Insights from the Analysis of Ancient and Modern DNAs with Population-specific SNPs

Abstract

Abstract Studies of ancient and modern DNAs have substantially improved our understanding of the early history of human populations. Despite the advancement of whole-genome sequencing technologies, present studies of ancient DNAs (aDNAs) are largely based on a panel of preselected genomic variants; thus, valuable genetic information in aDNAs is not being fully explored. In this work, we analyze 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 SNPs that were polymorphic in one reference population and monomorphic in the others. With the population-specific SNPs, we conducted ancestral spectrum analyses on the 19 aDNAs and the 16 modern DNAs to determine their coancestries with the modern reference populations. We show that ancestral spectrum analyses effectively reveal the genetic affinity between aDNAs and modern populations, which is also true for modern DNAs. Regarding the 11 aDNAs with normal transition to transversion ratios, the results agree with previous analyses. The other 8 aDNAs 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 aDNAs.