Fig. 1
From: Estimates of introgression as a function of pairwise distances
A graphical interpretation of the df estimate. The distance fraction (df) estimates the fraction of introgression (f) by relating the differences of the genetic distances between taxa, here hi-lit by path lengths between ingroup taxa (d13= light blue, d23= dark blue) to the overall sum of the path lengths to the archaic population P3 taking into account derived alleles resulting in a change of path length distance. a. The four-taxon (P1, P2, P3 and O) species tree (gray) with coalescence at nodes denoted as P12, P123 and P123O. Path length P12-P123 helps visualize the scale of relative distance between taxa and signifies the shared distance of P1 and P2 to P3. b. Illustrates introgression from P3 to P2, here marked by derived alleles arising in and replacing the P3 lineage after the split leading to P12 (black dot). c. Without introgression d13=d23 and resulting in df=0 (left a & c). d. Introgression of derived alleles reduces genetic distance between P2 and P3 at the time of gene-flow (tGF) causing d23<d13 and df to be positive (right b & d). Note, allele replacement in example (b, d) corresponds to SNP pattern ABBA. The df estimate relates the reduced distance caused by introgression to the total sum of path length distances after introgression. A mutation on the P12-P123 path corresponds to the SNP pattern BBAA and signifies shared distance