Ancient genomic evidence uncovers a 6th-century cross-border couple between South Asia and East Asia

The relationship between culture and ancestry is complex. Since the 2nd century, the Silk Road has facilitated human mobility across continents, complicating the determination of ancestry based on cultural traits, as evidenced by archaeological findings and historical accounts. In 2005, a 6th-century couple’s joint tomb was found east of Northern Zhou’s Chang’an city. According to conflicting epitaph texts, the male, Li Dan, has an ambiguous ancestry, possibly from East or South Asia. Archaeological materials blend Eastern and Western influences, posing challenges for researchers. In this study, we generated high-coverage genomes on the 1240k panel for the couple, covering 1,057,118 and 1,048,087 SNPs with average depths of 3.53x and 4.10x, respectively, revealing distinct northern South Asian and northern China-related ancestries. For Li Dan, genetic analysis reveals a close relationship with modern Brahmins, supporting his Brahmin status and his biography as the progeny of Brahmanic descent. Alongside the eclectic archaeological culture, we believe Li Dan preserved his ethnic heritage while forming an integrated Chinese cultural identity. This study highlights the value of integrating genetic studies with archaeological and historical research, providing the first genomic evidence of a cross-border couple between South Asia and East Asia in the 6th century.