Recent improvements in DNA extraction techniques from ancient human remains have dramatically expanded the availability of starting material for population level genetic studies. However sequencing costs remain the main limiting factor shaping the balance between number of samples and sequencing depth in any such study design. Consequently, population level studies are often characterized by low or ultra-low coverage sequences, invariably affecting the quality of the obtained genotype calls.
Here we introduce a novel approach to obtain population level allele frequency estimates from pools of ~20 ultra-low (0.1-1x) coverage samples. Particularly we will focus on two British populations from the same geographic site, before and after the 14th century Plague epidemic. Furthermore we show through empirical simulations how reads coming from multiple individuals from the same population can be combined to form a “chimeric” genome, representative of an average good-quality individual from that population.
The population level allele frequencies hence estimated, can be used to detect selective sweeps occurred during the Plague epidemic and, compared with the modern GBR samples from the 1000 Genomes Project inform us on putative adaptive responses to pathogens.