The new Ancient Environmental Genomics group will start February 2022, and will be headed by Benjamin Vernot. We will study human history, with a particular focus on ancient DNA extracted from sediments. Our primary approaches are computational, including the development of methods for analyzing challenging ancient DNA datasets, and bioninformatic assistance in the development of new laboratory methods. The group closely collaborates with other groups from the Departments of Evolutionary Genetics and Archaeogenetics, and generates data through the Ancient DNA Core Unit - all housed at MPI-EVA in Leipzig.
Most ancient DNA is retrieved from bones or teeth - but many sites lack such skeletal elements. Furthermore, bones and teeth are deposited upon death, but an individual sheds DNA throughout their entire life, in principle leaving a trace of their presence where they lived and worked. Recent work (Vernot et al, Science, 2021) has demonstrated that human DNA can be retrieved from ancient sediments - including human nuclear DNA - and that this DNA can even come from single individuals! In addition to human DNA, most sediment samples contain abundant DNA from flora and fauna, providing insight into the environment in which these people lived.
We plan to use sediment DNA to understand the lives of ancient humans. Projects include:
- Where does the human DNA in sediments come from?
- In Holocene settlements, can we map out neighborhood structure, or even identify the houses where individuals lived?
- How were wild and domestic animals integrated into the lived environment? Can we reconstruct trade networks from the trade of livestock?
Much of this work is conducted in collaboration with Matthias Meyer and his Ancient DNA Methods group, who work on new laboratory methods for the isolation and sequencing of archaic human DNA from sediments and other unconventional sources.
Computational Methods Development
Ancient DNA produces famously “bad” datasets - that is, sequencing reads are short and damaged, and samples may have substantial levels of modern human contamination. To overcome these unique challenges, many tools are designed specifically for working with ancient DNA - although too often, samples with high levels of human contamination or with very small amounts of data are simply discarded.
Sediment DNA complicates this even more, as samples are essentially metagenomic - that is, they are composed of DNA from multiple species, and often multiple individuals from each species. In (Vernot et al, Science, 2021) and (Zavala et al, Nature, 2021), we introduced new methods for dealing with such metagenomic datasets, allowing fine scale resolution of Neandertal and Denisovan mitochondrial DNA haplotypes, and the resolution of individual Neandertal populations from nuclear DNA.
New methods are needed to extend these analyses to other groups and populations, for example to modern humans, where contamination and true ancient human DNA can be challenging to disambiguate.