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.

Highlights

  • The field of ancient DNA (aDNA) has entered the new era of genomics and has provided valuable information when testing specific hypotheses related to the past

  • Each piece of target genomic DNA had to be amplified several times by PCR, ideally PCR amplicons had to be propagated using bacterial vectors, and a number of clones had to be sequenced before a consensus sequence devoid of sequencing errors could be generated [1]

  • This study demonstrated the immense potential of palaeogenomics towards reconstructing the population history of humans in much greater detail than what can be achieved from patterns of modern genomic variation alone

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Summary

The impossible genome

Ancient DNA (aDNA) research is full of surprises. Less than a decade ago, most experienced aDNA researchers believed that full genome sequencing of extinct species such as the woolly mammoth and Neandertals was impossible. Tworound multiplex reactions [9], whereby a set of PCR targets are co-amplified from the same microlitre of DNA extract, could help reduce material and time requirements by one or two orders of magnitude [10,11], but operational costs would still amount to billions of US dollars. This technology limited palaeogenomics to the shorter ancient microbial genomes [12]

Shotgun sequencing of the first ancient mammalian genome
The first ancient human genome
Ancient anatomically modern humans
The genomics of archaic hominins
Towards Middle Pleistocene genomes and proteomes
Non-mammalian palaeogenomics
What next?
37. Sanchez-Quinto F et al 2012 Genomic affinities
22. Rasmussen M et al 2010 Ancient human genome
26. Green RE et al 2006 Analysis of one million base
65. Miller W et al 2012 Polar and brown bear genomes
94. Fordyce SL et al 2013 Deep sequencing of RNA
96. Adler CJ et al 2013 Sequencing ancient calcified
Findings
72. Orlando L et al 2013 Recalibrating Equus evolution

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