Ancient DNA

:"Adna redirects here. For the unincorporated community in Washington, see Adna, Washington".Ancient DNA can be loosely described as any DNA recovered from biological samples that have not been preserved specifically for later DNA analyses. Examples include the analysis of DNA recovered from archaeological and historical skeletal material, mummified tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost cores, and so on. Unlike modern genetic analyses, ancient DNA studies are characterised by low quality DNA. This places limits on what analyses can achieve. Furthermore, due to degradation of the DNA molecules, a process which correlates loosely with factors such as time, temperature and presence of free water, upper limits exist beyond which no DNA is deemed likely to survive. Current estimates suggest that in optimal environments, i.e environments which are very cold, such as permafrost or ice, an upper limit of max 1 Million years exists. As such, early studies that reported recovery of much older DNA, for example, from Cretaceous dinosaur remains, have been proven to be wrong, with results stemming from sample or extract contamination, as opposed to authentic extracted DNA.

History of Ancient DNA studies

Arguably the first aDNA study was in 1984, with a publication by Russ Higuchi and colleagues at Berkeley that was to revolutionise the scope of molecular biology, 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 (Higuchi "et al." 1984). Over the next two years, through investigations into natural and artificially mummified specimens, Svante Pääbo both 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 (Pääbo 1985a; Pääbo 1985b; Pääbo1986).Nevertheless, 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) (Mullis and Faloona 1987; Saiki "et al." 1988) in the late 1980s the field was presented with the ability to rapidly progress.

Double primers 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.

Single primer extension (abr. SPEX) amplification was introduced in 2007 to address post mortem DNA modification damage. ["Novel high-resolution characterization of ancientDNA reveals C > U-type base modification events asthe sole cause of post mortem miscoding lesions";Paul Brotherton1, Phillip Endicott, Juan J. Sanchez3, Mark Beaumont, Ross Barnett, Jeremy Austin1 and Alan Cooper]

Antediluvian DNA studies

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 (Cano "et al." 1992a; Cano "et al." 1992b), termites (De Salle "et al." 1992; De Salle "et al." 1993) and wood gnats (De Salle and Grimaldi 1994), as well as plant (Poinar "et al." 1993) and bacterial (Cano "et al." 1994) 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 (Cano "et al." 1993). DNA retrieval was also not limited to amber. Several sediment-preserved plant remains dating to the Miocene were successfully investigated (Golenberg "et al." 1990; Golenberg 1991). 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 over 80 million years ago. When in 1995 two further studies reported dinosaur DNA sequences extracted from a Cretaceous egg (An "et al." 1995; Li "et al." 1995) it seemed that the field would truly revolutionise knowledge of the Earth’s evolutionary past. Unfortunately the golden days of aDNA did not last. A critical review of ancient DNA literature through the development of the field highlights that, with two famous but highly criticised exceptions that claim the retrieval of 250 million years old halobacterial sequences from Halite (Vreeland "et al." 2000; Fish "et al." 2002), few recent studies have succeeded in amplifying DNA from remains older than several hundred thousand years (ky) (c.f. Willerslev "et al." 2003).

Ancient DNA studies

Despite the problems associated with ‘antediluvian’ DNA, a wide, and ever-increasing range of aDNA sequences have now been published from a range of animal and plant taxa. Tissues examined include artificially or naturally mummified animal remains (c.f. Higuchi "et al." 1984; Thomas "et al." 1989), bone (c.f. Hagelberg "et al." 1989; Cooper "et al." 1992; Hänni "et al." 1994b; Hagelberg "et al." 1994), paleofaeces (Poinar "et al." 1998; Hofreiter "et al." 2000), alcohol preserved specimens (Junqueira "et al." 2002), rodent middens (Küch "et al." 2002), dried plant remains (Goloubinoff "et al." 1993; Dumolin-Lapegue "et al." 1999) and recently, extractions of animal and plant DNA directly from soil samples (Willerslev "et al." 2005).

Ancient DNA studies on human remains

Due to the considerable anthropological, archaeological, and public interest directed towards human remains, it is only natural that they have received a similar amount of attention from the DNA community. Due to their obvious signs of morphological preservation, many studies utilised mummified tissue as a source of ancient human DNA. Examples include both naturally preserved specimens, for example those preserved in ice, such as the Ötzi the Iceman (Handt "et al." 1994), or through rapid desiccation, for example high-altitude mummies from the Andes (c.f. Pääbo 1986; Montiel "et al." 2001)), as well as various sources of artificially preserved tissue (such as the chemically treated mummies of ancient Egypt (c.f. Hänni "et al." 1994a)). However, mummified remains are a limited resource, and the majority of human aDNA studies have focused on extracting DNA from two sources that are much more common in the archaeological record – bone and teeth. Recently, several other sources have also yielded DNA, including paleofaeces (Poinar "et al." 2001) and hair (Baker "et al." 2001, Gilbert "et al." 2004). Contamination remains a major problem when working on ancient human material.

Neanderthal

*mtDNA
Neanderthal ancient mtDNA was partially sequenced in in HVR region for following speciments: Feldhofer 1 ,Feldhofer 2 from Germany , Mezmaiskaya from the Russian Caucasus; Vindija 75 , Vindija 77, Vindija 80 from Croatia; Engis 2 from Belgium; La Chapelle-aux-Saints from France; El Sidrón: 441, 1253, and 1351c from Spain [http://anthropology.net/2007/10/18/neandertals-have-the-same-mutations-in-foxp2-the-language-gene-as-modern-humans/] [http://mbe.oxfordjournals.org/cgi/content/abstract/22/4/1077] ; and Rochers-de-Villeneuve from France and Riparo Mezzena [title: "A highly divergent mtDNA sequence in a Neandertal individual from Italy", [http://www.sciencedirect.com/science?_ob=ArticleURL&_udi=B6VRT-4KPFVNM-9&_user=10&_rdoc=1&_fmt=&_orig=search&_sort=d&view=c&_acct=C000050221&_version=1&_urlVersion=0&_userid=10&md5=586505ccdef813f608f61cc91ddf965d] ] from Itally.

*Chromosomal DNA

Two distinct neandertals from El Sidrón cave (1253 and 1351c) have the same mutations at position A-911, G-977 in exon 7 of FOXP2 gene as present day people. [Krause et al., The Derived FOXP2 Variant of Modern Humans Was Shared with Neandertals, Current Biology (2007), doi:10.1016/j.cub.2007.10.008]

Pathogen and microorganism aDNA analyses using human remains

The use of degraded human samples in aDNA analyses has not been limited to the amplification of human DNA. It is reasonable to assume that for a period of time post mortem, DNA may survive from any microorganisms present in the specimen at death. This not only includes pathogens present at the time of death (either the cause of death or long-term infections) but commensals and other associated microbes. Despite several studies that have reported limited preservation of such DNA, for example the lack of preservation of Helicobacter pylori in ethanol-preserved specimens dating to the 18th century (Barnes "et al." 2000), over 45 published studies report the successful retrieval of ancient pathogen DNA from samples dating back to over 5,000 years old in humans, and as long as 17,000 years ago in other species. As well as the usual sources of mummified tissue, bones and teeth, such studies have also examined a range of other tissue samples, including calcified pleura (Donoghue "et al." 1998), tissue embedded in paraffin (Jackson "et al." 1998; Basler "et al." 2001), and formalin-fixed tissue (Taubenberger "et al." 1997).la

Researchers specializing in ancient DNA

*Lori Baker
*Gila Kahila Bar-Gal [Hebrew University, Koret School of Veterinary Medicine: http://ksvm.agri.huji.ac.il/personalpages/gila-Kahila.htm]
*Ian Barnes
*Deborah Bolnick
*Abigail Bouwman
*Terry A. Brown
*Joachim Burger
*Graciela Cabana
*David Caramelli
*Jason A. Eshleman
*Marina Faerman [Hebrew University, Bioanthropology and Ancient DNA: http://bioanthropology.huji.ac.il/personal.asp]
*E.L. Rodriguez Florez
*Carles Lalueza Fox
*Eva-Maria Geigl
*M. Thomas P. Gilbert
*Chuck Greenblatt [Hebrew University, Faculty of Medicine, Kuvin Center: http://kuvin.huji.ac.il/default.aspx?pid=69]
*Michael Hofreiter
*K. Ann Horsburgh
*Susanne Hummel
*Frederika Kaestle
*Brian M. Kemp
*Diana M. Lawrence
*Cecil M. Lewis Jr.
*Odile Loreille
*Ripan Malhi
*Carney Matheson
*Lisa Matisoo-Smith
*Cara Monroe
*Connie Mulligan
*Dennis H. O'Rourke
*Svante Pääbo
*Hendrik Poinar
*Beth Shapiro
*Beth Shook
*David Glenn Smith
*Meradeth Snow
*Mark Spiegelman [Hebrew University, Department of Parasitology: http://parasitology-soc.md.huji.ac.il/o-s.htm]
*Anne C. Stone
*Eske Willerslev
*Dongya Yang

References

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*Willerslev E, Cooper A. 2005. Ancient DNA (Review Paper) Proc. R.Soc. B.272 3-16

Conferences

* [http://www.ancientDNA9.it/ ancientDNA9] - The 9th International Conference on Ancient DNA and Associated Biomolecules will be held in Pompeii (Naples), Italy, from October 19 to October 22, 2008

ee also

*List of DNA tested mummies
*List of genetic results derived from historical figures
*Human mitochondrial DNA haplogroups
*Human Y-chromosome DNA haplogroup
*Phylogenetic tree
*Tyrannosaurus#Soft tissue, Dinosaur mummy

External links

* [http://isogg.org/famousdna.htm Famous mtDNA]
* [http://www.isogg.org/ancientdna.htm Ancient mtDNA]
* [http://news.bbc.co.uk/2/hi/science/nature/5052414.stm Tooth gives up oldest human mtDNA]
* [http://news.bbc.co.uk/2/hi/science/nature/4602739.stm Extinct cave bear mtDNA sequenced]
* [http://www.standardtimes.com/daily/03-97/03-09-97/a09wn056.htm British teacher finds long-lost relative: 9,000-year-old man] - mtDNA analysis.
* [http://www.pnas.org/cgi/reprint/98/23/13460 Genetic characterization of the body attributed to the evangelist Luke] (PDF) better link http://www.pnas.org/cgi/content/full/98/23/13460 - mtDNA
* [http://www.egyptologyonline.com/using_dna.htm Unravelling the mummy mystery - using DNA] - no data on YDNA only mtDNA
* [http://www.friendsofpast.org/earliest-americans/map.html Evidence of the Past: A Map and Status of Ancient Remains] - samples from USA no sequence data here.