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).