First plastid phylogenomic study reveals potential cyto-nuclear discordance in the evolutionary history of Ficus L. (Moraceae)

Standard Sanger chloroplast markers provide limited information to resolve species level relationships within plants, in particular within large genera. Figs (Ficus L., Moraceae) compose one of the 50 largest genera of angiosperms with ∼750 species occurring in the tropics and subtropics worldwide. Figs, in addition to being a keystone food resource in rainforests, are well-known for the mutualistic interactions with their pollinating wasps. It is regarded as a model system for understanding co-evolution dating back more than 75 million years. However, despite significant taxon sampling, combinations of low copy nuclear, nuclear ribosomal and chloroplast regions have not been able to confidently resolve relationships among major groups of figs.

Using a high throughput sequencing approach we attempted to resolve the major lineages of Ficus based on plastome data. In this study, we show that the use of a de novo assembled plastome from within the genus provides less ambiguity and highe...