About 30% of protein-coding genes in the human genome are related through two whole genome duplication (WGD) events. Although WGD is often credited with great evolutionary importance, the processes governing the retention of these genes and their biological significance remain unclear. One increasingly popular hypothesis is that dosage balance constraints are a major determinant of duplicate gene retention. We test this hypothesis and show that WGD-duplicated genes (ohnologs) have rarely experienced subsequent small-scale duplication (SSD) and are also refractory to copy number variation (CNV) in human populations and are thus likely to be sensitive to relative quantities (i.e., they are dosage-balanced). By contrast, genes that have experienced SSD in the vertebrate lineage are more likely to also display CNV. This supports the hypothesis of biased retention of dosage-balanced genes after WGD. We also show that ohnologs have a strong association with human disease. In particular, Down Syndrome (DS) caused by trisomy 21 is widely assumed to be caused by dosage effects, and 75% of previously reported candidate genes for this syndrome are ohnologs that experienced no other copy number changes. We propose the remaining dosage-balanced ohnologs on chromosome 21 as candidate DS genes. These observations clearly show a persistent resistance to dose changes in genes duplicated by WGD. Dosage balance constraints simultaneously explain duplicate gene retention and essentiality after WGD. E arly in the vertebrate lineage the genome of our simple ancestor experienced radical upheaval from two rounds of whole genome duplication (WGD) and the subsequent chromosomal rearrangement and loss of many of the duplicate copies ("ohnologs") (1-3). Although only about 20-30% of the protein-coding genes in the human genome can be traced back to these events (ref. 3 and this study), the two tetraploid episodes in vertebrate history have frequently been credited with creating the conditions for the evolution of vertebrate complexity. Understanding the patterns of ohnolog retention is crucial to develop a unified model for the evolutionary impact of WGD and many groups have uncovered significant trends such as enrichment for developmental genes (4-6) and protein complex membership (7).Recently it was shown that mammalian ohnologs are more essential (i.e., knockout of one copy is more likely to lead to sterility or inviability) than paralogs generated by small-scale duplication (SSD) and are equally as essential as singleton genes (7). A prevalence of dosage-balanced genes among ohnologs was proposed to explain this contradiction of the theoretical, expected backup role of duplicated genes, which should buffer against such effects. Dosage balance may exist between two or more genes whose products interact or participate in the same pathway or process (8-10). According to the dosage balance hypothesis, changes in the relative dosage of gene product, such as would occur through duplication of some but not all of the balanced gene set, should...