A machine learning approach to study plant functional trait divergence

• Published in: Applications in plant sciences Vol. 12; no. 5; pp. e11576 - n/a
• Main Authors: Majumder, Sambadi, Mason, Chase M.
• Format: Journal Article
• Language: English
• Published: United States John Wiley & Sons, Inc 01.09.2024; John Wiley and Sons Inc; Wiley
• Subjects: Application; Diversification; ecophysiology; Environmental conditions; evolution; feature selection; Flowers & plants; genus; gradient boosting machine; Helianthus; Interspecific; intraspecific variation; Learning algorithms; Machine learning; Morphology; multidimensional; Observational learning; Phenotypic divergence; phenotypic variation; Phenotypic variations; Physiology; random forest; Seeds; species; gradient boosting machine; random forest; ecophysiology; multidimensional; Helianthus; feature selection
• ISSN: 2168-0450; 2168-0450
• DOI: 10.1002/aps3.11576

Premise Plant functional traits are often used to describe the spectra of ecological strategies used by different species. Here, we demonstrate a machine learning approach for identifying the traits that contribute most to interspecific phenotypic divergence in a multivariate trait space. Methods Descriptive and predictive machine learning approaches were applied to trait data for the genus Helianthus, including random forest and gradient boosting machine classifiers and recursive feature elimination. These approaches were applied at the genus level as well as within each of the three major clades within the genus to examine the variability in the major axes of trait divergence in three independent species radiations. Results Machine learning models were able to predict species identity from functional traits with high accuracy, and differences in functional trait importance were observed between the genus and clade levels indicating different axes of phenotypic divergence. Conclusions Applying machine learning approaches to identify divergent traits can provide insights into the predictability or repeatability of evolution through the comparison of parallel diversifications of clades within a genus. These approaches can be implemented in a range of contexts across basic and applied plant science from interspecific divergence to intraspecific variation across time, space, and environmental conditions.