Polyploidy and genome evolution

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Polyploidy, or whole-genome duplication (WGD), is a crucial driver of biodiversity, significantly impacting genome structure, organization, and evolution. Once thought to be a speciation process limited to plants, it is now acknowledged as a key factor in the evolution and gene content of most eukaryotic genomes. The diversity of eukaryotes is closely linked to multiple WGDs. This phenomenon creates new genomic interactions that lead to “genomic and transcriptomic shock,” which must be resolved in new polyploid lineages. Essentially, it acts as a “reset” button, prompting genomic changes that can foster adaptive speciation. This work synthesizes the theoretical foundations of polyploid genome evolution with empirical patterns observed in various polyploid groups. While the focus is primarily on plant models, recent research on vertebrates and fungi offers new insights into the mechanisms behind polyploid speciation and genome shaping. The emerging view is that polyploidy induces changes in genome structure and gene regulation, resulting in genetic and phenotypic novelty observable at chromosomal, physiological, and organismal levels, with significant ecological and evolutionary implications.