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4. Of Evolution, Systems and Complexity

Author

Jonathan Rouzaud-Cornabas, David P. Parsons, Vincent Liard, Guillaume Beslon, Artificial Evolution and Computational Biology (BEAGLE), Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Inria Grenoble - Rhône-Alpes, and Université de Lyon-Université Lumière - Lyon 2 (UL2)

Subjects
Cognitive science, 0303 health sciences, education.field_of_study, Fitness landscape, Systems biology, Population, Evolutionary algorithm, Complex system, Complex network, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Evolvability, 03 medical and health sciences, 0302 clinical medicine, Evolutionary dynamics, education, 030217 neurology & neurosurgery, 030304 developmental biology
Abstract

International audience; The question of complexity in biological systems is recurrent in evolutionary biology and is central in complex systems science for obvious reasons. But this question is surprisingly overlooked by Evolutionary Systems Biology. This comes unexpected given the roots of systems biology in complex systems science but also given that a proper understanding of the origin and evolution of complexity would provide clues for a better understanding of extant biological systems. In this chapter we will explore the links between evolutionary systems biology and biological systems complexity, in terms of concepts, tools, and results. In particular, we will show how complex models can be used to explore this question and show that complexity can spontaneously accumulate even in simple conditions owing to a “complexity ratchet” fuelled by sign-epistasis.

Published
2021

5. From terra incognita to hotspot: the largest South Pacific green turtle nesting population in the forgotten reefs of New Caledonia

Author

Jacques Fretey, Tyffen C. Read, Léa Carron, Christophe Fontfreyde, Aurélie Fourdrain, Julie-Anne Kerandel, Vincent Liardet, Marc Oremus, Morgane Reix-Tronquet, and Marc Girondot

Subjects
Chelonia mydas, coral sea, green turtles, New Caledonia, South Pacific, reef, trend, General. Including nature conservation, geographical distribution, QH1-199.5
Abstract

The green turtle Chelonia mydas is a large marine turtle present in tropical and subtropical seas of the Atlantic, Pacific and Indian Oceans. It is categorized as Endangered on the IUCN Red List based on the trend of nesting populations at 32 sites, of which only three are in the Pacific Ocean. New Caledonia is a sui generis overseas territory of France in the south-west Pacific Ocean c. 1,210 km east of Australia. The presence of green turtles in New Caledonian waters is known, although the main nesting sites are far from the main island, on remote uninhabited islands. Since 1988 field missions to these remote reefs, namely d'Entrecasteaux, Bellona and Chesterfield, have collected data to quantify the nesting of green turtles in New Caledonia. For the first time we analyse the data collected during these missions. D'Entrecasteaux, Bellona and Chesterfield Reefs host a large nesting colony of green turtles, with the upper credible estimate of nesting activities reaching 150,000 nesting tracks in some years. These numbers exceed the estimated number of green turtle activities in the Pacific. The trend of the number of nesting activities is stable and has the same relationship with the Southern Oscillation Index as observed at Australian nesting sites. Our recommendations for the French authorities are to continue monitoring these populations, collect new demographic parameters and ensure the protection of these remote reefs, which should be considered a national treasure for New Caledonia.

Published
2023
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6. The Complexity Ratchet: Stronger than selection, weaker than robustness

Author

David P. Parsons, Guillaume Beslon, Vincent Liard, Jonathan Rouzaud-Cornabas, Laboratoire d'InfoRmatique en Image et Systèmes d'information (LIRIS), Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Université de Lyon-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Artificial Evolution and Computational Biology (BEAGLE), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Lumière - Lyon 2 (UL2)-École Centrale de Lyon (ECL), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria)-Laboratoire de Biométrie et Biologie Evolutive - UMR 5558 (LBBE), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Institut National de Recherche en Informatique et en Automatique (Inria)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS)-VetAgro Sup - Institut national d'enseignement supérieur et de recherche en alimentation, santé animale, sciences agronomiques et de l'environnement (VAS)-Centre National de la Recherche Scientifique (CNRS), Service Expérimentation et Développement (SED [Grenoble]), Inria Grenoble - Rhône-Alpes, Institut National de Recherche en Informatique et en Automatique (Inria)-Institut National de Recherche en Informatique et en Automatique (Inria), Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Institut National des Sciences Appliquées (INSA)-Université de Lyon-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-École Centrale de Lyon (ECL), Université de Lyon-Université Lumière - Lyon 2 (UL2), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Institut National des Sciences Appliquées de Lyon (INSA Lyon), Université de Lyon-Université Lumière - Lyon 2 (UL2)-Inria Grenoble - Rhône-Alpes, SED [Grenoble], and Beslon, Guillaume

Subjects
0303 health sciences, Experimental evolution, Computer science, In silico, Ratchet, Robustness (evolution), 02 engineering and technology, 03 medical and health sciences, Evolutionary biology, 0202 electrical engineering, electronic engineering, information engineering, Epistasis, 020201 artificial intelligence & image processing, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], Mutational pressure, [INFO.INFO-BI] Computer Science [cs]/Bioinformatics [q-bio.QM], 030304 developmental biology
Abstract

International audience; Using the in silico experimental evolution platform Aevol, we evolved populations of digital organisms in conditions where a simple functional structure is best. Strikingly, we observed that in a large fraction of the simulations, organisms evolved a complex functional structure and that their complexity increased during evolution despite being a lot less fit than simple organisms in other populations. However, when submitted to a harsh mutational pressure, we observed that a significant proportion of complex individuals ended up with a simple functional structure. Our results suggest the existence of a complexity ratchet that is powered by epistasis and that cannot be beaten by selection. They also show that this ratchet can be overthrown by robustness because of the strong constraints it imposes on the coding capacity of the genome.

Published
2018

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