The genome sequence of a 45,000-year-old modern human from Ust'-Ishim

We present a high-quality genome sequence of a 45,000-year-old modern human from Siberia. This individual derives from a population that lived prior to – or simultaneously with – the separation of the populations in western and eastern Eurasia and carries a similar amount of Neandertal ancestry as present-day Eurasians. However, the genomic segments of Neandertal ancestry are substantially longer than those observed in present-day individuals, indicating that Neandertal gene flow into the ancestors of this individual occurred 7,000-13,000 years before he lived. We use the additional substitutions that have occurred in present-day non-Africans compared to this genome to estimate an autosomal mutation rate of 0.4-0.6×10-9/site/year and a Y chromosomal mutation rate of 0.7-0.9×10-9/site/year.