Phylogenomics reveals patterns of ancient hybridization and differential diversification contributing to phylogenetic conflict inPopulusL. andSalixL

Abstract

AbstractDespite the economic, ecological, and scientific importance of the generaPopulusL. (poplars, cottonwoods, and aspens) andSalixL. Salicaceae (willows), we know little about the sources of differences in species diversity between the genera and of the phylogenetic conflict that often confounds estimating phylogenetic trees.Salixsubgenera and sections, in particular, have been difficult to classify, with one recent attempt termed a ‘spectacular failure’ due to a speculated radiation of the subgeneraVetrixandChamaetia. Here we use targeted sequence capture to understand the evolutionary history of this portion of the Salicaceae plant family. Our phylogenetic hypothesis was based on 787 gene regions and identified extensive phylogenetic conflict among genes. Our analysis supported some previously described subgeneric relationships and confirmed polyphyly of others. Using an fbranchanalysis we identified several cases of hybridization in deep branches of the phylogeny, which likely contributed to discordance among gene trees. In addition, we identified a rapid increase in diversification rate near the origination of theVetrix-Chamaetiaclade inSalix. This region of the tree coincided with several nodes that lacked strong statistical support, indicating a possible increase in incomplete lineage sorting due to rapid diversification. The extraordinary level of both recent and ancient hybridization in bothPopulusandSalixhave played important roles in the diversification and diversity in these two genera.Supplementary data files will be provided by request tomatt.olson@ttu.edu