Jump to content

Ancient DNA

From Wikipedia, the free encyclopedia

This is an old revision of this page, as edited by Twikir (talk | contribs) at 16:49, 9 February 2009 (Correct grammar). The present address (URL) is a permanent link to this revision, which may differ significantly from the current revision.

Adna redirects here. For the unincorporated community in Washington, see Adna, Washington.
Cross-linked DNA extracted from the 4,000 year-old liver of an Ancient Egyptian priest Called Nekht-Ankh.

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, Holocene plankton in marine and lake sediments, 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.[1]

Problems and errors

aDNA may contain a large number of post mortem mutations, increasing with time. Some regions of polynucleotide are more susceptible to this degradation so sequence data can bypass statistical filters used to check the validity of data. [2]

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). The Dinosaur DNA was later reveiled to be human Y-Chromosome (Zischler et al. 1996)

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 the HVR region for following specimens: 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[3][4]; and Rochers-de-Villeneuve from France and Riparo Mezzena[5] from Itally.

  • Chromosomal DNA

Two distinct Neanderthals 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. [6]

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


References

  1. ^ Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions; Paul Brotherton1, Phillip Endicott, Juan J. Sanchez3, Mark Beaumont, Ross Barnett, Jeremy Austin1 and Alan Cooper
  2. ^ http://www.454genomics.net/downloads/news-events/geneticanalysisfromancientdna.pdf
  3. ^ http://anthropology.net/2007/10/18/neandertals-have-the-same-mutations-in-foxp2-the-language-gene-as-modern-humans/
  4. ^ http://mbe.oxfordjournals.org/cgi/content/abstract/22/4/1077
  5. ^ title: A highly divergent mtDNA sequence in a Neandertal individual from Italy, [1]
  6. ^ 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
  7. ^ Hebrew University, Koret School of Veterinary Medicine: http://ksvm.agri.huji.ac.il/personalpages/gila-Kahila.htm
  8. ^ Woods Hole Oceanographic Institution: http://www.whoi.edu/people/mcoolen/index.html
  9. ^ Hebrew University, Bioanthropology and Ancient DNA: http://bioanthropology.huji.ac.il/personal.asp
  10. ^ Hebrew University, Faculty of Medicine, Kuvin Center: http://kuvin.huji.ac.il/default.aspx?pid=69
  11. ^ Washington State University, Department of Anthropology: http://libarts.wsu.edu/anthro/faculty/kemp.html
  12. ^ Washington State University, School of Biological Sciences: http://sbs.wsu.edu/faculty/?faculty/150
  13. ^ University of Oklahoma, Department of Anthropology: http://www.ou.edu/anthropology/Faculty_staff/faculty_pages/lewis.html
  14. ^ Hebrew University, Department of Parasitology: http://parasitology-soc.md.huji.ac.il/o-s.htm

Bibliography

  • An C-C, Li Y, Zhu Y-X. . 1995. Molecular cloning and sequencing of the 18S rDNA from specialized dinosaur egg fossil found in Xixia Henan, China. Acta Sci Nat Univ Pekinensis 31:140-147
  • Baker LE. 2001. Mitochondrial DNA haplotype and sequence analysis of historic Choctaw and Menominee hair shaft samples. PhD Thesis. University of Tennessee, Knoxville.
  • Barnes I, Holton K, Vaira D, Spigelman M, Thomas MG. 2000. An assessment of the long-term preservation of the DNA of a bacterial pathogen in ethanol-preserved archival material. J Pathol 192:554-559
  • Basler CF, Reid AH, Dybing JK, Janczewski T A, Fanning TG, Zheng H, Salvatore M, Perdue ML, Swayne DE, Garcia-Sastre A, Palese P, Taubenberger JK. 2001. Sequence of the 1918 pandemic influenza virus non-structural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes. Proc Natl Acad Sci USA 98:2746-2751
  • Cano RJ, Poinar H, Poinar Jr GO. 1992a. Isolation and partial characterisation of DNA from the bee Problebeia dominicana (Apidae:Hymenoptera) in 25-40 million year old amber. Med Sci Res 20:249-251
  • Cano RJ, Poinar HN, Roubik DW, Poinar Jr GO. 1992b. Enzymatic amplification and nucleotide sequencing of portions of the 18S rRNA gene of the bee Problebeia dominicana (Apidae:Hymenoptera) isolated from 25-40 million year old Dominican amber. Med Sci Res 20:619-622
  • Cano RJ, Borucki MK, Higby-Schweitzer M, Poinar HN, Poinar GO Jr, Pollard KJ. 1994. Bacillus DNA in fossil bees: an ancient symbiosis? Appl Environ Microbiol 60:2164-167
  • Caramelli D, Vernesi C, Sanna S, Sampietro L, Lari M, Castrì L, Vona G, Floris R, Francalacci P, Tykot R, Casoli A, Bertranpetit J, Lalueza-Fox C, Bertorelle G, Barbujani G. Genetic variation in prehistoric Sardinia. Hum Genet. 2007 Nov;122(3-4):327-36.
  • Caramelli D, Lalueza-Fox C, Condemi S, Longo L, Milani L, Manfredini A, de Saint Pierre M, Adoni F, Lari M, Giunti P, Ricci S, Casoli A, Calafell F, Mallegni F, Bertranpetit J, Stanyon R, Bertorelle G, Barbujani G. A highly divergent mtDNA sequence in a Neandertal individual from Italy. Curr Biol. 2006 Aug 22;16(16):R630-2.
  • Caramelli D, Lalueza-Fox C, Vernesi C, Lari M, Casoli A, Mallegni F, Chiarelli B, Dupanloup I, Bertranpetit J, Barbujani G, Bertorelle G. Evidence for a genetic discontinuity between Neandertals and 24,000-year-old anatomically modern Europeans. Proc Natl Acad Sci U S A. 2003 May 27;100(11):6593-7. Epub 2003 May 12.
  • Cooper A, Mourer-Chauviré C, Chambers GK, von Haeseler A, Wilson A, Pääbo S. 1992. Independent origins of New Zealand moas and kiwis. Proc Natl Acad Sci USA 89:8741-8744
  • DeSalle R, Gatesy J, Wheeler W, Grimaldi D. 1992. DNA sequences from a fossil termite in Oligo-Miocene amber and their phylogenetic implications. Science 257:1933-1936
  • DeSalle R, Grimaldi D. 1994. Very old DNA. Curr Opin Genet Dev 4:810-815
  • DeSalle R, Barcia M, Wray C. 1993. PCR jumping in clones of 30-million-year-old DNA fragments from amber preserved termites (Mastotermes electrodominicus). Experientia 49:906-909
  • Díaz M.L. and Rodríguez E.L. The History of the Infectious Diseases is Written in the aDNA: Reality or Fiction. Bol. Int. Cienc. Básica. Vol.3, No.3:68-76. (Article N° BICB-08140200)
  • Donoghue HD, Spigelman M, Zias J, Gernaey-Child AM, Minnikin DE. 1998. Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old. Lett Appl Microbiol 27:265-269
  • Dumolin-Lapegue S, Pemonge H-M, Gielly L, Taberlet P, Petit RJ. 1999. Amplification of oak DNA from ancient and modern wood. Mol Ecol 8:2137-2140
  • Fish SA, Shepherd TJ, McGenity TJ, Grant WD. 2002. Recovery of 16S ribosomal RNA gene fragments from ancient halite. Nature 417:432-436
  • Gilbert MTP, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, Higham TFG, Richards MP, O’Connell TC, Tobin DJ, Janaway RC, Cooper A. 2004. Ancient mitochondrial DNA from hair. Current Biology 14:R463-464
  • Golenberg EM. 1991. Amplification and analysis of Miocene plant fossil DNA. Philos Trans R Soc Lond B 333:419-26; discussion 426-7
  • Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M, Henderson D, Zurawski G. 1990. Chloroplast DNA sequence from a Miocene Magnolia species. Nature 344:656-658
  • Goloubinoff P, Pääbo S, Wilson AC. 1993. Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens. Proc Natl Acad Sci U S A 90:1997-2001
  • Hagelberg E, Sykes B, Hedges R. 1989. Ancient bone DNA amplified. Nature 342: 485
  • Hagelberg E, Thomas MG, Cook Jr CE, Sher AV, Baryshnikov GF, Lister AM. 1994. DNA from ancient mammoth bones. Nature 370:333-334
  • Handt O, Richards M, Trommsdorf M, Kilger C, Simanainen J, Georgiev O, Bauer K, Stone A, Hedges R, Schaffner W, Utermann G, Sykes B, Pääbo S. 1994b. Molecular genetic analyses of the Tyrolean Ice Man. Science 264:1775-1778
  • Hänni C, Laudet V, Coll J, Stehelin D. 1994a. An unusual mitochondrial DNA sequence variant from an Egyptian mummy. Genomics 22:487-489
  • Hänni C, Laudet V, Stehelin D, Taberlet P. 1994b. Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequenceing. Proc Natl Acad Sci USA 91:12336-12340
  • Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC. 1984. DNA sequences from the quagga, and extinct member of the horse family. Nature 312:282-284
  • Hofreiter M, Poinar HN, Spaulding WG, Bauer K, Martin PS, Possnert G, Pääbo S. 2000. A molecular analysis of ground sloth diet through the last glaciation. Mol Ecol 9:1975-1984
  • Jackson PJ, Hugh-Jones ME, Adair DM, Green G, Hill KK, Kuske CR, Grinberg LM, Abramova FA, Keim P. 1998. PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: the presence of multiple Bacillus anthracis strains in different victims. Proc Natl Acad Sci USA 95:1224-1229
  • Junqueira ACM, Lessinger AC, Azeredo-Espin AML. 2002. Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis-causing flies. Med Vet Entomol 16:39-45
  • Küch M, Rohland N, Betancourt JL, Latorre C, Steppan S, Poinar HN. 2002. Molecular analysis of an 11,700-year-old rodent midden from the Atacama Desert, Chile. Mol Ecol 11:913-924
  • Lalueza-Fox C, Römpler H, Caramelli D, Stäubert C, Catalano G, Hughes D,Rohland N, Pilli E, Longo L, Condemi S, de la Rasilla M, Fortea J, Rosas A, Stoneking M, Schöneberg T, Bertranpetit J, Hofreiter M.A melanocortin 1 receptor allele suggests varying pigmentation among Neanderthals. Science. 2007 Nov 30;318(5855):1453-5.
  • Lalueza-Fox C, Krause J, Caramelli D, Catalano G, Milani L, Sampietro ML, Calafell F, Martínez-Maza C, Bastir M, García-Tabernero A, de la Rasilla M, Fortea J, Pääbo S, Bertranpetit J, Rosas A.Mitochondrial DNA of an Iberian Neandertal suggests a population affinity with other European Neandertals.Curr Biol. 2006 Aug 22;16(16):R629-30.
  • Lalueza-Fox C, Sampietro ML, Caramelli D, Puder Y, Lari M, Calafell F, Martínez-Maza C, Bastir M, Fortea J, de la Rasilla M, Bertranpetit J, Rosas A.Neandertal evolutionary genetics: mitochondrial DNA data from the iberian peninsula. Mol Biol Evol. 2005 Apr;22(4):1077-81.
  • Li Y, An C-C, Zhu Y-X. 1995. DNA isolation and sequence analysis of dinosaur DNA from Cretaceous dinosaur egg in Xixia Henan, China. Acta Sci Nat Univ Pekinensis 31:148-152
  • Lindahl T. 1993. Recovery of antediluvian DNA. Nature 365:700
  • Montiel R, Malgosa A, Francalacci P. 2001. Authenticating ancient human mitochondrial DNA. Hum Biol 73:689-713
  • Mullis KB, Faloona F. 1987. Specific synthesis of DNA in vitro via a polymerase-catalysed chain reaction. Methods Enzymol 155:335-350
  • Pääbo S. 1985a. Preservation of DNA in ancient Egyptian mummies. J Archeol Sci 12:411-417
  • Pääbo S. 1985b. Molecular cloning of ancient Egyptian mummy DNA. Nature. 314:644-645
  • Pääbo S. 1986. Molecular genetic investigations of ancient human remains. Cold Spring Harbour Symp Quant Biol. 51:441-446
  • Poinar H, Cano R, Poinar G. 1993. DNA from an extinct plant. Nature 363:677
  • Poinar H, Hofreiter M, Spaulding G, Martin P, Stankiewicz A, Bland H, Evershed R, Possnert G, Pääbo S. 1998. Molecular coproscopy: Dung and diet of the extinct ground sloth Nothrotheriops shastensis. Science 281:402-406
  • Poinar HN, Küch M, Sobolik KD, Barnes I, Stankiewicz AB, Kuder T, Spaulding WG, Bryant VM, Cooper A, Pääbo S. 2001. A molecular analysis of dietary diversity for three archaic Native Americans. Proc Natl Acad Sci USA 98:4317-4322
  • Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA. 1988. Primer-directed enzymatic amplification of DNA with thermostable DNA polymerase. Science 239:487-491
  • Taubenberger JK, Reid AH, Krafft AE, Bijwaard KE, Fanning TG. 1997. Initial genetic characterization of the 1918 “Spanish” Influenza virus. Science 275:1793-1796
  • Thomas RH, Schaffner W, Wilson AC, Pääbo. 1989. DNA phylogeny of the extinct marsupial wolf. Nature 340:465-7
  • Vreeland RH, Rozenwieg WD, Powers DW. 2000. Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal. Nature 407, 897-900
  • Willerslev E, Hansen AJ, Binladen J, Brandt TB, Gilbert MTP, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A. 2003. Diverse plant and animal genetic records from Holocene and Pleistocene sediments. Science 300:791-795
  • Woodward SR, Weyand NJ, Bunnell M. 1994. DNA sequence from Cretaceous period bone fragments. Science 266:1229-1232
  • Willerslev E, Cooper A. 2005. Ancient DNA (Review Paper) Proc. R.Soc. B.272 3-16

Conferences

  • 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

See also

Retrieved from "https://en.wikipedia.org/w/index.php?title=Ancient_DNA&oldid=269563063"