Sediment DNA reveals Neandertal population history

Abstract

The study of hominin history has progressed through both archaeological and genetic insights. However, many archaeological sites lack associated hominin fossils, frustrating genetic analyses. Even when fossils are found, they often do not cover the full time-span of a site, or sampling them for DNA may not be possible. Here we present targeted enrichment and sequencing of hominin nuclear DNA from sediments, and insights into human history derived from this DNA. We developed methods to capture hominin DNA even in the presence of homologous faunal DNA, and evaluate the extent of microbial and faunal DNA in our data. We applied these methods to sediment samples from Galería de las Estatuas, a site in northern Spain, and Denisova and Chagyrskaya caves, in the Altai Mountains in southern Siberia, and identified and sequenced Neandertal nuclear DNA in stratigraphic layers spanning 55k - 200 thousand years ago. We then placed each sample on the Neandertal phylogenetic tree, inferring the most likely divergence date from a lineage. In Estatuas we demonstrate a population transition, and associate this change with specific layers. In Chagyrskaya, all layers are associated with a single Neandertal lineage, suggesting a more homogenous occupation. This work demonstrates that detailed genetic analyses may be possible from many more archaeological sites than was previously thought, and is particularly encouraging for time-series studies of single sites, or for sites with a sparse fossil record.