Graph transformer for ancient ancestry inference

Local ancestry inference classifies segments of DNA in admixed individuals by their originating population. However, as the date of admixture becomes older, these segments become shorter and determining their ancestry becomes increasingly difficult. This limits many existing segment-based methods to relatively recent historical admixture events and more highly diverged populations. The rapidly expanding availability of ancient DNA offers a promising opportunity to use these ancient samples as references for local ancestry inference. A recent approach integrates ancient samples into the ancestral recombination graph (ARG) for local ancestry inference. Here, we introduce recent advances in deep learning for graphs into this ARG framework to create ARGMix, a graph transformer that infers local ancestry using the coalescent trees of the inferred ARG. Our approach employs ancient samples as references in the marginal trees to predict local ancestry. We train ARGMix on data reflecting the well-understood ancient European demography and demonstrate improved accuracy and robustness even under demographic misspecification. We then apply ARGMix to an ARG of ancient and present-day European samples for ancestry-specific analyses, finding evidence of continuity between Ötzi the Iceman and present-day individuals from nearby regions.