Abstract
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.
Highlights
There are few generic models and approaches able to unite the short timescales of interactions unraveled by systems biologists and ecologists, with the longer timescale of evolution
The phylogenetic dating of interaction networks offers a way to infer the local architecture of early eukaryotic gene coexpression networks (GCNs), gene regulatory networks (GRNs) and Protein–protein interaction networks (PPIs) by focusing on nodes and edges found in the last common ancestors of eukaryotes, including gene families that may have been contributed by the ancestral endosymbiotic bacteria and their archaeal hosts
In the late 1990s to early 2000s, the introduction of the term ‘phylogenomics’ supported the development of cutting-edge approaches to handle the wealth of molecular data, and probably contributed to a successful transition from phylogenetics, whose practices were traditionally centered on studies of single or a few gene families, towards broader, multimarker analyses
Summary
Phylosystemics: Merging Phylogenomics, Systems Biology, and Ecology to Study Evolution. 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. Phylosystemics could culminate with the development of multilayer temporal networks encompassing biotic and abiotic interactions, whose analyses could unravel ecological interactions with evolutionary consequences. There are few generic models and approaches able to unite the short timescales of interactions unraveled by systems biologists and ecologists, with the longer timescale of evolution
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