Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

Bapteste, Éric; Huneman, Philippe

doi:10.1186/s12915-018-0531-6

Cited by 29 publications

(25 citation statements)

References 217 publications

(185 reference statements)

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“…The study of the principles of evolution of the structure and function of gene networks is one of the most interesting and important tasks in biology [71]. The results of such analysis not only have theoretical interest, but also predictive power [72,73].…”

Section: Discussionmentioning

confidence: 99%

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Мустафин

Zamyatin

Konstantinov

et al. 2019

Genes

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Plants constantly fight with stressful factors as high or low temperature, drought, soil salinity and flooding. Plants have evolved a set of stress response mechanisms, which involve physiological and biochemical changes that result in adaptive or morphological changes. At a molecular level, stress response in plants is performed by genetic networks, which also undergo changes in the process of evolution. The study of the network structure and evolution may highlight mechanisms of plants adaptation to adverse conditions, as well as their response to stresses and help in discovery and functional characterization of the stress-related genes. We performed an analysis of Arabidopsis thaliana genes associated with several types of abiotic stresses (heat, cold, water-related, light, osmotic, salt, and oxidative) at the network level using a phylostratigraphic approach. Our results show that a substantial fraction of genes associated with various types of abiotic stress is of ancient origin and evolves under strong purifying selection. The interaction networks of genes associated with stress response have a modular structure with a regulatory component being one of the largest for five of seven stress types. We demonstrated a positive relationship between the number of interactions of gene in the stress gene network and its age. Moreover, genes of the same age tend to be connected in stress gene networks. We also demonstrated that old stress-related genes usually participate in the response for various types of stress and are involved in numerous biological processes unrelated to stress. Our results demonstrate that the stress response genes represent the ancient and one of the fundamental molecular systems in plants.

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Section: Discussionmentioning

confidence: 99%

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Мустафин

Zamyatin

Konstantinov

et al. 2019

Genes

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“…Examples are: West-Eberhard (2003) regarding the role of developmental plasticity in evolution; Odling-Smee et al 2003regarding the role of niche construction and niche selection, i.e. the active role of organisms changing or choosing their environments, in evolution; Jablonka & Lamb (2005) regarding the role of genetic as well as epigenetic, behavioral and symbolic variation and inheritance in evolution; Noble (2006Noble ( , 2015, Oyama et al (2001) and Bapteste & Huneman (2018) regarding the decentralized and complex nature of causality in development and evolution; and Sober & Wilson (1998) regarding the role of selection operating at multiple levels in evolution.…”

Section: Perspectives From the Debate About An Extended Evolutionary mentioning

confidence: 99%

“…(Oyama et al, 2001). Similarly, Bapteste & Huneman (2018) emphasize that "nothing on Earth evolves and makes sense in isolation, thereby challenging the key assumption of the Modern Synthesis Teaching evolution as an interdisciplinary science Conceptual clarification of evolution as an interdisciplinary science framework that targeting the individual gene or organism (even when in principle knowing that it is part of a set of complex interactions ) allows us to capture evolution in all its dimensions. Since the living world evolves as a dynamic network of interactions , we argue that evolutionary biology could become a science of evolving networks , which would allow biologists to explain organisational complexity, while providing a novel way to reframe and to unify evolutionary biology."…”

Section: Perspectives From the Debate About An Extended Evolutionary mentioning

confidence: 99%

Conceptual clarification of evolution as an interdisciplinary science

Hanisch¹,

Eirdosh²

2020

Preprint

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Evolutionary theory in the 21st century has been embraced, albeit with varying degrees of controversy and consensus, across wide ranging disciplines. From biology and anthropology, to medicine, psychology, economics, sustainability science, computer science, and many more, core concepts of heritable variation and selection have been utilized by scientists across academia to understand change in the natural and social world. This article aims to provide evolution educators with a short review of current discourse in evolution science and a conceptual clarification of core concepts in evolutionary theory, in the service of promoting deeper and transferable understanding of these concepts in evolution education.

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“…), can be compared to identify (i) nodes with similar roles and (ii) subtypes corresponding to subgraphs with similar architectures of microbial interaction between CNs. Such comparisons would detect stable patterns of interactions within the extant biodiversity [58] (Figure 3).…”

Section: Improved Understanding Of Ecosystems Evolution While Embracmentioning

confidence: 99%

Phylosystemics: Merging Phylogenomics, Systems Biology, and Ecology to Study Evolution

Watson

Habib

Bapteste

2020

Trends in Microbiology

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We define phylosystemics, a multidisciplinary strategy uniting short timescale interaction studies from systems biologists and ecologists with the longer timescale studies familiar to evolutionary biologists, taking advantage of methods from network sciences. Phylosystemics superimposes evolutionary information on entities/edges forming interaction networks produced by systems biology and ecology. At the molecular level, phylosystemics could provide evidence to infer and to time the evolution of molecular processes within a single branch of a phylogeny, in particular between the first and last common ancestors of a group arising during a major evolutionary transition. At the ecosystemic level, phylosystemics could culminate with the development of multilayer temporal networks encompassing biotic and abiotic interactions, whose analyses could unravel ecological interactions with evolutionary consequences. Trends in Microbiologyemergent field aiming to track the evolution of biological processes by general approaches of graph theory, then (ii) we demonstrate that phylosystemics is timely and actionable, and (iii) illustrate some major pay-offs expected from this approach.

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Towards a Dynamic Interaction Network of Life to unify and expand the evolutionary theory

Cited by 29 publications

References 217 publications

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Phylostratigraphic Analysis Shows the Earliest Origination of the Abiotic Stress Associated Genes in A. thaliana

Conceptual clarification of evolution as an interdisciplinary science

Phylosystemics: Merging Phylogenomics, Systems Biology, and Ecology to Study Evolution

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