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Zimm R, Berio F, Debiais-Thibaud M, Goudemand N. A shark-inspired general model of tooth morphogenesis unveils developmental asymmetries in phenotype transitions. Proc Natl Acad Sci U S A 2023; 120:e2216959120. [PMID: 37027430 PMCID: PMC10104537 DOI: 10.1073/pnas.2216959120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 02/07/2023] [Indexed: 04/08/2023] Open
Abstract
Developmental complexity stemming from the dynamic interplay between genetic and biomechanic factors canalizes the ways genotypes and phenotypes can change in evolution. As a paradigmatic system, we explore how changes in developmental factors generate typical tooth shape transitions. Since tooth development has mainly been researched in mammals, we contribute to a more general understanding by studying the development of tooth diversity in sharks. To this end, we build a general, but realistic, mathematical model of odontogenesis. We show that it reproduces key shark-specific features of tooth development as well as real tooth shape variation in small-spotted catsharks Scyliorhinus canicula. We validate our model by comparison with experiments in vivo. Strikingly, we observe that developmental transitions between tooth shapes tend to be highly degenerate, even for complex phenotypes. We also discover that the sets of developmental parameters involved in tooth shape transitions tend to depend asymmetrically on the direction of that transition. Together, our findings provide a valuable base for furthering our understanding of how developmental changes can lead to both adaptive phenotypic change and trait convergence in complex, phenotypically highly diverse, structures.
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Affiliation(s)
- Roland Zimm
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Lyon Cedex07 69364, France
| | - Fidji Berio
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Lyon Cedex07 69364, France
- Institut des Sciences de l’Evolution de Montpellier, University of Montpellier, CNRS, Institut de la Recherche pour le Développement, Montpellier34095, France
| | - Mélanie Debiais-Thibaud
- Institut des Sciences de l’Evolution de Montpellier, University of Montpellier, CNRS, Institut de la Recherche pour le Développement, Montpellier34095, France
| | - Nicolas Goudemand
- Institut de Génomique Fonctionnelle de Lyon, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5242, Lyon Cedex07 69364, France
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Essay the (unusual) heuristic value of Hox gene clusters; a matter of time? Dev Biol 2022; 484:75-87. [PMID: 35182536 DOI: 10.1016/j.ydbio.2022.02.007] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 02/11/2022] [Accepted: 02/14/2022] [Indexed: 12/22/2022]
Abstract
Ever since their first report in 1984, Antennapedia-type homeobox (Hox) genes have been involved in such a series of interesting observations, in particular due to their conserved clustered organization between vertebrates and arthropods, that one may legitimately wonder about the origin of this heuristic value. In this essay, I first consider different examples where Hox gene clusters have been instrumental in providing conceptual advances, taken from various fields of research and mostly involving vertebrate embryos. These examples touch upon our understanding of genomic evolution, the revisiting of 19th century views on the relationships between development and evolution and the building of a new framework to understand long-range and pleiotropic gene regulation during development. I then discuss whether the high value of the Hox gene family, when considered as an epistemic object, is related to its clustered structure (and the absence thereof in some animal species) and, if so, what is it in such particular genetic oddities that made them so generous in providing the scientific community with interesting information.
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Abstract
Twenty-five years ago, Lewis Wolpert, the eminent developmental biologist, asked the question, "Do We Understand Development?" He concluded that such rapid progress had been made in the preceding two decades that "It is not unreasonable to think that enough will eventually be known to program a computer and simulate some aspects of development." This prediction has been fulfilled, at least partially, with data-driven simulations of several different developmental processes being developed in the intervening years. Nevertheless, the question remains of whether we "understand" development and if simulations are sufficient to provide an explanation of development. While in silico replications and models are undoubtedly an important tool in the investigation and dissection of developmental processes, which complement traditional experimental methods, these need to be supplemented by theory that identifies principles and provides coherent explanations. Here, I use the example of pattern formation in the vertebrate neural tube to illustrate this idea.
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The emerging structure of the Extended Evolutionary Synthesis: where does Evo-Devo fit in? Theory Biosci 2018; 137:169-184. [PMID: 30132255 DOI: 10.1007/s12064-018-0269-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/26/2018] [Indexed: 12/23/2022]
Abstract
The Extended Evolutionary Synthesis (EES) debate is gaining ground in contemporary evolutionary biology. In parallel, a number of philosophical standpoints have emerged in an attempt to clarify what exactly is represented by the EES. For Massimo Pigliucci, we are in the wake of the newest instantiation of a persisting Kuhnian paradigm; in contrast, Telmo Pievani has contended that the transition to an EES could be best represented as a progressive reformation of a prior Lakatosian scientific research program, with the extension of its Neo-Darwinian core and the addition of a brand-new protective belt of assumptions and auxiliary hypotheses. Here, we argue that those philosophical vantage points are not the only ways to interpret what current proposals to 'extend' the Modern Synthesis-derived 'standard evolutionary theory' (SET) entail in terms of theoretical change in evolutionary biology. We specifically propose the image of the emergent EES as a vast network of models and interweaved representations that, instantiated in diverse practices, are connected and related in multiple ways. Under that assumption, the EES could be articulated around a paraconsistent network of evolutionary theories (including some elements of the SET), as well as models, practices and representation systems of contemporary evolutionary biology, with edges and nodes that change their position and centrality as a consequence of the co-construction and stabilization of facts and historical discussions revolving around the epistemic goals of this area of the life sciences. We then critically examine the purported structure of the EES-published by Laland and collaborators in 2015-in light of our own network-based proposal. Finally, we consider which epistemic units of Evo-Devo are present or still missing from the EES, in preparation for further analyses of the topic of explanatory integration in this conceptual framework.
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Tschopp P, Tabin CJ. Deep homology in the age of next-generation sequencing. Philos Trans R Soc Lond B Biol Sci 2017; 372:20150475. [PMID: 27994118 PMCID: PMC5182409 DOI: 10.1098/rstb.2015.0475] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2016] [Indexed: 12/14/2022] Open
Abstract
The principle of homology is central to conceptualizing the comparative aspects of morphological evolution. The distinctions between homologous or non-homologous structures have become blurred, however, as modern evolutionary developmental biology (evo-devo) has shown that novel features often result from modification of pre-existing developmental modules, rather than arising completely de novo. With this realization in mind, the term 'deep homology' was coined, in recognition of the remarkably conserved gene expression during the development of certain animal structures that would not be considered homologous by previous strict definitions. At its core, it can help to formulate an understanding of deeper layers of ontogenetic conservation for anatomical features that lack any clear phylogenetic continuity. Here, we review deep homology and related concepts in the context of a gene expression-based homology discussion. We then focus on how these conceptual frameworks have profited from the recent rise of high-throughput next-generation sequencing. These techniques have greatly expanded the range of organisms amenable to such studies. Moreover, they helped to elevate the traditional gene-by-gene comparison to a transcriptome-wide level. We will end with an outlook on the next challenges in the field and how technological advances might provide exciting new strategies to tackle these questions.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Patrick Tschopp
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Clifford J Tabin
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
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Erlich A, Moulton DE, Goriely A, Chirat R. Morphomechanics and Developmental Constraints in the Evolution of Ammonites Shell Form. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2016; 326:437-450. [DOI: 10.1002/jez.b.22716] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 10/12/2016] [Accepted: 10/20/2016] [Indexed: 01/02/2023]
Affiliation(s)
| | | | - Alain Goriely
- Mathematical Institute; University of Oxford; Oxford UK
| | - Regis Chirat
- Université Lyon 1; ENS de Lyon, CNRS, UMR 5276 LGL-TPE Villeurbanne Cedex France
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Signor SA, Arbeitman MN, Nuzhdin SV. Gene networks and developmental context: the importance of understanding complex gene expression patterns in evolution. Evol Dev 2016; 18:201-9. [PMID: 27161950 DOI: 10.1111/ede.12187] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Animal development is the product of distinct components and interactions-genes, regulatory networks, and cells-and it exhibits emergent properties that cannot be inferred from the components in isolation. Often the focus is on the genotype-to-phenotype map, overlooking the process of development that turns one into the other. We propose a move toward micro-evolutionary analysis of development, incorporating new tools that enable cell type resolution and single-cell microscopy. Using the sex determination pathway in Drosophila to illustrate potential avenues of research, we highlight some of the questions that these emerging technologies can address. For example, they provide an unprecedented opportunity to study heterogeneity within cell populations, and the potential to add the dimension of time to gene regulatory network analysis. Challenges still remain in developing methods to analyze this data and to increase the throughput. However this line of research has the potential to bridge the gaps between previously more disparate fields, such as population genetics and development, opening up new avenues of research.
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Affiliation(s)
- Sarah A Signor
- Program in Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Michelle N Arbeitman
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, FL 32306, USA
| | - Sergey V Nuzhdin
- Program in Molecular and Computation Biology, Dornsife College of Letters, Arts, and Sciences, University of Southern California, Los Angeles, CA 90089, USA.,Applied Mathematics, Saint Petersburg State Polytechnical University, St. Petersburg, Russia
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Crombach A, Wotton KR, Jiménez-Guri E, Jaeger J. Gap Gene Regulatory Dynamics Evolve along a Genotype Network. Mol Biol Evol 2016; 33:1293-307. [PMID: 26796549 PMCID: PMC4839219 DOI: 10.1093/molbev/msw013] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Developmental gene networks implement the dynamic regulatory mechanisms that pattern and shape the organism. Over evolutionary time, the wiring of these networks changes, yet the patterning outcome is often preserved, a phenomenon known as “system drift.” System drift is illustrated by the gap gene network—involved in segmental patterning—in dipteran insects. In the classic model organism Drosophila melanogaster and the nonmodel scuttle fly Megaselia abdita, early activation and placement of gap gene expression domains show significant quantitative differences, yet the final patterning output of the system is essentially identical in both species. In this detailed modeling analysis of system drift, we use gene circuits which are fit to quantitative gap gene expression data in M. abdita and compare them with an equivalent set of models from D. melanogaster. The results of this comparative analysis show precisely how compensatory regulatory mechanisms achieve equivalent final patterns in both species. We discuss the larger implications of the work in terms of “genotype networks” and the ways in which the structure of regulatory networks can influence patterns of evolutionary change (evolvability).
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Affiliation(s)
- Anton Crombach
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Karl R Wotton
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Eva Jiménez-Guri
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Johannes Jaeger
- EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain Universitat Pompeu Fabra (UPF), Barcelona, Spain
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O’Malley MA, Soyer OS, Siegal ML. A Philosophical Perspective on Evolutionary Systems Biology. BIOLOGICAL THEORY 2015; 10:6-17. [PMID: 26085823 PMCID: PMC4465572 DOI: 10.1007/s13752-015-0202-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Evolutionary systems biology (ESB) is an emerging hybrid approach that integrates methods, models, and data from evolutionary and systems biology. Drawing on themes that arose at a cross-disciplinary meeting on ESB in 2013, we discuss in detail some of the explanatory friction that arises in the interaction between evolutionary and systems biology. These tensions appear because of different modeling approaches, diverse explanatory aims and strategies, and divergent views about the scope of the evolutionary synthesis. We locate these discussions in the context of long-running philosophical deliberations on explanation, modeling, and theoretical synthesis. We show how many of the issues central to ESB's progress can be understood as general philosophical problems. The benefits of addressing these philosophical issues feed back into philosophy too, because ESB provides excellent examples of scientific practice for the development of philosophy of science and philosophy of biology.
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Affiliation(s)
| | - Orkun S. Soyer
- School of Life Sciences, University of Warwick, Coventry, UK
| | - Mark L. Siegal
- Department of Biology, Center for Genomics and Systems, Biology, New York University, New York, NY, USA
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