Insights from the Analysis of Ancient and Modern DNA with Population-Specific Single-Nucleotide Polymorphisms

Studies of modern and ancient DNA (aDNA) have substantially improved our understanding of the early history of human populations. Despite advances in whole-genome sequencing technologies, present studies of aDNA are largely based on a panel of preselected genomic variants; thus, valuable genetic information in aDNA should be further explored. This study analyzed genotype data from 19 ancient and 16 modern high-coverage shotgun human genomes. We used modern populations from the 1000 Genomes Project and the Human Genome Diversity Project as reference populations and selected single-nucleotide polymorphisms (SNPs) that were polymorphic in one reference population and monomorphic in the others. Ancestral spectrum analyses based on the population-specific SNPs were conducted on the 19 aDNA and 16 modern DNA samples to determine their coancestries with modern reference populations. These analyses effectively revealed the genetic affinity between aDNA and modern populations, which is also true for modern DNA. The results for the 11 aDNA samples with expected transition-to-transversion ratios agree with previous analyses; the 8 aDNA samples with excessive transition-to-transversion ratios revealed ancestral spectra indicative of a high level of DNA damage that cannot be fully explained by postmortem cytosine deamination. Additional biochemistry or bioinformatics treatments seem necessary for the meaningful study of such aDNA.