1
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Muñoz-Gómez SA. The energetic costs of cellular complexity in evolution. Trends Microbiol 2024; 32:746-755. [PMID: 38307786 DOI: 10.1016/j.tim.2024.01.003] [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: 11/04/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/04/2024]
Abstract
The evolutionary history of cells has been marked by drastic increases in complexity. Some hypothesize that such cellular complexification requires a massive energy flux as the origin of new features is hypothetically more energetically costly than their evolutionary maintenance. However, it remains unclear how increases in cellular complexity demand more energy. I propose that the early evolution of new genes with weak functions imposes higher energetic costs by overexpression before their functions are evolutionarily refined. In the long term, the accumulation of new genes deviates resources away from growth and reproduction. Accrued cellular complexity further requires additional infrastructure for its maintenance. Altogether, this suggests that larger and more complex cells are defined by increased survival but lower reproductive capacity.
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2
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Lingam M, Nichols R, Balbi A. A Bayesian Analysis of the Probability of the Origin of Life Per Site Conducive to Abiogenesis. ASTROBIOLOGY 2024; 24:813-823. [PMID: 39159441 DOI: 10.1089/ast.2024.0037] [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: 08/21/2024]
Abstract
The emergence of life from nonlife, or abiogenesis, remains a fundamental question in scientific inquiry. In this article, we investigate the probability of the origin of life (per conducive site) by leveraging insights from Earth's environments. If life originated endogenously on Earth, its existence is indeed endowed with informative value, although the interpretation of the attendant significance hinges critically upon prior assumptions. By adopting a Bayesian framework, for an agnostic prior, we establish a direct connection between the number of potential locations for abiogenesis on Earth and the probability of life's emergence per site. Our findings suggest that constraints on the availability of suitable environments for the origin(s) of life on Earth may offer valuable insights into the probability of abiogenesis and the frequency of life in the universe.
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Affiliation(s)
- Manasvi Lingam
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
- Department of Physics, The University of Texas at Austin, Austin, Texas, USA
| | - Ruth Nichols
- Department of Aerospace, Physics and Space Sciences, Florida Institute of Technology, Melbourne, Florida, USA
| | - Amedeo Balbi
- Dipartimento di Fisica, Università di Roma "Tor Vergata," Roma, Italy
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3
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Borg JM, Buskell A, Kapitany R, Powers ST, Reindl E, Tennie C. Evolved Open-Endedness in Cultural Evolution: A New Dimension in Open-Ended Evolution Research. ARTIFICIAL LIFE 2024; 30:417-438. [PMID: 37253238 DOI: 10.1162/artl_a_00406] [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: 06/01/2023]
Abstract
The goal of Artificial Life research, as articulated by Chris Langton, is "to contribute to theoretical biology by locating life-as-we-know-it within the larger picture of life-as-it-could-be." The study and pursuit of open-ended evolution in artificial evolutionary systems exemplify this goal. However, open-ended evolution research is hampered by two fundamental issues: the struggle to replicate open-endedness in an artificial evolutionary system and our assumption that we only have one system (genetic evolution) from which to draw inspiration. We argue not only that cultural evolution should be seen as another real-world example of an open-ended evolutionary system but that the unique qualities seen in cultural evolution provide us with a new perspective from which we can assess the fundamental properties of, and ask new questions about, open-ended evolutionary systems, especially with regard to evolved open-endedness and transitions from bounded to unbounded evolution. Here we provide an overview of culture as an evolutionary system, highlight the interesting case of human cultural evolution as an open-ended evolutionary system, and contextualize cultural evolution by developing a new framework of (evolved) open-ended evolution. We go on to provide a set of new questions that can be asked once we consider cultural evolution within the framework of open-ended evolution and introduce new insights that we may be able to gain about evolved open-endedness as a result of asking these questions.
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Affiliation(s)
- James M Borg
- Aston University School of Informatics and Digital Engineering.
| | | | - Rohan Kapitany
- Keele University School of Psychology University of Oxford School of Anthropology and Museum Ethnography
| | | | - Eva Reindl
- Durham University Department of Anthropology University of St. Andrews School of Psychology and Neuroscience
| | - Claudio Tennie
- University of Tübingen Department of Early Prehistory and Quaternary Ecology
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4
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Champagne-Ruel A, Zakaib-Bernier S, Charbonneau P. Diffusion and pattern formation in spatial games. Phys Rev E 2024; 110:014301. [PMID: 39160963 DOI: 10.1103/physreve.110.014301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 06/12/2024] [Indexed: 08/21/2024]
Abstract
Diffusion plays an important role in a wide variety of phenomena, from bacterial quorum sensing to the dynamics of traffic flow. While it generally tends to level out gradients and inhomogeneities, diffusion has nonetheless been shown to promote pattern formation in certain classes of systems. Formation of stable structures often serves as a key factor in promoting the emergence and persistence of cooperative behavior in otherwise competitive environments, however, an in-depth analysis on the impact of diffusion on such systems is lacking. We therefore investigate the effects of diffusion on cooperative behavior using a cellular automaton (CA) model of the noisy spatial iterated prisoner's dilemma (IPD), physical extension, and stochasticity being unavoidable characteristics of several natural phenomena. We further derive a mean-field (MF) model that captures the three-species predation dynamics from the CA model and highlight how pattern formation arises in this new model, then characterize how including diffusion by interchange similarly enables the emergence of large scale structures in the CA model as well. We investigate how these emerging patterns favors cooperative behavior for parameter space regions where IPD error rates classically forbid such dynamics. We thus demonstrate how the coupling of diffusion with nonlinear dynamics can, counterintuitively, promote large-scale structure formation and in return establish new grounds for cooperation to take hold in stochastic spatial systems.
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5
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Jaeger J, Riedl A, Djedovic A, Vervaeke J, Walsh D. Naturalizing relevance realization: why agency and cognition are fundamentally not computational. Front Psychol 2024; 15:1362658. [PMID: 38984275 PMCID: PMC11231436 DOI: 10.3389/fpsyg.2024.1362658] [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: 12/28/2023] [Accepted: 05/15/2024] [Indexed: 07/11/2024] Open
Abstract
The way organismic agents come to know the world, and the way algorithms solve problems, are fundamentally different. The most sensible course of action for an organism does not simply follow from logical rules of inference. Before it can even use such rules, the organism must tackle the problem of relevance. It must turn ill-defined problems into well-defined ones, turn semantics into syntax. This ability to realize relevance is present in all organisms, from bacteria to humans. It lies at the root of organismic agency, cognition, and consciousness, arising from the particular autopoietic, anticipatory, and adaptive organization of living beings. In this article, we show that the process of relevance realization is beyond formalization. It cannot be captured completely by algorithmic approaches. This implies that organismic agency (and hence cognition as well as consciousness) are at heart not computational in nature. Instead, we show how the process of relevance is realized by an adaptive and emergent triadic dialectic (a trialectic), which manifests as a metabolic and ecological-evolutionary co-constructive dynamic. This results in a meliorative process that enables an agent to continuously keep a grip on its arena, its reality. To be alive means to make sense of one's world. This kind of embodied ecological rationality is a fundamental aspect of life, and a key characteristic that sets it apart from non-living matter.
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Affiliation(s)
- Johannes Jaeger
- Department of Philosophy, University of Vienna, Vienna, Austria
- Complexity Science Hub (CSH) Vienna, Vienna, Austria
- Ronin Institute, Essex, NJ, United States
| | - Anna Riedl
- Middle European Interdisciplinary Master's Program in Cognitive Science, University of Vienna, Vienna, Austria
| | - Alex Djedovic
- Cognitive Science Program, University of Toronto, Toronto, ON, Canada
- Institute for the History and Philosophy of Science and Technology, University of Toronto, Toronto, ON, Canada
| | - John Vervaeke
- Department of Psychology, University of Toronto, Toronto, ON, Canada
| | - Denis Walsh
- Institute for the History and Philosophy of Science and Technology, University of Toronto, Toronto, ON, Canada
- Department of Philosophy, University of Toronto, Toronto, ON, Canada
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6
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Hartl B, Risi S, Levin M. Evolutionary Implications of Self-Assembling Cybernetic Materials with Collective Problem-Solving Intelligence at Multiple Scales. ENTROPY (BASEL, SWITZERLAND) 2024; 26:532. [PMID: 39056895 PMCID: PMC11275831 DOI: 10.3390/e26070532] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2024] [Revised: 06/10/2024] [Accepted: 06/14/2024] [Indexed: 07/28/2024]
Abstract
In recent years, the scientific community has increasingly recognized the complex multi-scale competency architecture (MCA) of biology, comprising nested layers of active homeostatic agents, each forming the self-orchestrated substrate for the layer above, and, in turn, relying on the structural and functional plasticity of the layer(s) below. The question of how natural selection could give rise to this MCA has been the focus of intense research. Here, we instead investigate the effects of such decision-making competencies of MCA agential components on the process of evolution itself, using in silico neuroevolution experiments of simulated, minimal developmental biology. We specifically model the process of morphogenesis with neural cellular automata (NCAs) and utilize an evolutionary algorithm to optimize the corresponding model parameters with the objective of collectively self-assembling a two-dimensional spatial target pattern (reliable morphogenesis). Furthermore, we systematically vary the accuracy with which the uni-cellular agents of an NCA can regulate their cell states (simulating stochastic processes and noise during development). This allows us to continuously scale the agents' competency levels from a direct encoding scheme (no competency) to an MCA (with perfect reliability in cell decision executions). We demonstrate that an evolutionary process proceeds much more rapidly when evolving the functional parameters of an MCA compared to evolving the target pattern directly. Moreover, the evolved MCAs generalize well toward system parameter changes and even modified objective functions of the evolutionary process. Thus, the adaptive problem-solving competencies of the agential parts in our NCA-based in silico morphogenesis model strongly affect the evolutionary process, suggesting significant functional implications of the near-ubiquitous competency seen in living matter.
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Affiliation(s)
- Benedikt Hartl
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA;
- Institute for Theoretical Physics, Center for Computational Materials Science (CMS), TU Wien, 1040 Wien, Austria
| | - Sebastian Risi
- Digital Design, IT University of Copenhagen, 2300 Copenhagen, Denmark;
| | - Michael Levin
- Allen Discovery Center, Tufts University, Medford, MA 02155, USA;
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
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7
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Crockett WW, Shaw JO, Simpson C, Kempes CP. Physical constraints during Snowball Earth drive the evolution of multicellularity. Proc Biol Sci 2024; 291:20232767. [PMID: 38924758 PMCID: PMC11271684 DOI: 10.1098/rspb.2023.2767] [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: 12/07/2023] [Accepted: 05/09/2024] [Indexed: 06/28/2024] Open
Abstract
Molecular and fossil evidence suggests that complex eukaryotic multicellularity evolved during the late Neoproterozoic era, coincident with Snowball Earth glaciations, where ice sheets covered most of the globe. During this period, environmental conditions-such as seawater temperature and the availability of photosynthetically active light in the oceans-likely changed dramatically. Such changes would have had significant effects on both resource availability and optimal phenotypes. Here, we construct and apply mechanistic models to explore (i) how environmental changes during Snowball Earth and biophysical constraints generated selective pressures, and (ii) how these pressures may have had differential effects on organisms with different forms of biological organization. By testing a series of alternative-and commonly debated-hypotheses, we demonstrate how multicellularity was likely acquired differently in eukaryotes and prokaryotes owing to selective differences on their size due to the biophysical and metabolic regimes they inhabit: decreasing temperatures and resource availability instigated by the onset of glaciations generated selective pressures towards smaller sizes in organisms in the diffusive regime and towards larger sizes in motile heterotrophs. These results suggest that changing environmental conditions during Snowball Earth glaciations gave multicellular eukaryotes an evolutionary advantage, paving the way for the complex multicellular lineages that followed.
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Affiliation(s)
- William W. Crockett
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Santa Fe Institute, Santa Fe, NM 87501, USA
| | | | - Carl Simpson
- Department of Geological Sciences and University of Colorado Museum of Natural History, University of Colorado, Boulder, CO 80309, USA
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Pineau RM, Libby E, Demory D, Lac DT, Day TC, Bravo P, Yunker PJ, Weitz JS, Bozdag GO, Ratcliff WC. Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment. Nat Ecol Evol 2024; 8:1010-1020. [PMID: 38486107 PMCID: PMC11090753 DOI: 10.1038/s41559-024-02367-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Accepted: 02/15/2024] [Indexed: 03/23/2024]
Abstract
The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth's ecosystems. Yet little is known about how early steps in the evolution of multicellularity affect eco-evolutionary dynamics. Through long-term experimental evolution, we observed niche partitioning and the adaptive divergence of two specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subjected to selection for rapid growth, followed by selection favouring larger group size. Small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations, specializing on divergent aspects of a trade-off between growth rate and survival. Through modelling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically impactful emergent properties of this evolutionary transition.
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Affiliation(s)
- Rozenn M Pineau
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Eric Libby
- Integrated Science Lab, Umeå university, Umeå, Sweden.
- Department of Mathematics and Mathematical Statistics, Umeå university, Umeå, Sweden.
| | - David Demory
- CNRS, Sorbonne Université, USR 3579 Laboratoire de Biodiversité et Biotechnologies Microbiennes (LBBM), Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Dung T Lac
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Thomas C Day
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Pablo Bravo
- Interdisciplinary Graduate Program in Quantitative Biosciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Peter J Yunker
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
| | - Joshua S Weitz
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
- School of Physics, Georgia Institute of Technology, Atlanta, GA, USA
- Department of Biology, University of Maryland, College Park, MD, USA
- Department of Physics, University of Maryland, College Park, MD, USA
| | - G Ozan Bozdag
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA.
- Department of Biology, University of Maryland, College Park, MD, USA.
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9
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Oszoli I, Zachar I. Group-selection via aggregative propagule-formation enables cooperative multicellularity in an individual based, spatial model. PLoS Comput Biol 2024; 20:e1012107. [PMID: 38713735 PMCID: PMC11101088 DOI: 10.1371/journal.pcbi.1012107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2023] [Revised: 05/17/2024] [Accepted: 04/24/2024] [Indexed: 05/09/2024] Open
Abstract
The emergence of multicellularity is one of the major transitions in evolution that happened multiple times independently. During aggregative multicellularity, genetically potentially unrelated lineages cooperate to form transient multicellular groups. Unlike clonal multicellularity, aggregative multicellular organisms do not rely on kin selection instead other mechanisms maintain cooperation against cheater phenotypes that benefit from cooperators but do not contribute to groups. Spatiality with limited diffusion can facilitate group selection, as interactions among individuals are restricted to local neighbourhoods only. Selection for larger size (e.g. avoiding predation) may facilitate the emergence of aggregation, though it is unknown, whether and how much role such selection played during the evolution of aggregative multicellularity. We have investigated the effect of spatiality and the necessity of predation on the stability of aggregative multicellularity via individual-based modelling on the ecological timescale. We have examined whether aggregation facilitates the survival of cooperators in a temporally heterogeneous environment against cheaters, where only a subset of the population is allowed to periodically colonize a new, resource-rich habitat. Cooperators constitutively produce adhesive molecules to promote aggregation and propagule-formation while cheaters spare this expense to grow faster but cannot aggregate on their own, hence depending on cooperators for long-term survival. We have compared different population-level reproduction modes with and without individual selection (predation) to evaluate the different hypotheses. In a temporally homogeneous environment without propagule-based colonization, cheaters always win. Predation can benefit cooperators, but it is not enough to maintain the necessary cooperator amount in successive dispersals, either randomly or by fragmentation. Aggregation-based propagation however can ensure the adequate ratio of cooperators-to-cheaters in the propagule and is sufficient to do so even without predation. Spatiality combined with temporal heterogeneity helps cooperators via group selection, thus facilitating aggregative multicellularity. External stress selecting for larger size (e.g. predation) may facilitate aggregation, however, according to our results, it is neither necessary nor sufficient for aggregative multicellularity to be maintained when there is effective group-selection.
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Affiliation(s)
- István Oszoli
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
| | - István Zachar
- Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös Loránd University, Budapest, Hungary
- HUN-REN Institute of Evolution, Centre for Ecological Research, Budapest, Hungary
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10
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Károlyi A, Scheuring I. Cooperation in public goods game does not require assortment and depends on population density. J Evol Biol 2024; 37:451-463. [PMID: 38459964 DOI: 10.1093/jeb/voae029] [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: 12/11/2023] [Revised: 03/01/2024] [Accepted: 03/06/2024] [Indexed: 03/11/2024]
Abstract
The threshold public goods game is one of the best-known models of non-linear public goods dilemmas. Cooperators and defectors typically coexist in this game when the population is assumed to follow the so-called structured deme model. In this article, we develop a dynamical model of a general N-player game in which there is no deme structure: Individuals interact with randomly chosen neighbours and selection occurs between randomly chosen pairs of individuals. We show that in the deterministic limit, the dynamics in this model leads to the same replicator dynamics as in the structured deme model, i.e., coexistence of cooperators and defectors is typical in threshold public goods game even when the population is completely well mixed. We extend the model to study the effect of density dependence and density fluctuation on the dynamics. We show analytically and numerically that decreasing population density increases the equilibrium frequency of cooperators till the fixation of this strategy, but below a critical density cooperators abruptly disappear from the population. Our numerical investigations show that weak density fluctuations enhance cooperation, while strong fluctuations suppress it.
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Affiliation(s)
- Adél Károlyi
- Department of Zoology, University of Veterinary Medicine, Budapest, Rottenbiller utca 50, Hungary
- University of Potsdam, Institute of Biochemistry and Biology, 14469 Potsdam, Germany
| | - István Scheuring
- HUN-REN, Centre for Ecological Research, Institute of Evolution, Budapest, Konkoly-Thege Miklós út 29-33, Hungary
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11
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Griebel U, Oller DK. From emotional signals to symbols. Front Psychol 2024; 15:1135288. [PMID: 38629043 PMCID: PMC11020113 DOI: 10.3389/fpsyg.2024.1135288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Accepted: 03/13/2024] [Indexed: 04/19/2024] Open
Abstract
The quest for the origins of language is a diverse enterprise, where research from a variety of disciplines brings area-specific ideas and area-specific terminology to bear. This variety often results in misunderstandings and misconceptions about communication in various species. In the present paper, we argue for focus on emotional systems as the primary motivators for social signals in animals in general. This focus can help resolve discrepancies of interpretation among different areas of inquiry and can illuminate distinctions among different social signals as well as their phylogenetic origins in animals and especially in humans. We advocate, following Jaak Panksepp, a view wherein the Seeking System, the endogenous tendency to search and explore, is the most fundamental emotional motivation. The Seeking System forms the basis for flexible, voluntary, and exploratory control of motor systems and makes much of learning possible. The relative lack of vocal learning and expression in nonhuman primates contrasted with extensive vocal learning and expression in humans began, we propose, with the evolution in ancient hominins of a necessary foundation for the many subsequent capabilities required for language. That foundation was, according to the reasoning, naturally selected in the form of neurological connections between the Seeking System and mechanisms of glottal/phonatory control. The new connections allowed ancient hominins to develop flexible, endogenous vocal fitness signals produced at very high rates and including large numbers of discrete syllables, recombinable to form syllable combinations with many prosodic variations. The increasing sociality of hominins supported evolution of massive expansion in the utilization of these flexible vocal forms to allow development of words and sentences.
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Affiliation(s)
- Ulrike Griebel
- School of Communication Sciences and Disorders, The University of Memphis, Memphis, TN, United States
- The Institute for Intelligent Systems, University of Memphis, Memphis, TN, United States
- The Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
| | - D. Kimbrough Oller
- School of Communication Sciences and Disorders, The University of Memphis, Memphis, TN, United States
- The Institute for Intelligent Systems, University of Memphis, Memphis, TN, United States
- The Konrad Lorenz Institute for Evolution and Cognition Research, Klosterneuburg, Austria
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12
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Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Diversity, origin, and evolution of the ESCRT systems. mBio 2024; 15:e0033524. [PMID: 38380930 PMCID: PMC10936438 DOI: 10.1128/mbio.00335-24] [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: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/22/2024] Open
Abstract
Endosomal sorting complexes required for transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold and using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The last archaeal common ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.IMPORTANCEAll eukaryotic cells possess complex intracellular membrane organization. Endosomal sorting complexes required for transport (ESCRT) play a central role in membrane remodeling which is essential for cellular functionality in eukaryotes. Recently, it has been shown that Asgard archaea, the archaeal phylum that includes the closest known relatives of eukaryotes, encode homologs of many components of the ESCRT systems. We employed protein sequence and structure comparisons to reconstruct the evolution of ESCRT systems in archaea and identified several previously unknown homologs of ESCRT subunits, some of which can be predicted to participate in cell division. The results of this reconstruction indicate that the last archaeal common ancestor already encoded a complex ESCRT system that was involved in protein sorting. In Asgard archaea, ESCRT systems evolved toward greater complexity, and in particular, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was established.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Victor Tobiasson
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université de Paris, Paris, France
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen, China
| | - Eugene V. Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, Maryland, USA
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13
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Szathmáry E. Nonadaptive onset of complex multicellularity. Proc Natl Acad Sci U S A 2024; 121:e2401220121. [PMID: 38437572 PMCID: PMC10945832 DOI: 10.1073/pnas.2401220121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/06/2024] Open
Affiliation(s)
- Eörs Szathmáry
- Institute of Evolution, HUN-REN Centre for Ecological Research, Budapest1121, Hungary
- Center for the Conceptual Foundations of Science, Parmenides Foundation, Pöcking82343, Germany
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14
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Girard C. The tri-flow adaptiveness of codes in major evolutionary transitions. Biosystems 2024; 237:105133. [PMID: 38336225 DOI: 10.1016/j.biosystems.2024.105133] [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: 11/17/2023] [Revised: 01/26/2024] [Accepted: 01/27/2024] [Indexed: 02/12/2024]
Abstract
Life codes increase in both number and variety with biological complexity. Although our knowledge of codes is constantly expanding, the evolutionary progression of organic, neural, and cultural codes in response to selection pressure remains poorly understood. Greater clarification of the selective mechanisms is achieved by investigating how major evolutionary transitions reduce spatiotemporal and energetic constraints on transmitting heritable code to offspring. Evolution toward less constrained flows is integral to enduring flow architecture everywhere, in both engineered and natural flow systems. Beginning approximately 4 billion years ago, the most basic level for transmitting genetic material to offspring was initiated by protocell division. Evidence from ribosomes suggests that protocells transmitted comma-free or circular codes, preceding the evolution of standard genetic code. This rudimentary information flow within protocells is likely to have first emerged within the geo-energetic and geospatial constraints of hydrothermal vents. A broad-gauged hypothesis is that major evolutionary transitions overcame such constraints with tri-flow adaptations. The interconnected triple flows incorporated energy-converting, spatiotemporal, and code-based informational dynamics. Such tri-flow adaptations stacked sequence splicing code on top of protein-DNA recognition code in eukaryotes, prefiguring the transition to sexual reproduction. Sex overcame the spatiotemporal-energetic constraints of binary fission with further code stacking. Examples are tubulin code and transcription initiation code in vertebrates. In a later evolutionary transition, language reduced metabolic-spatiotemporal constraints on inheritance by stacking phonetic, phonological, and orthographic codes. In organisms that reproduce sexually, each major evolutionary transition is shown to be a tri-flow adaptation that adds new levels of code-based informational exchange. Evolving biological complexity is also shown to increase the nongenetic transmissibility of code.
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Affiliation(s)
- Chris Girard
- Department of Global and Sociocultural Studies, Florida International University, Miami, FL 33199, United States.
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15
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Makarova KS, Tobiasson V, Wolf YI, Lu Z, Liu Y, Zhang S, Krupovic M, Li M, Koonin EV. Diversity, Origin and Evolution of the ESCRT Systems. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.06.579148. [PMID: 38903064 PMCID: PMC11188069 DOI: 10.1101/2024.02.06.579148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Endosomal Sorting Complexes Required for Transport (ESCRT) play key roles in protein sorting between membrane-bounded compartments of eukaryotic cells. Homologs of many ESCRT components are identifiable in various groups of archaea, especially in Asgardarchaeota, the archaeal phylum that is currently considered to include the closest relatives of eukaryotes, but not in bacteria. We performed a comprehensive search for ESCRT protein homologs in archaea and reconstructed ESCRT evolution using the phylogenetic tree of Vps4 ATPase (ESCRT IV) as a scaffold, using sensitive protein sequence analysis and comparison of structural models to identify previously unknown ESCRT proteins. Several distinct groups of ESCRT systems in archaea outside of Asgard were identified, including proteins structurally similar to ESCRT-I and ESCRT-II, and several other domains involved in protein sorting in eukaryotes, suggesting an early origin of these components. Additionally, distant homologs of CdvA proteins were identified in Thermoproteales which are likely components of the uncharacterized cell division system in these archaea. We propose an evolutionary scenario for the origin of eukaryotic and Asgard ESCRT complexes from ancestral building blocks, namely, the Vps4 ATPase, ESCRT-III components, wH (winged helix-turn-helix fold) and possibly also coiled-coil, and Vps28-like domains. The Last Archaeal Common Ancestor likely encompassed a complex ESCRT system that was involved in protein sorting. Subsequent evolution involved either simplification, as in the TACK superphylum, where ESCRT was co-opted for cell division, or complexification as in Asgardarchaeota. In Asgardarchaeota, the connection between ESCRT and the ubiquitin system that was previously considered a eukaryotic signature was already established.
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Affiliation(s)
- Kira S. Makarova
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Victor Tobiasson
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Yuri I. Wolf
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
| | - Zhongyi Lu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Yang Liu
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Siyu Zhang
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Mart Krupovic
- Archaeal Virology Unit, Institut Pasteur, Université de Paris, F-75015 Paris, France
| | - Meng Li
- Archaeal Biology Center, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
- Shenzhen Key Laboratory of Marine Microbiome Engineering, Institute for Advanced Study, Shenzhen University, Shenzhen 518060, China
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, Bethesda, MD 20894, USA
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16
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Miao L, Yin Z, Knoll AH, Qu Y, Zhu M. 1.63-billion-year-old multicellular eukaryotes from the Chuanlinggou Formation in North China. SCIENCE ADVANCES 2024; 10:eadk3208. [PMID: 38266082 PMCID: PMC10807817 DOI: 10.1126/sciadv.adk3208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2023] [Accepted: 12/21/2023] [Indexed: 01/26/2024]
Abstract
Multicellularity is key to the functional and ecological success of the Eukarya, underpinning much of their modern diversity in both terrestrial and marine ecosystems. Despite the widespread occurrence of simple multicellular organisms among eukaryotes, when this innovation arose remains an open question. Here, we report cellularly preserved multicellular microfossils (Qingshania magnifica) from the ~1635-million-year-old Chuanlinggou Formation, North China. The fossils consist of large uniseriate, unbranched filaments with cell diameters up to 190 micrometers; spheroidal structures, possibly spores, occur within some cells. In combination with spectroscopic characteristics, the large size and morphological complexity of these fossils support their interpretation as eukaryotes, likely photosynthetic, based on comparisons with extant organisms. The occurrence of multicellular eukaryotes in Paleoproterozoic rocks not much younger than those containing the oldest unambiguous evidence of eukaryotes as a whole supports the hypothesis that simple multicellularity arose early in eukaryotic history, as much as a billion years before complex multicellular organisms diversified in the oceans.
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Affiliation(s)
- Lanyun Miao
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Zongjun Yin
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
| | - Andrew H. Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Yuangao Qu
- Institute of Deep-sea Science and Engineering, Chinese Academy of Sciences, Sanya 572000, China
| | - Maoyan Zhu
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, Nanjing 210008, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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17
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Schoenmakers LLJ, Reydon TAC, Kirschning A. Evolution at the Origins of Life? Life (Basel) 2024; 14:175. [PMID: 38398684 PMCID: PMC10890241 DOI: 10.3390/life14020175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2023] [Revised: 01/19/2024] [Accepted: 01/23/2024] [Indexed: 02/25/2024] Open
Abstract
The role of evolutionary theory at the origin of life is an extensively debated topic. The origin and early development of life is usually separated into a prebiotic phase and a protocellular phase, ultimately leading to the Last Universal Common Ancestor. Most likely, the Last Universal Common Ancestor was subject to Darwinian evolution, but the question remains to what extent Darwinian evolution applies to the prebiotic and protocellular phases. In this review, we reflect on the current status of evolutionary theory in origins of life research by bringing together philosophy of science, evolutionary biology, and empirical research in the origins field. We explore the various ways in which evolutionary theory has been extended beyond biology; we look at how these extensions apply to the prebiotic development of (proto)metabolism; and we investigate how the terminology from evolutionary theory is currently being employed in state-of-the-art origins of life research. In doing so, we identify some of the current obstacles to an evolutionary account of the origins of life, as well as open up new avenues of research.
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Affiliation(s)
- Ludo L. J. Schoenmakers
- Konrad Lorenz Institute for Evolution and Cognition Research (KLI), 3400 Klosterneuburg, Austria
| | - Thomas A. C. Reydon
- Institute of Philosophy, Centre for Ethics and Law in the Life Sciences (CELLS), Leibniz University Hannover, 30159 Hannover, Germany;
| | - Andreas Kirschning
- Institute of Organic Chemistry, Leibniz University Hannover, 30167 Hannover, Germany;
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18
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Krishnan N, Csiszár V, Móri TF, Garay J. Genesis of ectosymbiotic features based on commensalistic syntrophy. Sci Rep 2024; 14:1366. [PMID: 38228651 DOI: 10.1038/s41598-023-47211-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 11/10/2023] [Indexed: 01/18/2024] Open
Abstract
The symbiogenetic origin of eukaryotes with mitochondria is considered a major evolutionary transition. The initial interactions and conditions of symbiosis, along with the phylogenetic affinity of the host, are widely debated. Here, we focus on a possible evolutionary path toward an association of individuals of two species based on unidirectional syntrophy. With the backing of a theoretical model, we hypothesize that the first step in the evolution of such symbiosis could be the appearance of a linking structure on the symbiont's membrane, using which it forms an ectocommensalism with its host. We consider a commensalistic model based on the syntrophy hypothesis in the framework of coevolutionary dynamics and mutant invasion into a monomorphic resident system (evolutionary substitution). We investigate the ecological and evolutionary stability of the consortium (or symbiotic merger), with vertical transmissions playing a crucial role. The impact of the 'effectiveness of vertical transmission' on the dynamics is also analyzed. We find that the transmission of symbionts and the additional costs incurred by the mutant determine the conditions of fixation of the consortia. Additionally, we observe that small and highly metabolically active symbionts are likely to form the consortia.
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Affiliation(s)
- Nandakishor Krishnan
- HUN-REN Centre for Ecological Research, Institute of Evolution, Konkoly-Thege M. Út 29-33, Budapest, 1121, Hungary.
- Doctoral School of Biology, Institute of Biology, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary.
| | - Villő Csiszár
- Department of Probability Theory and Statistics, Eötvös Loránd University, Pázmány Péter Sétány 1/C, Budapest, 1117, Hungary
| | - Tamás F Móri
- HUN-REN Alfréd Rényi Institute of Mathematics, Reáltanoda U. 13-15, Budapest, 1053, Hungary
| | - József Garay
- HUN-REN Centre for Ecological Research, Institute of Evolution, Konkoly-Thege M. Út 29-33, Budapest, 1121, Hungary
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19
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Søgaard Jørgensen P, Weinberger VP, Waring TM. Evolution and sustainability: gathering the strands for an Anthropocene synthesis. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220251. [PMID: 37952619 PMCID: PMC10645096 DOI: 10.1098/rstb.2022.0251] [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: 10/02/2023] [Accepted: 10/18/2023] [Indexed: 11/14/2023] Open
Abstract
How did human societies evolve to become a major force of global change? What dynamics can lead societies on a trajectory of global sustainability? The astonishing growth in human population, economic activity and environmental impact has brought these questions to the fore. This theme issue pulls together a variety of traditions that seek to address these questions using different theories and methods. In this Introduction, we review and organize the major strands of work on how the Anthropocene evolved, how evolutionary dynamics are influencing sustainability efforts today, and what principles, strategies and capacities will be important to guide us towards global sustainability in the future. We present a set of synthetic insights and highlight frontiers for future research efforts which could contribute to a consolidated synthesis. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.
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Affiliation(s)
- Peter Søgaard Jørgensen
- Stockholm Resilience Centre, Stockholm University, Stockholm, Stockholm 10691, Sweden
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, Stockholm, Stockholm 10405, Sweden
- Anthropocene Laboratory, Royal Swedish Academy of Sciences, Stockholm, Stockholm 10405, Sweden
| | - Vanessa P. Weinberger
- Center for Resilience, Adaptation and Mitigation (CReAM), Universidad Mayor, Temuco, 4801043, Chile
| | - Timothy M. Waring
- Mitchell Center for Sustainability Solutions, University of Maine Orono, ME 04473, USA
- School of Economics, University of Maine Orono, ME 04473, USA
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20
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Luo Y, Liang M, Yu C, Ma W. Circular at the very beginning: on the initial genomes in the RNA world. RNA Biol 2024; 21:17-31. [PMID: 39016036 PMCID: PMC11259081 DOI: 10.1080/15476286.2024.2380130] [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] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Abstract
It is likely that an RNA world existed in early life, when RNA played both the roles of the genome and functional molecules, thereby undergoing Darwinian evolution. However, even with only one type of polymer, it seems quite necessary to introduce a labour division concerning these two roles because folding is required for functional molecules (ribozymes) but unfavourable for the genome (as a template in replication). Notably, while ribozymes tend to have adopted a linear form for folding without constraints, a circular form, which might have been topologically hindered in folding, seems more suitable for an RNA template. Another advantage of involving a circular genome could have been to resist RNA's end-degradation. Here, we explore the scenario of a circular RNA genome plus linear ribozyme(s) at the precellular stage of the RNA world through computer modelling. The results suggest that a one-gene scene could have been 'maintained', albeit with rather a low efficiency for the circular genome to produce the ribozyme, which required precise chain-break or chain-synthesis. This strict requirement may have been relieved by introducing a 'noncoding' sequence into the genome, which had the potential to derive a second gene through mutation. A two-gene scene may have 'run well' with the two corresponding ribozymes promoting the replication of the circular genome from different respects. Circular genomes with more genes might have arisen later in RNA-based protocells. Therefore, circular genomes, which are common in the modern living world, may have had their 'root' at the very beginning of life.
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Affiliation(s)
- Yufan Luo
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Minglun Liang
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
| | - Chunwu Yu
- College of Computer Sciences, Wuhan University, Wuhan, China
| | - Wentao Ma
- Hubei Key Laboratory of Cell Homeostasis, College of Life Sciences, Wuhan University, Wuhan, China
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21
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Søgaard Jørgensen P, Jansen REV, Avila Ortega DI, Wang-Erlandsson L, Donges JF, Österblom H, Olsson P, Nyström M, Lade SJ, Hahn T, Folke C, Peterson GD, Crépin AS. Evolution of the polycrisis: Anthropocene traps that challenge global sustainability. Philos Trans R Soc Lond B Biol Sci 2024; 379:20220261. [PMID: 37952617 PMCID: PMC10645130 DOI: 10.1098/rstb.2022.0261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/22/2023] [Indexed: 11/14/2023] Open
Abstract
The Anthropocene is characterized by accelerating change and global challenges of increasing complexity. Inspired by what some have called a polycrisis, we explore whether the human trajectory of increasing complexity and influence on the Earth system could become a form of trap for humanity. Based on an adaptation of the evolutionary traps concept to a global human context, we present results from a participatory mapping. We identify 14 traps and categorize them as either global, technology or structural traps. An assessment reveals that 12 traps (86%) could be in an advanced phase of trapping with high risk of hard-to-reverse lock-ins and growing risks of negative impacts on human well-being. Ten traps (71%) currently see growing trends in their indicators. Revealing the systemic nature of the polycrisis, we assess that Anthropocene traps often interact reinforcingly (45% of pairwise interactions), and rarely in a dampening fashion (3%). We end by discussing capacities that will be important for navigating these systemic challenges in pursuit of global sustainability. Doing so, we introduce evolvability as a unifying concept for such research between the sustainability and evolutionary sciences. This article is part of the theme issue 'Evolution and sustainability: gathering the strands for an Anthropocene synthesis'.
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Affiliation(s)
- Peter Søgaard Jørgensen
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Global Economic Dynamics and the Biosphere Programme, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
- Anthropocene Laboratory, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
| | - Raf E. V. Jansen
- Global Economic Dynamics and the Biosphere Programme, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
| | - Daniel I. Avila Ortega
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Global Economic Dynamics and the Biosphere Programme, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
| | - Lan Wang-Erlandsson
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Anthropocene Laboratory, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
- Potsdam Institute for Climate Impact Research, Member of the Leibnitz Association, 14473 Potsdam, Germany
| | - Jonathan F. Donges
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Potsdam Institute for Climate Impact Research, Member of the Leibnitz Association, 14473 Potsdam, Germany
| | - Henrik Österblom
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Anthropocene Laboratory, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
| | - Per Olsson
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Magnus Nyström
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Steven J. Lade
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Fenner School of Environment & Society, Australian National University, Canberra 2601, Australia
| | - Thomas Hahn
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Carl Folke
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Global Economic Dynamics and the Biosphere Programme, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
- Anthropocene Laboratory, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
- Beijer Institute of Ecological Economics, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
| | - Garry D. Peterson
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
| | - Anne-Sophie Crépin
- Stockholm Resilience Centre, Stockholm University, SE-106 91 Stockholm, Sweden
- Beijer Institute of Ecological Economics, Royal Swedish Academy of Sciences, SE-104 05 Stockholm, Sweden
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22
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Bourke AFG. Conflict and conflict resolution in the major transitions. Proc Biol Sci 2023; 290:20231420. [PMID: 37817595 PMCID: PMC10565403 DOI: 10.1098/rspb.2023.1420] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2023] [Accepted: 09/14/2023] [Indexed: 10/12/2023] Open
Abstract
Conflict and conflict resolution have been argued to be fundamental to the major transitions in evolution. These were key events in life's history in which previously independently living individuals cooperatively formed a higher-level individual, such as a multicellular organism or eusocial colony. Conflict has its central role because, to proceed stably, the evolution of individuality in each major transition required within-individual conflict to be held in check. This review revisits the role of conflict and conflict resolution in the major transitions, addressing recent work arguing for a minor role. Inclusive fitness logic suggests that differences between the kin structures of clones and sexual families support the absence of conflict at the origin of multicellularity but, by contrast, suggest that key conflicts existed at the origin of eusociality. A principal example is conflict over replacing the founding queen (queen replacement). Following the origin of each transition, conflict remained important, because within-individual conflict potentially disrupts the attainment of maximal individuality (organismality) in the system. The conclusion is that conflict remains central to understanding the major transitions, essentially because conflict arises from differences in inclusive fitness optima while conflict resolution can help the system attain a high degree of coincidence of inclusive fitness interests.
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Affiliation(s)
- Andrew F. G. Bourke
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
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23
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Jacob MS. Toward a Bio-Organon: A model of interdependence between energy, information and knowledge in living systems. Biosystems 2023:104939. [PMID: 37295595 DOI: 10.1016/j.biosystems.2023.104939] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2023] [Revised: 06/01/2023] [Accepted: 06/06/2023] [Indexed: 06/12/2023]
Abstract
What is an organism? In the absence of a fundamental biological definition, what constitutes a living organism, whether it is a unicellular microbe, a multicellular being or a multi-organismal society, remains an open question. New models of living systems are needed to address the scale of this question, with implications for the relationship between humanity and planetary ecology. Here we develop a generic model of an organism that can be applied across multiple scales and through major evolutionary transitions to form a toolkit, or bio-organon, for theoretical studies of planetary-wide physiology. The tool identifies the following core organismic principles that cut across spatial scale: (1) evolvability through self-knowledge, (2) entanglement between energy and information, and (3) extrasomatic "technology" to scaffold increases in spatial scale. Living systems are generally defined by their ability to self-sustain against entropic forces of degradation. Life "knows" how to survive from the inside, not from its genetic code alone, but by utilizing this code through dynamically embodied and functionally specialized flows of information and energy. That is, entangled metabolic and communication networks bring encoded knowledge to life in order to sustain life. However, knowledge is itself evolved and is evolving. The functional coupling between knowledge, energy and information has ancient origins, enabling the original, cellular "biotechnology," and cumulative evolutionary creativity in biochemical products and forms. Cellular biotechnology also enabled the nesting of specialized cells into multicellular organisms. This nested organismal hierarchy can be extended further, suggesting that an organism of organisms, or a human "superorganism," is not only possible, but in keeping with evolutionary trends.
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Affiliation(s)
- Michael S Jacob
- Human Energy, 21 Orinda Way, Suite C 208, Orinda, CA, 94563, United States; Mental Health Service, San Francisco VA Medical Center, 4150 Clement St, San Francisco, CA, 94121, United States; Department of Psychiatry and Weill Institute for Neurosciences, University of California, San Francisco, 505 Parnassus Ave, San Francisco, CA, 94143, United States.
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24
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Galanics C, Sintár V, Szalai I. Autocatalytic flow chemistry. Sci Rep 2023; 13:9211. [PMID: 37280425 DOI: 10.1038/s41598-023-36360-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Accepted: 06/02/2023] [Indexed: 06/08/2023] Open
Abstract
Autocatalysis is a crucial process of nonequilibrium self-organization in nature and is assumed to play a role in the origin of life. The essential dynamical phenomena of an autocatalytic reaction network are bistability and the development of propagating front when combined with diffusion. The presence of bulk fluid motion may widen the range of emerging behavior in those systems. Many aspects of the dynamics of autocatalytic reactions in a continuous flow have already been studied, especially the shape and dynamics of the chemical front and the influence of the chemical reactions on hydrodynamic instabilities. This paper aims to provide experimental evidence of bistability and related dynamical phenomena, such as excitability and oscillations in autocatalytic reactions performed in a tubular flow reactor, where the flow is laminar and advection is the dominating transport process. We show that the linear residence time ramp may result in the simultaneous appearance of different dynamic states along the length of the pipe. Therefore, long tubular reactors offer a unique opportunity to quickly explore the dynamics of reaction networks. These findings enhance our understanding of nonlinear flow chemistry and its role in natural pattern formation.
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Affiliation(s)
- Csenge Galanics
- Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary
| | - Virág Sintár
- Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary
| | - István Szalai
- Institute of Chemistry, Eötvös Loránd University, Budapest, 1117, Hungary.
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25
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Levin M. Darwin's agential materials: evolutionary implications of multiscale competency in developmental biology. Cell Mol Life Sci 2023; 80:142. [PMID: 37156924 PMCID: PMC10167196 DOI: 10.1007/s00018-023-04790-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 04/24/2023] [Accepted: 04/27/2023] [Indexed: 05/10/2023]
Abstract
A critical aspect of evolution is the layer of developmental physiology that operates between the genotype and the anatomical phenotype. While much work has addressed the evolution of developmental mechanisms and the evolvability of specific genetic architectures with emergent complexity, one aspect has not been sufficiently explored: the implications of morphogenetic problem-solving competencies for the evolutionary process itself. The cells that evolution works with are not passive components: rather, they have numerous capabilities for behavior because they derive from ancestral unicellular organisms with rich repertoires. In multicellular organisms, these capabilities must be tamed, and can be exploited, by the evolutionary process. Specifically, biological structures have a multiscale competency architecture where cells, tissues, and organs exhibit regulative plasticity-the ability to adjust to perturbations such as external injury or internal modifications and still accomplish specific adaptive tasks across metabolic, transcriptional, physiological, and anatomical problem spaces. Here, I review examples illustrating how physiological circuits guiding cellular collective behavior impart computational properties to the agential material that serves as substrate for the evolutionary process. I then explore the ways in which the collective intelligence of cells during morphogenesis affect evolution, providing a new perspective on the evolutionary search process. This key feature of the physiological software of life helps explain the remarkable speed and robustness of biological evolution, and sheds new light on the relationship between genomes and functional anatomical phenotypes.
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Affiliation(s)
- Michael Levin
- Allen Discovery Center at Tufts University, 200 Boston Ave. 334 Research East, Medford, MA, 02155, USA.
- Wyss Institute for Biologically Inspired Engineering at Harvard University, 3 Blackfan St., Boston, MA, 02115, USA.
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26
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Van Cleve J. Evolutionarily stable strategy analysis and its links to demography and genetics through invasion fitness. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210496. [PMID: 36934754 PMCID: PMC10024993 DOI: 10.1098/rstb.2021.0496] [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: 11/16/2022] [Accepted: 02/07/2023] [Indexed: 03/21/2023] Open
Abstract
Evolutionarily stable strategy (ESS) analysis pioneered by Maynard Smith and Price took off in part because it often does not require explicit assumptions about the genetics and demography of a population in contrast to population genetic models. Though this simplicity is useful, it obscures the degree to which ESS analysis applies to populations with more realistic genetics and demography: for example, how does ESS analysis handle complexities such as kin selection, group selection and variable environments when phenotypes are affected by multiple genes? In this paper, I review the history of the ESS concept and show how early uncertainty about the method lead to important mathematical theory linking ESS analysis to general population genetic models. I use this theory to emphasize the link between ESS analysis and the concept of invasion fitness. I give examples of how invasion fitness can measure kin selection, group selection and the evolution of linked modifier genes in response to variable environments. The ESSs in these examples depend crucially on demographic and genetic parameters, which highlights how ESS analysis will continue to be an important tool in understanding evolutionary patterns as new models address the increasing abundance of genetic and long-term demographic data in natural populations. This article is part of the theme issue 'Half a century of evolutionary games: a synthesis of theory, application and future directions'.
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Affiliation(s)
- Jeremy Van Cleve
- Department of Biology, University of Kentucky, Lexington, KY 40506 USA
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Weber GW. Quantum Leaps in Human Biocultural Evolution and the Relationship to Cranial Capacity. Life (Basel) 2023; 13:life13041030. [PMID: 37109559 PMCID: PMC10145355 DOI: 10.3390/life13041030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/22/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023] Open
Abstract
The evolution of the genus Homo can only be understood by considering both of the inheritance systems that interact to shape human nature: biology and culture. While growing intellectual abilities are a key factor of human evolution, they are rarely contrasted with cultural progress. Cranial capacity data of 193 hominin fossils from the last seven million years and artefacts of increasing number and complexity in the archaeological record are used to demonstrate the concordant progression of brain-size increase and cultural development, starting approximately two million years ago. Our biocultural evolution shows a number of quantum leaps along the time axis applying to both domains. At first, humans left the canonical evolutionary pathway, which pertains to all other organisms, by enhancing their fitness using sophisticated tools and fire; secondly, they turned into a symbolic species; and finally, humanity now faces a new challenge: "intentional evolution". Chronologically, these quantum leaps correspond to cranial capacity data used here as a proxy for cognitive performance. This contribution tries to demonstrate this parallel development and argues for a simple and generalized model of human biocultural evolution. An extrapolation of the model into the future shows that humans, as biological entities, will not necessarily persist.
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Affiliation(s)
- Gerhard W Weber
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
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Andersson C, Czárán T. The transition from animal to human culture-simulating the social protocell hypothesis. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210416. [PMID: 36688383 PMCID: PMC9869448 DOI: 10.1098/rstb.2021.0416] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The origin of human cumulative culture is commonly envisioned as the appearance (some 2.0-2.5 million years ago) of a capacity to faithfully copy the know-how that underpins socially learned traditions. While certainly plausible, this story faces a steep 'startup problem'. For example, it presumes that ape-like early Homo possessed specialized cognitive capabilities for faithful know-how copying and that early toolmaking actually required such a capacity. The social protocell hypothesis provides a leaner story, where cumulative culture may have originated even earlier-as cumulative systems of non-cumulative traditions ('institutions' and 'cultural lifestyles'), via an emergent group-level channel of cultural inheritance. This channel emerges as a side-effect of a specific but in itself unremarkable suite of social group behaviours. It is independent of faithful know-how copying, and an ancestral version is argued to persist in Pan today. Hominin cultural lifestyles would thereby have gained in complexity and sophistication, eventually becoming independent units of selection (socionts) via a cultural evolutionary transition in individuality, abstractly similar to the origin of early cells. We here explore this hypothesis by simulating its basic premises. The model produces the expected behaviour and reveals several additional and non-trivial phenomena as fodder for future work. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Claes Andersson
- Department of Space, Earth and Environment, Division for Physical Resource Theory, Complex System Group, Chalmers University of Technology, 412 96 Gothenburg, Sweden,European Centre for Living Technology, University of Venice Ca’ Foscari, Ca' Bottacin, Dorsoduro 3911, Calle Crosera, 30123 Venice, Italy
| | - Tamás Czárán
- Evolutionary Systems Research Group, ELKH Centre for Ecological Research, Karolina Road 29, H-1113 Budapest, Hungary,Institute of Evolution, ELKH Centre for Ecological Research, Karolina Road 29, H-1113 Budapest, Hungary,ELKH-ELTE Theoretical Biology and Evolutionary Research Group, Eötvös Loránd University, Egyetem tér 1–3, H-1053 Budapest, Hungary
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29
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Denton KK, Ram Y, Feldman MW. Conditions that favour cumulative cultural evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210400. [PMID: 36688392 PMCID: PMC9869458 DOI: 10.1098/rstb.2021.0400] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The emergence of human societies with complex language and cumulative culture is considered a major evolutionary transition. Why such a high degree of cumulative culture is unique to humans is perplexing given the potential fitness advantages of cultural accumulation. Here, Boyd & Richerson's (1996 Why culture is common, but cultural evolution is rare. Proc. Br. Acad. 88, 77-93) discrete-cultural-trait model is extended to incorporate arbitrarily strong selection; conformist, anti-conformist and unbiased frequency-dependent transmission; random and periodic environmental variation; finite population size; and multiple 'skill levels.' From their infinite-population-size model with success bias and a single skill level, Boyd and Richerson concluded that social learning is favoured over individual learning under a wider range of conditions when social learning is initially common than initially rare. We find that this holds only if the number n of individuals observed by a social learner is sufficiently small, but with a finite population and/or a combination of success-biased and conformist or unbiased transmission, this result holds with larger n. Assuming social learning has reached fixation, the increase in a population's mean skill level is lower if cumulative culture is initially absent than initially present, if population size is finite, or if cultural transmission has a frequency-dependent component. Hence, multiple barriers to cultural accumulation may explain its rarity. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Kaleda K. Denton
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Yoav Ram
- School of Zoology, Faculty of Life Sciences, Tel Aviv University, Tel Aviv 6997801, Israel,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv 6997801, Israel
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Kish Bar-On K, Lamm E. The interplay of social identity and norm psychology in the evolution of human groups. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210412. [PMID: 36688389 PMCID: PMC9869443 DOI: 10.1098/rstb.2021.0412] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
People's attitudes towards social norms play a crucial role in understanding group behaviour. Norm psychology accounts focus on processes of norm internalization that influence people's norm-following attitudes but pay considerably less attention to social identity and group identification processes. Social identity theory in contrast studies group identity but works with a relatively thin and instrumental notion of social norms. We argue that to best understand both sets of phenomena, it is important to integrate the insights of both approaches. Social status, social identity and social norms are considered separate phenomena in evolutionary accounts. We discuss assumptions and views that support this separation, and suggest an integrated view of our own. We argue that we should be open to the early origins of human social complexity, and conjecture that the longer that the human social world involved multi-level societies the more probable it is that norm psychology and social identity interacted in rich ways. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Kati Kish Bar-On
- The Science, Technology, and Society program, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Ehud Lamm
- The Cohn Institute for the History and Philosophy of Science and Ideas, Tel Aviv University, Tel Aviv 69978, Israel
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McShea DW. Four reasons for scepticism about a human major transition in social individuality. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210403. [PMID: 36688394 PMCID: PMC9869438 DOI: 10.1098/rstb.2021.0403] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The 'major transitions in evolution' are mainly about the rise of hierarchy, new individuals arising at ever higher levels of nestedness, in particular the eukaryotic cell arising from prokaryotes, multicellular individuals from solitary protists and individuated societies from multicellular individuals. Some lists include human societies as a major transition, but based on a comparison with the non-human transitions, there are reasons for scepticism. (i) The foundation of the major transitions is hierarchy, but the cross-cutting interactions in human societies undermine hierarchical structure. (ii) Natural selection operates in three modes-stability, growth and reproductive success-and only the third produces the complex adaptations seen in fully individuated higher levels. But human societies probably evolve mainly in the stability and growth modes. (iii) Highly individuated entities are marked by division of labour and commitment to morphological differentiation, but in humans differentiation is mostly behavioural and mostly reversible. (iv) As higher-level individuals arise, selection drains complexity, drains parts, from lower-level individuals. But there is little evidence of a drain in humans. In sum, a comparison with the other transitions gives reasons to doubt that human social individuation has proceeded very far, or if it has, to doubt that it is a transition of the same sort. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Griesemer J, Shavit A. Scaffolding individuality: coordination, cooperation, collaboration and community. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210398. [PMID: 36688398 PMCID: PMC9869437 DOI: 10.1098/rstb.2021.0398] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Processes of evolutionary transition (ET), becoming part of a new reproducing collective while losing the capacity of independent reproduction, seem difficult to track without circularity, since their features-units of selection, individuality, inheritance at multiple levels (MLS1, MLS2)-are products of one process. We describe ET in a non-circular way, noting kinds of interactions among community members necessary for such major transitions that are not instances of those same interactions within community members. Reproducing 'systems' tend to hybridize with environmental components, employing eco-devo scaffolding interactions forming communities. Communities are developmentally scaffolded systems of diverse members engaged in heterogeneous interactions. They may become individuals in their own right with the potential to evolve an inheritance system at the emergent community level. We argue for the explanatory benefits of treating 'individuality' as a special case of 'collectivity'. We characterize an idealized sequence of collective processes-coordination, cooperation and collaboration (3Cs)-which scaffolds transitions to new forms of collective individuality: communities. Hominid evolution and learning draw attention to developmental interactions driving both dimensions of ET: new 'levels of individuality' and inherited 'information systems'. Here, we outline a theoretical perspective that we suggest applies across a wide range of cases and scenarios. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- James Griesemer
- Department of Philosophy, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA
| | - Ayelet Shavit
- Department of Interdisciplinary Studies, Tel Hai College 12208, Israel,Department of Humanities and Arts, Technion, 3200003 Israel
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Carmel Y, Shavit A, Lamm E, Szathmáry E. Human socio-cultural evolution in light of evolutionary transitions: introduction to the theme issue. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210397. [PMID: 36688397 PMCID: PMC9869440 DOI: 10.1098/rstb.2021.0397] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Human societies are no doubt complex. They are characterized by division of labour, multiple hierarchies, intricate communication networks and transport systems. These phenomena and others have led scholars to propose that human society may be, or may become, a new hierarchical level that may dominate the individual humans within it, similar to the relations between an organism and its cells, or an ant colony and its members. Recent discussions of the possibility of this major evolutionary transition in individuality (ETI) raise interesting and controversial questions that are explored in the present issue from four different complementary perspectives. (i) The general theory of ETIs. (ii) The unique aspects of cultural evolution. (iii) The evolutionary history and pre-history of humans. (iv) Specific routes of a possible human ETI. Each perspective uses different tools provided by different disciplines: biology, anthropology, cultural evolution, systems theory, psychology, economy, linguistics and philosophy of science. Altogether, this issue provides a broad and rich application of the notion of ETI to human past, present and perhaps also future evolution. It presents important case studies, new theoretical results and novel questions for future research. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Yohay Carmel
- Department of Environmental Engineering, Technion, Haifa, 32000, Israel
| | - Ayelet Shavit
- Department of Interdisciplinary Studies, Tel Hai College, 12208, Israel,Department of Humanities and Arts, Technion, 3200003, Israel
| | - Ehud Lamm
- The Cohn Institute for History and Philosophy of Science, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Eörs Szathmáry
- Institute of Evolution, Centre for Ecological Research, 1121 Budapest, Hungary,Parmenides Foundation, 82343 Pöcking, Germany,Department of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest 1117, Hungary
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Rainey PB. Major evolutionary transitions in individuality between humans and AI. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210408. [PMID: 36688400 PMCID: PMC9869444 DOI: 10.1098/rstb.2021.0408] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
That humans might undergo future evolutionary transitions in individuality (ETIs) seems fanciful. However, drawing upon recent thinking concerning the origins of properties that underpin ETIs, I argue that certain ETIs are imminently realizable. Central to my argument is recognition that heritable variance in fitness at higher levels of organization can be externally imposed (scaffolded) by specific ecological structures and cultural practices. While ETIs to eusociality seem highly improbable, ETIs involving symbioses between humans and artificial intelligence (AI) can be readily envisaged. A necessary requirement is that fitness-affecting interactions between humans and AI devices are inherited by offspring. The Mendelian nature of human reproduction ensures that offspring resemble parents. Reproduction of AI devices requires nothing more than transference of algorithms from parental AI devices to devices that are assigned to offspring. This simple copying, combined with societal structures that require humans to carry AI devices, ensures heritable variance in fitness at the level of both interacting partners. Selection at the collective level will drive alignment of replicative fates and increase co-dependency, thus alleviating need for continual imposition of externally imposed scaffolds. I conclude by drawing attention to the immediacy of such transitions and express concern over possibilities for malevolent manipulation. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Paul B. Rainey
- Department of Microbial Population Biology, Max Planck Institute for Evolutionary Biology, 24306 Plön, Germany,Laboratoire Biophysique et Évolution, CBI, ESPCI Paris, Université PSL, CNRS, 75005 Paris, France
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35
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Dor D. Communication for collaborative computation: two major transitions in human evolution. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210404. [PMID: 36688385 PMCID: PMC9869436 DOI: 10.1098/rstb.2021.0404] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
This paper presents and defends the following theoretical arguments: (1) The uniqueness of the human condition lies in the fact that only humans engage in collaborative computation, where different individuals work together on shared computational challenges. Collaborative computation is the foundation of our cumulative cultures. (2) Collaborative computation requires individuals to engage in instructive communication, where senders do not just send messages to receivers-but also send them instructions that the receivers are obliged to follow in the course of computing the messages. (3) The process of human evolution was driven throughout by the invention and development of tools of instructive communication. (4) In this process, two separate major transitions should be identified. The first was made possible by the toolkit of representational gestures (pointing, eye contact, manual demonstration, pantomime and more) that Merlin Donald called the toolkit of mimesis. Mimesis allows for collaborative computation as long as the information requiring computation is available for direct experiencing by the participants. The second was made possible by language, the tool that allowed its users, for the first time, to engage in collaborative computations of information they did not experience together-through the systematic instruction of the mental computations of imagination. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Daniel Dor
- Department of Communication, Tel Aviv University, Tel Aviv 69978, Israel
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36
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Keasar T, Pourtallier O, Wajnberg E. Can sociality facilitate learning of complex tasks? Lessons from bees and flowers. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210402. [PMID: 36688396 PMCID: PMC9869446 DOI: 10.1098/rstb.2021.0402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The emergence of animal societies is a major evolutionary transition, but its implications for learning-dependent innovations are insufficiently understood. Bees, with lifestyles ranging from solitary to eusocial, are ideal models for exploring social evolution. Here, we ask how and why bees may acquire a new 'technology', foraging on morphologically complex flowers, and whether eusociality facilitates this technological shift. We consider 'complex' flowers that produce high food rewards but are difficult to access, versus 'simple' flowers offering easily accessible yet lower rewards. Complex flowers are less profitable than simple flowers to naive bees but become more rewarding after a learning period. We model how social bees optimally choose between simple and complex flowers over time, to maximize their colony's food balance. The model predicts no effect of colony size on the bees' flower choices. More foraging on complex flowers is predicted as colony longevity, its proportion of foragers, individual longevity and learning ability increase. Of these traits, only long-lived colonies and abundant foragers characterize eusocial bees. Thus, we predict that eusociality supports, but is not mandatory for, learning to exploit complex flowers. A re-analysis of a large published dataset of bee-flower interactions supports these conclusions. We discuss parallels between the evolution of insect sociality and other major transitions that provide scaffolds for learning innovations. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Tamar Keasar
- Biology and Environment, University of Haifa, Oranim, Tivon 36006, Israel
| | | | - Eric Wajnberg
- INRIA, Projet Hephaistos, 06902 Sophia Antipolis, France,Inrae, 400 Route des Chappes, BP 167 06903 Sophia Antipolis Cedex, France
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37
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Prentiss AM, Laue C, Gjesfjeld E, Walsh MJ, Denis M, Foor TA. Evolution of the Okvik/Old Bering Sea culture of the Bering Strait as a major transition. Philos Trans R Soc Lond B Biol Sci 2023; 378:20210415. [PMID: 36688384 PMCID: PMC9869439 DOI: 10.1098/rstb.2021.0415] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Great transitions are thought to embody major shifts in locus of selection, labour diversification and communication systems. Such expectations are relevant for biological and cultural systems as decades of research has demonstrated similar dynamics within the evolution of culture. The evolution of the Neo-Inuit cultural tradition in the Bering Strait provides an ideal context for examination of cultural transitions. The Okvik/Old Bering Sea (Okvik/OBS) culture of Bering Strait is the first representative of the Neo-Inuit tradition. Archaeological evidence drawn for settlement and subsistence data, technological traditions and mortuary contexts suggests that Okvik/OBS fits the definition of a major transition given change in the nature of group membership (from families to political groups with social ranking), task organization (emergent labour specialization) and communication (advent of complex art forms conveying social and ideological information). This permits us to develop a number of implications about the evolutionary process recognizing that transitions may occur on three scales: (1) ephemeral variants, as for example, simple technological entities; (2) integrated systems, spanning modular technology to socio-economic strategies; and (3) simultaneous change across all scales with emergent properties. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
| | - Cheyenne Laue
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
| | - Erik Gjesfjeld
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, England
| | - Matthew J. Walsh
- Modern History and World Cultures Section, The National Museum of Denmark, Ny Vestergade 10 Prinsens Palæ 1471, Copenhagen, Denmark
| | - Megan Denis
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
| | - Thomas A. Foor
- Department of Anthropology, University of Montana, Missoula, MT 59812, USA
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38
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Carmel Y. Human societal development: is it an evolutionary transition in individuality? Philos Trans R Soc Lond B Biol Sci 2023; 378:20210409. [PMID: 36688399 PMCID: PMC9869447 DOI: 10.1098/rstb.2021.0409] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
An evolutionary transition in individuality (ETI) occurs when a previously independent organism becomes a lower level unit within a higher hierarchical level (for example, cells in an organism, ants in a colony). Using archaeological and historical accounts from the last 12 000 years, I empirically examine the proposition that human society increasingly functions as a higher hierarchical level within which individuals integrate as lower level units. I evaluate human societal development with respect to three criteria that together indicate complexity in biological systems and serve as an operationalization scheme for ETIs: size, inseparability and specialization. The size of the largest polity has increased seven orders of magnitude, from hundreds to billions. Inseparability became nearly complete since Mesopotamian city-states, following the first appearance of intricate specialization (division of labour). Connectivity within a polity has increased rapidly during the last few centuries, and particularly within the last few decades. In view of these results, I formulate the following hypothesis: human society is undergoing an evolutionary transition in individuality, driven by socio-cultural-technological processes. This proposition requires a detailed theoretical basis and further empirical testing. I propose four predictions derived from the hypothesis that may be used to test it. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Yohay Carmel
- Faculty of Civil and Environmental Engineering, The Technion, Haifa 32000, Israel
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Shavit A, Sharon G. Can models of evolutionary transition clarify the debates over the Neolithic Revolution? Philos Trans R Soc Lond B Biol Sci 2023; 378:20210413. [PMID: 36688395 PMCID: PMC9869441 DOI: 10.1098/rstb.2021.0413] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The 'Neolithic Revolution,' sometimes referred to as the emergence of agriculture at its earliest in the southern Levant, is the most significant shift in human history, shaping the world we live in today. Yet, after 100 years of study, its major cause, tempo (gradual or revolutionary), and impact of human intentionality remain disputed. Here, we examine the research potential of an evolutionary transition in individuality (ETI) to clarify this dramatic shift. Applying an ETI research perspective reveals how different causes and conditions lead to the same result, enabling a holistic view rather than a reduction of 'Neolithic' to 'agriculture,' or to one major climatic condition, inheritance system or standard evolutionary model, thus allowing us to clarify and bypass some of these heated, unresolved disputes. Additionally, unlike current archaeological emphasis on 'where,' 'when,' 'why' and 'how' questions, the ETI perspective offers a productive path for resolving a fundamental preliminary anomaly: why and how could the Neolithic lifeway evolve at all, given the selfish interest of individuals in a hunter-gatherer group? We do not intend to solve the shift to Neolithic lifeways, only to offer a fresh lens for examining it, emphasizing the relevance of tracking within and between group differences. This article is part of the theme issue 'Human socio-cultural evolution in light of evolutionary transitions'.
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Affiliation(s)
- Ayelet Shavit
- Department of Interdisciplinary Studies, Tel Hai College, 1220800, Israel,Department of Humanities and Arts, Technion, 3200003 Israel
| | - Gonen Sharon
- Department of Humanities and Arts, Technion, 3200003 Israel
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Tang S, Pichugin Y, Hammerschmidt K. An environmentally induced multicellular life cycle of a unicellular cyanobacterium. Curr Biol 2023; 33:764-769.e5. [PMID: 36854263 DOI: 10.1016/j.cub.2023.01.069] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/19/2022] [Accepted: 01/04/2023] [Indexed: 03/02/2023]
Abstract
Understanding the evolutionary transition to multicellularity is a key problem in biology.1,2,3,4 Nevertheless, the ecological conditions driving such transitions are not well understood. The first known transition to multicellularity occurred 2.5 billion years ago in cyanobacteria,5,6,7 and today's cyanobacteria are characterized by enormous morphological diversity. They range from unicellular species; unicellular cyanobacteria with packet-like phenotypes, e.g., tetrads; and simple filamentous species to highly differentiated filamentous species.8,9,10 The cyanobacterium Cyanothece sp. ATCC 51142, an isolate from the intertidal zone of the U.S. Gulf Coast,11 was classified as a unicellular species.12 We report a facultative life cycle of Cyanothece sp. in which multicellular filaments alternate with unicellular stages. In a series of experiments, we identified salinity and population density as environmental factors triggering the phenotypic switch between the two morphologies. Then, we used numerical models to test hypotheses regarding the nature of the environmental cues and the mechanisms underlying filament dissolution. While the results predict that the observed response is likely caused by an excreted compound in the medium, we cannot fully exclude changes in nutrient availability (as in Tuomi et al.13 and Matz and Jürgens14). The best-fit modeling results show a nonlinear effect of the compound, which is characteristic of density-dependent sensing systems.15,16 Furthermore, filament fragmentation is predicted to occur by connection cleavage rather than cell death of each alternating cell, which is supported by fluorescent and scanning electron microscopy results. The switch between unicellular and multicellular morphology constitutes an environmentally dependent life cycle that is likely an important step en route to permanent multicellularity.
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Affiliation(s)
- Si Tang
- Institute of General Microbiology, Kiel University, Kiel, Germany
| | - Yuriy Pichugin
- Department of Evolutionary Theory, Max Planck Institute for Evolutionary Biology, Plön, Germany.
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41
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Goldman AD. How did life become cellular? Proc Biol Sci 2023; 290:20222327. [PMID: 36750189 PMCID: PMC9904939 DOI: 10.1098/rspb.2022.2327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023] Open
Affiliation(s)
- Aaron D. Goldman
- Department of Biology, Oberlin College, Oberlin, OH, USA,Blue Marble Space Institute of Science, Seattle, WA, USA
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Pineau RM, Demory D, Libby E, Lac DT, Day TC, Bravo P, Yunker PJ, Weitz JS, Bozdag GO, Ratcliff WC. Emergence and maintenance of stable coexistence during a long-term multicellular evolution experiment. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.19.524803. [PMID: 36711513 PMCID: PMC9882323 DOI: 10.1101/2023.01.19.524803] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The evolution of multicellular life spurred evolutionary radiations, fundamentally changing many of Earth’s ecosystems. Yet little is known about how early steps in the evolution of multicellularity transform eco-evolutionary dynamics, e.g., via niche expansion processes that may facilitate coexistence. Using long-term experimental evolution in the snowflake yeast model system, we show that the evolution of multicellularity drove niche partitioning and the adaptive divergence of two distinct, specialized lineages from a single multicellular ancestor. Over 715 daily transfers, snowflake yeast were subject to selection for rapid growth in rich media, followed by selection favoring larger group size. Both small and large cluster-forming lineages evolved from a monomorphic ancestor, coexisting for over ~4,300 generations. These small and large sized snowflake yeast lineages specialized on divergent aspects of a trade-off between growth rate and survival, mirroring predictions from ecological theory. Through modeling and experimentation, we demonstrate that coexistence is maintained by a trade-off between organismal size and competitiveness for dissolved oxygen. Taken together, this work shows how the evolution of a new level of biological individuality can rapidly drive adaptive diversification and the expansion of a nascent multicellular niche, one of the most historically-impactful emergent properties of this evolutionary transition.
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Xue ZP, Chindelevitch L, Guichard F. Supply-driven evolution: Mutation bias and trait-fitness distributions can drive macro-evolutionary dynamics. Front Ecol Evol 2023. [DOI: 10.3389/fevo.2022.1048752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
Many well-documented macro-evolutionary phenomena still challenge current evolutionary theory. Examples include long-term evolutionary trends, major transitions in evolution, conservation of certain biological features such as hox genes, and the episodic creation of new taxa. Here, we present a framework that may explain these phenomena. We do so by introducing a probabilistic relationship between trait value and reproductive fitness. This integration allows mutation bias to become a robust driver of long-term evolutionary trends against environmental bias, in a way that is consistent with all current evolutionary theories. In cases where mutation bias is strong, such as when detrimental mutations are more common than beneficial mutations, a regime called “supply-driven” evolution can arise. This regime can explain the irreversible persistence of higher structural hierarchies, which happens in the major transitions in evolution. We further generalize this result in the long-term dynamics of phenotype spaces. We show how mutations that open new phenotype spaces can become frozen in time. At the same time, new possibilities may be observed as a burst in the creation of new taxa.
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Nonacs P, Denton KK, Robin AN, Helanterä H, Kapheim KM. Editorial: Social evolution and the what, when, why and how of the major evolutionary transitions in the history of life. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.1109484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Hakala SM, Fujioka H, Gapp K, De Gasperin O, Genzoni E, Kilner RM, Koene JM, König B, Linksvayer TA, Meurville MP, Negroni MA, Palejowski H, Wigby S, LeBoeuf AC. Socially transferred materials: why and how to study them. Trends Ecol Evol 2022; 38:446-458. [PMID: 36543692 DOI: 10.1016/j.tree.2022.11.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Revised: 11/21/2022] [Accepted: 11/25/2022] [Indexed: 12/23/2022]
Abstract
When biological material is transferred from one individual's body to another, as in ejaculate, eggs, and milk, secondary donor-produced molecules are often transferred along with the main cargo, and influence the physiology and fitness of the receiver. Both social and solitary animals exhibit such social transfers at certain life stages. The secondary, bioactive, and transfer-supporting components in socially transferred materials have evolved convergently to the point where they are used in applications across taxa and type of transfer. The composition of these materials is typically highly dynamic and context dependent, and their components drive the physiological and behavioral evolution of many taxa. Our establishment of the concept of socially transferred materials unifies this multidisciplinary topic and will benefit both theory and applications.
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Tóth A, Székvölgyi L, Vellai T. The genome loading model for the origin and maintenance of sex in eukaryotes. Biol Futur 2022; 73:345-357. [PMID: 36534301 DOI: 10.1007/s42977-022-00148-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 12/08/2022] [Indexed: 12/23/2022]
Abstract
Understanding why sexual reproduction-which involves syngamy (union of gametes) and meiosis-emerged and how it has subsisted for millions of years remains a fundamental problem in biology. Considered as the essence of sex, meiotic recombination is initiated by a DNA double-strand break (DSB) that forms on one of the pairing homologous chromosomes. This DNA lesion is subsequently repaired by gene conversion, the non-reciprocal transfer of genetic information from the intact homolog. A major issue is which of the pairing homologs undergoes DSB formation. Accumulating evidence shows that chromosomal sites where the pairing homologs locally differ in size, i.e., are heterozygous for an insertion or deletion, often display disparity in gene conversion. Biased conversion tends to duplicate insertions and lose deletions. This suggests that DSB is preferentially formed on the "shorter" homologous region, which thereby acts as the recipient for DNA transfer. Thus, sex primarily functions as a genome (re)loading mechanism. It ensures the restoration of formerly lost DNA sequences (deletions) and allows the efficient copying and, mainly in eukaryotes, subsequent spreading of newly emerged sequences (insertions) arising initially in an individual genome, even if they confer no advantage to the host. In this way, sex simultaneously repairs deletions and increases genetic variability underlying adaptation. The model explains a remarkable increase in DNA content during the evolution of eukaryotic genomes.
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Affiliation(s)
- András Tóth
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary
| | - Lóránt Székvölgyi
- MTA-DE Momentum Genome Architecture and Recombination Research Group, Department of Biochemistry and Molecular Biology, Faculty of Medicine, University of Debrecen, Debrecen, 4032, Hungary
| | - Tibor Vellai
- Department of Genetics, Eötvös Loránd University, Pázmány Péter Stny. 1/C, Budapest, 1117, Hungary.
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Scott AD, King DM, Ordway SW, Bahar S. Phase transitions in evolutionary dynamics. CHAOS (WOODBURY, N.Y.) 2022; 32:122101. [PMID: 36587338 DOI: 10.1063/5.0124274] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2022] [Accepted: 12/05/2022] [Indexed: 06/17/2023]
Abstract
Sharp changes in state, such as transitions from survival to extinction, are hallmarks of evolutionary dynamics in biological systems. These transitions can be explored using the techniques of statistical physics and the physics of nonlinear and complex systems. For example, a survival-to-extinction transition can be characterized as a non-equilibrium phase transition to an absorbing state. Here, we review the literature on phase transitions in evolutionary dynamics. We discuss directed percolation transitions in cellular automata and evolutionary models, and models that diverge from the directed percolation universality class. We explore in detail an example of an absorbing phase transition in an agent-based model of evolutionary dynamics, including previously unpublished data demonstrating similarity to, but also divergence from, directed percolation, as well as evidence for phase transition behavior at multiple levels of the model system's evolutionary structure. We discuss phase transition models of the error catastrophe in RNA virus dynamics and phase transition models for transition from chemistry to biochemistry, i.e., the origin of life. We conclude with a review of phase transition dynamics in models of natural selection, discuss the possible role of phase transitions in unraveling fundamental unresolved questions regarding multilevel selection and the major evolutionary transitions, and assess the future outlook for phase transitions in the investigation of evolutionary dynamics.
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Affiliation(s)
- Adam D Scott
- Department of Physics and Astronomy and Center for Neurodynamics, University of Missouri at St. Louis, One University Blvd., St. Louis, Missouri 63121, USA
| | - Dawn M King
- Department of Physics and Astronomy and Center for Neurodynamics, University of Missouri at St. Louis, One University Blvd., St. Louis, Missouri 63121, USA
| | - Stephen W Ordway
- Department of Physics and Astronomy and Center for Neurodynamics, University of Missouri at St. Louis, One University Blvd., St. Louis, Missouri 63121, USA
| | - Sonya Bahar
- Department of Physics and Astronomy and Center for Neurodynamics, University of Missouri at St. Louis, One University Blvd., St. Louis, Missouri 63121, USA
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Abstract
Viruses are the most abundant biological entities on Earth, and yet, they have not received enough consideration in astrobiology. Viruses are also extraordinarily diverse, which is evident in the types of relationships they establish with their host, their strategies to store and replicate their genetic information and the enormous diversity of genes they contain. A viral population, especially if it corresponds to a virus with an RNA genome, can contain an array of sequence variants that greatly exceeds what is present in most cell populations. The fact that viruses always need cellular resources to multiply means that they establish very close interactions with cells. Although in the short term these relationships may appear to be negative for life, it is evident that they can be beneficial in the long term. Viruses are one of the most powerful selective pressures that exist, accelerating the evolution of defense mechanisms in the cellular world. They can also exchange genetic material with the host during the infection process, providing organisms with capacities that favor the colonization of new ecological niches or confer an advantage over competitors, just to cite a few examples. In addition, viruses have a relevant participation in the biogeochemical cycles of our planet, contributing to the recycling of the matter necessary for the maintenance of life. Therefore, although viruses have traditionally been excluded from the tree of life, the structure of this tree is largely the result of the interactions that have been established throughout the intertwined history of the cellular and the viral worlds. We do not know how other possible biospheres outside our planet could be, but it is clear that viruses play an essential role in the terrestrial one. Therefore, they must be taken into account both to improve our understanding of life that we know, and to understand other possible lives that might exist in the cosmos.
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Affiliation(s)
- Ignacio de la Higuera
- Department of Biology, Center for Life in Extreme Environments, Portland State University, Portland, OR, United States
| | - Ester Lázaro
- Centro de Astrobiología (CAB), CSIC-INTA, Torrejón de Ardoz, Spain
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Ishida T. Emergence Simulation of Biological Cell-like Shapes Satisfying the Conditions of Life Using a Lattice-Type Multiset Chemical Model. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101580. [PMID: 36295015 PMCID: PMC9605168 DOI: 10.3390/life12101580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 10/04/2022] [Accepted: 10/08/2022] [Indexed: 11/06/2022]
Abstract
Simple Summary One of the great challenges in science is determining when, where, why, and how life first arose as well as the form taken by this life. In the present study, life was assumed to be (1) bounded, (2) replicating, (3) able to inherit information, and (4) able to metabolize energy. The various existing hypotheses provide little explanation of how these four conditions for life were established. Indeed, “how” a chemical process that simultaneously satisfies all four conditions emerged after the materials for life were in place is not always clear. In this study, a multiset chemical lattice model, which allows for virtual molecules of multiple types to be placed in each cell on a two-dimensional space, was considered. Using only the processes of molecular diffusion, reaction, and polymerization and modeling the chemical reactions of 15 types of molecules and 2 types of polymerized molecules, as well as using the morphogenesis rule of the Turing model, the process of emergence of a cell-like form with all three conditions except evolution ability was modeled and demonstrated. Abstract Although numerous reports using methods such as molecular dynamics, cellular automata, and artificial chemistry have clarified the process connecting non-life and life on protocell simulations, none of the models could simultaneously explain the emergence of cell shape, continuous self-replication, and replication control solely from molecular reactions and diffusion. Herein, we developed a model to generate all three conditions, except evolution ability, from hypothetical chains of chemical and molecular polymerization reactions. The present model considers a 2D lattice cell space, where virtual molecules are placed in each cell, and molecular reactions in each cell are based on a multiset rewriting rule, indicating stochastic transition of molecular species. The reaction paths of virtual molecules were implemented by replacing the rules of cellular automata that generate Turing patterns with molecular reactions. The emergence of a cell-like form with all three conditions except evolution ability was modeled and demonstrated using only molecular diffusion, reaction, and polymerization for modeling the chemical reactions of 15 types of molecules and 2 types of polymerized molecules. Furthermore, controlling self-replication is possible by changing the initial arrangement of a specific molecule. In summary, the present model is capable of investigating and refining existing hypotheses on the emergence of life.
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Affiliation(s)
- Takeshi Ishida
- Department of Ocean Mechanical Engineering, National Fisheries University, Shimonoseki 759-6595, Japan
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50
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Belpaire TER, Pešek J, Lories B, Verstrepen KJ, Steenackers HP, Ramon H, Smeets B. Permissive aggregative group formation favors coexistence between cooperators and defectors in yeast. THE ISME JOURNAL 2022; 16:2305-2312. [PMID: 35778439 PMCID: PMC9477849 DOI: 10.1038/s41396-022-01275-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 06/08/2022] [Accepted: 06/16/2022] [Indexed: 06/01/2023]
Abstract
In Saccharomyces cerevisiae, the FLO1 gene encodes flocculins that lead to formation of multicellular flocs, that offer protection to the constituent cells. Flo1p was found to preferentially bind to fellow cooperators compared to defectors lacking FLO1 expression, enriching cooperators within the flocs. Given this dual function in cooperation and kin recognition, FLO1 has been termed a "green beard gene". Because of the heterophilic nature of the Flo1p bond however, we hypothesize that kin recognition is permissive and depends on the relative stability of the FLO1+/flo1- versus FLO1+/FLO1+ detachment force F. We combine single-cell measurements of adhesion, individual cell-based simulations of cluster formation, and in vitro flocculation to study the impact of relative bond stability on the evolutionary stability of cooperation. We identify a trade-off between both aspects of the green beard mechanism, with reduced relative bond stability leading to increased kin recognition at the expense of cooperative benefits. We show that the fitness of FLO1 cooperators decreases as their frequency in the population increases, arising from the observed permissive character (F+- = 0.5 F++) of the Flo1p bond. Considering the costs associated with FLO1 expression, this asymmetric selection often results in a stable coexistence between cooperators and defectors.
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Affiliation(s)
- Tom E R Belpaire
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001, Leuven, Belgium.
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium.
| | - Jiří Pešek
- Team SIMBIOTX, Inria Saclay, 91120, Palaiseau, France
| | - Bram Lories
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
| | - Kevin J Verstrepen
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
- Laboratory of Systems Biology, VIB-KU Leuven Center for Microbiology, 3001, Leuven, Belgium
| | - Hans P Steenackers
- Centre for Microbial and Plant Genetics, KU Leuven, 3001, Leuven, Belgium
| | - Herman Ramon
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001, Leuven, Belgium
| | - Bart Smeets
- Division of Mechatronics, Biostatistics, and Sensors, KU Leuven, 3001, Leuven, Belgium
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