Ancient mitochondrial DNA analysis of human remains in the era of next- generation sequencing

Abstract

The analysis of ancient DNA (aDNA) has become important in recent years, providing new insights on human evolution and population history. Since the emergence of ancient DNA analysis in the mid-eighties, mitochondrial DNA (mtDNA) analysis has been an essential tool in paleogenomic research. Compared to nuclear DNA, its small, circular, multicopy genome is collectively less susceptible to chemical damage and fragmentation and has more potential for retrievability. Despite its longevity, mtDNA's maternal inheritance with no recombination allows researchers to reconstruct maternal lineages and thus partially track human ancestry and migratory patterns. The accuracy and authenticity of mtDNA data retrieved from paleontological and archaeological remains have improved significantly over the past three decades, driven by advances ranging from enhanced contamination control to next-generation genome sequencing and target enrichment. The current review highlights the challenges of recovering and authenticating ancient mtDNA, including DNA fragmentation, postmortem DNA damage, contamination, heteroplasmy, and nuclear mitochondrial sequences (Numts), which can complicate research results. Within this context, the review addresses the rapidly changing sequencing technologies and the use of specialized bioinformatics software that tackle these challenges and enable researchers to reconstruct almost complete mtDNA genomes from human remains. Although mtDNA analysis has limitations and provides only a partial view of the human genomic architecture, it remains an important tool for analyzing maternal ancestry and generating authenticated genomic information of ancient human populations.