1
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Griffing AH, Gamble T, Cohn MJ, Sanger TJ. Convergent developmental patterns underlie the repeated evolution of adhesive toe pads among lizards. Biol J Linn Soc Lond 2022; 135:518-532. [PMID: 35185322 PMCID: PMC8842688 DOI: 10.1093/biolinnean/blab164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 11/24/2021] [Accepted: 11/25/2021] [Indexed: 01/07/2023]
Abstract
How developmental modifications produce key innovations, which subsequently allow for rapid diversification of a clade into new adaptive zones, has received much attention. However, few studies have used a robust comparative framework to investigate the influence of evolutionary and developmental constraints on the origin of key innovations, such as the adhesive toe pad of lizards. Adhesive toe pads evolved independently at least 16 times in lizards, allowing us to examine whether the patterns observed are general evolutionary phenomena or unique, lineage-specific events. We performed a high-resolution comparison of plantar scale development in 14 lizard species in Anolis and geckos, encompassing five independent origins of toe pads (one in Anolis, four in geckos). Despite substantial evolutionary divergence between Anolis and geckos, we find that these clades have undergone similar developmental modifications to generate their adhesive toe pads. Relative to the ancestral plantar scale development, in which scale ridges form synchronously along the digit, both padded geckos and Anolis exhibit scansor formation in a distal-to-proximal direction. Both clades have undergone developmental repatterning and, following their origin, modifications in toe pad morphology occurred through relatively minor developmental modifications, suggesting that developmental constraints governed the diversification of the adhesive toe pad in lizards.
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Affiliation(s)
- Aaron H Griffing
- Department of Biological Sciences, Marquette University, PO Box 1881, Milwaukee, WI 53201, USA,Corresponding author. E-mail:
| | - Tony Gamble
- Department of Biological Sciences, Marquette University, PO Box 1881, Milwaukee, WI 53201, USA,Milwaukee Public Museum, 800 W. Wells St., Milwaukee, WI 53233, USA,Bell Museum of Natural History, University of Minnesota, 2088 Larpenteur Ave. W., St. Paul, MN 55113, USA
| | - Martin J Cohn
- Department of Molecular Genetics and Microbiology, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Thomas J Sanger
- Department of Molecular Genetics and Microbiology, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA,Department of Biology, Loyola University Chicago, 1032 W. Sheridan Rd, Chicago, IL 60660, USA
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2
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Andrade MP, Santos D, Bueno GM, Santos CMD. What if… Sponges Originated 890 Million Years Ago? On the Emergence of Some Precursors of Animal Sentience. Evol Biol 2021. [DOI: 10.1007/s11692-021-09551-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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3
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Konagurthu AS, Subramanian R, Allison L, Abramson D, Stuckey PJ, Garcia de la Banda M, Lesk AM. Universal Architectural Concepts Underlying Protein Folding Patterns. Front Mol Biosci 2021; 7:612920. [PMID: 33996891 PMCID: PMC8120156 DOI: 10.3389/fmolb.2020.612920] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Accepted: 12/16/2020] [Indexed: 11/17/2022] Open
Abstract
What is the architectural “basis set” of the observed universe of protein structures? Using information-theoretic inference, we answer this question with a dictionary of 1,493 substructures—called concepts—typically at a subdomain level, based on an unbiased subset of known protein structures. Each concept represents a topologically conserved assembly of helices and strands that make contact. Any protein structure can be dissected into instances of concepts from this dictionary. We dissected the Protein Data Bank and completely inventoried all the concept instances. This yields many insights, including correlations between concepts and catalytic activities or binding sites, useful for rational drug design; local amino-acid sequence–structure correlations, useful for ab initio structure prediction methods; and information supporting the recognition and exploration of evolutionary relationships, useful for structural studies. An interactive site, Proçodic, at http://lcb.infotech.monash.edu.au/prosodic (click), provides access to and navigation of the entire dictionary of concepts and their usages, and all associated information. This report is part of a continuing programme with the goal of elucidating fundamental principles of protein architecture, in the spirit of the work of Cyrus Chothia.
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Affiliation(s)
- Arun S Konagurthu
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Ramanan Subramanian
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Lloyd Allison
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - David Abramson
- Research Computing Center, University of Queensland, Brisbane, QLD, Australia
| | - Peter J Stuckey
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia.,School of Computing and Information Systems, University of Melbourne, Melbourne, VIC, Australia
| | - Maria Garcia de la Banda
- Department of Data Science and Artificial Intelligence, Faculty of Information Technology, Monash University, Clayton, VIC, Australia
| | - Arthur M Lesk
- Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, PA, United States.,MRC Laboratory of Molecular Biology, Cambridge, United Kingdom
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4
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Uesaka M, Kuratani S, Irie N. The developmental hourglass model and recapitulation: An attempt to integrate the two models. JOURNAL OF EXPERIMENTAL ZOOLOGY PART B-MOLECULAR AND DEVELOPMENTAL EVOLUTION 2021; 338:76-86. [PMID: 33503326 PMCID: PMC9292893 DOI: 10.1002/jez.b.23027] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 01/03/2021] [Accepted: 01/04/2021] [Indexed: 12/18/2022]
Abstract
Recapitulation is a hypothetical concept that assumes embryogenesis of an animal parallels its own phylogenetic history, sequentially developing from more ancestral features to more derived ones. This concept predicts that the earliest developmental stage of various animals should represent the most evolutionarily conserved patterns. Recent transcriptome‐based studies, on the other hand, have reported that mid‐embryonic, organogenetic periods show the highest level of conservation (the developmental hourglass model). This, however, does not rule out the possibility that recapitulation would still be detected after the mid‐embryonic period. In accordance with this, recapitulation‐like morphological features are enriched in late developmental stages. Moreover, our recent chromatin accessibility‐based study provided molecular evidence for recapitulation in the mid‐to‐late embryogenesis of vertebrates, as newly evolved gene regulatory elements tended to be activated at late embryonic stages. In this review, we revisit the recapitulation hypothesis, together with recent molecular‐based studies that support the developmental hourglass model. We contend that the recapitulation hypothesis does not entirely contradict the developmental hourglass model and that these two may even coexist in later embryonic stages of vertebrates. Finally, we review possible mechanisms underlying the recapitulation pattern of chromatin accessibility together with the hourglass‐like evolutionary conservation in vertebrate embryogenesis. Recapitulation pattern has been reported for chromatin accessibility during the mid‐to‐late embryogenesis. The observed recapitulation pattern and the developmental hourglass model may coexist. The possible evolutionary mechanisms underlying tendencies of embryonic evolution were discussed.
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Affiliation(s)
- Masahiro Uesaka
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
| | - Shigeru Kuratani
- Laboratory for Evolutionary Morphology, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan.,Laboratory for Evolutionary Morphology, RIKEN Cluster for Pioneering Research, Kobe, Japan
| | - Naoki Irie
- Department of Biological Sciences, The University of Tokyo, Tokyo, Japan.,Universal Biology Institute, The University of Tokyo, Tokyo, Japan
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5
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On the specificity of gene regulatory networks: How does network co-option affect subsequent evolution? Curr Top Dev Biol 2020; 139:375-405. [PMID: 32450967 DOI: 10.1016/bs.ctdb.2020.03.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The process of multicellular organismal development hinges upon the specificity of developmental programs: for different parts of the organism to form unique features, processes must exist to specify each part. This specificity is thought to be hardwired into gene regulatory networks, which activate cohorts of genes in particular tissues at particular times during development. However, the evolution of gene regulatory networks sometimes occurs by mechanisms that sacrifice specificity. One such mechanism is network co-option, in which existing gene networks are redeployed in new developmental contexts. While network co-option may offer an efficient mechanism for generating novel phenotypes, losses of tissue specificity at redeployed network genes could restrict the ability of the affected traits to evolve independently. At present, there has not been a detailed discussion regarding how tissue specificity of network genes might be altered due to gene network co-option at its initiation, as well as how trait independence can be retained or restored after network co-option. A lack of clarity about network co-option makes it more difficult to speculate on the long-term evolutionary implications of this mechanism. In this review, we will discuss the possible initial outcomes of network co-option, outline the mechanisms by which networks may retain or subsequently regain specificity after network co-option, and comment on some of the possible evolutionary consequences of network co-option. We place special emphasis on the need to consider selectively-neutral outcomes of network co-option to improve our understanding of the role of this mechanism in trait evolution.
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6
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Eiden LE, Gundlach AL, Grinevich V, Lee MR, Mecawi AS, Chen D, Buijs RM, Hernandez VS, Fajardo-Dolci G, Zhang L. Regulatory peptides and systems biology: A new era of translational and reverse-translational neuroendocrinology. J Neuroendocrinol 2020; 32:e12844. [PMID: 32307768 DOI: 10.1111/jne.12844] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 03/11/2020] [Indexed: 12/15/2022]
Abstract
Recently, there has been a resurgence in regulatory peptide science as a result of three converging trends. The first is the increasing population of the drug pipeline with peptide-based therapeutics, mainly in, but not restricted to, incretin-like molecules for treatment of metabolic disorders such as diabetes. The second is the development of genetic and optogenetic tools enabling new insights into how peptides actually function within brain and peripheral circuits to accomplish homeostatic and allostatic regulation. The third is the explosion in defined structures of the G-protein coupled receptors to which most regulatory peptides bind and exert their actions. These trends have closely wedded basic systems biology to drug discovery and development, creating a "two-way street" on which translational advances travel from basic research to the clinic, and, equally importantly, "reverse-translational" information is gathered, about the molecular, cellular and circuit-level mechanisms of action of regulatory peptides, comprising information required for the fine-tuning of drug development through testing in animal models. This review focuses on a small group of 'influential' peptides, including oxytocin, vasopressin, pituitary adenylate cyclase-activating polypeptide, ghrelin, relaxin-3 and glucagon-like peptide-1, and how basic discoveries and their application to therapeutics have intertwined over the past decade.
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Affiliation(s)
- Lee E Eiden
- Section on Molecular Neuroscience, National Institute of Mental Heath-Intramural Research Program, NIH, Bethesda, MD, USA
| | - Andrew L Gundlach
- The Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, VIC, Australia
| | - Valery Grinevich
- Department of Neuropeptide Research in Psychiatry, Central Institute of Mental Health, University Heidelberg, Mannheim, Germany
| | - Mary R Lee
- Section on Clinical Psychoneuroendocrinology and Neuropsychopharmacology, NIAAA and NIDA, NIH, Bethesda, MD, USA
| | - André S Mecawi
- Laboratory of Neuroendocrinology, Department of Biophysics, Escola Paulista de Medicina, Universidade Federal de São Paulo, São Paulo, Brazil
| | - Duan Chen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Ruud M Buijs
- Department of Cell Biology and Physiology, Institute for Biomedical Research, Universidad Nacional Autonoma de Mexico, Mexico City, Mexico
| | - Vito S Hernandez
- Department of Physiology, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Germán Fajardo-Dolci
- School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
| | - Limei Zhang
- Department of Physiology, School of Medicine, National Autonomous University of Mexico, Mexico City, Mexico
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7
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The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries. Trends Microbiol 2020; 28:372-386. [DOI: 10.1016/j.tim.2020.01.005] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2019] [Revised: 11/21/2019] [Accepted: 01/16/2020] [Indexed: 02/07/2023]
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8
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Lord E, Pathmanathan JS, Corel E, Makarenkov V, Lopez P, Bouchard F, Bhattacharya D, Antoine PO, Le Guyader H, Lapointe FJ, Bapteste E. Introducing Trait Networks to Elucidate the Fluidity of Organismal Evolution Using Palaeontological Data. Genome Biol Evol 2019; 11:2653-2665. [PMID: 31504500 PMCID: PMC6761957 DOI: 10.1093/gbe/evz182] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2019] [Indexed: 11/25/2022] Open
Abstract
Explaining the evolution of animals requires ecological, developmental, paleontological, and phylogenetic considerations because organismal traits are affected by complex evolutionary processes. Modeling a plurality of processes, operating at distinct time-scales on potentially interdependent traits, can benefit from approaches that are complementary treatments to phylogenetics. Here, we developed an inclusive network approach, implemented in the command line software ComponentGrapher, and analyzed trait co-occurrence of rhinocerotoid mammals. We identified stable, unstable, and pivotal traits, as well as traits contributing to complexes, that may follow to a common developmental regulation, that point to an early implementation of the postcranial Bauplan among rhinocerotoids. Strikingly, most identified traits are highly dissociable, used repeatedly in distinct combinations and in different taxa, which usually do not form clades. Therefore, the genes encoding these traits are likely recruited into novel gene regulation networks during the course of evolution. Our evo-systemic framework, generalizable to other evolved organizations, supports a pluralistic modeling of organismal evolution, including trees and networks.
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Affiliation(s)
- Etienne Lord
- Département d'informatique, Université du Québec à Montréal, Montréal, Québec, Canada
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
| | - Jananan S Pathmanathan
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eduardo Corel
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Vladimir Makarenkov
- Département d'informatique, Université du Québec à Montréal, Montréal, Québec, Canada
| | - Philippe Lopez
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Frédéric Bouchard
- Département de Philosophie, Université de Montreal, Montréal, Quebec, Canada
| | | | - Pierre-Olivier Antoine
- Institut des Sciences de l'Evolution, cc64, Université de Montpellier, CNRS, Université des Antilles, IRD, EPHE, Montpellier, France
| | - Hervé Le Guyader
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - François-Joseph Lapointe
- Département de sciences biologiques, Université de Montréal, Montréal, Québec, Canada
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
| | - Eric Bapteste
- Institut de Systématique, Evolution, Biodiversité (ISYEB), Sorbonne Université, CNRS, Museum National d'Histoire Naturelle, EPHE, Université des Antilles, Paris, France
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9
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Hoke KL, Adkins-Regan E, Bass AH, McCune AR, Wolfner MF. Co-opting evo-devo concepts for new insights into mechanisms of behavioural diversity. ACTA ACUST UNITED AC 2019; 222:222/8/jeb190058. [PMID: 30988051 DOI: 10.1242/jeb.190058] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We propose that insights from the field of evolutionary developmental biology (or 'evo-devo') provide a framework for an integrated understanding of the origins of behavioural diversity and its underlying mechanisms. Towards that goal, in this Commentary, we frame key questions in behavioural evolution in terms of molecular, cellular and network-level properties with a focus on the nervous system. In this way, we highlight how mechanistic properties central to evo-devo analyses - such as weak linkage, versatility, exploratory mechanisms, criticality, degeneracy, redundancy and modularity - affect neural circuit function and hence the range of behavioural variation that can be filtered by selection. We outline why comparative studies of molecular and neural systems throughout ontogeny will provide novel insights into diversity in neural circuits and behaviour.
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Affiliation(s)
- Kim L Hoke
- Department of Biology, Colorado State University, Fort Collins, CO 80523, USA
| | - Elizabeth Adkins-Regan
- Department of Psychology, Cornell University, Ithaca, NY 14853, USA.,Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Andrew H Bass
- Department of Neurobiology and Behavior, Cornell University, Ithaca, NY 14853, USA
| | - Amy R McCune
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca, NY 14853, USA
| | - Mariana F Wolfner
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
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10
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Salvador-Martínez I, Coronado-Zamora M, Castellano D, Barbadilla A, Salazar-Ciudad I. Mapping Selection within Drosophila melanogaster Embryo's Anatomy. Mol Biol Evol 2019; 35:66-79. [PMID: 29040697 DOI: 10.1093/molbev/msx266] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
We present a survey of selection across Drosophila melanogaster embryonic anatomy. Our approach integrates genomic variation, spatial gene expression patterns, and development with the aim of mapping adaptation over the entire embryo's anatomy. Our adaptation map is based on analyzing spatial gene expression information for 5,969 genes (from text-based annotations of in situ hybridization data directly from the BDGP database, Tomancak et al. 2007) and the polymorphism and divergence in these genes (from the project DGRP, Mackay et al. 2012).The proportion of nonsynonymous substitutions that are adaptive, neutral, or slightly deleterious are estimated for the set of genes expressed in each embryonic anatomical structure using the distribution of fitness effects-alpha method (Eyre-Walker and Keightley 2009). This method is a robust derivative of the McDonald and Kreitman test (McDonald and Kreitman 1991). We also explore whether different anatomical structures differ in the phylogenetic age, codon usage, or expression bias of the genes they express and whether genes expressed in many anatomical structures show more adaptive substitutions than other genes.We found that: 1) most of the digestive system and ectoderm-derived structures are under selective constraint, 2) the germ line and some specific mesoderm-derived structures show high rates of adaptive substitution, and 3) the genes that are expressed in a small number of anatomical structures show higher expression bias, lower phylogenetic ages, and less constraint.
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Affiliation(s)
- Irepan Salvador-Martínez
- Evo-devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland
| | - Marta Coronado-Zamora
- Departament de Genètica i de Microbiologia, Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - David Castellano
- Bioinformatics Research Centre, Aarhus University, Aarhus, Denmark
| | - Antonio Barbadilla
- Departament de Genètica i de Microbiologia, Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
| | - Isaac Salazar-Ciudad
- Evo-devo Helsinki Community, Centre of Excellence in Experimental and Computational Developmental Biology, Institute of Biotechnology, University of Helsinki, Helsinki, Finland.,Departament de Genètica i de Microbiologia, Genomics, Bioinformatics and Evolution, Departament de Genètica i Microbiologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Spain
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11
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Moreno-Villena JJ, Dunning LT, Osborne CP, Christin PA. Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis. Mol Biol Evol 2019; 35:94-106. [PMID: 29040657 PMCID: PMC5850498 DOI: 10.1093/molbev/msx269] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Novel adaptations are generally assembled by co-opting pre-existing genetic components, but the factors dictating the suitability of genes for new functions remain poorly known. In this work, we used comparative transcriptomics to determine the attributes that increased the likelihood of some genes being co-opted for C4 photosynthesis, a convergent complex trait that boosts productivity in tropical conditions. We show that independent lineages of grasses repeatedly co-opted the gene lineages that were the most highly expressed in non-C4 ancestors to produce their C4 pathway. Although ancestral abundance in leaves explains which genes were used for the emergence of a C4 pathway, the tissue specificity has surprisingly no effect. Our results suggest that levels of key genes were elevated during the early diversification of grasses and subsequently repeatedly used to trigger a weak C4 cycle via relatively few mutations. The abundance of C4-suitable transcripts therefore facilitated physiological innovation, but the transition to a strong C4 pathway still involved consequent changes in expression levels, leaf specificity, and coding sequences. The direction and amount of changes required for the strong C4 pathway depended on the identity of the genes co-opted, so that ancestral gene expression both facilitates adaptive transitions and constrains subsequent evolutionary trajectories.
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Affiliation(s)
| | - Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Colin P Osborne
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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12
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Abstract
The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology.
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Affiliation(s)
- Eric Bapteste
- Sorbonne Universités, UPMC Université Paris 06, Institut de Biologie Paris-Seine (IBPS), F-75005 Paris, France
- CNRS, UMR7138, Institut de Biologie Paris-Seine, F-75005 Paris, France
| | - Philippe Huneman
- Institut d’Histoire et de Philosophie des Sciences et des Techniques (CNRS / Paris I Sorbonne), F-75006 Paris, France
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13
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Moreno-Villena JJ, Dunning LT, Osborne CP, Christin PA. Highly Expressed Genes Are Preferentially Co-Opted for C4 Photosynthesis. Mol Biol Evol 2018. [PMID: 29040657 DOI: 10.1093/molbev/msx269/4457558] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Novel adaptations are generally assembled by co-opting pre-existing genetic components, but the factors dictating the suitability of genes for new functions remain poorly known. In this work, we used comparative transcriptomics to determine the attributes that increased the likelihood of some genes being co-opted for C4 photosynthesis, a convergent complex trait that boosts productivity in tropical conditions. We show that independent lineages of grasses repeatedly co-opted the gene lineages that were the most highly expressed in non-C4 ancestors to produce their C4 pathway. Although ancestral abundance in leaves explains which genes were used for the emergence of a C4 pathway, the tissue specificity has surprisingly no effect. Our results suggest that levels of key genes were elevated during the early diversification of grasses and subsequently repeatedly used to trigger a weak C4 cycle via relatively few mutations. The abundance of C4-suitable transcripts therefore facilitated physiological innovation, but the transition to a strong C4 pathway still involved consequent changes in expression levels, leaf specificity, and coding sequences. The direction and amount of changes required for the strong C4 pathway depended on the identity of the genes co-opted, so that ancestral gene expression both facilitates adaptive transitions and constrains subsequent evolutionary trajectories.
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Affiliation(s)
| | - Luke T Dunning
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
| | - Colin P Osborne
- Animal and Plant Sciences, University of Sheffield, Sheffield, United Kingdom
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14
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Constrained vertebrate evolution by pleiotropic genes. Nat Ecol Evol 2017; 1:1722-1730. [PMID: 28963548 DOI: 10.1038/s41559-017-0318-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 08/16/2017] [Indexed: 02/06/2023]
Abstract
Despite morphological diversification of chordates over 550 million years of evolution, their shared basic anatomical pattern (or 'bodyplan') remains conserved by unknown mechanisms. The developmental hourglass model attributes this to phylum-wide conserved, constrained organogenesis stages that pattern the bodyplan (the phylotype hypothesis); however, there has been no quantitative testing of this idea with a phylum-wide comparison of species. Here, based on data from early-to-late embryonic transcriptomes collected from eight chordates, we suggest that the phylotype hypothesis would be better applied to vertebrates than chordates. Furthermore, we found that vertebrates' conserved mid-embryonic developmental programmes are intensively recruited to other developmental processes, and the degree of the recruitment positively correlates with their evolutionary conservation and essentiality for normal development. Thus, we propose that the intensively recruited genetic system during vertebrates' organogenesis period imposed constraints on its diversification through pleiotropic constraints, which ultimately led to the common anatomical pattern observed in vertebrates.
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15
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Franchini A, Ottaviani E. Thymus: Conservation in evolution. Gen Comp Endocrinol 2017; 246:46-50. [PMID: 28322763 DOI: 10.1016/j.ygcen.2017.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 03/16/2017] [Accepted: 03/16/2017] [Indexed: 11/17/2022]
Abstract
From an evolutionary point of view, the thymus is a new organ observed for the first time in fish concomitantly with the appearance of adaptive clonotypical immunity. Hormone and neuropeptide expression was demonstrated in different species suggesting a conserved role of these molecules. An integrated evolution of immune and neuroendocrine responses appears to have been realized by means of the re-use of ancestral material, such as neuroendocrine cells and mediators, to create a thymic microenvironment for the maturation and differentiation of T cells.
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Affiliation(s)
- Antonella Franchini
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy
| | - Enzo Ottaviani
- Department of Life Sciences, University of Modena and Reggio Emilia, Modena, Italy.
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16
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Control of Hoxd gene transcription in the mammary bud by hijacking a preexisting regulatory landscape. Proc Natl Acad Sci U S A 2016; 113:E7720-E7729. [PMID: 27856734 DOI: 10.1073/pnas.1617141113] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Vertebrate Hox genes encode transcription factors operating during the development of multiple organs and structures. However, the evolutionary mechanism underlying this remarkable pleiotropy remains to be fully understood. Here, we show that Hoxd8 and Hoxd9, two genes of the HoxD complex, are transcribed during mammary bud (MB) development. However, unlike in other developmental contexts, their coexpression does not rely on the same regulatory mechanism. Hoxd8 is regulated by the combined activity of closely located sequences and the most distant telomeric gene desert. On the other hand, Hoxd9 is controlled by an enhancer-rich region that is also located within the telomeric gene desert but has no impact on Hoxd8 transcription, thus constituting an exception to the global regulatory logic systematically observed at this locus. The latter DNA region is also involved in Hoxd gene regulation in other contexts and strongly interacts with Hoxd9 in all tissues analyzed thus far, indicating that its regulatory activity was already operational before the appearance of mammary glands. Within this DNA region and neighboring a strong limb enhancer, we identified a short sequence conserved in therian mammals and capable of enhancer activity in the MBs. We propose that Hoxd gene regulation in embryonic MBs evolved by hijacking a preexisting regulatory landscape that was already at work before the emergence of mammals in structures such as the limbs or the intestinal tract.
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Guerreiro I, Gitto S, Novoa A, Codourey J, Nguyen Huynh TH, Gonzalez F, Milinkovitch MC, Mallo M, Duboule D. Reorganisation of Hoxd regulatory landscapes during the evolution of a snake-like body plan. eLife 2016; 5. [PMID: 27476854 PMCID: PMC4969037 DOI: 10.7554/elife.16087] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 07/10/2016] [Indexed: 12/15/2022] Open
Abstract
Within land vertebrate species, snakes display extreme variations in their body plan, characterized by the absence of limbs and an elongated morphology. Such a particular interpretation of the basic vertebrate body architecture has often been associated with changes in the function or regulation of Hox genes. Here, we use an interspecies comparative approach to investigate different regulatory aspects at the snake HoxD locus. We report that, unlike in other vertebrates, snake mesoderm-specific enhancers are mostly located within the HoxD cluster itself rather than outside. In addition, despite both the absence of limbs and an altered Hoxd gene regulation in external genitalia, the limb-associated bimodal HoxD chromatin structure is maintained at the snake locus. Finally, we show that snake and mouse orthologous enhancer sequences can display distinct expression specificities. These results show that vertebrate morphological evolution likely involved extensive reorganisation at Hox loci, yet within a generally conserved regulatory framework.
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Affiliation(s)
- Isabel Guerreiro
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Sandra Gitto
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | - Ana Novoa
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Julien Codourey
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Federico Gonzalez
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland
| | | | - Moises Mallo
- Instituto Gulbenkian de Ciência, Lisbon, Portugal
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, Geneva, Switzerland.,School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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Abstract
During the past 20 years, the studies on genetics or pharmacogenomics of primary hypertension provided interesting results supporting the role of genetics, but no actionable finding ready to be translated into personalized medicine. Two types of approaches have been applied: a "hypothesis-driven" approach on the candidate genes, coding for proteins involved in the biochemical machinery underlying the regulation of BP, and an "unbiased hypothesis-free" approach with GWAS, based on the randomness principles of frequentist statistics. During the past 10-15 years, the application of the latter has overtaken the application of the former leading to an enlargement of the number of previously unknown candidate loci or genes but without any actionable result for the therapy of hypertension. In the present review, we summarize the results of our hypothesis-driven approach based on studies carried out in rats with genetic hypertension and in humans with essential hypertension at the pre-hypertensive and early hypertensive stages. These studies led to the identification of mutant adducin and endogenous ouabain as candidate genetic-molecular mechanisms in both species. Rostafuroxin has been developed for its ability to selectively correct Na(+) pump abnormalities sustained by the two abovementioned mechanisms and to selectively reduce BP in rats and in humans carrying the gene variants underlying the mutant adducin and endogenous ouabain (EO) effects. A clinical trial is ongoing to substantiate these findings. Future studies should apply both the candidate gene and GWAS approaches to fully exploit the potential of genetics in optimizing the personalized therapy.
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Miquel PA, Hwang SY. From physical to biological individuation. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2016; 122:51-57. [PMID: 27431501 DOI: 10.1016/j.pbiomolbio.2016.07.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 07/12/2016] [Accepted: 07/14/2016] [Indexed: 12/25/2022]
Abstract
In this paper, we insist on stressing the epistemic and metaphysical difference between individual and individuation, a distinction originally developed by Gilbert Simondon. Individuation occurs in complex physical systems by the coupling (R1) between the system and its outside conditions. As such the system is not well defined by its sole constituents. Let's characterize (R2) as follows: the system is not entirely defined by its structure at a given time because this structure will change and global emergent properties will appear, as in the paradigmatic example of phase transition. Thus physical individuation is defined both by the coupling of a physical system with its environment (R1) and by its diachronic dynamics taking place (R2). We interpret biological individuation as a second order one, i.e. as a recursive procedure through which physical individuation is also acting on "its own theatre". We represent this procedure like a mapping through which (R1R2) are applied to themselves, so that: RN = (R1R2)N. We highlight the relation between this assumption and the concept of extended criticality developed by Bailly, Longo and Montévil.
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Affiliation(s)
- Paul-Antoine Miquel
- Université de Toulouse 2, 5 Allée Antonio Machado, 31058, Toulouse Cedex 9, France.
| | - Su-Young Hwang
- Department of Liberal Arts and Science, Hongik University, Sejong-Ro, 2639, Jochiwon-eup, The New City of Sejong, South Korea.
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20
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Díaz-Hernández V, Marmolejo-Valencia A, Merchant-Larios H. Exogenous estradiol alters gonadal growth and timing of temperature sex determination in gonads of sea turtle. Dev Biol 2015; 408:79-89. [DOI: 10.1016/j.ydbio.2015.05.022] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Revised: 05/27/2015] [Accepted: 05/30/2015] [Indexed: 10/22/2022]
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Londe S, Monnin T, Cornette R, Debat V, Fisher BL, Molet M. Phenotypic plasticity and modularity allow for the production of novel mosaic phenotypes in ants. EvoDevo 2015; 6:36. [PMID: 26629324 PMCID: PMC4666092 DOI: 10.1186/s13227-015-0031-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 11/12/2015] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND The origin of discrete novelties remains unclear. Some authors suggest that qualitative phenotypic changes may result from the reorganization of preexisting phenotypic traits during development (i.e., developmental recombination) following genetic or environmental changes. Because ants combine high modularity with extreme phenotypic plasticity (queen and worker castes), their diversified castes could have evolved by developmental recombination. We performed a quantitative morphometric study to investigate the developmental origins of novel phenotypes in the ant Mystrium rogeri, which occasionally produces anomalous 'intercastes.' Our analysis compared the variation of six morphological modules with body size using a large sample of intercastes. RESULTS We confirmed that intercastes are conspicuous mosaics that recombine queen and worker modules. In addition, we found that many other individuals traditionally classified as workers or queens also exhibit some level of mosaicism. The six modules had distinct profiles of variation suggesting that each module responds differentially to factors that control body size and polyphenism. Mosaicism appears to result from each module responding differently yet in an ordered and predictable manner to intermediate levels of inducing factors that control polyphenism. The order of module response determines which mosaic combinations are produced. CONCLUSIONS Because the frequency of mosaics and their canalization around a particular phenotype may evolve by selection on standing genetic variation that affects the plastic response (i.e., genetic accommodation), developmental recombination is likely to play an important role in the evolution of novel castes in ants. Indeed, we found that most mosaics have queen-like head and gaster but a worker-like thorax congruent with the morphology of ergatoid queens and soldiers, respectively. Ergatoid queens of M. oberthueri, a sister species of M. rogeri, could have evolved from intercastes produced ancestrally through such a process.
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Affiliation(s)
- Sylvain Londe
- />UMR 7618 Institute of Ecology and Environmental Sciences of Paris, Sorbonne Universités, UPMC Univ Paris 06, 7 quai St Bernard, 75 252 Paris, France
| | - Thibaud Monnin
- />UMR 7618 Institute of Ecology and Environmental Sciences of Paris, Sorbonne Universités, UPMC Univ Paris 06, 7 quai St Bernard, 75 252 Paris, France
| | - Raphaël Cornette
- />Département Systématique et Évolution, Muséum National d’Histoire Naturelle; CNRS UMR 7205, Institut de Systématique, Evolution, Biodiversité, Paris, France
| | - Vincent Debat
- />Département Systématique et Évolution, Muséum National d’Histoire Naturelle; CNRS UMR 7205, Institut de Systématique, Evolution, Biodiversité, Paris, France
| | - Brian L. Fisher
- />Department of Entomology, California Academy of Sciences, Golden Gate Park, 55 Music Concourse Drive, San Francisco, CA 94118 USA
| | - Mathieu Molet
- />UMR 7618 Institute of Ecology and Environmental Sciences of Paris, Sorbonne Universités, UPMC Univ Paris 06, 7 quai St Bernard, 75 252 Paris, France
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Sears KE, Maier JA, Rivas-Astroza M, Poe R, Zhong S, Kosog K, Marcot JD, Behringer RR, Cretekos CJ, Rasweiler JJ, Rapti Z. The Relationship between Gene Network Structure and Expression Variation among Individuals and Species. PLoS Genet 2015; 11:e1005398. [PMID: 26317994 PMCID: PMC4552942 DOI: 10.1371/journal.pgen.1005398] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 06/27/2015] [Indexed: 01/01/2023] Open
Abstract
Variation among individuals is a prerequisite of evolution by natural selection. As such, identifying the origins of variation is a fundamental goal of biology. We investigated the link between gene interactions and variation in gene expression among individuals and species using the mammalian limb as a model system. We first built interaction networks for key genes regulating early (outgrowth; E9.5-11) and late (expansion and elongation; E11-13) limb development in mouse. This resulted in an Early (ESN) and Late (LSN) Stage Network. Computational perturbations of these networks suggest that the ESN is more robust. We then quantified levels of the same key genes among mouse individuals and found that they vary less at earlier limb stages and that variation in gene expression is heritable. Finally, we quantified variation in gene expression levels among four mammals with divergent limbs (bat, opossum, mouse and pig) and found that levels vary less among species at earlier limb stages. We also found that variation in gene expression levels among individuals and species are correlated for earlier and later limb development. In conclusion, results are consistent with the robustness of the ESN buffering among-individual variation in gene expression levels early in mammalian limb development, and constraining the evolution of early limb development among mammalian species.
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Affiliation(s)
- Karen E. Sears
- School of Integrative Biology, University of Illinois, Urbana, Illinois, United States of America
- Institute for Genomic Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Jennifer A. Maier
- School of Integrative Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Marcelo Rivas-Astroza
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Rachel Poe
- Department of Mathematics, University of Illinois, Urbana, Illinois, United States of America
| | - Sheng Zhong
- Department of Bioengineering, University of California, San Diego, La Jolla, California, United States of America
| | - Kari Kosog
- School of Integrative Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Jonathan D. Marcot
- School of Integrative Biology, University of Illinois, Urbana, Illinois, United States of America
| | - Richard R. Behringer
- Department of Genetics, University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Chris J. Cretekos
- Department of Biological Sciences, Idaho State University, Pocatello, Idaho, United States of America
| | - John J. Rasweiler
- Department of Obstetrics and Gynecology, State University of New York Downstate Medical Center, Brooklyn, New York, United States of America
| | - Zoi Rapti
- Department of Mathematics, University of Illinois, Urbana, Illinois, United States of America
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23
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Woltering JM, Duboule D. Tetrapod axial evolution and developmental constraints; Empirical underpinning by a mouse model. Mech Dev 2015; 138 Pt 2:64-72. [PMID: 26238020 PMCID: PMC4678112 DOI: 10.1016/j.mod.2015.07.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2015] [Revised: 07/19/2015] [Accepted: 07/20/2015] [Indexed: 02/05/2023]
Abstract
The tetrapod vertebral column has become increasingly complex during evolution as an adaptation to a terrestrial life. At the same time, the evolution of the vertebral formula became subject to developmental constraints acting on the size of the cervical and thoraco-lumbar regions. In the course of our studies concerning the evolution of Hox gene regulation, we produced a transgenic mouse model expressing fish Hox genes, which displayed a reduced number of thoraco-lumbar vertebrae and concurrent sacral homeotic transformations. Here, we analyze this mutant stock and conclude that the ancestral, pre-tetrapodial Hox code already possessed the capacity to induce vertebrae with sacral characteristics. This suggests that alterations in the interpretation of the Hox code may have participated to the evolution of this region in tetrapods, along with potential modifications of the HOX proteins themselves. With its reduced vertebral number, this mouse stock violates a previously described developmental constraint, which applies to the thoraco-lumbar region. The resulting offset between motor neuron morphology, vertebral patterning and the relative positioning of hind limbs illustrates that the precise orchestration of the Hox-clock in parallel with other ontogenetic pathways places constraints on the evolvability of the body plan. A transgenic mouse line expressing fish Hox genes has anterior homeotic transformations. Fish Hox genes are capable of inducing tetrapod specific vertebral characters. A sacral Hox-code influences adult hindlimb position, yet not the position of limb budding.
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Affiliation(s)
- Joost M Woltering
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland
| | - Denis Duboule
- Department of Genetics and Evolution, University of Geneva, 30 quai Ernest Ansermet, 1211 Geneva, Switzerland; School of Life Sciences, Ecole Polytechnique Fédérale de Lausanne (EPFL), 1015 Lausanne, Switzerland.
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24
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Projecto-Garcia J, Jollivet D, Mary J, Lallier FH, Schaeffer SW, Hourdez S. Selective forces acting during multi-domain protein evolution: the case of multi-domain globins. SPRINGERPLUS 2015; 4:354. [PMID: 26191481 PMCID: PMC4503718 DOI: 10.1186/s40064-015-1124-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 06/29/2015] [Indexed: 11/10/2022]
Abstract
Multi-domain proteins form the majority of proteins in eukaryotes. During their formation by tandem duplication or gene fusion, new interactions between domains may arise as a result of the structurally-forced proximity of domains. The proper function of the formed proteins likely required the molecular adjustment of these stress zones by specific amino acid replacements, which should be detectable by the molecular signature of selection that governed their changes. We used multi-domain globins from three different invertebrate lineages to investigate the selective forces that acted throughout the evolution of these molecules. In the youngest of these molecules [Branchipolynoe scaleworm; original duplication ca. 60 million years (Ma)], we were able to detect some amino acids under positive selection corresponding to the initial duplication event. In older lineages (didomain globin from bivalve mollusks and nematodes), there was no evidence of amino acid positions under positive selection, possibly the result of accumulated non-adaptative mutations since the original duplication event (165 and 245 Ma, respectively). Some amino acids under positive selection were sometimes detected in later branches, either after speciation events, or after the initial duplication event. In Branchipolynoe, the position of the amino acids under positive selection on a 3D model suggests some of them are located at the interface between two domains; while others are locate in the heme pocket.
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Affiliation(s)
- Joana Projecto-Garcia
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - Didier Jollivet
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - Jean Mary
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - François H Lallier
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
| | - Stephen W Schaeffer
- />Department of Biology and Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park, PA 16802 USA
| | - Stéphane Hourdez
- />CNRS UMR 7144, Station Biologique de Roscoff, Places Georges Teissier, 29680 Roscoff, France
- />Laboratoire Adaptation et Diversité en Milieu Marin, UPMC Université Paris 06, Place Georges Teissier, 29680 Roscoff Cedex, France
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25
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Winata CL, Kondrychyn I, Korzh V. Changing Faces of Transcriptional Regulation Reflected by Zic3. Curr Genomics 2015; 16:117-27. [PMID: 26085810 PMCID: PMC4467302 DOI: 10.2174/1389202916666150205124519] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2014] [Revised: 01/27/2015] [Accepted: 01/29/2015] [Indexed: 02/07/2023] Open
Abstract
The advent of genomics in the study of developmental mechanisms has brought a trove of information
on gene datasets and regulation during development, where the Zic family of zinc-finger proteins
plays an important role. Genomic analysis of the modes of action of Zic3 in pluripotent cells demonstrated its
requirement for maintenance of stem cells pluripotency upon binding to the proximal regulatory regions
(promoters) of genes associated with cell pluripotency (Nanog, Sox2, Oct4, etc.) as well as cell cycle, proliferation, oncogenesis
and early embryogenesis. In contrast, during gastrulation and neurulation Zic3 acts by binding the distal regulatory
regions (enhancers, etc) associated with control of gene transcription in the Nodal and Wnt signaling pathways, including
genes that act to break body symmetry. This illustrates a general role of Zic3 as a transcriptional regulator that
acts not only alone, but in many instances in conjunction with other transcription factors. The latter is done by binding to
adjacent sites in the context of multi-transcription factor complexes associated with regulatory elements.
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Affiliation(s)
- Cecilia Lanny Winata
- International Institute of Molecular and Cell Biology, Warsaw, Poland; Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany
| | | | - Vladimir Korzh
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research, Singapore; Department of Biological Sciences, National University of Singapore, Singapore
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26
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Morange M. Synthetic Biology: A Bridge Between Functional and Evolutionary Biology. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot_a_00003] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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28
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Newman SA. The Developmental Genetic Toolkit and the Molecular Homology—Analogy Paradox. ACTA ACUST UNITED AC 2015. [DOI: 10.1162/biot.2006.1.1.12] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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29
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Lonfat N, Montavon T, Darbellay F, Gitto S, Duboule D. Convergent evolution of complex regulatory landscapes and pleiotropy at Hox loci. Science 2014; 346:1004-6. [DOI: 10.1126/science.1257493] [Citation(s) in RCA: 111] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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30
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Lapébie P, Ruggiero A, Barreau C, Chevalier S, Chang P, Dru P, Houliston E, Momose T. Differential responses to Wnt and PCP disruption predict expression and developmental function of conserved and novel genes in a cnidarian. PLoS Genet 2014; 10:e1004590. [PMID: 25233086 PMCID: PMC4169000 DOI: 10.1371/journal.pgen.1004590] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 07/09/2014] [Indexed: 11/19/2022] Open
Abstract
We have used Digital Gene Expression analysis to identify, without bilaterian bias, regulators of cnidarian embryonic patterning. Transcriptome comparison between un-manipulated Clytia early gastrula embryos and ones in which the key polarity regulator Wnt3 was inhibited using morpholino antisense oligonucleotides (Wnt3-MO) identified a set of significantly over and under-expressed transcripts. These code for candidate Wnt signaling modulators, orthologs of other transcription factors, secreted and transmembrane proteins known as developmental regulators in bilaterian models or previously uncharacterized, and also many cnidarian-restricted proteins. Comparisons between embryos injected with morpholinos targeting Wnt3 and its receptor Fz1 defined four transcript classes showing remarkable correlation with spatiotemporal expression profiles. Class 1 and 3 transcripts tended to show sustained expression at "oral" and "aboral" poles respectively of the developing planula larva, class 2 transcripts in cells ingressing into the endodermal region during gastrulation, while class 4 gene expression was repressed at the early gastrula stage. The preferential effect of Fz1-MO on expression of class 2 and 4 transcripts can be attributed to Planar Cell Polarity (PCP) disruption, since it was closely matched by morpholino knockdown of the specific PCP protein Strabismus. We conclude that endoderm and post gastrula-specific gene expression is particularly sensitive to PCP disruption while Wnt-/β-catenin signaling dominates gene regulation along the oral-aboral axis. Phenotype analysis using morpholinos targeting a subset of transcripts indicated developmental roles consistent with expression profiles for both conserved and cnidarian-restricted genes. Overall our unbiased screen allowed systematic identification of regionally expressed genes and provided functional support for a shared eumetazoan developmental regulatory gene set with both predicted and previously unexplored members, but also demonstrated that fundamental developmental processes including axial patterning and endoderm formation in cnidarians can involve newly evolved (or highly diverged) genes.
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Affiliation(s)
- Pascal Lapébie
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Antonella Ruggiero
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Carine Barreau
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Sandra Chevalier
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Patrick Chang
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Philippe Dru
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Evelyn Houliston
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
| | - Tsuyoshi Momose
- Sorbonne Universités, UPMC Univ Paris 06, and CNRS, Laboratoire de Biologie du Développement de Villefranche-sur-mer, Observatoire Océanographique, Villefranche-sur-mer, France
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31
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de Laat W, Duboule D. Topology of mammalian developmental enhancers and their regulatory landscapes. Nature 2013; 502:499-506. [PMID: 24153303 DOI: 10.1038/nature12753] [Citation(s) in RCA: 353] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2013] [Accepted: 09/02/2013] [Indexed: 12/26/2022]
Abstract
How a complex animal can arise from a fertilized egg is one of the oldest and most fascinating questions of biology, the answer to which is encoded in the genome. Body shape and organ development, and their integration into a functional organism all depend on the precise expression of genes in space and time. The orchestration of transcription relies mostly on surrounding control sequences such as enhancers, millions of which form complex regulatory landscapes in the non-coding genome. Recent research shows that high-order chromosome structures make an important contribution to enhancer functionality by triggering their physical interactions with target genes.
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Affiliation(s)
- Wouter de Laat
- Hubrecht Institute-KNAW and University Medical Center Utrecht, Uppsalalaan 8, 3584 CT, Utrecht, the Netherlands
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Abstract
The oskar gene is critical for germ plasm formation and reproduction in higher insects. A recent study reports that oskar has more ancient roots than previously thought, indicating it was co-opted for its reproductive role in higher insects.
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Affiliation(s)
- Ehab Abouheif
- Department of Biology, McGill University, Montreal, Quebec H3A 1B1, Canada.
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33
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Using evolutionary computations to understand the design and evolution of gene and cell regulatory networks. Methods 2013; 62:39-55. [PMID: 23726941 DOI: 10.1016/j.ymeth.2013.05.013] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Revised: 11/30/2012] [Accepted: 05/21/2013] [Indexed: 12/21/2022] Open
Abstract
This paper surveys modeling approaches for studying the evolution of gene regulatory networks (GRNs). Modeling of the design or 'wiring' of GRNs has become increasingly common in developmental and medical biology, as a means of quantifying gene-gene interactions, the response to perturbations, and the overall dynamic motifs of networks. Drawing from developments in GRN 'design' modeling, a number of groups are now using simulations to study how GRNs evolve, both for comparative genomics and to uncover general principles of evolutionary processes. Such work can generally be termed evolution in silico. Complementary to these biologically-focused approaches, a now well-established field of computer science is Evolutionary Computations (ECs), in which highly efficient optimization techniques are inspired from evolutionary principles. In surveying biological simulation approaches, we discuss the considerations that must be taken with respect to: (a) the precision and completeness of the data (e.g. are the simulations for very close matches to anatomical data, or are they for more general exploration of evolutionary principles); (b) the level of detail to model (we proceed from 'coarse-grained' evolution of simple gene-gene interactions to 'fine-grained' evolution at the DNA sequence level); (c) to what degree is it important to include the genome's cellular context; and (d) the efficiency of computation. With respect to the latter, we argue that developments in computer science EC offer the means to perform more complete simulation searches, and will lead to more comprehensive biological predictions.
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Weisbrod A, Cohen M, Chipman AD. Evolution of the insect terminal patterning system--insights from the milkweed bug, Oncopeltus fasciatus. Dev Biol 2013; 380:125-31. [PMID: 23665175 DOI: 10.1016/j.ydbio.2013.04.030] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2012] [Revised: 03/27/2013] [Accepted: 04/23/2013] [Indexed: 10/26/2022]
Abstract
The anterior and posterior ends of the insect embryo are patterned through the terminal patterning system, which is best known from the fruitfly Drosophila melanogaster. In Drosophila, the RTK receptor Torso and its presumed co-activator Torso-like initiate a signaling cascade, which activates two terminal gap genes, tailless and huckebein. These in turn interact with various patterning genes to define terminal structures. Work on other insect species has shown that this system is poorly conserved, and not all of its components have been found in all cases studied. We place the variability of the system within a broader phylogenetic framework. We describe the expression and knock-down phenotypes of the homologues of terminal patterning genes in the hemimetabolous Oncopeltus fasciatus. We have examined the interactions among these genes and between them and other patterning genes. We demonstrate that all of these genes have different roles in Oncopeltus relative to Drosophila; torso-like is expressed in follicle cells during oogenesis and is involved in the invagination of the blastoderm to form the germ band, and possibly also in defining the growth zone; tailless is regulated by orthodenticle and has a role only in anterior determination; huckebein is expressed only in the middle of the blastoderm; finally, torso was not found in Oncopeltus and its role in terminal patterning seems novel within holometabolous insects. We then use our data, together with published data on other insects, to reconstruct the evolution of the terminal patterning gene network in insects. We suggest that the Drosophila terminal patterning network evolved recently in the lineage leading to the Diptera, and represents an example of evolutionary "tinkering", where pre-existing pathways are co-opted for a new function.
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Affiliation(s)
- Anat Weisbrod
- The Deparment of Ecology, Evolution and Behavior, Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, 91904 Jerusalem, Israel
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Merchant-Larios H, Díaz-Hernández V. Environmental Sex Determination Mechanisms in Reptiles. Sex Dev 2013; 7:95-103. [DOI: 10.1159/000341936] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
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Spirov AV, Sabirov MA, Holloway DM. In silico evolution of gene cooption in pattern-forming gene networks. ScientificWorldJournal 2012; 2012:560101. [PMID: 23365523 PMCID: PMC3540831 DOI: 10.1100/2012/560101] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2012] [Accepted: 11/13/2012] [Indexed: 11/17/2022] Open
Abstract
Gene recruitment or cooption occurs when a gene, which may be part of an existing gene regulatory network (GRN), comes under the control of a new regulatory system. Such re-arrangement of pre-existing networks is likely more common for increasing genomic complexity than the creation of new genes. Using evolutionary computations (EC), we investigate how cooption affects the evolvability, outgrowth and robustness of GRNs. We use a data-driven model of insect segmentation, for the fruit fly Drosophila, and evaluate fitness by robustness to maternal variability—a major constraint in biological development. We compare two mechanisms of gene cooption: a simpler one with gene Introduction and Withdrawal operators; and one in which GRN elements can be altered by transposon infection. Starting from a minimal 2-gene network, insufficient for fitting the Drosophila gene expression patterns, we find a general trend of coopting available genes into the GRN, in order to better fit the data. With the transposon mechanism, we find co-evolutionary oscillations between genes and their transposons. These oscillations may offer a new technique in EC for overcoming premature convergence. Finally, we comment on how a differential equations (in contrast to Boolean) approach is necessary for addressing realistic continuous variation in biochemical parameters.
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Affiliation(s)
- Alexander V Spirov
- Computer Science and CEWIT, SUNY Stony Brook, 1500 Stony Brook Road, Stony Brook, NY 11794, USA.
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Tension and Robustness in Multitasking Cellular Networks. PLoS Comput Biol 2012; 8:e1002491. [PMID: 22577355 PMCID: PMC3343128 DOI: 10.1371/journal.pcbi.1002491] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2011] [Accepted: 03/09/2012] [Indexed: 11/27/2022] Open
Abstract
Cellular networks multitask by exhibiting distinct, context-dependent dynamics. However, network states (parameters) that generate a particular dynamic are often sub-optimal for others, defining a source of “tension” between them. Though multitasking is pervasive, it is not clear where tension arises, what consequences it has, and how it is resolved. We developed a generic computational framework to examine the source and consequences of tension between pairs of dynamics exhibited by the well-studied RB-E2F switch regulating cell cycle entry. We found that tension arose from task-dependent shifts in parameters associated with network modules. Although parameter sets common to distinct dynamics did exist, tension reduced both their accessibility and resilience to perturbation, indicating a trade-off between “one-size-fits-all” solutions and robustness. With high tension, robustness can be preserved by dynamic shifting of modules, enabling the network to toggle between tasks, and by increasing network complexity, in this case by gene duplication. We propose that tension is a general constraint on the architecture and operation of multitasking biological networks. To this end, our work provides a framework to quantify the extent of tension between any network dynamics and how it affects network robustness. Such analysis would suggest new ways to interfere with network elements to elucidate the design principles of cellular networks. Multitasking pervades our daily lives. For example, the technological devices that we increasingly rely upon are now engineered with such multifunctionality or “integration” in mind. Similarly, cellular networks also multitask in that they generate multiple, distinct dynamics according to their operating context. Here we show that differences in parameter spaces that underlie different dynamics thus cause a “tension”, which ultimately constrains network operation. In particular, our analysis reveals that tension negatively impacts robustness by reducing accessibility of parameters able to accomplish two tasks and reduces their ability to withstand perturbations. The presence of tension and its negative impact on network robustness represents a fundamental, generic constraint on the operation of different multitasking networks.
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Bertossa RC. Morphology and behaviour: functional links in development and evolution. Philos Trans R Soc Lond B Biol Sci 2011; 366:2056-68. [PMID: 21690124 PMCID: PMC3130372 DOI: 10.1098/rstb.2011.0035] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Development and evolution of animal behaviour and morphology are frequently addressed independently, as reflected in the dichotomy of disciplines dedicated to their study distinguishing object of study (morphology versus behaviour) and perspective (ultimate versus proximate). Although traits are known to develop and evolve semi-independently, they are matched together in development and evolution to produce a unique functional phenotype. Here I highlight similarities shared by both traits, such as the decisive role played by the environment for their ontogeny. Considering the widespread developmental and functional entanglement between both traits, many cases of adaptive evolution are better understood when proximate and ultimate explanations are integrated. A field integrating these perspectives is evolutionary developmental biology (evo-devo), which studies the developmental basis of phenotypic diversity. Ultimate aspects in evo-devo studies--which have mostly focused on morphological traits--could become more apparent when behaviour, 'the integrator of form and function', is integrated into the same framework of analysis. Integrating a trait such as behaviour at a different level in the biological hierarchy will help to better understand not only how behavioural diversity is produced, but also how levels are connected to produce functional phenotypes and how these evolve. A possible framework to accommodate and compare form and function at different levels of the biological hierarchy is outlined. At the end, some methodological issues are discussed.
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Affiliation(s)
- Rinaldo C Bertossa
- Centre for Behaviour and Neurosciences & Centre for Ecological and Evolutionary Studies, University of Groningen, PO Box 11103, 9700 Groningen, The Netherlands.
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Hudson C, Ba M, Rouvière C, Yasuo H. Divergent mechanisms specify chordate motoneurons: evidence from ascidians. Development 2011; 138:1643-52. [DOI: 10.1242/dev.055426] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Ascidians are members of the vertebrate sister group Urochordata. Their larvae exhibit a chordate body plan, which forms by a highly accelerated embryonic strategy involving a fixed cell lineage and small cell numbers. We report a detailed analysis of the specification of three of the five pairs of motoneurons in the ascidian Ciona intestinalis and show that despite well-conserved gene expression patterns and embryological outcomes compared with vertebrates, key signalling molecules have adopted different roles. We employed a combination of cell ablation and gene manipulation to analyse the function of two signalling molecules with key roles in vertebrate motoneuron specification that are known to be expressed equivalently in ascidians: the inducer Sonic hedgehog, produced ventrally by the notochord and floorplate; and the inhibitory BMP2/4, produced on the lateral/dorsal side of the neural plate. Our surprising conclusion is that neither BMP2/4 signalling nor the ventral cell lineages expressing hedgehog play crucial roles in motoneuron formation in Ciona. Furthermore, BMP2/4 overexpression induced ectopic motoneurons, the opposite of its vertebrate role. We suggest that the specification of motoneurons has been modified during ascidian evolution, such that BMP2/4 has adopted a redundant inductive role rather than a repressive role and Nodal, expressed upstream of BMP2/4 in the dorsal neural tube precursors, acts as a motoneuron inducer during normal development. Thus, our results uncover significant differences in the mechanisms used for motoneuron specification within chordates and also highlight the dangers of interpreting equivalent expression patterns as indicative of conserved function in evo-devo studies.
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Affiliation(s)
- Clare Hudson
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
| | - Moly Ba
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
| | - Christian Rouvière
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
| | - Hitoyoshi Yasuo
- UPMC University of Paris 06, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, BP28, 06230, Villefranche-sur-mer, France
- CNRS, UMR7009, Developmental Biology Unit, Observatoire Océanologique de Villefranche-sur-mer, 06230, BP28, Villefranche-sur-mer, France
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Morange M. What will result from the interaction between functional and evolutionary biology? STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2011; 42:69-74. [PMID: 21300317 DOI: 10.1016/j.shpsc.2010.11.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The modern synthesis has been considered to be wrongly called a "synthesis", since it had completely excluded embryology, and many other disciplines. The recent developments of Evo-Devo have been seen as a step in the right direction, as complementing the modern synthesis, and probably leading to a "new synthesis". My argument is that the absence of embryology from the modern synthesis was the visible sign of a more profound lack: the absence of functional biology in the evolutionary synthesis. I will consider the reasons for this absence, as well as the recent transformations which favoured a closer interaction between these two branches of biology. Then I will describe two examples of recent work in which functional and evolutionary questioning were tightly linked. The most significant part of the paper will be devoted to the transformation of evolutionary theory that can be expected from this encounter: a deep transformation, or simply an experimental confirmation of this theory? I will not choose between these two different possibilities, but will discuss some of the difficulties which make the choice problematic.
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Affiliation(s)
- Michel Morange
- Centre Cavaillès, USR 3308, Ecole Normale Supérieure, 29 rue d'Ulm, 75230 Paris Cedex 05, France.
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Abstract
Where is ‘evo-devo' going and how will it get there? Denis Duboule analyses the fields of evolution and development and argues that their current marriage is likely a transitory affair.
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Affiliation(s)
- Denis Duboule
- University of Geneva, Ecole Polytechnique Fédérale, Lausanne, Switzerland.
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Cell state switching factors and dynamical patterning modules: complementary mediators of plasticity in development and evolution. J Biosci 2009; 34:553-72. [DOI: 10.1007/s12038-009-0074-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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Newman SA, Bhat R, Mezentseva NV. Cell state switching factors and dynamical patterning modules: complementary mediators of plasticity in development and evolution. J Biosci 2009. [DOI: 10.1007/s12038-009-0001-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Stochasticity in evolution. Trends Ecol Evol 2009; 24:157-65. [DOI: 10.1016/j.tree.2008.09.014] [Citation(s) in RCA: 126] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2008] [Revised: 09/24/2008] [Accepted: 09/25/2008] [Indexed: 11/30/2022]
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Milde S, Hemmrich G, Anton-Erxleben F, Khalturin K, Wittlieb J, Bosch TCG. Characterization of taxonomically restricted genes in a phylum-restricted cell type. Genome Biol 2009; 10:R8. [PMID: 19161630 PMCID: PMC2687796 DOI: 10.1186/gb-2009-10-1-r8] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2008] [Revised: 12/11/2008] [Accepted: 01/22/2009] [Indexed: 12/04/2022] Open
Abstract
Computational and functional genomic analyses in Hydra magnipapillata suggest that taxonomically-restricted genes are involved in the evolution of morphological novelties such as the cnidarian nematocyte Background Despite decades of research, the molecular mechanisms responsible for the evolution of morphological diversity remain poorly understood. While current models assume that species-specific morphologies are governed by differential use of conserved genetic regulatory circuits, it is debated whether non-conserved taxonomically restricted genes are also involved in making taxonomically relevant structures. The genomic resources available in Hydra, a member of the early branching animal phylum Cnidaria, provide a unique opportunity to study the molecular evolution of morphological novelties such as the nematocyte, a cell type characteristic of, and unique to, Cnidaria. Results We have identified nematocyte-specific genes by suppression subtractive hybridization and find that a considerable portion has no homologues to any sequences in animals outside Hydra. By analyzing the transcripts of these taxonomically restricted genes and mining of the Hydra magnipapillata genome, we find unexpected complexity in gene structure and transcript processing. Transgenic Hydra expressing the green fluorescent protein reporter under control of one of the taxonomically restricted gene promoters recapitulate faithfully the described expression pattern, indicating that promoters of taxonomically restricted genes contain all elements essential for spatial and temporal control mechanisms. Surprisingly, phylogenetic footprinting of this promoter did not reveal any conserved cis-regulatory elements. Conclusions Our findings suggest that taxonomically restricted genes are involved in the evolution of morphological novelties such as the cnidarian nematocyte. The transcriptional regulatory network controlling taxonomically restricted gene expression may contain not yet characterized transcription factors or cis-regulatory elements.
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Affiliation(s)
- Sabine Milde
- Zoological Institute, Christian-Albrechts-University Kiel, Kiel, Germany.
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High nucleotide divergence in developmental regulatory genes contrasts with the structural elements of olfactory pathways in caenorhabditis. Genetics 2008; 181:1387-97. [PMID: 19001295 DOI: 10.1534/genetics.107.082651] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Almost all organismal function is controlled by pathways composed of interacting genetic components. The relationship between pathway structure and the evolution of individual pathway components is not completely understood. For the nematode Caenorhabditis elegans, chemosensory pathways regulate critical aspects of an individual's life history and development. To help understand how olfaction evolves in Caenorhabditis and to examine patterns of gene evolution within transduction pathways in general, we analyzed nucleotide variation within and between species across two well-characterized olfactory pathways, including regulatory genes controlling the fate of the cells in which the pathways are expressed. In agreement with previous studies, we found much higher levels of polymorphism within C. remanei than within the related species C. elegans and C. briggsae. There are significant differences in the rates of nucleotide evolution for genes across the two pathways but no particular association between evolutionary rate and gene position, suggesting that the evolution of functional pathways must be considered within the context of broader gene network structure. However, developmental regulatory genes show both higher levels of divergence and polymorphism than the structural genes of the pathway. These results show that, contrary to the emerging paradigm in the evolution of development, important structural changes can accumulate in transcription factors.
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Evolution in biological and nonbiological systems under different mechanisms of generation and inheritance. Theory Biosci 2008; 127:343-58. [PMID: 18946696 DOI: 10.1007/s12064-008-0052-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Accepted: 09/18/2008] [Indexed: 10/21/2022]
Abstract
The majority of definitions of life and evolution include the notion that part of an organism has to be copied to its offspring and that this includes some form of coded information. This article presents the thesis that this conception is too restrictive and that evolution can occur in systems in which there is no copy of information between generations. For that purpose, this article introduces a new set of concepts and a theoretical framework that is designed to be equally applicable to the study of the evolution of biological and nonbiological systems. In contrast to some theoretical approaches in evolution, like neo-Darwinism, the approach presented here is not focused on the transmission and change of hereditary information that can be copied (like in the case of DNA). Instead, multiple mechanisms by which a system can generate offspring (with and without copying) and by which information in it affects the structure and evolution of its offspring are considered. The first part of this article describes in detail these new concepts. The second part of this article discusses how these concepts are directly applicable to the diversity of systems that can evolve. The third part introduces hypotheses concerning (1) how different mechanisms of generation and inheritance can arise from each other during evolution, and (2) how the existence of several inheritance mechanisms in an organism can affect its evolution.
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Kopantzev EP, Monastyrskaya GS, Vinogradova TV, Zinovyeva MV, Kostina MB, Filyukova OB, Tonevitsky AG, Sukhikh GT, Sverdlov ED. Differences in gene expression levels between early and later stages of human lung development are opposite to those between normal lung tissue and non-small lung cell carcinoma. Lung Cancer 2008; 62:23-34. [DOI: 10.1016/j.lungcan.2008.02.011] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2007] [Revised: 12/21/2007] [Accepted: 02/14/2008] [Indexed: 12/12/2022]
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Kräußlich H. Exploitable genetic variation can be changed under environmental and genetic stress. Consequences for livestock breeding - a review. J Anim Breed Genet 2008. [DOI: 10.1111/j.1439-0388.2000.00254.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Labbé P, Berticat C, Berthomieu A, Unal S, Bernard C, Weill M, Lenormand T. Forty years of erratic insecticide resistance evolution in the mosquito Culex pipiens. PLoS Genet 2008; 3:e205. [PMID: 18020711 PMCID: PMC2077897 DOI: 10.1371/journal.pgen.0030205] [Citation(s) in RCA: 103] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2007] [Accepted: 10/03/2007] [Indexed: 11/26/2022] Open
Abstract
One view of adaptation is that it proceeds by the slow and steady accumulation of beneficial mutations with small effects. It is difficult to test this model, since in most cases the genetic basis of adaptation can only be studied a posteriori with traits that have evolved for a long period of time through an unknown sequence of steps. In this paper, we show how ace-1, a gene involved in resistance to organophosphorous insecticide in the mosquito Culex pipiens, has evolved during 40 years of an insecticide control program. Initially, a major resistance allele with strong deleterious side effects spread through the population. Later, a duplication combining a susceptible and a resistance ace-1 allele began to spread but did not replace the original resistance allele, as it is sublethal when homozygous. Last, a second duplication, (also sublethal when homozygous) began to spread because heterozygotes for the two duplications do not exhibit deleterious pleiotropic effects. Double overdominance now maintains these four alleles across treated and nontreated areas. Thus, ace-1 evolution does not proceed via the steady accumulation of beneficial mutations. Instead, resistance evolution has been an erratic combination of mutation, positive selection, and the rearrangement of existing variation leading to complex genetic architecture. Adaptation is not always a straightforward process, and often results from natural selection tinkering with available variation. We present in this study just such a tortuous natural selection pathway, which allows the mosquito Culex pipiens to resist organophosphorous insecticides. In the Montpellier area, following the use of insecticide to control mosquito populations, a high-resistance allele of the insecticide target enzyme appeared. But this allele also displayed strong deleterious side effects. Recently, several duplicated haplotypes began to spread in natural population that put in tandem a susceptible and a resistant allele. We show that the duplicated haplotypes actually display reduced side effects compared to the resistant allele when in the heterozygous state, but also new and strong costs in the homozygote. This pattern leads to an unexpected equilibrium between four different alleles across treated and nontreated areas. The story of resistance in C. pipiens is indeed far from a slow progression toward a “perfect” adaptation. Rather, selection for resistance to insecticide is a long process of trial and error leading to an uncommon genetic architecture.
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Affiliation(s)
- Pierrick Labbé
- Equipe Génétique de l'Adaptation, Institut des Sciences de l'Evolution, CNRS Université Montpellier 2, Montpellier, France.
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