For RASPberry analyses, SNPs with missing data in the parental genotypes were removed using Plink 1.07 (Purcell et al. 2007), the parental genotypes (50) were phased with fastphase (Scheet & Stephens 2006) by creating the input files with FCGENE (Roshyara & Scholz 2014), and ancestries for each admixed individual were estimated in ADMIXTURE (Alexander et al. 2009). For the local ancestry analysis, we called SNPs across the whole sequence of chromosome 6, 12 and 15 based on 118 individuals, and obtained the probabilities for P. balsamifera, P. trichocarpa or mixed ancestry for each SNP and considered only those with probabilities >95% in one of the three categories with RASPberry.