Our closest evolutionary relatives, Neandertals and Denisovans, died out roughly 40,000 years ago. Understanding how we differ from them is a major goal of paleoanthropology. Technical improvements in the retrieval of DNA from fossil bones, teeth and sediments have recently provided access to genetic data from the Middle and Upper Palaeolithic, the crucial time period where early modern humans expanded out of Africa and met Neandertals and Denisovans. The genetic study of these time periods is mainly limited by sample availability: under ideal conditions, DNA is preserved for up to two million years, but preservation varies highly between regions and climatic conditions; in Europe, DNA older than 40,000 years old is rare. Thus, despite advances in sequencing technologies and ancient DNA protocols, many samples that come from the time when both Neandertals and modern humans lived in the same place have little DNA.
The key objective of the project is to learn on when, how, and where Neandertal, Denisovans and modern humans met. We want to learn about their interactions, and what the biological consequences were of the gene flow. To do this, we need to analyze genetic data from people that lived (nearly) contemporaneous to Neandertals and Denisovans. This requires the development of novel theory, and their implementation in new computational and statistical method to analyze ancient DNA. To achieve this, we will develop novel population genetic theory, first in the simplified case of a single, neutral population, but later extend this to incorporate both natural selection and population structure. This will be then applied in a software that aims at characterizing the parts of an individuals genome they have inherited from a Neandertal and Denisovan ancestor. Our tools will be targeted towards addressing the issues with ancient DNA, namely that they are often low quality, that the DNA is highly fragmented and damaged, and very frequently contaminated.
We will then apply our tools to a comprehensive data set of present-day and early modern human genomes. We will generate comprehensive genetic maps, flagging for each individual where in its genome it has genetic material inherited from Neandertals or Denisovans. We will then use these data to precisely date when, and over which duration, humans met with Neandertals and Denisovans. We will also be able to say which regions were under positive or negative natural selection, and over which time periods this took place. We will also investigate how these patterns change over time and space. Overall, this study will give us unique and novel insights into our relationship with Neandertals and Denisovans, and so clarifies what makes us human.
