Unveiling Genetic Sex, Ancestry, Kinship, and Osteopetrosis Genetic Disease Through Ancient DNA From Highly Degraded Remains

Severe degradation of human remains often impedes effective anthropological and morphological analyses based on skeletal in archeology. However, advances in ancient DNA research have provided new perspectives on genetic sex determination, genetic ancestry, and the genetic architecture underlying phenotypic traits and inherited diseases. Here, we successfully retrieved DNA from three individuals of the Song Dynasty period from the Zhangliu site in Huai'an City, Jiangsu Province, China. Population genomic analyses demonstrate that these individuals are genetically continuous with Late Neolithic Yellow River millet farmers, indicating a north‐to‐south dispersal into the Huai River region with limited subsequent admixture from Yangtze River rice‐related populations. Through genome‐wide relatedness estimation combined with uniparental markers, we reconstructed a first‐degree pedigree comprising a father, mother, and their son. Within this pedigree, the mother and son share an osteopetrosis‐associated LEMD3 variant, a pattern fully consistent with autosomal dominant inheritance and the reconstructed familial relationships. Furthermore, we also identified East Asian‐specific variants, including EDAR rs3827760‐G associated with shovel‐shaped incisors and ABCC11 ‐rs17822931‐T associated with earwax. Despite the extremely poor preservation of these three individuals, which completely precluded morphological sex assessment, we successfully determined their genetic ancestry and obtained reliable genetic sex identification using a genetic approach. Our findings demonstrate the power of aDNA analysis in overcoming challenges posed by degraded remains and in linking genetic variants to inherited diseases in archeological contexts.