Data from: 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
higher coverage across the 59 Ficus and 6 outgroup plastome assemblies
compared to using the nearest available reference plastome outside the
genus resulting in improved resolution and higher support of the
phylogenetic relationships within Ficus inferred from plastome data.
Chloroplast genome data confidently resolved relationships among major
groups of figs and largely support current understanding based on nuclear
sequence data including passively pollinated Neotropical section
Pharmacosycea as sister lineage to all other Ficus. However, conflicts
between the new plastome topology and previous nuclear studies are
observed for both individual species as well as relationships among some
sections at deeper levels. Conflicts could be caused by lack of resolution
in the nuclear data or may indicate potential cyto-nuclear discordance as
previously observed in an African lineage of Ficus.