Evolutionary systems biology: What it is and why it matters

Abstract

Evolutionary systems biology (ESB) is a rapidly growing integrative approach that has the core aim of generating mechanistic and evolutionary understanding of genotype-phenotype relationships at multiple levels. ESB's more specific objectives include extending knowledge gained from model organisms to non-model organisms, predicting the effects of mutations, and defining the core network structures and dynamics that have evolved to cause particular intracellular and intercellular responses. By combining mathematical, molecular, and cellular approaches to evolution, ESB adds new insights and methods to the modern evolutionary synthesis, and offers ways in which to enhance its explanatory and predictive capacities. This combination of prediction and explanation marks ESB out as a research manifesto that goes further than its two contributing fields. Here, we summarize ESB via an analysis of characteristic research examples and exploratory questions, while also making a case for why these integrative efforts are worth pursuing.

Evolution of gene network activity by tuning the strength of negative-feedback regulation

“…Further, despite our increasing level of knowledge about the effect of feedback regulation 4,9,25,26 on gene network activity in single species and the effect of carbon metabolism gene regulation on fitness 27 , a systematic experimental and quantitative study characterizing the role of feedback-mediating promoters on the evolved activity of modular gene networks has been missing. At the cross section 28 of evolutionary biology and systems biology, our work provides an example to how gene network evolution could occur through tuning the strength of negative-feedback regulation. .…”

Deep homology in the age of next-generation sequencing

“…Concluding remarks and outlook NGS has already significantly advanced our ability to address questions of homology, both experimentally as well as conceptually, and will probably continue to do so. Overall, it's fair to assume that the trend of incorporating technological advances from different fields of biology, and indeed the natural sciences in general, will continue in the field of evolutionary and developmental biology, to make it a more inclusive science [86,87]. Already, the next revolution in transcriptome sequencing is on its way, with the recent ability to use single cells as input material in high-throughput experiments [88].…”

“…In particular, a combination of experimental data and modelling approaches might help to delineate a 'configuration space', in which different individualized developmental and gene regulatory systems were free to evolve [87,103]. Following such synthesis, evo-devo research in general might indeed gain certain predictive powers about possible evolutionary trajectories, by defining the range of possible ontogenetic roadmaps [47,48,87]. The concept of deep homology, with its emphasis on how gene transcription can be co-opted in an evolutionary novel context, is likely to prove particularly powerful in delineating the gene regulatory dimension of such configuration spaces.…”

The contribution of Nicolae Botnariuc to evolutionary biology using systems theory

“…In a similar manner, the rapidly growing field of evolutionary systems biology (ESB) integrates methods from evolutionary biology and system biology. The field has the central goal of understanding the genotypephenotype relationships at multiple levels of organizational hierarchy (Soyer and O'Malley 2013). For example, ecological genomics techniques are suitable for multilevel selection studies carried out within diverse hierarchical systems (cf.…”