Transposable elements as a source of structural rearrangements, genetic conflicts and constraints to gene flow

Hybridisation between species is recognised as a process that can lead to the fast evolution of new phenotypes, but it can also introduce additional genetic conflicts or escalate them.

The hypothesis behind this project is that transposable elements (TEs) in hybrid genomes can increase in activity and cause new insertions that in turn can trigger the formation of new SVs like inversions. These new SVs can be a new source of genetic barriers.

Therefore, in this view, hybridisation will cause the escalation of genetic conflicts and the very elements underpinning the conflicts will create the barriers to further hybridisation and gene flow.In this project I aim to test this hypothesis using 240 phased genome assemblies for the species complex hispanica(and its hybrids) within the avian genus Oenanthe (wheatears) and I will: 1) detect TEs and SVs in all individuals; 2) find signatures of increased TE activity and SV formation; 3) detect and compare patterns of gene flow and test if regions resilient to gene flow are indeed enriched in new TE insertions and SVs.

Thanks to multiple hybrid zones involving different combinations of species I will be able to find common and lineage-specific patterns of gene flow.

This project therefore aims to investigate the core question of evolutionary biology regarding which molecular mechanisms underpin species formation and isolation. The results of this project can be important for the conservation of hybridising endangered species.