Extensive lineage-specific rediploidisation masks shared whole genome duplication in the sturgeon-paddlefish ancestor

Whole genome duplication (WGD) is a dramatic evolutionary event generating many new genes and which may play a role in survival through mass extinctions. Paddlefish and sturgeon are sister lineages that both show genomic evidence for ancient WGD. Until now this has been interpreted as two independent WGD events due to a preponderance of duplicate genes with independent histories. Here we show that although there is indeed a plurality of apparently ‘independent’ gene duplications, these derive from a shared genome duplication event occurring close to the Permian-Triassic mass extinction period, followed by a prolonged process of reversion to stable diploid inheritance (rediploidisation). We show that the sharing of this WGD is masked by the fact that paddlefish and sturgeon lineage divergence occurred before rediploidisation had proceeded even half-way. Thus, for most genes the resolution to diploidy was lineage-specific. Because genes are only truly duplicated once diploid inheritance is established, the paddlefish and sturgeon genomes are a mosaic of shared and non-shared gene duplications resulting from a shared genome duplication event. This is the first time that lineage-specific resolution of genes from a common WGD event has been shown to affect such a large proportion of the genome.