Evolutionary change through genomic admixture in a hybrid fish

• Applicant: Dr. Stefan Dennenmoser
• Subject Area: Evolution, Anthropology
• Term: from 2019 to 2023
• Project identifier: Deutsche Forschungsgemeinschaft (DFG) - Project number 418090872

Evidence that admixture between divergent lineages may enhance evolutionary processes is accumulating, but how exactly it affects evolutionary change is still highly contentious. One effect of great relevance is broadly summarized under the terms “genomic shock” or “genomic instability”. For example, activation of transposable elements (TEs) or increased rates of non- homologous recombination may introduce new copies. However, despite the fact that transposition has been known since before the genomic era, it remains largely unknown which of the proposed mechanisms explain the accumulation of TE copies in natural hybrid lineages. Herein, I propose to address questions regarding evolutionary dynamics of admixed genomes by taking advantage of technological advances, a young lineage of hybrid origin (Invasive Cottus) and the extensive experience and resources available to study it. In my recent genome wide analysis of gene duplications and transposition in European Cottus I have found a conspicuous increase of copy numbers of repetitive and transposable elements invasive Cottus. This could be explained by a transposition burst, but also by an expansion of centromeric regions where repetitive elements and TEs are abundant. Centromere expansion could represent a mechanism that compensates for unequal centromere lengths when two parental species hybridize (centromere drive). Hence, TE accumulation in hybrids could be explained by a transposition burst or alternatively, as an indirect effect of genomic stabilization. I propose to combine long-read sequencing with different experimental approaches designed to distinguish between TE activity and expansions of repetitive regions as possible causes of TE accumulation. Evolutionary change of genomic stability will be assessed through population-wide data of structural re-arrangements. This data will be collected from both hybrid and parental populations using nanopore sequencing. The generation of ultra-long sequences will allow to assemble centromeric regions, which can be tested for size expansions in hybrids with ChIP-seq experiments that use a CENP-A antibody to obtain individual centromeric sequence reads. Changes in methylation patterns that may affect transposon silencing will also be investigated using the nanopore sequencing data. Finally, I will use small-RNA sequencing to test for rapid evolution of small-RNA-mediated TE silencing in invasive Cottus.

• DFG Programme: Research Grants