Backbone phylogeny of Salix based on genome skimming data

The genus <i>Salix</i> is a common component of the Northern Hemisphere dendroflora with important ecological and economic value. However, taxonomy and systematics of <i>Salix</i> is extremely difficult and relationships between main lineages, especially deep phylogenies, remain largely unresolved. In this study, we used genome-skimming, plastome assembly, and single-copy orthologs (SCOs) from 66 <i>Salix</i> accessions, along with publicly available plastome and sequence read archive (SRA) datasets to obtain a robust backbone phylogeny of <i>Salix</i>, clarify relationships between its main lineages, and gain a more precise understanding of the origin and diversification of this species-rich genus. The plastome and SCO datasets resolved <i>Salix</i> into two robust clades, with plastome-based phylogenies lacking inner resolution and SCO offering fully resolved phylogenies. Our results support the classification of <i>Salix</i> into five subgenera: <i>Salix</i>, <i>Urbaniana</i>, <i>Triandrae</i>, <i>Longifoliae</i> and <i>Vetrix</i>. We observed a significant acceleration in the diversification rate within the <i>Chamaetia-Vetrix</i> clade, while <i>Salix</i> exhibited increased rates of diversification spanning from the early Oligocene to the late Miocene. These changes coincided with contemporaneous tectonic and climate change events. Our results provide a foundation for future systematic and evolutionary studies of <i>Salix</i>. Additionally, we showed that genome skimming data is an efficient, rapid, and reliable approach for obtaining extensive genomic data for phylogenomic studies, enabling the comprehensive elucidation of <i>Salix</i> relationships.