Technical Advances and Challenges in Genome-Scale Analysis of Ancient DNA

  • Tianying Lan
  • Charlotte LindqvistEmail author
Part of the Population Genomics book series (POGE)


Through improvements in methods to recover ancient DNA (aDNA) and applications of high-throughput DNA sequencing technology, aDNA research has entered into a new era of paleogenomics. Technical advances, including improved knowledge of DNA degradation patterns, identification of variation in endogenous DNA yield in particular skeletal elements, and aDNA-specific modifications to DNA extraction and library construction methods, significantly improved aDNA recovery rates and conversion efficiency of aDNA into sequencing libraries. Thus, in recent years, this has enabled whole-genome sequencing of numerous ancient individuals and extinct species, as well as substantial growth in the volume of ancient DNA studies and sequence data. These ever-growing datasets as well as the degraded nature of ancient DNA have also brought in challenges and innovations to bioinformatic methods for data processing and analysis. Applications of bioinformatic tools should be proceeded with caution by evaluating their feasibility and accuracy on aDNA data, and more standardized analytical pipelines are in high demand. In this chapter, we provide an overview of some of the major technical advances and challenges in aDNA and paleogenomic research.


Bioinformatics Contamination Library preparation Next-generation sequencing Paleogenomics Postmortem DNA damage Targeted enrichment 


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© Springer International Publishing AG, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Department of Biological SciencesUniversity at Buffalo (SUNY)BuffaloUSA
  2. 2.School of Biological SciencesNanyang Technological UniversitySingaporeSingapore

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