Fig. 2. Performance of ancIBD on simulated IBD segments.
a, Power and segment length errors. We copied-in IBD segments of lengths 4, 8, 12, 16 and 20 cM into synthetic diploid samples. We simulated shotgun-like and 1240k-like data (Supplementary Note 2) and visualize false positive, power and length bias for 2×, 1×, 0.5× and 0.25× coverage (rows). For each parameter set and IBD length, we simulated 500 replicates of pairs of chromosome 3, each pair with a single, randomly placed, copied-in IBD segment. The power (or recall) of detecting IBD segments of each simulated length is indicated in the text next to the corresponding grey vertical bar. Results for other coverages are shown in Supplementary Fig. 4. b, False positive rate. We downsampled high-quality empirical aDNA data without IBD segments (Supplementary Table 6) to establish false positive rates of IBD segments for various coverage and IBD lengths (Supplementary Note 7). The y axis shows the mean number of false positive IBD segments per pair of chromosome 3 in each length bin (bin width 0.25 cM). To contextualize these false positive rates, we also depict expected IBD sharing assuming various constant population sizes (dotted lines, calculated as described in ref. 58). If the false positive rate is on a similar order of magnitude or larger than expected for a population of that effective population size (Ne), individual IBD calls of that length for that coverage and demographic scenario are likely to be false positives.