Scalable ARG-free Detection of Denisovan-mediated Superarchaic Introgression Reveals Heterogeneous Patterns across Populations

Ghost introgression from unsampled hominin lineages has emerged as an increasingly important component of human evolutionary history. Recent studies suggest that deeply divergent hominin lineages may have contributed ancestry either directly to modern humans or indirectly through Denisovan introgression, while inference remains difficult due to few reference genomes, weak signal, and uncertainty in reconstructing deep genealogies. Here we show analytically and through simulations that Denisovan-mediated superarchaic introgression produces predictable shifts in local coalescent depth that can be approximated by scalable summary statistics, particularly pairwise sequence divergence, suggesting