What Genome Sequencing May Be Hiding From You: Lake Whitefish (Coregonus clupeaformis) as a Cytogenetic Case Study

Progress has been made towards whole genome characterization of many species of fishes, which is a powerful tool in conservation genetics. However, a neglected component of these studies is the use modern cytogenetic, especially in diverging lineages to understand the genomic causes and consequences of divergence, and thus the conservation of unique wild populations.

In Northeastern North America, two lake whitefish lineages have colonized post-glacial lakes ~12,000 YBP following an allopatric period of ~60 000Y. A dwarf limnetic ecotype has then evolved repeatedly from the normal benthic ecotype. Evidence suggest that the accumulation of genetic incompatibilities in allopatry might have facilitated this divergence, despite ongoing gene flow and low nucleotide divergence. In order to improve our understanding of this divergence, we applied modern cytogenetic methods to three natural lake whitefish sympatric pairs. Conventional approaches revealed a salmonid karyotype of type A, combined with extensive polymorphism mostly shared by the three species pairs. FISH results are consistent with transposition burst of rDNA genes. Our results indicate ongoing genomic rearrangements between these diverging ecotypes, mainly involving the labile portion of the genome. As such, cytogenetic is highly complementary to genomic approaches and should be incorporated towards a full understanding of natural populations.