Genome-wide study of a Neolithic Wartberg grave community reveals distinct HLA variation and hunter-gatherer ancestry

The Wartberg culture (WBC, 3500-2800 BCE) dates to the Late Neolithic period, a time of important demographic and cultural transformations in western Europe. We performed genome-wide analyses of 42 individuals who were interred in a WBC collective burial in Niedertiefenbach, Germany (3300-3200 cal. BCE). The results showed that the farming population of Niedertiefenbach carried a surprisingly large hunter-gatherer ancestry component (34–58%). This component was most likely introduced during the cultural transformation that led to the WBC. In addition, the Niedertiefenbach individuals exhibited a distinct human leukocyte antigen gene pool, possibly reflecting an immune response that was geared towards detecting viral infections. ; Introduction Results Discussion Methods - Samples - Osteological analysis - Radiocarbon dating - aDNA extraction and sequencing - Pathogen screening - Mapping and aDNA damage patterns - Genotyping - Genetic sex determination - Contamination estimation and authentication - Principal component analysis - ADMIXTURE analysis - Admixture dating - F3 outgroup statistics - qpAdm analysis - Kinship analysis - Determination of mitochondrial and Y chromosome haplotypes - Calling of phenotypic SNPs - HLA typing and analysis - Statistics and reproducibility - Reporting summary