Phylogenomics reveals patterns ancient hybridization and differential diversification that contribute to phylogenetic conflict in willows, poplars, and close relatives

Despite the economic, ecological, and scientific importance of the genera
Salix L. (willows) and Populus L. (poplars, cottonwoods, and aspens)
Salicaceae, 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. Salix subgenera and sections, in
particular, have been difficult to classify, with one recent attempt
termed a ‘spectacular failure’ due to a speculated radiation of the
subgenera Vetrix and Chamaetia. 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 fbranch analysis 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 the
Vetrix-Chamaetia clade in Salix. 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 both Salix and Populus have played important roles in the
diversification and diversity in these two genera.