As Celian Diblasi reaches the end of his PhD at NMBU, his work provides new insight into how complex genetic changes have shaped evolution in Atlantic Salmon over time and in different world regions.
Species evolution depends on variation in characteristics, or traits, between species members.
Structural variants as a driving force in evolution
Such variation typically comes from genetic mutations, where changes in the DNA sequence give some individuals a competitive advantage over others, and thus the ‘new’ DNA sequence becomes more prominent in subsequent generations.
Mutations come in many shapes and sizes, from simple edits in a single base pair (the building blocks of DNA), to more complex changes that affect broad parts of the genome. Examples of more complex mutations are so called structural variants, where DNA regions can be deleted, inverted, or – in more extreme examples – the entire DNA sequence (genome) can be duplicated. Such whole genome duplication (WGD) is like copying and pasting the organism’s entire instruction manual, and has happened in many species throughout history.
WGD can impact the development of new characteristics, where one copy of each gene maintains its usual function in its usual organ or body part while the other is able to take on a new role or to become active in a different place in the body. This, in turn, can make the species more adaptable to new environments, thereby guiding species evolution. However, complex genomic mutations such as WGD are difficult to study, and their precise role in driving evolution in different species is unclear.
Salmon as an ideal model to study structural variants
In this context, Atlantic salmon (Salmo salar) is an interesting model for studying a role for structural variants in shaping evolutionary processes. Salmonids underwent WGD approximately 100 million years ago, meaning they had double the number of gene copies (four instead of two). Since then, salmon have undergone a slow evolutionary transition returning from four copies of each gene back to behaving like a genome with the ‘normal’ two copies – a process termed rediploidization. However, not all ‘extra’ copies of the genes are necessarily lost during rediploidization; sometimes they take on new or shared roles in controlling cell behavior and are maintained alongside their ‘original’ counterpart.
Scientists have used Atlantic salmon to try to understand the mechanisms that control the activity of different genes after WGD, which are more complex than in species with only one copy of each gene. This helps improve our understanding of how structural variants such as WGD influence evolution. In addition, since different populations of wild and domesticated Atlantic salmon have evolved in different geographical locations, researchers are also able to assess the impact of different environments and breeding practices on evolution.
Old duplicates still performing important roles
The fact that this is still happening after 100 million years provides insight into how important this balance has been for the species to survive and adapt.
In his doctoral studies, Diblasi used Atlantic salmon to investigate patterns of gene regulation after genome duplication. In gill tissue, Diblasi’s work revealed that many duplicated gene pairs show compensatory gene expression – that is, the duplicated gene has been maintained over millions of years and still contributes to controlling cell behaviour today.
PhD student at Faculty of Biosciences, Department of Animal and Aquaculture SciencesPhoto: Tommy Normann
Genetic traces of domestication
When salmon are farmed, they are exposed to different environments and, therefore, selection forces compared to salmon that exist in the wild. Diblasi's PhD studies indicate that genes controlling the immune system have been particularly exposed to selection in domesticated populations.
Further, since European and North American Salmon have existed independently, Diblasi was able to investigate how these distant environments have differently shaped the salmon genome over time. Interestingly, two immune-related genes, called daxx and tapbp, have been under selection in domesticated populations in both continents, suggesting they have played an important role in the survival of domesticated fish irrespective of geographical location. In other cases, Diblasi identified gene pairs where one copy was affected by selection in Europe and the other was under selection in North America, demonstrating that duplicated genes can evolve differently when environments and/or breeding goals are different.
Improved understanding of genome duplication and its role in evolution
Overall, Diblasi ’s results provide a better understanding of how complex variants such as WGDs shape diversity in Atlantic salmon, including how domestication has influenced the health and robustness of these fish, which form an important part of global food systems. Many genes found in vertebrates today are known to originate from duplicated genes that arose after ancient WGD events, before the emergence of different vertebrate groups such as fishes, amphibians, reptiles, birds and mammals, including humans. Diblasi’s research into how duplicated genes function and evolve in Atlantic salmon can therefore provide broader insight into genome evolution across vertebrates.
Célian Diblasi will defend his doctoral thesis, “Structural variants and whole genome duplication in Atlantic salmon evolution”, on 16 March at NMBU.
Postdoctoral fellow Marie Saitou has been Diblasi’s main supervisor.
Co-supervisors: Associate Professor Simen Rød Sandve and researcher Nicola Jane Barson.