Estimating the time since admixture from phased and unphased molecular data

After admixture, recombination breaks down genomic blocks of contiguous ancestry. The breakdown of these blocks forms a new ‘molecular clock’, that ticks at a much faster rate than the mutation clock, enabling accurate dating of admixture events in the recent past. However, existing theory on the break down of these blocks, or the accumulation of delineations between blocks, so called ‘junctions’, has mostly been limited to using regularly spaced markers on phased data. Here, we present an extension to the theory of junctions using the Ancestral Recombination Graph that describes the expected number of junctions for any distribution of markers along the genome. Furthermore, we provide a new framework to infer the time since admixture using unphased data. We demonstrate both the phased and unphased methods on simulated data and show that our new extensions performs better than previous methods, especially for smaller population sizes and for more ancient admixture times. Lastly, we demonstrate the applicability of our method on an empirical dataset of labcrosses of yeast ( Saccharomyces cerevisae ) and on two case studies of hybridization in swordtail fish and Populus trees.