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      Adaptation, fitness landscape learning and fast evolution

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          Abstract

          We consider evolution of a large population, where fitness of each organism is defined by many phenotypical traits. These traits result from expression of many genes. Under some assumptions on  fitness we prove that such model organisms  are capable, to some extent, to recognize the fitness landscape. That fitness landscape learning sharply reduces the number of mutations needed for adaptation. Moreover, this learning increases phenotype robustness with respect to mutations, i.e., canalizes the phenotype.  We show that learning and canalization work only when evolution is gradual. Organisms can be adapted to  many constraints associated with a hard environment, if that environment becomes harder step by step. Our results explain why evolution can involve genetic changes of a relatively large effect and why the total number of changes are surprisingly small.

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          The complexity of theorem-proving procedures

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            The genetic theory of adaptation: a brief history.

            Theoretical studies of adaptation have exploded over the past decade. This work has been inspired by recent, surprising findings in the experimental study of adaptation. For example, morphological evolution sometimes involves a modest number of genetic changes, with some individual changes having a large effect on the phenotype or fitness. Here I survey the history of adaptation theory, focusing on the rise and fall of various views over the past century and the reasons for the slow development of a mature theory of adaptation. I also discuss the challenges that face contemporary theories of adaptation.
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              Adaptive prediction of environmental changes by microorganisms.

              Natural habitats of some microorganisms may fluctuate erratically, whereas others, which are more predictable, offer the opportunity to prepare in advance for the next environmental change. In analogy to classical Pavlovian conditioning, microorganisms may have evolved to anticipate environmental stimuli by adapting to their temporal order of appearance. Here we present evidence for environmental change anticipation in two model microorganisms, Escherichia coli and Saccharomyces cerevisiae. We show that anticipation is an adaptive trait, because pre-exposure to the stimulus that typically appears early in the ecology improves the organism's fitness when encountered with a second stimulus. Additionally, we observe loss of the conditioned response in E. coli strains that were repeatedly exposed in a laboratory evolution experiment only to the first stimulus. Focusing on the molecular level reveals that the natural temporal order of stimuli is embedded in the wiring of the regulatory network-early stimuli pre-induce genes that would be needed for later ones, yet later stimuli only induce genes needed to cope with them. Our work indicates that environmental anticipation is an adaptive trait that was repeatedly selected for during evolution and thus may be ubiquitous in biology.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: MethodologyRole: Writing – Review & Editing
                Role: ConceptualizationRole: Formal AnalysisRole: InvestigationRole: MethodologyRole: SoftwareRole: Writing – Original Draft PreparationRole: Writing – Review & Editing
                Role: Formal AnalysisRole: MethodologyRole: ValidationRole: Writing – Review & Editing
                Role: SoftwareRole: VisualizationRole: Writing – Review & Editing
                Journal
                F1000Res
                F1000Res
                F1000Research
                F1000Research
                F1000 Research Limited (London, UK )
                2046-1402
                13 September 2019
                2019
                : 8
                : 358
                Affiliations
                [1 ]Departments of Statistics, Ecology and Evolution, Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
                [2 ]Saint Petersburg National Research University of Information Technologies, Mechanics and Optics, Saint Petersburg, Russian Federation
                [3 ]CNRS, Mathématiques, Université de Lille, Villeneuve d'Ascq, France
                [4 ]Department of Computer Science, University of Bonn, Bonn, Germany
                [1 ]Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary
                [2 ]Parmenides Center for the Conceptual Foundations of Science, Pullach, Germany
                [3 ]Deparment of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary
                [1 ]Systems & Computational Biology Department, Albert Einstein College of Medicine, New York, NY, USA
                [1 ]Systems & Computational Biology Department, Albert Einstein College of Medicine, New York, NY, USA
                [1 ]Evolutionary Systems Research Group, MTA Centre for Ecological Research, Tihany, Hungary
                [2 ]Parmenides Center for the Conceptual Foundations of Science, Pullach, Germany
                [3 ]Deparment of Plant Systematics, Ecology and Theoretical Biology, Eötvös University, Budapest, Hungary
                Author notes

                No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Competing interests: No competing interests were disclosed.

                Author information
                https://orcid.org/0000-0001-5624-3368
                Article
                10.12688/f1000research.18575.2
                6798318
                31656586
                052c18cc-e687-4a36-a100-413587db64fe
                Copyright: © 2019 Reinitz J et al.

                This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 5 September 2019
                Funding
                Funded by: Government of Russian Federation
                Award ID: Grant08-08
                Funded by: Russian Ministry of Education
                Award ID: 2012-1.2.1-12-000-1013-016
                Funded by: National Institutes of Health
                Award ID: RO1OD010936
                Funded by: RSF
                Award ID: 16-11-10075
                The second author was supported by the grant of Russian Ministry of Education, 2012-1.2.1-12-000-1013-016. Additionally, the second author was financially supported by Government of Russian Federation, Grant Grant 08-08. D. Grigoriev is grateful to the grant RSF 16-11-10075 and to both MCCME and MPI f\"ur Mathematik for wonderful working conditions and inspiring atmosphere. J. Reinitz and S. Vakulenko were supported by US NIH grant RO1 OD010936 (formerly RO1 RR07801).
                The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.
                Categories
                Research Article
                Articles

                evolution,gene networks,fitness landscape learning
                evolution, gene networks, fitness landscape learning

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