Haplotype sharing among modern Australians and the two highest-coverage ancient individuals (KP1 and MH8) was inferred using ChromoPainter (48). Haplotype phase was reconstructed for the full set of individuals with diploid genotypes using Shape-IT (49). We then performed chromosome painting for the two ancient individuals as recipients, using all modern Australians, as well as selected outgroups (French, Han, Papuan, and Bougainville) as potential donors. Differential sharing for the pair of ancient individuals was quantified using the symmetry statistic (50)Embedded ImageSEs were obtained using a block jackknife across the 22 autosomes.

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