Figure 1: Overview of the ancIBD algorithm.

a) Sketch of the ancIBD Hidden Markov Model. The ancIBD HMM has five states: one background state of no allele sharing, and four states modeling the four possible IBD sharing states between two phased diploid genomes. We model phase switch errors within a true IBD segment as a transition between the four IBD states. b) Visualization of the full pipeline to call IBD. First, ancient DNA data is imputed and phased using published software (GLIMPSE) and a panel of modern reference haplotypes, and then our HMM (ancIBD) is applied to screen for IBD. The final output consists of two .tsv tables, one listing all inferred IBD segments and one listing IBD summary statistics for each pair of individuals.