The slow, and sometimes incomplete, journey to diploidy

Whether you are reading this as a plant, an animal, or fungus, it is likely that some ancestor of yours doubled up on genomes. However, it is likely that these extra genomes disappeared over evolutionary time. What gives? Where are those extra genomes that I should have rightfully inherited?

Diploidization, the mysterious process that reigns extra genomes back to a diploid state, has been a vexing complexity for those who are trying to piece together the evolutionary history of ancient polyploids. For example, diploidization appears to happen at different rates at different chromosomes/loci in fish and maize.
So there are two outstanding questions. First, what taxa have undergone paleopolyploidy events? Second, how did they get back to diploidy?
The gradual descent into diploidy
One of the more recent whole-genome duplication events occurred in Salmonid fishes ~80 million years ago, making it a group of interest for understanding some long term evolutionary consequences of diploidization while still having enough genomic resolution to actually detect those consequences. In a recent issue of Nature, Lien et al. characterize the Atlantic Salmon genome in an attempt to document the ongoing process of diploidization in this species.
Indeed, Atlantic Salmon are still returning to diploidy:

Without exception, duplicated regions exhibiting rearrangements at telomeres in the form of inversions, translocations or larger deletions all displayed a sequence similarity of ∼87%. This clear correspondence between the degree of intra-block sequence similarity and blocks predicted to still participate in tetrasomic inheritance (or recently have done so) suggests that up to 25% of the salmon genome experienced delayed rediploidization after the initial large chromosome rearrangements, and that as much as 10% of the genome may still retain residual tetrasomy

From Figure 3c of Lien et al. (2016), displaying a hypothetical model of post genome duplication (Ss4R) rediploidization.

From Figure 3c of Lien et al. (2016), displaying a hypothetical model of post genome duplication (Ss4R) rediploidization in Atlantic Salmon.

During this process of diploidization, duplicated genes that are nonfunctional are often lost. Those functional duplicates that stick around can be the result of neofunctionalization, where one duplicate acquires a new function compared to the other, or subfunctionalization, where each duplicate retains only one part of the function from their ancestral gene. Lien et al. suggest more instances of neofunctionalization in Atlantic Salmon compared to subfunctionalization.

The predominance of cases where only one copy has changed its regulation compared to the assumed ancestral state indicates that regulatory subfunctionalization has not been a dominant duplicate retention mechanism post [genome duplication event], unless it was followed by subsequent neofunctionalization, which has been suggested as a common process.

When diploidization gets odd
Where the Atlantic Salmon may be steadily becoming diploid while retaining genes with new functions, another recent publication highlights a taxon in which diploidization got…odd.
The heartleaf bittercress (Cardamine cordifolia) is a widespread and ecologically-successful flowering plant in Western North America that happens to be triploid. This scenario is unusual because other triploid relatives are sterile. What makes C. cordifolia so special?

"Chromosome painting"

“Chromosome painting” is a technique to visualize happy little chromosomes using in situ hybridization

Mandakova et al. used chromosome painting to investigate the paradoxical genome number in C. cordifolia, and it turns out that the chromosome counts of C. cordifolia were not what they seemed. Due to four separate chromosome translocations, the ancestral tetraploidy of C. cordifolia has been reduced to (pseudo)triploidy in this species:

…the pseudotriploid genome of C. cordifolia originated through diploidization of a primary tetraploid ancestral genome. Hence, C. cordifolia , while being a functionally diploid species, arose from a tetraploid genome. The extant genome of C. cordifolia originated from its tetraploid progenitor through descending dysploidy, whereby the origin of four translocation (“fusion”) chromosomes reduced the original number of linkage groups from 16 to 12.

The authors justifiably conclude that chromosome counts can be misleading when interpreting the evolutionary histories of polyploid species, especially when “diploidization” doesn’t result in a diploid at all.
Lien, S., Koop, B. F., Sandve, S. R., Miller, J. R., Kent, M. P., Nome, T., … & Grammes, F. (2016). The Atlantic salmon genome provides insights into rediploidization. Nature. doi:10.1038/nature17164
Mandáková, T., Gloss, A. D., Whiteman, N. K., & Lysak, M. A. (2016). How diploidization turned a tetraploid into a pseudotriploid. American Journal of Botany. doi:10.3732/ajb.1500452

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