Quantifying chemodiversity considering biochemical and structural properties of compounds with the R package chemodiv

• Published in: The New phytologist 2023-03, Vol.237 (6), p.2478-2492
• Main Authors: Petrén, Hampus, Köllner, Tobias G., Junker, Robert R.
• Format: Article
• Language: English
• Subjects: chemical communication; chemical ecology; chemodiversity; Databases, Factual; Ecology; Mathematical analysis; Phenotype; Phenotypes; Phytochemicals; plant defence; Plant physiology; Plants; Properties; R package; Relative abundance; secondary metabolites
• ISSN: 0028-646X; 1469-8137
• DOI: 10.1111/nph.18685

Summary Plants produce large numbers of phytochemical compounds affecting plant physiology and interactions with their biotic and abiotic environment. Recently, chemodiversity has attracted considerable attention as an ecologically and evolutionary meaningful way to characterize the phenotype of a mixture of phytochemical compounds. Currently used measures of phytochemical diversity, and related measures of phytochemical dissimilarity, generally do not take structural or biosynthetic properties of compounds into account. Such properties can be indicative of the compounds' function and inform about their biosynthetic (in)dependence, and should therefore be included in calculations of these measures. We introduce the R package chemodiv, which retrieves biochemical and structural properties of compounds from databases and provides functions for calculating and visualizing chemical diversity and dissimilarity for phytochemicals and other types of compounds. Our package enables calculations of diversity that takes the richness, relative abundance and – most importantly – structural and/or biosynthetic dissimilarity of compounds into account. We illustrate the use of the package with examples on simulated and real datasets. By providing the R package chemodiv for quantifying multiple aspects of chemodiversity, we hope to facilitate investigations of how chemodiversity varies across levels of biological organization, and its importance for the ecology and evolution of plants and other organisms.