Nonadaptive molecular evolution of plastome during the speciation of Actaea purpurea and its relatives

We have seen an explosive increase of plant plastid genome (plastome) sequences in the last decade, and the view that sequence variation in plastomes is maintained by the mutation-drift balance has been challenged by new evidence. Although comparative genomic and population-level studies provided us with evidence for positive evolution of plastid genes at both the macro- and micro-evolution levels, less studies have systematically investigated how plastomes have evolved during the speciation process. We here sequenced 13 plastomes of Actaea purpurea (P.K. Hsiao) J. Compton, and its closest relatives, and conducted a systematic survey of positive selection in their plastid genes using the McDonald-Kreitman test and codon-based methods using maximum likelihood to estimate the ratio of nonsynonymous to synonymous substitutions (ω) across a phylogeny. We found that during the speciation of A. purpurea and its relatives, all plastid genes evolved neutrally or were under purifying selection. Genome size, gene order, and number were highly conserved. Comparing to A. purpurea, plastomes of Actaea japonica and Actaea biternata had low genetic diversity, consistent with previous studies. Our work not only sheds important light on the evolutionary history of A. purpurea and its kin, but also on the evolution of plastomes during plant speciation.