Phylogeography of Y-chromosome haplogroup Q1a1a-M120, a paternal lineage connecting populations in Siberia and East Asia

<b>Background:</b> Previous studies have suggested that the human Y-chromosome haplogroup Q1a1a-M120, a widespread paternal lineage in East Asian populations, originated in South Siberia. However, much uncertainty remains regarding the origin, diversification, and expansion of this paternal lineage. <b>Aim:</b> To explore the origin and diffusion of paternal Q-M120 lineages in East Asia. <b>Subjects and methods:</b> The authors generated 26 new Y chromosome sequences of Q-M120 males and co-analysed 45 Y chromosome sequences of this haplogroup. A highly-revised phylogenetic tree of haplogroup Q-M120 with age estimates was reconstructed. Additionally, a comprehensive phylogeographic analysis of this lineage was performed including 15,007 samples from 440 populations in eastern Eurasia. <b>Results:</b> An ancient connection of this lineage with populations in Siberia was revealed. However, this paternal lineage experienced an <i>in-situ</i> expansion between 5000 and 3000 years ago in northwestern China. Ancient populations with high frequencies of Q-M120 were involved in the formation of ancient Huaxia populations before 2000 years ago; this haplogroup eventually became one of the founding paternal lineages of modern Han populations. <b>Conclusion:</b> This study provides a clear pattern of the origin and diffusion process of haplogroup Q1a1a-M120, as well as the role of this paternal lineage during the formation of ancient Huaxia populations and modern Han populations.