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

Whole genome duplications are a common occurrence in plants, but this creates challenges for reconstructing the evolutionary history between species, especially when polyploidy is a result of hybridization. While multiple methods have been developed to try to tackle these issues, most are computationally intensive, restrictive on the number of taxa that can be evaluated, and benefit immensely from a priori hypotheses about the allopolyploid progenitors, rendering these methods unfeasible for many understudied polyploids. We present a rapid, low-cost, and computationally light method for determining the relative time of hybridization as well as the most likely progenitor species of a given allopolyploid species, including progenitors that are extinct, ancestral, or unknown. The method utilizes a combined approach of first mapping sequencing reads from the polyploid against a diploid pantranscriptome to generate hypotheses about possible progenitor pairs and then modeling various hybridization scenarios to estimate the likelihood of each hypothesis. We demonstrate the utility of our methods by identifying likely progenitors and times of origin for six allotetraploid species from the genus Clarkia. While the methods outlined here do not conclusively confirm the origins of these allopolyploids, they provide well-supported working hypotheses for further intensive exploration.