Ancient DNA

Ancient DNA (aDNA) is DNA isolated from ancient specimens. Due to degradation processes (including cross-linking, deamination and fragmentation) ancient DNA is of lower quality in comparison with modern genetic material. Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for contemporary sequencing technologies. Genetic material has been recovered from archaeological and historical skeletal material, mummified tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost cores as well as marine and lake sediments. Ancient DNA (aDNA) is DNA isolated from ancient specimens. Due to degradation processes (including cross-linking, deamination and fragmentation) ancient DNA is of lower quality in comparison with modern genetic material. Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for contemporary sequencing technologies. Genetic material has been recovered from archaeological and historical skeletal material, mummified tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost cores as well as marine and lake sediments. The first study of what would come to be called aDNA was conducted in 1984, when Russ Higuchi and colleagues at the University of California, Berkeley reported that traces of DNA from a museum specimen of the Quagga not only remained in the specimen over 150 years after the death of the individual, but could be extracted and sequenced. Over the next two years, through investigations into natural and artificially mummified specimens, Svante Pääbo confirmed that this phenomenon was not limited to relatively recent museum specimens but could apparently be replicated in a range of mummified human samples that dated as far back as several thousand years. The laborious processes that were required at that time to sequence such DNA (through bacterial cloning) were an effective brake on the development of the field of ancient DNA (aDNA). However, with the development of the Polymerase Chain Reaction (PCR) in the late 1980s, the field began to progress rapidly. Double primer PCR amplification of aDNA (jumping-PCR) can produce highly skewed and non-authentic sequence artifacts. Multiple primer, nested PCR strategy was used to overcome those shortcomings. The post-PCR era heralded a wave of publications as numerous research groups tried their hands at aDNA. Soon a series of incredible findings had been published, claiming authentic DNA could be extracted from specimens that were millions of years old, into the realms of what Lindahl (1993b) has labelled Antediluvian DNA. The majority of such claims were based on the retrieval of DNA from organisms preserved in amber. Insects such as stingless bees, termites, and wood gnats, as well as plant and bacterial sequences were extracted from Dominican amber dating to the Oligocene epoch. Still older sources of Lebanese amber-encased weevils, dating to within the Cretaceous epoch, reportedly also yielded authentic DNA. DNA retrieval was not limited to amber. Several sediment-preserved plant remains dating to the Miocene were successfully investigated. Then, in 1994 and to international acclaim, Woodward et al. reported the most exciting results to date — mitochondrial cytochrome b sequences that had apparently been extracted from dinosaur bones dating to more than 80 million years ago. When in 1995 two further studies reported dinosaur DNA sequences extracted from a Cretaceous egg, it seemed that the field would revolutionize knowledge of the Earth's evolutionary past. Even these extraordinary ages were topped by the claimed retrieval of 250-million-year-old halobacterial sequences from halite. Whole genome sequencing started to yield results in 1995. Single primer extension (abr. SPEX) amplification was introduced in 2007 to address postmortem DNA modification damage. Since 2009 the field of aDNA-studies has been revolutionzed, with the introduction of much cheaper research-techniques, leading to new insights in human migrations. Due to degradation processes (including cross-linking, deamination and fragmentation) ancient DNA is of lower quality in comparison with modern genetic material. The damage characteristics and ability of aDNA to survive through time restricts possible analyses and places an upper limit on the age of successful samples Allentoft et al. (2012). There is a theoretical correlation between time and DNA degradation, although differences in environmental conditions complicates things. Samples subjected to different conditions are unlikely to predictably align to a uniform age-degradation relationship. The environmental effects may even matter after excavation, as DNA decay rates may increase, particularly under fluctuating storage conditions. Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for contemporary sequencing technologies.