Evidence for post-allopolyploidy genetic exchanges between duplicated regions in three ancient polyploidies

Many successful lineages, including flowering plants and vertebrates, owe some of their evolutionary prosperity to whole genome duplications (WGD). However, in the immediate aftermath of a WGD, the new polyploid species that is formed often experiences multivalent pairings during meiosis, which can produce inviable gametes. To mitigate the potential harm caused by such pairings, most lineages eventually undergo "diploidization" to restore typical bivalent pairing. A key component of this process is the loss of duplicated genes. While diploidization was once thought to be rapid, recent analyses of polyploidies suggest the process may be more drawn out, with multivalent pairing persisting long after the initial WGD event. Here, we assess evidence for "late" diploidization after three different polyploidies: the teleost genome duplication (TGD), nested polyploidies in Paramecium lineages, and the ancient WGD in bakers yeast. Using our tool POInT (the Polyploidy Orthology Inference Tool), we model the resolution of these events. By analyzing discordance between expected species trees and observed gene trees, we argue that late diploidization was a likely feature in the resolution of all three polyploidies.