Plastome phylogeny and lineage diversification of Salicaceae with focus on poplars and willows

Abstract

Phylogenetic relationships and lineage diversification of the family Salicaceae <i>sensu lato</i> (<i>s.l</i>.) remain poorly understood. In this study, we examined phylogenetic relationships between 42 species from six genera based on the complete plastomes. Phylogenetic analyses of 77 protein coding genes of the plastomes produced good resolution of the interrelationships among most sampled species and the recovered clades. Of the sampled genera from the family, <i>Flacourtia</i> was identified as the most basal and the successive clades comprised both <i>Itoa</i> and <i>Poliothyrsis</i>, <i>Idesia</i>, two genera of the Salicaceae <i>sensu stricto</i> (<i>s.s</i>.) (<i>Populus</i> and <i>Salix</i>). Five major subclades were recovered within the <i>Populus</i> clade. These subclades and their interrelationships are largely inconsistent with morphological classifications and molecular phylogeny based on nuclear internal transcribed spacer sequence variations. Two major subclades were identified for the <i>Salix</i> clade. Molecular dating suggested that species diversification of the major subclades in the <i>Populus</i> and <i>Salix</i> clades occurred mainly within the recent Pliocene. In addition, we found that the <i>rpl32</i> gene was lost and the <i>rps7</i> gene evolved into a pseudogene multiple times in the sampled genera of the Salicaceae <i>s.l</i>. Compared with previous studies, our results provide a well-resolved phylogeny from the perspective of the plastomes.