Convergent evolution of polyploid genomes from across the eukaryotic tree of life

By modeling the homoeologous gene losses that occurred in 50 genomes deriving from ten distinct polyploidy events, we show that the evolutionary forces acting on polyploids are remarkably similar, regardless of whether they occur in flowering plants, ciliates, fishes, or yeasts. We show that many of the events show a relative rate of duplicate gene loss before the first postpolyploidy speciation that is significantly higher than in later phases of their evolution. The relatively weak selective constraint experienced by the single-copy genes these losses produced leads us to suggest that most of the purely selectively neutral duplicate gene losses occur in the immediate postpolyploid period. Nearly all of the events show strong evidence of biases in the duplicate losses, consistent with them being allopolyploidies, with 2 distinct progenitors contributing to the modern species. We also find ongoing and extensive reciprocal gene losses (alternative losses of duplicated ancestral genes) between these genomes. With the exception of a handful of closely related taxa, all of these polyploid organisms are separated from each other by tens to thousands of reciprocal gene losses. As a result, it is very unlikely that viable diploid hybrid species could form between these taxa, since matings between such hybrids would tend to produce offspring lacking essential genes. It is, therefore, possible that the relatively high frequency of recurrent polyploidies in some lineages may be due to the ability of new polyploidies to bypass reciprocal gene loss barriers.

Automated summary

The study finds that the evolutionary forces acting on polyploids are remarkably similar regardless of the species they occur in. The rate of duplicate gene loss is relatively high in the early stages of polyploid evolution, suggesting that most selectively neutral duplicate gene losses occur during this period. There is strong evidence of biases in the duplicate losses, indicating that allopolyploidies with distinct progenitors are common. Additionally, reciprocal gene losses are ongoing and extensive between these polyploid genomes, making the formation of viable diploid hybrid species highly unlikely. The ability of new polyploidies to bypass reciprocal gene loss barriers may explain the relatively high frequency of recurrent polyploidy in certain lineages.