An organism’s phenotype depends on a multitude of genetic variants, spread over a linear genome. This is widely understood, and yet in practice, has hardly been incorporated into population genetic analysis. Recent developments in theory, computation, and sequencing technology now make it possible to obtain and analyse whole haploid genomes on a large scale.
We were recently awarded an ERC grant, HaplotypeStructure, which will support analysis of genetic variation that is spread over continuous linear genomes. Theory and methods will be developed in close interaction with empirical data from artificial selection experiments and from the intensely studied hybrid zone in Antirrhinum; for both, we have a known pedigree, and phased whole-genome sequence. The project will develop better tools for inferring selection and population structure from DNA sequence data, and more fundamentally, will give us a deeper understanding of how the abundant variation that is carried on linear genomes is shaped by evolution.
Arka Pal and Sean Stankowski are analysing whole-genome data from the Antirrhinum hybrid zone, using the new “haplotagging” method, developed by Frank Chan (MPI Tübingen; Meier et al., 2020). Anastasia Tsyhanova is working with Matthew Robinson to find ways to include haplotype structure into large GWAS analyses. Diego Garcia and Anja Westram are using whole-genome sequence from the marine snail Littorina to understand local adaptation.
Daria Shipilina, Sean Stankowski, Arka Pal, et al. 2022. On the origin and structure of haplotype blocks. Authorea. DOI: 10.22541/au.164425910.09070763/v1
Meier, J.I., Salazar, P.A., Kucka, M., Davied, R.W., Dreau, A., Aldas, I., Power, O.B., Nadeau, N.J., Bridle, J.R., Rolian, C., Barton, N.H., McMillan, O., Jiggins, C.D., Chan, Y.F. 2020. Haplotype tagging reveals parallel formation of hybrid races in two butterfly species. PNAS 118:e2015005118