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Corresponding author: Manaaki Whenua Landcare Research, PO Box 69040, Lincoln, Canterbury 7640, New Zealand. E-mail: [email protected]
INTRODUCTION
Ancient DNA research has evolved markedly since the first pioneering studies were published in the 1980s. While these early studies typically retrieved relatively short regions of mitochondrial DNA from museum, or Holocene age, specimens (e.g. Higuchi et al. 1984; Pääbo et al. 1988) near-complete genomes are now routinely being sequenced from Pleistocene age remains (Der Sarkissian et al. 2015). Moreover, the ever-expanding set of substrates from which ancient DNA has been retrieved (Green and Speller, 2017) is allowing new insights into diverse aspects of the past, such as palaeofaunas (Grealy et al. 2015), ancient oral microbiomes (e.g. Weyrich et al. 2017), palaeodiets (e.g. Wood et al. 2013a) and palaeoenvironments (Anderson-Carpenter et al. 2011; Parducci et al. 2017).
The extraction, amplification, sequencing and analysis of DNA molecules from long-dead organisms present several unique challenges. As a result of natural degradation processes, DNA from old specimens is usually present at a much lower copy number than in recent specimens (Pääbo et al. 2004), and is therefore at risk of contamination by modern DNA (Yang and Watt, 2005; Skoglund et al. 2014). Moreover, DNA molecules break into shorter fragments over time and accumulate damage that can alter nucleotide sequences (Brotherton et al. 2007; Sawyer et al. 2012). Early ancient DNA research was hampered by a poor understanding of these issues and several claims of antediluvian DNA (>1 million years old, sensu Lindahl, 1993) have since been disproven (Hofreiter et al. 2001). Authentication criteria have subsequently been developed to help improve the rigor of ancient DNA research, including the use of specialized ancient DNA facilities, inclusion of negative controls in PCR experiments, ensuring reproducibility and providing independent replication of results (Cooper and Poinar, 2000; Hofreiter et al. 2001; Gilbert et al. 2005).
Although somewhat challenging, the study of DNA from ancient specimens represents an approach that can provide certain insights about the past that are unattainable by other means (Rizzi et al. 2012; Leonardi et al. 2017; Cole and Wood, in press). Ancient DNA research provides us with a ‘real-time’ view of ecological and evolutionary processes that otherwise could only be inferred from current genetic variation (Krause and Pääbo,...