The History and Future of Plant Molecular Ecology

Abstract Molecular ecology links the smallest units of genetic variation to the largest patterns of ecological organization, encompassing the phenotypes, interactions, and fitness outcomes on which natural selection acts. Here we review plant molecular ecology as a series of transitions. Molecular markers first made natural variation visible and reconstructed the histories shaping plant distributions. A genomic era followed, in which reference genomes and population-scale sequencing identified the genetic basis of adaptation, though association alone could not reveal gene function in nature. Attention then shifted from correlation to function, testing the ecological roles of genes in native habitats. Advances in single-cell analysis have made it possible to link genes to function with far greater precision. Other technological advances have simultaneously pushed the field’s questions outward, toward communities and ecosystems increasingly reshaped by climate change. We discuss emerging approaches that seek to bridge this widening gap, and argue that a discipline born from the molecule must ultimately account for the ecosystem.