You are here

Whole genomes: the holy grail. A commentary on: ‘Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastidgenomes’

TitleWhole genomes: the holy grail. A commentary on: ‘Molecular phylogenomics of the tribe Shoreeae (Dipterocarpaceae) using whole plastidgenomes’
Publication TypeJournal Article
Year of Publication2019
AuthorsOlmstead RG, Bedoya AM
JournalAnnals of Botany
Date Published05

This is a good case study of a problem that is common enough that anyone in this field encounters it sooner or later, and that occurs in many groups of organisms. Specifically, the situation in which extant members of a group form three clades resulting from divergence early in the evolutionary history of the group, and the crown of each clade is subtended by a relatively long branch going back to the early divergence events (Fig. 1).The authors offer two commonly attributed causes for this conflict, (1) hybridization and subsequent introgression leading to conflict among loci, or (2) incomplete lineage sorting in which individual loci may have evolutionary histories with different branching patterns as a result of retained polymorphisms that sort out differentially sometime after the branching event. The short internode and relatively long stem branches leading to each clade suggest that recent hybridization is not involved. This is further supported by their SplitsTree analysis. However, hybridization is generally thought of as a phenomenon restricted primarily to recently diverged species, and, other things being equal (e.g., population size, outcrossing rate) incomplete lineage sorting is more likely to occur when branches in a phylogeny occur in close temporal proximity. This makes distinguishing the two difficult, even with large amounts of data. In a similar study, Lee-Yaw et al. (2019) use whole plastid genomes and RADseq data to test introgression vs. incomplete lineage sorting among annual species of Helianthus, an extraordinarily well-studied group, where divergence times are estimated to be no more than 50 000 to 250 000 years. In what may be an ideal situation, they were able to tease apart evidence for multiple introgression events from lineage sorting. In the Dipterocarpaceae, with the estimated age of 28My (+/- 9My) for the critical nodes (Heckenhauer et al., 2017), it is unlikely that even the most sophisticated analyses currently available will be able to determine what process may have been at play.