AbstractWhole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD–derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance are still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliateParamecium tetraureliaand two of its sister species from theParamecium aureliacomplex. Here, we report the genome sequence and analysis of 10 additionalP. aureliaspecies and 1 additional out group, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the crypticP. aureliacomplex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower inParameciumthan in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong inParamecium. A near complete lack of recent single-gene duplications inParameciumprovides additional evidence for strong selective pressures against gene dosage changes. This exceptional data set of 13 species sharing an ancestral WGD and 2 closely related out group species will be a useful resource for future studies onParameciumas a major model organism in the evolutionary cell biology.