Toward high-resolution population genomics using archaeological samples

Abstract

The term 'ancient DNA' (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of 'molecular paleontology'. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.

Keywords: ancient DNA; bioinformatics; epigenetics; next-generation sequencing; population genetics.

Figure 1.

Major milestones of development of high-resolution ancient human genomics.

Figure 2.

Geographic distribution of existing whole genome aDNA sequences.

Figure 3.

Flowchart of a typical bioinformatics pipeline for aDNA analysis using NGS data.

Figure 4.

Epigenetic analysis of aDNA. As a result of cytosine and methyl-cytosine deamination in postmortem sample, we observe C→U and mC→T conversions. When Taq polymerase is used for DNA amplification, both C→U and mC→T will be recorded as T (this is the major difference between ancient and bisulphite-treated samples when only unmethylated cytosine in converted to U while mC remains unchanged). When Pfu polymerase is used, U will not be amplified, while those T that appeared as a result of mC→T conversion will be read as T. The pie charts demonstrate the ratio of sequenced C to T. This C/T ratio with Taq and Pfu along with comparison with the reference genome allows detection of methylated cytosines: in the case of postmortem deamination C→U and PCR by Pfu the frequency of T will be decreased.