Extended Data Fig. 6: Effect of phasing errors on IBD dates.
From: Paths and timings of the peopling of Polynesia inferred from genomic networks
IBD segments on the island of Rapa Nui were identified between all male X chromosomes. The log of the number of IBD segments (y axis) of a given genetic length (x axis) is plotted (orange; bottom left). The expected exponential decay of IBD segment lengths (linear semilog plot) is seen. The slope of this line (−0.161) is the exponential (decay) constant lambda. Since the X chromosome is perfectly phased in men, because it is haploid, the identification of these IBD segments is unaffected by errors introduced through phasing algorithms. To quantify the effect of such errors, synthetic-female individuals were constructed by combining two male X chromosomes to make a diploid pair and to erase the phase information by recording only the genotype. The unphased diploid genotypes so constructed were phased and IBD segments were again identified and plotted (green; bottom right). The difference between the exponential decay constant (−0.166) of these statistically phased genotypes and the previous one is seen to be minor (top panel), amounting to three per cent (3.01%), which corresponds to a difference of around 25 years for dates approximately eight hundred years ago (as in Polynesia). Uncertainty in the slope of the lines (equivalent to the uncertainty in the estimate exponential decay constant) is shaded.
