Heterozygote frequencies in Juglans and Pistacia P1+P2 datasets are 0.003 and 0.002 respectively, 20-50X lower than in their corresponding P1 and P2 datasets (Table 1). The proportion of heterozygous genotypes in P1 and P2 datasets increases strongly with increasing read depth, whereas the proportion in P1+P2 datasets is not affected by read depth (Figure 2). Most heterozygous genotypes in P1+P2 datasets are concentrated in a few individuals, probably due to cross-contamination during DNA extraction or library preparation (Figure 2). Therefore, the dual alignment strategy for interspecific hybrids results in effectively haploid datasets and enables simple detection and removal of cross-contaminated samples.