication: 24.1% of α-duplicated gene pairs in Arabidopsis remain in dosage balance with interacting partners, versus 12.9% and 9.4% for the earlier β-duplication and γ-triplication. GO-slim (a cut-down version of gene ontologies) terms reinforce evidence from protein-protein interactions, showing that the putatively diverged gene pairs are adapted to different cellular components. We identified a group of α-duplicated genes that show higher than average single-nucleotide polymorphism density, indicating that a period of positive selection, potentially driving functional divergence, may have preceded the current phase of purifying selection. We propose three possible paths for the evolution of duplicated genes following WGD.
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Vilhena DA, Harris EB, Bergstrom CT, Maliska ME, Ward PD, Sidor CA, Strömberg CAE, Wilson GP. Bivalve network reveals latitudinal selectivity gradient at the end-Cretaceous mass extinction. Sci Rep 2013. [PMCID: PMC3646391 DOI: 10.1038/srep01790] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Biogeographic patterns of survival help constrain the causal factors responsible for mass extinction. To test whether biogeography influenced end-Cretaceous (K-Pg) extinction patterns, we used a network approach to delimit biogeographic units (BUs) above the species level in a global Maastrichtian database of 329 bivalve genera. Geographic range is thought to buffer taxa from extinction, but the number of BUs a taxon occurred in superseded geographic range as an extinction predictor. Geographically, we found a latitudinal selectivity gradient for geographic range in the K-Pg, such that higher latitude BUs had lower extinction than expected given the geographic ranges of the genera, implying that (i) high latitude BUs were more resistant to extinction, (ii) the intensity of the K-Pg kill mechanism declined with distance from the tropics, or (iii) both. Our results highlight the importance of macroecological structure in constraining causal mechanisms of extinction and estimating extinction risk of taxa.
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Ponge JF. Disturbances, organisms and ecosystems: a global change perspective. Ecol Evol 2013; 3:1113-24. [PMID: 23610648 PMCID: PMC3631418 DOI: 10.1002/ece3.505] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2012] [Revised: 01/05/2013] [Accepted: 01/17/2013] [Indexed: 12/29/2022] Open
Abstract
The present text exposes a theory of the role of disturbances in the assemblage and evolution of species within ecosystems, based principally, but not exclusively, on terrestrial ecosystems. Two groups of organisms, doted of contrasted strategies when faced with environmental disturbances, are presented, based on the classical r-K dichotomy, but enriched with more modern concepts from community and evolutionary ecology. Both groups participate in the assembly of known animal, plant, and microbial communities, but with different requirements about environmental fluctuations. The so-called "civilized" organisms are doted with efficient anticipatory mechanisms, allowing them to optimize from an energetic point of view their performances in a predictable environment (stable or fluctuating cyclically at the scale of life expectancy), and they developed advanced specializations in the course of evolutionary time. On the opposite side, the so-called "barbarians" are weakly efficient in a stable environment because they waste energy for foraging, growth, and reproduction, but they are well adapted to unpredictably changing conditions, in particular during major ecological crises. Both groups of organisms succeed or alternate each other in the course of spontaneous or geared successional processes, as well as in the course of evolution. The balance of "barbarians" against "civilized" strategies within communities is predicted to shift in favor of the first type under present-day anthropic pressure, exemplified among others by climate warming, land use change, pollution, and biological invasions.
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Affiliation(s)
- Jean-François Ponge
- Muséum National d'Histoire Naturelle, CNRS UMR 7179 4 avenue du Petit-Château, Brunoy, 91800, France
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50
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Self-Organized Criticality: Consequences for Statistics and Predictability of Earthquakes. ACTA ACUST UNITED AC 2013. [DOI: 10.1029/gm083p0069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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