Population Genomic Analyses of DNA from Ancient Remains

The possibility of obtaining genomic data from ancient biological material has opened the time dimension to genetic research. Obtaining genomic data from individuals and populations before, during, and after particular events allows us to study the individuals that were directly involved in these events. Such an approach can overcome the limitations of studying data from present-day individuals and trying to make inferences about past events from these data. Studies on present-day samples do not include potential groups that went extinct or have not contributed substantially to present-day populations, and some of the signals of ancient events may have been erased by later demographic processes. In this chapter we outline some of the specific approaches working with ancient population-genetic data and point to some of the known methodological and statistical specifics for working with empirical genetic data from ancient samples. The chapter mainly focuses on the power and possibilities of genomic approaches, in contrast to single-marker studies. The prime advantage of moving towards genome-wide studies is that data from even single individuals can lead to new insights as the thousands of different loci across the genome can be seen as (relatively) independent samples of the same evolutionary history. After we have described the statistical challenges and opportunities in working with ancient human DNA, we conclude with some examples on topics where this approach has led to new and better understanding of human evolution and prehistory.