Global architecture of metabolite distributions across species and its formation mechanisms

TL;DR

This study reveals that the distribution of plant metabolites across species exhibits complex structural patterns like nested and modular structures, which can be explained by simple evolutionary processes rather than trait-based mechanisms.

Contribution

It demonstrates that metabolite distribution structures can be modeled by simple evolution processes, challenging previous trait-based explanations.

Findings

Model predicts nested and modular structures accurately.

Structural properties explained by evolution processes without traits.

Better fit to observed metabolite distribution patterns.

Abstract

Living organisms produce metabolites of many types via their metabolisms. Especially, flavonoids, a kind of secondary metabolites, of plant species are interesting examples. Since plant species are believed to have specific flavonoids with respect to diverse environment, elucidation of design principles of metabolite distributions across plant species is important to understand metabolite diversity and plant evolution. In the previous work, we found heterogeneous connectivity in metabolite distributions, and proposed a simple model to explain a possible origin of heterogeneous connectivity. In this paper, we show further structural properties in the metabolite distribution among families inspired by analogy with plant-animal mutualistic networks: nested structure and modular structure. An earlier model represents that these structural properties in bipartite relationships are determined based on traits of elements and external factors. However, we find that the architecture of metabolite distributions is described by simple evolution processes without trait-based mechanisms by comparison between our model and the earlier model. Our model can better predict nested structure and modular structure in addition to heterogeneous connectivity both qualitatively and quantitatively. This finding implies an alternative possible origin of these structural properties, and suggests simpler formation mechanisms of metabolite distributions across plant species than expected.