Advances in ancient DNA studies

The first aDNA studies used bacterial cloning to amplify small sequences retrieved from skins of animal and human mummies, and revealed the inefficient reaction kinetics of this technique (Higuchi et al., 1984; Pääbo 1985, 1989). These studies demonstrated that the genetic material surviving in ancient specimens was often principally microbial or fungal in origin. Endogenous DNA was generally limited to very low concentrations of short, damaged fragments of multi-copy loci such as mitochondrial DNA (mtDNA). The invention of the polymerase chain reaction (PCR) made it possible to routinely amplify and study even single surviving molecules, allowing the number and range of aDNA studies to diversify rapidly (Pääbo 1989; Pääbo & Wilson 1988; Pääbo et al., 1989; Thomas, 1989). However, the enormous amplifying power of PCR also means that contamination from modern DNA becomes a major problem. Contamination is especially likely when previously amplified PCR products are present. False positives from intra-laboratory contamination remain a major problem in aDNA research. The large number of PCR cycles used to amplify aDNA means that it is actually quite difficult not to obtain positive (although not authentic) results. Many of the most extravagant aDNA reports have since been either disproved or effectively disregarded including early, spectacular claims of DNA sequences surviving for millions of years (Myr) in plants (Golenberg et al., 1990; Soltis et al., 1992, although see Kim et al., 2004), dinosaur bones (Woodward et al., 1994) and amber inclusions (Cano et al., 1992a, b, 1993; DeSalle et al., 1992, 1993; Poinar et al., 1993; DeSalle, 1994). Despite this somewhat tarnished history, recent have improved standards, and aDNA is now emerging as a viable scientific discipline. A series of large scale studies have begun to reveal the true potential of aDNA to record the methods and processes of evolution, providing a unique way to test models and assumptions commonly used to reconstruct patterns of evolution, population genetics and palaeoecological change.