Ancient genomics

Abstract

The past decade has witnessed a revolution in ancient DNA (aDNA) research. Although the field's focus was previously limited to mitochondrial DNA and a few nuclear markers, whole genome sequences from the deep past can now be retrieved. This breakthrough is tightly connected to the massive sequence throughput of next generation sequencing platforms and the ability to target short and degraded DNA molecules. Many ancient specimens previously unsuitable for DNA analyses because of extensive degradation can now successfully be used as source materials. Additionally, the analytical power obtained by increasing the number of sequence reads to billions effectively means that contamination issues that have haunted aDNA research for decades, particularly in human studies, can now be efficiently and confidently quantified. At present, whole genomes have been sequenced from ancient anatomically modern humans, archaic hominins, ancient pathogens and megafaunal species. Those have revealed important functional and phenotypic information, as well as unexpected adaptation, migration and admixture patterns. As such, the field of aDNA has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past.

Keywords: ancient DNA; genomics; next generation sequencing.

Figure 1.

Accessing single-strand information from aDNA templates. Comparison of template preparation for (a) Helicos tSMS [77] and (b) single-stranded library building [51], in the case of a double-stranded DNA molecule showing a single-strand break ‘|’ and two cytosines deaminated to uracils (U). Both methods lead to three sequence reads, each represented by a different colour (pink, blue and green), thus providing strand information. Conversely, double-stranded molecules with a single-strand break built into double-stranded libraries lead to the sequencing of one read. Cytosine deamination in overhangs leads to an artefactual increase in G → A transitions in Helicos tSMS sequence reads and C → T transitions in sequence reads obtained from single-stranded libraries. (a) ‘B’, dCTP, dGTP or dATP virtual terminator. (b) ‘X’, ‘Y’ and ‘Z’ adapter/primer sequence.

Figure 2.

Endogenous content of ancient genomic extracts. Datasets are ordered from the most ancient sample to the most recent. ‘yBP’, years before present.