Evaluating the applicability of kinship analyses for sedimentary ancient DNA datasets

Abstract Kinship reconstruction in ancient populations provides key insights into past social organization and evolutionary history. Sedimentary ancient DNA (sedaDNA) enables access to deep-time human populations in the absence of skeletal remains. However, it is characterized by severe degradation and the potential mixture of genetic material from multiple individuals, raising questions about its suitability for kinship inference. Here, we use extensive simulations to evaluate the feasibility and limitations of kinship inference in sparse and damaged sedaDNA data, with a focus on Neandertals. We find that the main obstacle to accurate kinship inference in sedaDNA is the presence of multiple contributors to a given sample. To address this, we introduce a simple heterozygosity-based test to identify samples containing DNA from multiple individuals. Guided by these results, we analyze published Neandertal sedaDNA from the Galería de las Estatuas site to assess the practical limits of kinship inference in real sedimentary ancient DNA data. Together, our results define methodological considerations and practical limits for kinship inference in sedimentary ancient DNA.