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The phylogenetic tree reveals deep divergences between Y chromosomes indigenous to Sahul, the ancient continent that included both Australia and New Guinea, and those from all other populations ( Figures 1 B and 1C). Complete sequence data allow direct and accurate inference of the timing of these divergences. Applying a point mutation rate of 0.76 × 10per site per year inferred from the number of missing mutations on the Y chromosome of a ∼45-ky-old radiocarbon-dated Eurasian sample [], we infer a divergence time of 54.3 ky (95% confidence interval [CI]: 48.0–61.6 ky) between K/M chromosomes in Sahul and their closest relatives in the R and Q haplogroups ( Figure 1 B), and a divergence time of 54.1 KY (95% CI: 47.8–61.4 ky) between Sahul C chromosomes and their closest relatives in the C5 haplogroup ( Figure 1 C), a distinction noted previously on the basis of a single SNP, M347 []. These dates are consistent with the archeological record documenting human occupation in Australia by ∼47 kya [] and with genome-wide analyses that have found an early divergence between the ancestors of Eurasian populations and the ancestors of Aboriginal Australians and Papuans []. They thus provide no evidence for any later Y chromosome gene flow into Australia between the early separation and the beginning of recent European colonization. Specifically, these results refute earlier findings based on short tandem repeat (STR) variation that Aboriginal Australian Y chromosomes in the C haplogroup descend from populations in southern India and Sri Lanka 1.3–13.3 kya []. Although the closest chromosomes to the Aboriginal Australian Cs in our phylogeny are found in South Asian populations, the deep divergence time and the fact that the Aboriginal Australian Cs share a more recent common ancestor with Papuan Cs show that this is not the result of recent genetic contact. The CIs reported above take into account the uncertainty of the Y chromosome point mutation rate, but not necessarily other possible sources of technical uncertainty (such as read alignment and genotype calling). We tested whether accounting for such additional uncertainty could affect the conclusion of a deep divergence between Aboriginal Australian and South Asian C chromosomes by re-estimating this divergence time from 100 bootstrap samples of sites from the full ∼10 million analyzed Y chromosome sites. The 95% CI for these estimates was 50.9–58.1 kya, and very conservative application of the mutation rate uncertainty multiplicatively to the bootstrap estimates gives a combined CI of 44.9–65.9 kya. Technical uncertainty is thus not large enough to affect our overall conclusion. The disparity between our findings and the earlier report can be attributed to improvements in technology, as none of the methods previously used to study the history of the paternal lineage offered the level of phylogenetic or dating precision afforded by complete Y chromosome sequencing. Redd et al. employed ten widely used Y STRs (three simple trinucleotides, three simple tetranucleotides, one of which was bilocal, and four complex tetranucleotides), applying the same fast genealogical mutation rate of 2.08 × 10per STR per 25 years to all of them []. It has been shown that Y STRs tend to massively under-estimate ancient divergence times [], perhaps because of a combination of the fast mutation rate assumed, saturation of STR distances, and in this case the short generation time used.