From Candidate Genes to Macroevolution: An Integrated Approach to Modeling the Evolution of Plant Innovations

Understanding how plant innovations arise and persist requires connecting mechanisms across biological scales. The growing accessibility of genomic data and methodological advances in phylogenetic comparative methods provide unprecedented opportunities to achieve this integration. Yet, functional tools remain unevenly distributed across the plant Tree of Life, and conceptual differences across scales of inquiry limit integration. Here, we highlight emerging approaches that bridge developmental, genomic, and macroevolutionary research to generate a more comprehensive view of plant evolution. We propose building a "Functional Tree of Plant Life" by investing in shared infrastructure and funding programs for developing transformation techniques and building genetic resources to incentivize research in nonmodel taxa. Concurrently, further methodological advances in phylogenetic comparative methods are needed to continue accommodating complex developmental, genomic, and transcriptomic data. Combined, these efforts would enable experimental validation of gene function across diverse lineages and improve reconstructions of the evolution of genetic pathways and the developmental origins of key phenotypes. Building this integrative framework will require both conceptual synthesis, collaboration, and community investment but offers a transformative path toward understanding the evolution of plant form and function.