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Duran-Nebreda S, Bentley RA, Vidiella B, Spiridonov A, Eldredge N, O'Brien MJ, Valverde S. On the multiscale dynamics of punctuated evolution. Trends Ecol Evol 2024; 39:734-744. [PMID: 38821781 DOI: 10.1016/j.tree.2024.05.003] [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: 10/04/2023] [Revised: 05/07/2024] [Accepted: 05/07/2024] [Indexed: 06/02/2024]
Abstract
For five decades, paleontologists, paleobiologists, and ecologists have investigated patterns of punctuated equilibria in biology. Here, we step outside those fields and summarize recent advances in the theory of and evidence for punctuated equilibria, gathered from contemporary observations in geology, molecular biology, genetics, anthropology, and sociotechnology. Taken in the aggregate, these observations lead to a more general theory that we refer to as punctuated evolution. The quality of recent datasets is beginning to illustrate the mechanics of punctuated evolution in a way that can be modeled across a vast range of phenomena, from mass extinctions hundreds of millions of years ago to the possible future ahead in the Anthropocene. We expect the study of punctuated evolution to be applicable beyond biological scenarios.
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Affiliation(s)
- Salva Duran-Nebreda
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain
| | - R Alexander Bentley
- Department of Anthropology, University of Tennessee, Knoxville, TN 37996, USA
| | - Blai Vidiella
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain
| | - Andrej Spiridonov
- Department of Geology and Mineralogy, Vilnius University, Vilnius, Lithuania
| | - Niles Eldredge
- The American Museum of Natural History, New York, NY 10024, USA
| | - Michael J O'Brien
- Department of History, Philosophy, and Geography and Department of Life Sciences, Texas A&M University-San Antonio, San Antonio, TX 78224, USA; Department of Anthropology, University of Missouri, Columbia, MO 65205, USA.
| | - Sergi Valverde
- Evolution of Networks Lab, Institut de Biologia Evolutiva, Passeig Marítim de la Barceloneta 37 49, Barcelona 08003, Spain; European Centre for Living Technology, Ca' Bottacin, Dorsoduro 3911, 30123 Venice, Italy.
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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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Venkatakrishnan A, Holzknecht ZE, Holzknecht R, Bowles DE, Kotzé SH, Modliszewski JL, Parker W. Evolution of bacteria in the human gut in response to changing environments: An invisible player in the game of health. Comput Struct Biotechnol J 2021; 19:752-758. [PMID: 33552447 PMCID: PMC7829112 DOI: 10.1016/j.csbj.2021.01.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 01/23/2023] Open
Abstract
Several factors in Western society, including widespread use of antibiotics, chronic inflammation, and loss of complex eukaryotic symbionts such as helminths, have a dramatic impact on the ecosystem of the gut, affecting the microbiota hosted there. In addition, reductions in dietary fiber are profoundly impactful on the microbiota, causing extensive destruction of the niche space that supports the normally diverse microbial community in the gut. Abundant evidence now supports the view that, following dramatic alterations in the gut ecosystem, microorganisms undergo rapid change via Darwinian evolution. Such evolutionary change creates functionally distinct bacteria that may potentially have properties of pathogens but yet are difficult to distinguish from their benign predecessors.
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Affiliation(s)
| | - Zoie E Holzknecht
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Rob Holzknecht
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Dawn E Bowles
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
| | - Sanet H Kotzé
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, University of Stellenbosch, Cape Town 8000, South Africa
| | - Jennifer L Modliszewski
- Genomic Analysis and Bioinformatics Shared Resource, Duke Center for Genomic and Computational Biology, Duke University School of Medicine, Durham, NC, USA
| | - William Parker
- Department of Surgery, Duke University School of Medicine, Durham, NC, USA
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Impacts of speciation and extinction measured by an evolutionary decay clock. Nature 2020; 588:636-641. [PMID: 33299185 DOI: 10.1038/s41586-020-3003-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2020] [Accepted: 09/16/2020] [Indexed: 02/03/2023]
Abstract
The hypothesis that destructive mass extinctions enable creative evolutionary radiations (creative destruction) is central to classic concepts of macroevolution1,2. However, the relative impacts of extinction and radiation on the co-occurrence of species have not been directly quantitatively compared across the Phanerozoic eon. Here we apply machine learning to generate a spatial embedding (multidimensional ordination) of the temporal co-occurrence structure of the Phanerozoic fossil record, covering 1,273,254 occurrences in the Paleobiology Database for 171,231 embedded species. This facilitates the simultaneous comparison of macroevolutionary disruptions, using measures independent of secular diversity trends. Among the 5% most significant periods of disruption, we identify the 'big five' mass extinction events2, seven additional mass extinctions, two combined mass extinction-radiation events and 15 mass radiations. In contrast to narratives that emphasize post-extinction radiations1,3, we find that the proportionally most comparable mass radiations and extinctions (such as the Cambrian explosion and the end-Permian mass extinction) are typically decoupled in time, refuting any direct causal relationship between them. Moreover, in addition to extinctions4, evolutionary radiations themselves cause evolutionary decay (modelled co-occurrence probability and shared fraction of species between times approaching zero), a concept that we describe as destructive creation. A direct test of the time to over-threshold macroevolutionary decay4 (shared fraction of species between two times ≤ 0.1), counted by the decay clock, reveals saw-toothed fluctuations around a Phanerozoic mean of 18.6 million years. As the Quaternary period began at a below-average decay-clock time of 11 million years, modern extinctions further increase life's decay-clock debt.
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Veenstra F, de Prado Salas PG, Stoy K, Bongard J, Risi S. Death and Progress: How Evolvability is Influenced by Intrinsic Mortality. ARTIFICIAL LIFE 2020; 26:90-111. [PMID: 32027531 DOI: 10.1162/artl_a_00311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Many factors influence the evolvability of populations, and this article illustrates how intrinsic mortality (death induced through internal factors) in an evolving population contributes favorably to evolvability on a fixed deceptive fitness landscape. We test for evolvability using the hierarchical if-and-only-if (h-iff) function as a deceptive fitness landscape together with a steady state genetic algorithm (SSGA) with a variable mutation rate and indiscriminate intrinsic mortality rate. The mutation rate and the intrinsic mortality rate display a relationship for finding the global maximum. This relationship was also found when implementing the same deceptive fitness landscape in a spatial model consisting of an evolving population. We also compared the performance of the optimal mutation and mortality rate with a state-of-the-art evolutionary algorithm called age-fitness Pareto optimization (AFPO) and show how the two approaches traverse the h-iff landscape differently. Our results indicate that the intrinsic mortality rate and mutation rate induce random genetic drift that allows a population to efficiently traverse a deceptive fitness landscape. This article gives an overview of how intrinsic mortality influences the evolvability of a population. It thereby supports the premise that programmed death of individuals could have a beneficial effect on the evolvability of the entire population.
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Cabrol NA. Alien Mindscapes-A Perspective on the Search for Extraterrestrial Intelligence. ASTROBIOLOGY 2016; 16:661-76. [PMID: 27383691 PMCID: PMC5111820 DOI: 10.1089/ast.2016.1536] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2016] [Accepted: 05/23/2016] [Indexed: 05/15/2023]
Abstract
UNLABELLED Advances in planetary and space sciences, astrobiology, and life and cognitive sciences, combined with developments in communication theory, bioneural computing, machine learning, and big data analysis, create new opportunities to explore the probabilistic nature of alien life. Brought together in a multidisciplinary approach, they have the potential to support an integrated and expanded Search for Extraterrestrial Intelligence (SETI (1) ), a search that includes looking for life as we do not know it. This approach will augment the odds of detecting a signal by broadening our understanding of the evolutionary and systemic components in the search for extraterrestrial intelligence (ETI), provide more targets for radio and optical SETI, and identify new ways of decoding and coding messages using universal markers. KEY WORDS SETI-Astrobiology-Coevolution of Earth and life-Planetary habitability and biosignatures. Astrobiology 16, 661-676.
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