Uncovering the importance of structural genomic changes for speciation and adaptation in a changing world: a pangenomic approach

This project is focussed on characterization and quantification of SVs, an aspect of genetic variation that has until recently received relatively little attention within population genetics.

With the advent of new sequencing techniques, especially the application of long reads and new pangenomic approaches to construct a high-confidence SV-truthset against which short-read genomes can be mapped, it is now entirely feasible to investigate the population genetic nature of SVs.

I will study grouse (genus Lagopus) and will be able to rely to a large extent on existing whole genome sequence data gathered in my previous projects. With limited additional sequencing efforts, I will identify and genotype SVs across natural populations. Furthermore, I can use these data to address whether SVs are associated with speciation and local adaptation.

Moreover, I can investigate whether SVs are involved in generating Bateson-Dobzhansky-Muller incompatibilities and thus generate outbreeding depression.

The latter is of fundamental importance for understanding how locally adapted phenotypes may persists in the face of gene flow, and in practical conservation when choosing individuals for ex-situ conservation populations (populations kept in captivity for the purpose of reintroduction), as well as translocations among fragmented and endangered populations.

These approaches are becoming increasingly more relevant, more important, and applied to the conservation of threatened species.