Fig. 6: ARG-based detection of archaic introgression tracts.
From: Robust and accurate Bayesian inference of genome-wide genealogies for hundreds of genomes
a, The demography model involving introgression and the un-introgressed (red) and introgressed (blue) lineages under the model. The time interval from the introgression time to the divergence time of the two populations is called the ‘introgression window’. b, The receiver operating characteristic (AUROC) plot of using coalescence ratio (CR) and long branch proportion (LB) from Relate and SINGER to differentiate the inferred introgressed and un-introgressed tracts from IBDmix. c, Identification of potential archaic introgression tracts. For a given leaf node, its pairwise coalescence times with every other leaf node in the marginal tree are summarized as a distribution. In the plot, each column represents such a distribution from marginal trees within a 10 kb window. The two white horizontal lines delineate the interval between the introgression time and the split time. A tract indicative of introgression should exhibit a depletion of coalescence events within this interval and an enrichment of coalescence events above the split time. Regions shaded in red denote putative introgression tracts. d, The ratio of pairwise coalescence density above the split time to that within the interval between the introgression time and the split time.
