Molecular phylogenetic tree, whole-genome duplication and divergence events
Based on collinear homologous gene pairs, including interspecific orthologs and intraspecific paralogs without tandem repeats, we aligned protein sequences using MUSCLE (Edgar, 2004), then used PAL2NAL to carry out codon alignment (Suyama, Torrents, & Bork, 2006). The YN model-based Ka and Ks calculation was performed using KaKs_Calculator (Z. Zhang et al., 2006). Finally, we constructed a molecular phylogenetic tree using RAxML (Stamatakis, 2014) based on the GAMMA+GTR model. Assuming the divergence time of Populus andSalix –48 Mya (Manchester et al., 1986) as fossil calibration, we estimated dates for divergent events of poplar species using r8s (Sanderson, 2003). We also contructed a phylogenetic tree of the chloroplast genomes derived from 15 white poplar species and P. trichocarpa(File S1).