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Landa CR, Ariza-Mateos A, Briones C, Perales C, Wagner A, Domingo E, Gómez J. Adapting the rhizome concept to an extended definition of viral quasispecies and the implications for molecular evolution. Sci Rep 2024; 14:17914. [PMID: 39095425 PMCID: PMC11297277 DOI: 10.1038/s41598-024-68760-6] [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: 02/18/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
The rhizome concept proposed by Gilles Deleuze and Félix Guattari offers a novel perspective on the organization and interdependence of complex constellations of heterogeneous entities, their mapping and their ruptures. The emphasis of the present study is placed on the dynamics of contacts and communication among such entities that arise from experimentation, without any favored hierarchy or origin. When applied to biological evolution, the rhizome concept integrates all types of heterogeneity resulting from "symbiotic" relationships among living beings (or their genomic material), horizontal genetic transfer, recombination and mutation, and breaks away from the approach that gives rise to the phylogenetic tree of life. It has already been applied to describe the dynamics and evolution of RNA viruses. Thus, here we introduce a novel framework for the interpretation the viral quasispecies concept, which explains the evolution of RNA virus populations as the result of dynamic interconnections and multifaceted interdependence between highly heterogeneous viral sequences and its inherently heterogeneous host cells. The rhizome network perspective underlines even further the medical implications of the broad mutant spectra of viruses that are in constant flow, given the multiple pathways they have available for fitness loss and gain.
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Affiliation(s)
- Carlos Raico Landa
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Avd. Conocimiento 17, 18016, Armilla, Granada, Spain
| | - Ascensión Ariza-Mateos
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Avd. Conocimiento 17, 18016, Armilla, Granada, Spain
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Carlos Briones
- Department of Molecular Evolution, Centro de Astrobiología (CSIC-INTA), Madrid, Spain
| | - Celia Perales
- Centro Nacional de Biotecnología (CNB-CSIC), Campus de Cantoblanco, Madrid, Spain
- Department of Clinical Microbiology, IIS-Fundación Jiménez Díaz, UAM, Madrid, Spain
| | | | - Esteban Domingo
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Campus de Cantoblanco, Madrid, Spain
| | - Jordi Gómez
- Laboratory of RNA Archaeology, Instituto de Parasitología y Biomedicina "López-Neyra" (CSIC), Avd. Conocimiento 17, 18016, Armilla, Granada, Spain.
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González-Pech RA, Li VY, Garcia V, Boville E, Mammone M, Kitano H, Ritchie KB, Medina M. The Evolution, Assembly, and Dynamics of Marine Holobionts. ANNUAL REVIEW OF MARINE SCIENCE 2024; 16:443-466. [PMID: 37552896 DOI: 10.1146/annurev-marine-022123-104345] [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: 08/10/2023]
Abstract
The holobiont concept (i.e., multiple living beings in close symbiosis with one another and functioning as a unit) is revolutionizing our understanding of biology, especially in marine systems. The earliest marine holobiont was likely a syntrophic partnership of at least two prokaryotic members. Since then, symbiosis has enabled marine organisms to conquer all ocean habitats through the formation of holobionts with a wide spectrum of complexities. However, most scientific inquiries have focused on isolated organisms and their adaptations to specific environments. In this review, we attempt to illustrate why a holobiont perspective-specifically, the study of how numerous organisms form a discrete ecological unit through symbiosis-will be a more impactful strategy to advance our understanding of the ecology and evolution of marine life. We argue that this approach is instrumental in addressing the threats to marine biodiversity posed by the current global environmental crisis.
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Affiliation(s)
- Raúl A González-Pech
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vivian Y Li
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Vanessa Garcia
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Elizabeth Boville
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | - Marta Mammone
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
| | | | - Kim B Ritchie
- Department of Natural Sciences, University of South Carolina, Beaufort, South Carolina, USA;
| | - Mónica Medina
- Department of Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; , , , , ,
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3
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Rosenberg E. Rapid acquisition of microorganisms and microbial genes can help explain punctuated evolution. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.957708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The punctuated mode of evolution posits that evolution occurs in rare bursts of rapid evolutionary change followed by long periods of genetic stability (stasis). The accepted cause for the rapid changes in punctuated evolution is special ecological circumstances – selection forces brought about by changes in the environment. This article presents a complementary explanation for punctuated evolution by the rapid formation of genetic variants in animals and plants by the acquisition of microorganisms from the environment into microbiomes and microbial genes into host genomes by horizontal gene transfer. Several examples of major evolutionary events driven by microorganisms are discussed, including the formation of the first eukaryotic cell, the ability of some animals to digest cellulose and other plant cell-wall complex polysaccharides, dynamics of root system architecture, and the formation of placental mammals. These changes by cooperation were quantum leaps in the evolutionary development of complex bilolgical systems and can contribute to an understanding of the mechanisms underlying punctuated evolution.
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Vidal B, Gulez B, Cao WX, Leyva-Diaz E, Reilly MB, Tekieli T, Hobert O. The enteric nervous system of the C. elegans pharynx is specified by the Sine oculis-like homeobox gene ceh-34. eLife 2022; 11:76003. [PMID: 35324425 PMCID: PMC8989417 DOI: 10.7554/elife.76003] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 03/23/2022] [Indexed: 11/29/2022] Open
Abstract
Overarching themes in the terminal differentiation of the enteric nervous system, an autonomously acting unit of animal nervous systems, have so far eluded discovery. We describe here the overall regulatory logic of enteric nervous system differentiation of the nematode Caenorhabditis elegans that resides within the foregut (pharynx) of the worm. A C. elegans homolog of the Drosophila Sine oculis homeobox gene, ceh-34, is expressed in all 14 classes of interconnected pharyngeal neurons from their birth throughout their life time, but in no other neuron type of the entire animal. Constitutive and temporally controlled ceh-34 removal shows that ceh-34 is required to initiate and maintain the neuron type-specific terminal differentiation program of all pharyngeal neuron classes, including their circuit assembly. Through additional genetic loss of function analysis, we show that within each pharyngeal neuron class, ceh-34 cooperates with different homeodomain transcription factors to individuate distinct pharyngeal neuron classes. Our analysis underscores the critical role of homeobox genes in neuronal identity specification and links them to the control of neuronal circuit assembly of the enteric nervous system. Together with the pharyngeal nervous system simplicity as well as its specification by a Sine oculis homolog, our findings invite speculations about the early evolution of nervous systems.
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Affiliation(s)
- Berta Vidal
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Burcu Gulez
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Wen Xi Cao
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Eduardo Leyva-Diaz
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Molly B Reilly
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Tessa Tekieli
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
| | - Oliver Hobert
- Department of Biological Sciences, Columbia University, Howard Hughes Medical Institute, New York, United States
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Formosinho J, Bencard A, Whiteley L. Environmentality in biomedicine: microbiome research and the perspectival body. STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE 2022; 91:148-158. [PMID: 34922182 DOI: 10.1016/j.shpsa.2021.11.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 10/18/2021] [Accepted: 11/07/2021] [Indexed: 06/14/2023]
Abstract
Microbiome research shows that human health is foundationally intertwined with the ecology of microbial communities living on and in our bodies. This challenges the categorical separation of organisms from environments that has been central to biomedicine, and questions the boundaries between them. Biomedicine is left with an empirical problem: how to understand causal pathways between host health, microbiota and environment? We propose a conceptual tool - environmentality - to think through this problem. Environmentality is the state or quality of being an environment for something else in a particular context: a fully perspectival proposition. Its power lies partly in what Isabelle Stengers has called the efficacy of the word itself, contrasting the dominant sense of the word environment as something both external and fixed. Through three case studies, we argue that environmentality can help think about the causality of microbiota vis-a-vis host health in a processual, relational and situated manner, across scales and temporalities. We situate this intervention within historical trajectories of thought in biomedicine, focusing on the challenge microbiome research poses to an aperspectival body. We argue that addressing entanglements between microbial and human lives requires that the environment is brought into the clinic, thus shortening the conceptual gap between medicine and public health.
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Affiliation(s)
- Joana Formosinho
- Medical Museion, Department of Public Health and Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), University of Copenhagen, Denmark.
| | - Adam Bencard
- Medical Museion, Department of Public Health and Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), University of Copenhagen, Denmark
| | - Louise Whiteley
- Medical Museion, Department of Public Health and Novo Nordisk Foundation Center for Basic Metabolic Research (CBMR), University of Copenhagen, Denmark
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Boesmans W, Nash A, Tasnády KR, Yang W, Stamp LA, Hao MM. Development, Diversity, and Neurogenic Capacity of Enteric Glia. Front Cell Dev Biol 2022; 9:775102. [PMID: 35111752 PMCID: PMC8801887 DOI: 10.3389/fcell.2021.775102] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 12/09/2021] [Indexed: 12/15/2022] Open
Abstract
Enteric glia are a fascinating population of cells. Initially identified in the gut wall as the "support" cells of the enteric nervous system, studies over the past 20 years have unveiled a vast array of functions carried out by enteric glia. They mediate enteric nervous system signalling and play a vital role in the local regulation of gut functions. Enteric glial cells interact with other gastrointestinal cell types such as those of the epithelium and immune system to preserve homeostasis, and are perceptive to luminal content. Their functional versatility and phenotypic heterogeneity are mirrored by an extensive level of plasticity, illustrated by their reactivity in conditions associated with enteric nervous system dysfunction and disease. As one of the hallmarks of their plasticity and extending their operative relationship with enteric neurons, enteric glia also display neurogenic potential. In this review, we focus on the development of enteric glial cells, and the mechanisms behind their heterogeneity in the adult gut. In addition, we discuss what is currently known about the role of enteric glia as neural precursors in the enteric nervous system.
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Affiliation(s)
- Werend Boesmans
- Biomedical Research Institute (BIOMED), Hasselt University, Hasselt, Belgium
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Amelia Nash
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Kinga R. Tasnády
- Biomedical Research Institute (BIOMED), Hasselt University, Hasselt, Belgium
- Department of Pathology, GROW-School for Oncology and Developmental Biology, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Wendy Yang
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
- Graduate Institute of Clinical Medicine, College of Medicine, National Taiwan University, Taiwan, Taiwan
| | - Lincon A. Stamp
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
| | - Marlene M. Hao
- Department of Anatomy and Physiology, The University of Melbourne, Melbourne, VIC, Australia
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Sharifi R, Ryu C. Social networking in crop plants: Wired and wireless cross-plant communications. PLANT, CELL & ENVIRONMENT 2021; 44:1095-1110. [PMID: 33274469 PMCID: PMC8049059 DOI: 10.1111/pce.13966] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Revised: 11/18/2020] [Accepted: 11/22/2020] [Indexed: 05/03/2023]
Abstract
The plant-associated microbial community (microbiome) has an important role in plant-plant communications. Plants decipher their complex habitat situations by sensing the environmental stimuli and molecular patterns and associated with microbes, herbivores and dangers. Perception of these cues generates inter/intracellular signals that induce modifications of plant metabolism and physiology. Signals can also be transferred between plants via different mechanisms, which we classify as wired- and wireless communications. Wired communications involve direct signal transfers between plants mediated by mycorrhizal hyphae and parasitic plant stems. Wireless communications involve plant volatile emissions and root exudates elicited by microbes/insects, which enable inter-plant signalling without physical contact. These producer-plant signals induce microbiome adaptation in receiver plants via facilitative or competitive mechanisms. Receiver plants eavesdrop to anticipate responses to improve fitness against stresses. An emerging body of information in plant-plant communication can be leveraged to improve integrated crop management under field conditions.
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Affiliation(s)
- Rouhallah Sharifi
- Department of Plant ProtectionCollege of Agriculture and Natural Resources, Razi UniversityKermanshahIran
| | - Choong‐Min Ryu
- Molecular Phytobacteriology LaboratoryInfectious Disease Research Center, KRIBBDaejeonSouth Korea
- Biosystem and Bioengineering ProgramUniversity of Science and Technology (UST)DaejeonSouth Korea
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9
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Bosch TCG, McFall-Ngai M. Animal development in the microbial world: Re-thinking the conceptual framework. Curr Top Dev Biol 2021; 141:399-427. [PMID: 33602495 PMCID: PMC8214508 DOI: 10.1016/bs.ctdb.2020.11.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Animals have evolved within the framework of the microbes and are constantly exposed to diverse microbiota. This dominance of the microbial world is forcing all fields of biology to question some of their most basic premises, with developmental biology being no exception. While animals under laboratory conditions can develop and live without microbes, they are far from normal, and would not survive under natural conditions, where their fitness would be strongly compromised. Since much of the undescribed biodiversity on Earth is microbial, any consideration of animal development in the absence of the recognition of microbes will be incomplete. Here, we show that animal development may never have been autonomous, rather it requires transient or persistent interactions with the microbial world. We propose that to formulate a comprehensive understanding of embryogenesis and post-embryonic development, we must recognize that symbiotic microbes provide important developmental signals and contribute in significant ways to phenotype production. This offers limitless opportunities for the field of developmental biology to expand.
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Affiliation(s)
- Thomas C G Bosch
- Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany.
| | - Margaret McFall-Ngai
- Pacific Biosciences Research Center, Kewalo Marine Laboratory, University of Hawai'i at Mānoa, Honolulu, HI, United States
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10
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Hadfield MG. Developmental Symbiosis: A Sponge Larva Needs Symbiotic Bacteria to Succeed on the Benthos. Curr Biol 2021; 31:R88-R90. [PMID: 33497640 DOI: 10.1016/j.cub.2020.11.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Settlement and metamorphosis of marine invertebrate larvae are processes of profound developmental, morphological, physiological and ecological change. That these processes in larvae of a marine sponge critically rely on products supplied by endosymbiotic bacteria signals the importance of developmental symbiosis among the most basal metazoans.
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Affiliation(s)
- Michael G Hadfield
- Kewalo Marine Laboratory, University of Hawai'i at Mānoa, 41 Ahui Street, Honolulu, HI 96813, USA.
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11
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Farias AP, Camargo RDS, Andrade Sousa KK, Caldato N, Forti LC. Nest Architecture and Colony Growth of Atta bisphaerica Grass-Cutting Ants. INSECTS 2020; 11:E741. [PMID: 33137875 PMCID: PMC7693648 DOI: 10.3390/insects11110741] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 10/23/2020] [Accepted: 10/26/2020] [Indexed: 06/11/2023]
Abstract
Atta grass-cutting ants (Formicidae: Myrmicinae: Attini) are found in the Cerrado biome and build giant nests with hundreds or thousands of large chambers. We assessed for Atta bisphaerica grass-cutting ants whether the total volume of fungus chambers and other nest parameters grow at close or similar proportions to worker numbers in the colony. Data on fungus garden biomass, population, external area, number of entrance holes, number of fungus chambers, total fungus chambers volume, and nest depth were obtained during colony growth/nest development. Our results reveal that the fungus garden biomass, external area, and total fungus chamber volume increased at rates similar to the increase in the number of workers. The total volume of chambers, and external area increased at a similar proportion to the increase in number of workers, probably due to the fungus garden allocation needs of the colony. The number of fungus chambers, number of entrance holes, and nest depth increased less than 4-fold for every 10-fold increase in the worker number. In addition, the height of the fungus chambers increased as the width increased, a pattern not observed for tunnel height and length, and the chamber volume increased according to worker number. Thus, this study demonstrates for A. bisphaerica that nest development in terms of chamber volume is similar to the increase in number of colony workers, and this contributes to a better understanding of Atta nest architecture.
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Affiliation(s)
- Adriano Pimentel Farias
- Department of Vegetal Protection, School of Agronomical Sciences, São Paulo State University, Botucatu, SP CEP 18603-970, Brazil; (R.d.S.C.); (K.K.A.S.); (N.C.); (L.C.F.)
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12
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Ronai I, Greslehner GP, Boem F, Carlisle J, Stencel A, Suárez J, Bayir S, Bretting W, Formosinho J, Guerrero AC, Morgan WH, Prigot-Maurice C, Rodeck S, Vasse M, Wallis JM, Zacks O. "Microbiota, symbiosis and individuality summer school" meeting report. MICROBIOME 2020; 8:117. [PMID: 32795355 PMCID: PMC7427737 DOI: 10.1186/s40168-020-00898-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/24/2020] [Indexed: 05/13/2023]
Abstract
How does microbiota research impact our understanding of biological individuality? We summarize the interdisciplinary summer school on "Microbiota, symbiosis and individuality: conceptual and philosophical issues" (July 2019), which was supported by a European Research Council starting grant project "Immunity, DEvelopment, and the Microbiota" (IDEM). The summer school centered around interdisciplinary group work on four facets of microbiota research: holobionts, individuality, causation, and human health. The conceptual discussion of cutting-edge empirical research provided new insights into microbiota and highlights the value of incorporating into meetings experts from other disciplines, such as philosophy and history of science. Video Abstract.
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Affiliation(s)
- Isobel Ronai
- Columbia University, 1200 Amsterdam Ave, New York, 10027 NY USA
| | - Gregor P. Greslehner
- ImmunoConcept, UMR5164, CNRS & University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076 France
| | - Federico Boem
- Dipartimento di Filosofia e Scienze dell’Educazione, Università degli Studi di Torino, Palazzo Nuovo, Via Sant’Ottavio, 20, Torino, 10124 Italy
| | - Judith Carlisle
- Washington University in St. Louis, Department of Philosophy, One Brookings Drive, St. Louis, 63130-4899 MO USA
| | - Adrian Stencel
- Institute of Philosophy, Jagiellonian University, Grodzka 52, Kraków, 33-332 Poland
| | - Javier Suárez
- Abteilung Philosophie, Universität Bielefeld, Universitätsstraße 25, Bielefeld, 33615 Germany
| | - Saliha Bayir
- Institut für Philosophie,Universität Kassel, Henschelstr. 2, Kassel, 34127 Germany
| | - Wiebke Bretting
- ImmunoConcept, UMR5164, CNRS & University of Bordeaux, 146 Rue Léo Saignat, Bordeaux, 33076 France
| | - Joana Formosinho
- Medical Museion, Department of Public Health, University of Copenhagen, Fredericiagade 18, Copenhagen, 1310 Denmark
| | - Anna C. Guerrero
- Arizona State University, Center for Biology and Society, 427 E Tyler Mall, Tempe, 85281 AZ USA
| | - William H. Morgan
- The University of Sheffield, Department of Philosophy, 45 Victoria Street, Sheffield, S3 7QB UK
| | - Cybèle Prigot-Maurice
- Université de Poitiers, Laboratoire Écologie et Biologie des Interactions, UMR CNRS 7267, Bâtiment B35, 5 rue Albert Turpain, TSA 51106, Poitiers Cedex 9, 86073 France
| | - Salome Rodeck
- Leibniz Center for Literary and Cultural Research, Schützenstr. 18, Berlin, 10117 Germany
| | - Marie Vasse
- Institute for Integrative Biology, ETH Zürich, Universitätstrasse 16, Zürich, 8092 Switzerland
| | - Jacqueline M. Wallis
- University of Bristol, Department of Philosophy, Cotham House, Bristol, BS6 6JL UK
| | - Oryan Zacks
- Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, 6997801 Israel
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Baedke J, Fábregas‐Tejeda A, Nieves Delgado A. The holobiont concept before Margulis. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2020; 334:149-155. [DOI: 10.1002/jez.b.22931] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Revised: 01/22/2020] [Accepted: 01/24/2020] [Indexed: 12/13/2022]
Affiliation(s)
- Jan Baedke
- Department of Philosophy IRuhr University BochumBochum Germany
- Institute of Zoology and Evolutionary ResearchFriedrich‐Schiller‐UniversityJena Germany
| | - Alejandro Fábregas‐Tejeda
- Department of Philosophy IRuhr University BochumBochum Germany
- Institute of BiologyNational Autonomous University of Mexico (UNAM) Circuito Exterior Ciudad Universitaria S/N Mexico City Mexico
| | - Abigail Nieves Delgado
- Department of Philosophy IRuhr University BochumBochum Germany
- Centre for Anthropological Knowledge in Scientific and Technological Cultures (CAST)Ruhr University BochumBochum Germany
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Collens A, Kelley E, Katz LA. The concept of the hologenome, an epigenetic phenomenon, challenges aspects of the modern evolutionary synthesis. JOURNAL OF EXPERIMENTAL ZOOLOGY. PART B, MOLECULAR AND DEVELOPMENTAL EVOLUTION 2019; 332:349-355. [PMID: 31709760 PMCID: PMC6904923 DOI: 10.1002/jez.b.22915] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2019] [Revised: 09/22/2019] [Accepted: 10/02/2019] [Indexed: 12/12/2022]
Abstract
John Tyler Bonner's call to re-evaluate evolutionary theory in light of major transitions in life on Earth (e.g., from the first origins of microbial life to the evolution of sex, and the origins of multicellularity) resonate with recent discoveries on epigenetics and the concept of the hologenome. Current studies of genome evolution often mistakenly focus only on the inheritance of DNA between parent and offspring. These are in line with the widely accepted Neo-Darwinian framework that pairs Mendelian genetics with an emphasis on natural selection as explanations for the evolution of biodiversity on Earth. Increasing evidence for widespread symbioses complicates this narrative, as is seen in Scott Gilbert's discussion of the concept of the holobiont in this series: Organisms across the tree of life coexist with substantial influence on one another through endosymbiosis, symbioses, and host-associated microbiomes. The holobiont theory, coupled with observations from molecular studies, also requires us to understand genomes in a new way-by considering the interactions underlain by the genome of a host plus its associated microbes, a conglomerate entity referred to as the hologenome. We argue that the complex patterns of inheritance of these genomes coupled with the influence of symbionts on host gene expression make the concept of the hologenome an epigenetic phenomenon. We further argue that the aspects of the hologenome challenge of the modern evolutionary synthesis, which requires updating to remain consistent with Darwin's intent of providing natural laws that underlie the evolution of life on Earth.
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Affiliation(s)
- Adena Collens
- Department of Biological Sciences, Smith College, Northampton MA, 01063 USA
| | - Emma Kelley
- Department of Biological Sciences, Smith College, Northampton MA, 01063 USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith College, Northampton MA, 01063 USA
- Program in Organismic and Evolutionary Biology, University of Massachusetts, Amherst MA, 01003
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