From ISOGG Wiki
Ancient DNA (aDNA) refers to the study of DNA extracted from specimens that died decades, hundreds or sometimes thousands of years ago. Examples include the analysis of DNA recovered from archaeological finds, museum specimens, fossil remains and other unusual specimens. In general these specimens were not preserved for the purpose of genetic and genomic studies. The techniques used in extracting aDNA are 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.
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 almost 60 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 60 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 Proteinase K 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 the petrous bone. Teeth are also favoured for ancient DNA. 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. Any other dense compact bone, such as a femur or another long bone, can also be used.
- Marx V (2017). Genetics: new tales from ancient DNA. Nature Methods 14: 771-774. Published online 24 July 2017. An overview of current ancient DNA methdology and findings.
- Hansen HH , Damgaard PB , Margaryan A et al (2017). Comparing ancient DNA preservation in petrous bone and tooth cementum. PLOS One published online 27 January 2017.
- Orlando L, Gilbert MTP, Willerslev E (2015). Reconstructing ancient genomes and epigenomes. Nature Reviews Genetics. Published online 09 June 2015.
- Raff, Jennifer (2014). How to tell if an ancient DNA study is legitimate? Violent Metaphors blog, 7 February 2014
- Rohland N and Hofreiter M (2007). Ancient DNA extraction from bones and teeth. Nature Protocols 2 1756-1762.
Published online: 12 July 2007 | doi:10.1038/nprot.2007.247
- Gilbert, M TP; Bandelt H-J, Hofreiter M, Barnes I (2005). Assessing ancient DNA studies. Trends in Ecology and Evolution 20 (10): 541-544.
- Pääbo S. Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Vigilant L, Hofreiter M (2004). Genetic aanalyses from ancient DNA. Annual Review of Genetics 38: 645–679. Includes an overview of the criteria for authenticity.
- Cooper, A and Poinar, HN (2000). Ancient DNA: Do It Right or Not at All. Science; 289 1139.
- BODIES - The British and Irish On-line Database Index to Excavated human remainS
- Evidence of the past: a map and status of ancient remains in the USA
- Jean Manco. Introduction to ancient DNA. Ancestral Journeys website. Includes links to tables documenting results from various ancient DNA studies, including charts of mitochondrial and Y-chromosome haplogroups extracted from historic and prehistoric human remains
- A list of ancient DNA Y-chromosome studies from Dienekes' blog
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)
Other news stories
- Eske Willerslev Is Rewriting History With DNA by Carl Zimmer, New York Times, 16 May 2016.
- What's old is new again by Bob Grant, The Scientist, 1 June 2015.
- Ancient DNA tells a new human story by Matt Ridley, Wall Street Journal, 1 May 2015.
- Human evolution: the Neanderthal in the family by Ewen Callaway, Nature News and Comment, 26 March 2014
- Cleaning up ancient DNA
- Tooth gives up oldest human mtDNA
- Extinct cave bear mtDNA sequenced
- 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
- "Better" DNA out of fossil bones by Alison Ross, BBC News, 19 September 2005
- Ancient hair gives up its DNA secrets by Anna Salleh, ABC Science Online, 22 June 2004
- Kivisild T (2017). The study of human Y chromosome variation through ancient DNA. Human Genetics. Published online 4 March 2017. A useful review article.
- Krause J, Pääbo S (2016). Genetic time travel. Genetics 203(1): 9-12.
- From mammoths to Neandertals, ancient DNA unlocks the mysteries of the past A special issue of Science devoted to ancient DNA, 23 July 2015.
- Ancient DNA: the first three decades A discussion meeting issue of the Royal Society's Philosophical Transactions B organised and edited by by Erika Hagelberg, Michael Hofreiter and Christine Keyser
- Luca Ermini, Clio Der Sarkissian, Eske Willerslev, Ludovic Orlando. Major transitions in human evolution revisited: A tribute to ancient DNA. Journal of Human Evolution (in press). Available online 19 December 2014. An excellent, comprehensive review article.
- Guido Brandt, Szécsényi-Nagy, Christina Roth, Kurt Werner Alt, Wolfgang Haak (2014). Human paleogenetics of Europe – The known knowns and the known unknowns. Journal of Human Evolution (in press). Available online 13 November 2014. A review article focusing mainly on ancient DNA findings from mitochondrial DNA and Y-DNA.
- Pickrell J, Reich D (2014). Towards a new history and geography of human genes informed by ancient DNA. Trends in Genetics 2014; 30 (9): 377-389 (subscription required). Available as a preprint from BioRxiv.
- Ermanno Rizzi, Martina Lari, Elena Gigli, Gianluca De Bellis and David Caramelli. Ancient DNA studies: new perspectives on old samples. Genetics Selection Evolution 2012, 44:21. A very good review article on the history of ancient DNA studies.
- Christiane Maria Bauera, Martin Bodnera, Harald Niederstättera, Daniela Niederwiesera, Gabriela Hubera, Petra Hatzer-Grubwiesera, Karl Holubarb, Walther Parsona. Molecular genetic investigations on Austria's patron saint Leopold III. Forensic Science International Genetics, 8 November 2012.
- Haak W, Balanovsky O, Sanchez JJ et al. Ancient DNA from European Early Neolithic Farmers Reveals Their Near Eastern Affinities PLoS Biol 2010 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.
- 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.
- ISOGG page on famous mtDNA
- ISOGG page on ancient mtDNA
- Wikipedia list of haplogroups of historical and famous figures
- Wikipedia article on ancient DNA
- How long does DNA last? by Forrest Wickman. Slate, 5 February 2013.
- Terry Brown and Kerry Brown. Biomolecular Archaeology: An Introduction. Wiley-Blackwell, February 2011.
- Elizabeth Matisoo-Smith and K. Ann Horsburgh. DNA for Archaeologists. Left Coast Press, November 2012.
- Svante Pääbo. Neanderthal Man: In Search of Lost Genomes. Basic Books, New York, 2014.
- aDNA in the life by Tom Booth. Day of Archaeology website, 28 July 2017.
- The hype cycle of ancient DNA by Patrícia Pečnerová, The Molecular Ecologist, 20 April 2017.
- Petrous bone is the new black by Patrícia Pečnerová, The Molecular Ecologist, 22 February 2016.
- Palaeogenomes - are they influencing us a bit too much? by Tom Gilbert, OpenQuaternary Discussions blog, 6 October 2014.
- Day 1 at the Royal Society's 2013 Ancient DNA meeting by Debbie Kennett, Cruwys News blog, 21 November 2013.
- Day 2 at the Royal Society's 2013 Ancient DNA meeting by Debbie Kennett, Cruwys News blog, 21 November 2013.
- Ancient European ancient DNA A Eupedia page showing Y-DNA and mtDNA haplogroup frequencies in ancient DNA samples in Europe
- Map of ancient DNA An open source map showing with a description and the location of all the ancient DNA samples found to date.
- Online Ancient Genome Repository An open access repository for ancient human DNA data.
- Ancient DNA samples on GedMatch Felix Immanuel has processed some of the publicly available ancient DNA raw files and uploaded to them GEDMatch for comparison purposes.