For the 11 trisomic chromosomes, it is not possible to determine whether these duplications are recent or ancestral, because even a recent duplication of a single chromosome leading to trisomy would result in previously disomic frequencies appearing trisomic. Nevertheless, the trisomic plots and the clear absence of frequencies resembling disomy or tetrasomy demonstrate that all of these chromosomes are trisomic in this sample rather than a combination of disomic and tetrasomic states. This method, in combination with read depth coverage, can be used to discriminate between recent and established aneuploidy in the case of tetrasomic chromosomes, or other chromosomes that exist as multiples of 2n. The same analysis was performed on L. braziliensis, which shows that 30 of 35 chromosomes are clearly trisomic (Fig. 4E), three are tetrasomic (chromosomes 4, 5, 29) (Fig. 4F), and one hexasomic (chromosome 31) (Fig. 4G), closely matching read depth analysis (Fig. 3D). One chromosome (chromosome 14) has an ambiguous profile closely resembling that of the tetrasomic chromosomes (data not shown). Taken together, these data indicate that L. braziliensis strain M2904 is primarily triploid but contains several tetrasomic chromosomes, and intriguingly six copies of chromosome 31.