Plastome Phylogenetics: 30 Years of Inferences Into Plant Evolution

Abstract From restriction site analyses to whole plastid genome sequences, our understanding of green plant (Viridiplantae; ~ 500,000 extant species) evolutionary relationships over the past three decades has largely been informed by analyses of the plastid genome. The plastid genome has informed studies ranging from population genetics to phylogenetics, the latter ranging from the intraspecific level to studies of all green plants. Diverse portions of the genome ranging from plastid spacers to entire genomes provide valuable data for plant evolutionary biologists. Recent phylogenetic analyses using whole plastid genomes sampled from over 2000 species representing all major groups of green plants have both solidified our understanding of relationships and highlighted the few key nodes in plant evolutionary history that remain unresolved. Likewise, detailed large-scale analyses of plastomes across angiosperms reinforce firmly supported nodes but fail to resolve a handful of remaining questionable relationships. The long history of plastid phylogenetics will serve as a reference point as scientists continue to expand beyond the plastid genome and include more nuclear and mitochondrial data in their analyses. These comparisons are crucial in that recent studies indicate some discordance between nuclear and plastid gene trees both across green plants as a whole and within angiosperms. Rather than being a source of concern, these discordances point to the complex and intriguing one-billion-year evolutionary history of the green plant clade, a clade that is foundational to life on Earth.