Plastid genomes of Shoreeae

Phylogenetic relationships in the ecologically and economically important tribe Shoreeae present a long-standing problem in the systematics of Dipterocarpaceae. Heckenhauer et al. employ next-generation sequencing (NGS)-based genome skimming to obtain whole plastid genome sequences of the tribe.

The team successfully used phylogenomic analyses of the entire plastid genomes for inferring phylogenetic relationships among genera and groups of Shorea sensu Ashton. Discordance in the placement of Parashorea was observed between phylogenetic trees obtained from plastome analyses and from previously available nuclear DNA datasets. This discordance could indicate ancient hybridization or incomplete lineage sorting.

In their commentary, Olmstead and Dvorsky say: “For as long as we have been constructing trees of evolutionary relationships using DNA sequences in plants, authors have been able to pass off responsibility for resolving conflict to future generations, or at least to future studies, by suggesting that with more taxa and more sequence data, the relationships will become clear. What happens when we meet the end of the road? In this study, excellent representative sampling is assessed for complete plastid genome sequences AND reduced representation data of the nuclear genome derived from RADseq to the tune of nearly 20 000 loci and over 100 000 SNPs. Despite the vast amount of data, the conflict between chloroplast and nuclear phylogenetic trees remains. The authors are left to speculate why.”

Heckenhauer and colleagues conclude: “Given the economic and ecological importance of tribe Shoreeae, the molecular phylogenetic studies must now prompt a search for diagnostic characters, a necessary prerequisite for any systematic and taxonomic revision.”