Julien Dutheil

For further information on the project refer to <https://molsysevol.github.io/> or contact Julien Dutheil <dutheil@evolbio.mpg.de> after having read the recommended literature.

Please submit your application via our online portal.

Efficient and robust inference of (and with) the ancestral recombination graph (ARG)

The ancestry of a sample of genomes taken in one or multiple populations is a complex entity, owing to the presence of recombination that makes the genealogy change along the genome. The resulting ancestral recombination graph (ARG) is at the core of statistical inference in population genomics. Because it is largely unknown, the ARG has traditionally been considered as a virtual object, modeled but not directly inferred. As the amount of available data exploded and new, efficient models of genome evolution within populations emerged, reconstructing the ARG is now a reachable goal, with the promise to unravel the evolutionary history of populations with unprecedented resolution.

In this project, we will explore ARG reconstruction methods from pairs of genomes. While the number of genealogies of a sample increases hyper-exponentially with its size, the ARG of a pair of genomes is comparatively simple. It consists in the set of times to the most recent common ancestor (TMRCA) of the two genomes, which can be efficiently inferred using hidden Markov chains under the sequentially Markov coalescent model. The doctoral project has two goals: 1) explore methods to obtain the most robust pairwise TMRCA estimates, and 2) design a method to efficiently combine pairwise estimates into a full ARG. The resulting inferred ARG will then be used, for instance, to infer demography and reconstruct recombination maps and ancestral alleles.

Reference:

- Gustavo V Barroso, Nataša Puzović, Julien Y Dutheil. Inference of recombination maps from a single pair of genomes and its application to ancient samples. PLoS Genetics (2019); 15(11):e1008449

Further reading:

- Alexander L Lewanski, Michael C Grundler, Gideon S Bradburd. The era of the ARG: An introduction to ancestral recombination graphs and their significance in empirical evolutionary genomics. PLoS Genetics (2024) 18;20(1):e1011110.