Ancient genomes reveal structural shifts and pinpoint arrival of Steppe-related ancestry during the Chalcolithic/Bronze Age Transition in Italy

Across Europe, the Chalcolithic/Bronze Age transition was largely characterised by an influx of Steppe-related ancestry. The effect of this major shift on the genetic and kinship structure of populations in the Italian peninsula remains underexplored. We generated 46 whole-genome sequences from commingled and single burials in Northeastern and Central Italy dated between 3200 - 1500 BCE, filling a gap in the literature between 1950 - 1500 BCE. Our study confirms a diversity of ancestry components in the Chalcolithic in Italy and pinpoints the arrival of Steppe-related ancestry to at least 1950 BCE in Northeast Italy with an increase in this component in all samples through time. We detect patrilineal kinship in Chalcolithic commingled burials in Northeastern and Central Italy with a possible shift in population structure in the Bronze Age despite continuity of burial practice. We find an increase in the frequency of variants associated with protection against pathogenic mycobacterial infections between Italian Neolithic/Chalcolithic populations and Near Eastern Neolithic/Chalcolithic and post-Bronze Age populations in Italy. Our study provides a closer look at local dynamics of demography and selection as they occurred in the midst of a wide-spread phenomenon.