Resolving Allopolyploid Origins Within the Genus Clarkia Using a Novel Read-Mapping and Modeling Approach

Whole genome duplications are frequent in plants, but they pose difficulties in tracing the evolutionary relationships between species, particularly when the polyploidy results from hybridization. Numerous methods have been developed to address these challenges, yet most are computationally demanding, restricted in the number of species they can analyze, and heavily reliant on prior knowledge about the hybrid progenitors.

In this study, researchers introduce a streamlined, cost-effective, and computationally efficient technique to ascertain the approximate timing of hybridization and the most probable parent species of a specific allopolyploid species, even if those parents are extinct, ancestral, or unidentified. This method employs a dual strategy, first generating potential progenitor pair hypotheses by mapping sequencing reads from the polyploid onto a diploid pantranscriptome, and subsequently evaluating various hybridization scenarios to gauge the likelihood of each hypothesis.

To validate the effectiveness of their approach, the researchers apply their methods to six allotetraploid species within the Clarkia genus. Although their findings do not definitively establish the origins of these allopolyploids, they offer well-supported working hypotheses for further in-depth investigation.