To study genome doublings, we used homologous copy-number information – that is, the copy numbers, bi and ci, of the two homologous chromosome segments at each locus. By looking at the distribution of bi, ci across the genome, we could draw inferences regarding genome doubling. Immediately following genome doubling, both, bi and ci would be even numbers. Following the loss of a single copy of a region, the larger of bi and ci will remain even, but the smaller would become odd. In fact, when we looked at high-ploidy samples, we discerned that the higher of bi and ci was usually even throughout the genome, consistent with their having arisen by doubling of the entire genome (Supplementary Fig. 9). Using simulations, we found that the observed profiles were unlikely to arise due to SCNAs occurring in serial fashion at multiple independent chromosomes (P < 1e-3; Online Methods).
