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In our prior work by Hose  et al. , we performed a genome-sequencing survey and reported that aneuploidy was frequently observed in wild strains of  S. cerevisiae.  We also profiled transcriptome abundance in naturally aneuploid isolates compared to isogenic euploid controls and found that 10–30% of amplified genes, depending on the strain and affected chromosome, show lower-than-expected expression compared to gene copy number. In Hose  et al.,  we argued that this gene group is enriched for genes subject to one or more modes of dosage compensation, where mRNA abundance is decreased in response to higher dosage of that gene. A recent manuscript by Torres  et al.  refutes our prior work. Here, we provide a response to Torres  et al. , along with additional analysis and controls to support our original conclusions. We maintain that aneuploidy is well tolerated in the wild strains of  S. cerevisiae  that we studied and that the group of genes enriched for those subject to dosage compensation show unique evolutionary signatures.

Further support for aneuploidy tolerance in wild yeast and effects of dosage compensation on gene copy-number evolution