# Open data phylometabolomics reveals turnover‐dominated chemical divergence and clade‐specific physicochemical regimes across angiosperms

## TL;DR

This study shows that plant chemical diversity in angiosperms evolves mainly through replacement, not accumulation, and that major plant groups have distinct chemical strategies.

## Contribution

A reproducible phylometabolomics pipeline reveals turnover-driven chemical divergence and clade-specific physicochemical regimes in angiosperms.

## Key findings

- Chemical divergence in angiosperms is dominated by metabolite replacement rather than accumulation.
- Major plant clades occupy distinct physicochemical and elemental niches, indicating conserved evolutionary constraints.
- Turnover explains nearly all β-diversity in plant chemical composition across angiosperm lineages.

## Abstract

Specialized metabolites are central to plant defense, signaling and ecological interactions, yet we still lack a macroevolutionary framework explaining how this diversity is structured across angiosperms. Here, we integrate the open LOTUS chemical repository with standardized taxonomy to map a curated ‘chemical core’ comprising 77 404 family‐supported occurrences across 12 representative families spanning Magnoliids, Monocots, and Eudicots. Chemical composition shows strong higher‐level structure, delineating major lineages while revealing a striking evolutionary topology: inter‐lineage divergence is dominated by metabolite replacement rather than accumulation. Across family pairs, β‐diversity is overwhelmingly explained by turnover, indicating that chemical disparity rarely arises from one lineage retaining subsets of another's repertoire. Despite this universal turnover regime, lineages occupy distinct physicochemical and elemental neighborhoods, consistent with divergent evolutionary strategies under shared allocation constraints. Magnoliids define a lipophilic boundary characterized by greater investment in nitrogen‐bearing and aromatic‐rich defenses; Monocots occupy a more hydrophilic, high‐molecular‐weight and structurally saturated niche; and Eudicots expand oxygen‐rich carbon scaffolds with reduced nitrogen dependence. Together, our results indicate that angiosperm chemical evolution is highly dynamic at the compositional level, yet constrained at the architectural level, with persistent turnover generating lineage‐specific chemical identities within inherited physicochemical corridors. This work provides a reproducible open data foundation for testing mechanistic links between biosynthetic organization, ecological antagonists, and evolutionary diversification of plant chemistry.

Using an open, reproducible phylometabolomics pipeline (LOTUS + standardized taxonomy; ~77 000 occurrences), we show that angiosperm chemodiversity diverges primarily by turnover (replacement), not nested accumulation. Despite this dynamism, major clades occupy distinct physicochemical regimes, revealing conserved constraints that channel chemical innovation across deep time.

Angiosperm specialized metabolism is often portrayed as cumulative, with derived lineages adding new chemical classes. Using a reproducible framework linking LOTUS occurrences to standardized taxonomy, we show that deep‐lineage chemical divergence is driven by replacement: turnover explains nearly all β‐diversity, while nestedness is minimal; clades occupy distinct physicochemical and elemental regimes that constrain chemical evolution across angiosperms.