Ancient mitogenomics

Abstract

The mitochondrial genome has been the traditional focus of most research into ancient DNA, owing to its high copy number and population-level variability. Despite this long-standing interest in mitochondrial DNA, it was only in 2001 that the first complete ancient mitogenomic sequences were obtained. As a result of various methodological developments, including the introduction of high-throughput sequencing techniques, the total number of ancient mitogenome sequences has increased rapidly over the past few years. In this review, we present a brief history of ancient mitogenomics and describe the technical challenges that face researchers in the field. We catalogue the diverse sequencing methods and source materials used to obtain ancient mitogenomic sequences, summarise the associated genetic and phylogenetic studies that have been conducted, and evaluate the future prospects of the field.

Introduction

Over the past 25 years, ancient DNA research has maintained a consistently high profile in scientific journals and in the public domain. This is partly owing to appreciation of the attendant technical and methodological challenges, as well as the spectacular, and often controversial, claims that have characterised the field. In addition, ancient DNA work is often associated with charismatic animals such as the woolly mammoth, dodo, and Tasmanian tiger.

Ancient DNA, broadly defined here as any degraded DNA obtained from specimens not deliberately preserved for genetic analysis, differs from modern DNA in several important respects. As a result of post-mortem damage, such as that caused by hydrolytic and oxidative reactions, ancient DNA molecules are often highly fragmented and usually found in low concentrations (Pääbo, 1989). This presents practical obstacles for sequence analysis and heightens the risk of contamination. Consequently, specialised facilities and the implementation of strict laboratory protocols are often regarded as essential for ancient DNA research, especially when human, common domestic, or microbial samples are involved.

The earliest report of ancient DNA appeared in the mid-1980s, when Higuchi et al. (1984) obtained mitochondrial sequence fragments from a 150-year-old museum specimen of the extinct quagga. Shortly afterwards, Pääbo (1985) published a partial mitochondrial DNA sequence from a 2430-year-old Egyptian mummy. Neither of these analyses was reproducible and the sequences are now viewed cautiously (Pääbo et al., 2004). At the time, however, these studies had considerable impact because they suggested that DNA molecules were able to survive for extended periods of time and could still be sequenced. Such ancient genetic data would allow unprecedented access to information that could not be gleaned from palaeontological, archaeological, or documentary evidence alone.

Progress in ancient DNA research gained substantial impetus with the development of the polymerase chain reaction (PCR), which enabled the amplification of very small amounts of starting DNA (Mullis and Faloona, 1987). Recognising its potential for helping to recover genetic information from even trace amounts of nucleic acids, the nascent ancient DNA community rapidly took up this new methodology. However, the application of PCR to ancient specimens soon revealed the ubiquity of DNA sequence damage and the pervasiveness of contamination (Pääbo, 1989, Pääbo and Wilson, 1988). Nevertheless, the magnitude and gravity of these risks did little to dampen enthusiasm within the field, with reports of DNA from Miocene plant fossils (Golenberg et al., 1990, Soltis et al., 1992), a 120-million-year-old insect trapped in amber (Cano et al., 1993), and dinosaurs (Li et al., 1995, Woodward et al., 1994). These optimistic studies, among several others, helped to instigate sensational media coverage of ancient DNA research.

Subsequent empirical and theoretical evidence has placed the maximum survival time of DNA at under a million years (Lindahl, 1993, Lindahl, 1997, Smith et al., 2001, Willerslev et al., 2003), casting grave doubt on studies claiming the successful retrieval of ‘geologically ancient’ or ‘antediluvian’ DNA. Indeed, most or all of these sequences are now strongly suspected to be artefactual (Hebsgaard et al., 2005), and claims of geologically ancient DNA have become far less frequent in the 21st century (but see Fish et al., 2002, Kim et al., 2004, Veiga-Crespo et al., 2007, Veiga-Crespo et al., 2008, Veiga-Crespo et al., 2004, Vreeland et al., 2006). Serious concern over the reliability and credibility of ancient DNA studies has led numerous authors to publish detailed and rigorous guidelines for evaluating the authenticity of ancient DNA sequences (e.g., Cooper and Poinar, 2000, Gilbert et al., 2005, Hofreiter et al., 2001, Pääbo et al., 2004, Ward and Stringer, 1997).