Fig. 1.

Homoploid hybridization—gene flow between individuals with the same ploidy level (which in this example are both polyploid individuals)—can lead to differential introgression in subgenomes, either due to random events or in association with natural selection against some admixed genotypes as shown above. The parental populations (populations 1 and 2) are assumed to have two subgenomes with disomic inheritance (indicated with light blue and dark blue or red and purple, respectively, with color differences within each subgenome representing population subdivision). Gametogenesis in a hybrid individual produces gametes with a mosaic of population variation in each subgenome, depicted here as blocks that include entire chromosomes (in reality, recombination would likely generate smaller blocks of population-specific variation within each chromosome). If some backcrossed individuals have low fitness (gray) and high fitness individuals successfully breed in one parental population, different proportions of each subgenome may introgress, here shown as an extreme example of introgression only in subgenome 2.