Ancient DNA
From ISOGG Wiki
Ancient DNA (aDNA) refers to DNA extracted from ancient specimens. Examples include the analysis of DNA recovered from archaeological and historical skeletal material, mummified tissues and archival collections of non-frozen medical specimens. The techniques used in extracting aDNA are however applicable to any situation where DNA has degraded to the extent that conventional fresh DNA extraction techniques cannot be used. Practically speaking, the term aDNA relates to the condition of the DNA, not necessarily the age.
Different techniques are required to extract ancient DNA, and the extraction therefore needs to be handled at a specialist aDNA laboratory. A fresh DNA sample can be on the order of micrograms. If the lab is exposed to low levels of alien DNA on the order of nanograms or picograms, the contamination will not show up in the results. In contrast an aDNA sample is typically on the order of nanograms or even picograms, so that extra nanograms or picograms of contamination could be fatal to the analysis.
Colleen Fitzpatrick reports: "Over the last year or two, I have been involved in several projects where misidentifications have been made and DNA from remains has been consumed or destroyed because the DNA sample was brought to a commercial testing lab, not an aDNA lab. Commercial labs are rarely equipped to handle the small quantities of aDNA, and often do not know they cannot handle it. These labs commonly produce results that are contaminated. This was true in the recent misidentification of the Navajo skeleton as Everett Reuss, the poet who died in the Utah desert in the 1920s. Cross-contamination occurred at the commercial lab that handled it between Reuss family members and the remains, giving a false positive identification."[1]
The issue with aDNA extraction is simply that DNA is a very complex structure that degrades as soon as the organism dies due to bacteria that cause the corpse to decompose. This is accelerated if the DNA is exposed to "the elements", and by any chemicals that might be present (such as embalming fluid). The oldest specimens that have yielded aDNA tend to be found in cool dry climates at high altitudes that helped retard the bacterial action and kept the DNA away from heat and moisture.
The Y-chromosome is 50 million base pairs long and there is only one per cell. DNA analysis of the Y depends on extracting enough DNA from certain regions within those 50 million base pairs for analysis. For highly degraded remains, it's highly unlikely that enough of the right Y survives for analysis.
There is a much better chance of recovering enough Mitochondrial DNA (mtDNA) for an identification. This makes it easier for the laboratory to extract usable DNA, but a lot harder on the genealogists looking for the family reference, as you have to follow the female line. There are up to 1,000 mitochondria per cell, each with five to ten copies of its own 16,569 base-pairs genome. Therefore, there can be as many as 10,000 copies per cell of the mtDNA genome. This results in a much higher probability of recovering mtDNA from severely degraded remains.
Embalming creates further problems. The formaldehyde found in embalming fluid not only denatures DNA, but also causes DNA strands to cross link to themselves and other strands of DNA, much like a wadded up ball of duct tape. The damage is permanent. The formaldehyde oxidizes to paraformaldehyde, which can inhibit the ProteinaseK used during the extraction. So for embalmed remains, the extraction of aDNA must overcome the issues of degradation by bacterial action involved in decomposition and degradation due to exposure to the elements, in addition to the inhibition of the extraction process by the presence of oxidized formaldehyde. There have been protocols developed to try to break the cross-links formed by the formaldehyde. These involve microwaving and temperature cycling bone powder. Unfortunately, for very fragile specimens, this protocol can destroy the DNA as well. What has been more successful is to soak the bone powder in a PBS solution that allows the paraformaldehyde to float to the top, with the bone powder sinking to the bottom. Once the paraformaldehyde is removed, the remaining bone powder is dissolved with a demineralization process, releasing DNA that is hiding deep in the bone matrix that has not been affected by the embalming process. This can double the yield of aDNA.
The best place to look for aDNA is in teeth. Enamel is the hardest substance in the body and although it does not contain DNA, it provides physical protection to the dentine within it and helps to protect the DNA in the dentine. After the teeth, dense compact bone is the best place to look for DNA, and therefore a femur or another long bone is favoured.
Contents |
The Spitalfields Princess
The "Spitalfields Princess" was found in a Roman Cemetery at Spitalfields Market, London, England, in 1999 and was the subject of a BBC TV programme "Meet the Ancestors":
- Digging up the Romans: Discovering people at Spitalfields Market
- Girl power by Jenny Hall Classical Association News Number 24, June 2001.
- Roman "yuppie" had Spanish Genes Steve Connor, The Independent, 2nd August 1999.
Roman remains from Butt Road Cemetery, Colchester, Essex, England
- Colchester Man
- Patricia Smith. "The Secrets of the Romano-Britons' genes: New data from old bones". The Colchester Archaeologist, Number 11, 1998, 18-19.
- Nina Crummy, Philip Crummy and Carl Cross. Excavations of Roman and later cemeteries, churches and monastic sites in Colchester, 1971-88 (46 megabytes)
Forensic and ancient DNA laboratories
Australia
Canada
Denmark
Germany
New Zealand
United Kingdom
- LGC Forensics
- DNA Worldwide - Forensic DNA testing
- Cellmark Forensic Services
- Keri Brown, University of Manchester
- Dr Ian Barnes, Royal Holloway, University of London
- Glyn Daniel Laboratory For Archaeogenetics, Cambridge
- Dr Greger Larson, Department of Archaeology, Durham University
- Prof Michael Hofreiter, Department of Biology, University of York
- University College London Proposals are currently being reviewed for building a new laboratory specifically designed for extracting ancient DNA
USA
- Mitotyping Technologies
- Beth Shapiro's lab: Molecular Evolution, ancient DNA, viruses, and phylogenetics
- Prof Noreen Tuross, Department of Human Evolutionary Biology, Harvard University
Scientific papers
- Kemp BM, Malhi RS, McDonough J et al. Genetic analysis of early holocene skeletal remains from Alaska and its implications for the settlement of the Americas. Am J Phys Anthropol 2007 Apr;132(4):605-21.
- Haak W, Balanovsky O, Sanchez JJ et al. Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities PLoS Biol 8(11): e1000536. doi:10.1371/journal.pbio.1000536.
- Melchior L, Kivisild T, Lynnerup N, Dissing J, 2008. Evidence of Authentic DNA from Danish Viking Age Skeletons Untouched by Humans for 1,000 Years. PLoS ONE 3(5): e2214.
External links
- ISOGG page on famous mtDNA
- ISOGG page on ancient mtDNA
- BODIES - The British and Irish On-line Database Index to Excavated human remainS
- Ancient Eurasian DNA Mitochondrial and Y-chromosome haplogroups extracted from historic and prehistoric human remains in Europe and related remains in Asia, arranged chronologically
- Tooth gives up oldest human mtDNA
- Extinct cave bear mtDNA sequenced
- British teacher finds long-lost relative: 9,000-year-old man
- Genetic characterization of the body attributed to the evangelist Luke
- Unravelling the mummy mystery - using DNA
- The mitochondrial lineage of Ötzi is not like other Europeans
- King Tut's family secrets and Curse of the Pharaoh's DNA
- Evidence of the past: a map and status of ancient remains in the USA
- A list of ancient DNA Y-chromosome studies from Dienekes' blog
Further reading
- Terry Brown and Kerry Brown. Biomolecular Archaeology: An Introduction. Wiley-Blackwell, February 2011.
References
- ↑ Colleen Fitzpatrick. Ancient DNA. Posting on the ISOGG project administrators’ mailing list, 13 September 2010.
