Concordance between genotypes before and after downsampling
To assess the robustness of each alignment strategy to reduced sequencing depth, raw Illumina files were downsampled by 50%, and genotype calls for each taxon from the imputed, downsampled datasets were compared to genotype calls from the full imputed datasets. Concordance between full and downsampled datasets is much higher using dual alignment (P1+P2; Figure 3). Downsampling also results in a one-third reduction in heterozygosity in P1 and P2 datasets but does not affect the proportion of heterozygous genotypes in P1+P2 datasets (Table 1). With increasing sequencing depth, concordance in P1+P2 datasets increases as expected, whereas concordance in P1 and P2 datasets is unexpectedly higher at low depth than at intermediate sequencing depth.