Ancient DNA

Cross-linked DNA extracted from the 4,000-year-old liver of the ancient Egyptian priest Nekht-Ankh.

Ancient DNA is DNA isolated from ancient specimens.[1] It can be also 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. Allentoft et al. (2012) tried to calculate this limit by studying the decay of mitochondrial and nuclear DNA in Moa bones. The DNA degrades in an exponential decay process. According to their model, mitochondrial DNA is degraded to an average length of 1 base pair after 6,830,000 years at −5 °C.[2] The decay kinetics have been measured by accelerated aging experiments further displaying the strong influence of storage temperature and humidity on DNA decay.[3] Nuclear DNA degrades at least twice as fast as mtDNA. As such, early studies that reported recovery of much older DNA, for example from Cretaceous dinosaur remains, may have stemmed from contamination of the sample.

History of ancient DNA studies

The first study of what would come to be called aDNA came in 1984, when Russ Higuchi and colleagues at 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.[4] 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 (Pääbo 1985a; Pääbo 1985b; Pääbo 1986). 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) in the late 1980s the field began to progress rapidly.[5][6]

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.

Single primer extension (abr. SPEX) amplification was introduced in 2007 to address postmortem DNA modification damage.[7]

Problems and errors

aDNA may contain a large number of postmortem 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.[8] Due to sequencing errors, great caution should be applied to interpretation of population size.[9] Substitutions resulting from deamination cytosine residues are vastly overrepresented in the ancient DNA sequences. Miscoding of C to T and G to A accounts for the majority of errors.[10] Another problem with ancient DNA samples is contamination by modern human DNA and by microbial DNA (most of which is also ancient).[11]

"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 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[12] — 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 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.[13][14]

Unfortunately, the golden days of antediluvian DNA did not last. A critical review of ancient DNA literature through the development of the field highlights that few studies after about 2002 have succeeded in amplifying DNA from remains older than several hundred thousand years.[15] A greater appreciation for the risks of environmental contamination and studies on the chemical stability of DNA have resulted in concerns being raised over previous reported results. The dinosaur DNA was later revealed to be human Y-chromosome,[16] while the DNA reported from encapsulated halobacteria has been criticized based on its similarity to modern bacteria, which hints at contamination.[17] A 2007 study also suggest that these bacterial DNA samples may not have survived from ancient times but may instead be the product of long-term, low-level metabolic activity.[18]

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,[4][19] bone (c.f. Hagelberg et al. 1989; Cooper et al. 1992; Hagelberg et al. 1994),[20] paleofaeces,[21][22] alcohol preserved specimens (Junqueira et al. 2002), rodent middens,[23] dried plant remains (Goloubinoff et al. 1993; Dumolin-Lapegue et al. 1999) and recently, extractions of animal and plant DNA directly from soil samples.[24] In June 2013, a group of researchers announced that they had sequenced the DNA of a 560–780 thousand year old horse, using material extracted from a leg bone found buried in permafrost in Canada's Yukon territory.[25] In 2013, a German team reconstructed the mitochondrial genome of an Ursus deningeri more than 300,000 years old, proving that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost.[26]

Ancient DNA studies on human remains

Due to the considerable anthropological, archaeological, and public interest directed toward 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, such as high-altitude mummies from 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).[27] 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. In November 2015, scientists reported finding a 110,000-year-old fossil tooth containing DNA from Denisovan hominin, an extinct species of human in the genus Homo.[28][29]

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 postmortem, DNA may survive from any microorganisms present in the specimen at death. These include not only 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,[30] 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,[31][32] and formalin-fixed tissue.[33]

Researchers specializing in ancient DNA

See also

References

  1. ↑ Bioinformatics and Functional Genomics By Jonathan Pevsner ISBN 978-0-470-08585-1, ISBN 0-470-08585-1
  2. ↑ Allentoft ME; Collins M; Harker D; Haile J; Oskam CL; Hale ML; Campos PF; Samaniego JA; Gilbert MTP; Willerslev E; Zhang G; Scofield RP; Holdaway RN; Bunce M (2012). "The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils". Proceedings of the Royal Society B 279 (1748): 4724–33. doi:10.1098/rspb.2012.1745.
  3. ↑ Grass, R. N.; Heckel, R.; Puddu, M.; Paunescu, D.; Stark, W. J. (2015). "Robust Chemical Preservation of Digital Information on DNA in Silica with Error-Correcting Codes". Angewandte Chemie International Edition 54 (8): 2552–2555. doi:10.1002/anie.201411378.
  4. 1 2 Higuchi R; Bowman B; Freiberger M; Ryder OA; Wilson AC (1984). "DNA sequences from the quagga, an extinct member of the horse family". Nature 312 (5991): 282–4. Bibcode:1984Natur.312..282H. doi:10.1038/312282a0. PMID 6504142.
  5. ↑ Mullis KB; Faloona FA (1987). "Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction". Meth. Enzymol. Methods in Enzymology 155: 335–50. doi:10.1016/0076-6879(87)55023-6. ISBN 978-0-12-182056-5. PMID 3431465.
  6. ↑ Saiki RK, Gelfand DH, Stoffel S, et al. (January 1988). "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase". Science 239 (4839): 487–91. Bibcode:1988Sci...239..487S. doi:10.1126/science.2448875. PMID 2448875.
  7. ↑ Brotherton, P; Endicott, P; Sanchez, Jj; Beaumont, M; Barnett, R; Austin, J; Cooper, A (2007). "Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post-mortem miscoding lesions" (Free full text). Nucleic Acids Research 35 (17): 5717–28. doi:10.1093/nar/gkm588. ISSN 0305-1048. PMC 2034480. PMID 17715147.
  8. ↑ (PDF) http://web.archive.org/web/20081217110352/http://www.454genomics.net/downloads/news-events/geneticanalysisfromancientdna.pdf. Archived from the original (PDF) on December 17, 2008. Retrieved December 1, 2008. Missing or empty |title= (help)
  9. ↑ Johnson, Pl; Slatkin, M (Jan 2008). "Accounting for bias from sequencing error in population genetic estimates" (Free full text). Molecular Biology and Evolution 25 (1): 199–206. doi:10.1093/molbev/msm239. ISSN 0737-4038. PMID 17981928.
  10. ↑ Briggs, Aw; Stenzel, U; Johnson, Pl; Green, Re; Kelso, J; Prüfer, K; Meyer, M; Krause, J; Ronan, Mt; et al. (Sep 2007). "Patterns of damage in genomic DNA sequences from a Neandertal" (Free full text). Proceedings of the National Academy of Sciences of the United States of America 104 (37): 14616–21. Bibcode:2007PNAS..10414616B. doi:10.1073/pnas.0704665104. ISSN 0027-8424. PMC 1976210. PMID 17715061.
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  12. ↑ Woodward SR; Weyand NJ; Bunnell M (November 1994). "DNA sequence from Cretaceous period bone fragments". Science 266 (5188): 1229–32. Bibcode:1994Sci...266.1229W. doi:10.1126/science.7973705. PMID 7973705.
  13. ↑ Vreeland RH; Rosenzweig WD; Powers DW (October 2000). "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal". Nature 407 (6806): 897–900. doi:10.1038/35038060. PMID 11057666.
  14. ↑ Fish SA; Shepherd TJ; McGenity TJ; Grant WD (May 2002). "Recovery of 16S ribosomal RNA gene fragments from ancient halite". Nature 417 (6887): 432–6. Bibcode:2002Natur.417..432F. doi:10.1038/417432a. PMID 12024211.
  15. ↑ Willerslev E, Hansen AJ, Binladen J, et al. (May 2003). "Diverse plant and animal genetic records from Holocene and Pleistocene sediments". Science 300 (5620): 791–5. Bibcode:2003Sci...300..791W. doi:10.1126/science.1084114. PMID 12702808.
  16. ↑ Zischler H; Höss M; Handt O; von Haeseler A; van der Kuyl AC; Goudsmit J (May 1995). "Detecting dinosaur DNA". Science 268 (5214): 1192–3; author reply 1194. doi:10.1126/science.7605504. PMID 7605504.
  17. ↑ Nicholls H (February 2005). "Ancient DNA Comes of Age". PLOS Biology 3 (2): e56. doi:10.1371/journal.pbio.0030056. PMC 548952. PMID 15719062.
  18. ↑ Johnson SS; Hebsgaard MB; Christensen TR; Mastepanov M; Nielsen R; Munch K; Brand T; Gilbert MT; Zuber MT; Bunce M; Rønn R; Gilichinsky D; Froese D; Willerslev E (September 2007). "Ancient bacteria show evidence of DNA repair". PNAS 104 (36): 14401–5. Bibcode:2007PNAS..10414401J. doi:10.1073/pnas.0706787104. PMC 1958816. PMID 17728401.
  19. ↑ Thomas RH; Schaffner W; Wilson AC; Pääbo S (August 1989). "DNA phylogeny of the extinct marsupial wolf". Nature 340 (6233): 465–7. Bibcode:1989Natur.340..465T. doi:10.1038/340465a0. PMID 2755507.
  20. ↑ Hänni C; Laudet V; Stehelin D; Taberlet P (December 1994). "Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing". Proceedings of the National Academy of Sciences of the United States of America 91 (25): 12336–40. Bibcode:1994PNAS...9112336H. doi:10.1073/pnas.91.25.12336. PMC 45432. PMID 7991628.
  21. ↑ Poinar HN, Hofreiter M, Spaulding WG, et al. (July 1998). "Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis". Science 281 (5375): 402–6. Bibcode:1998Sci...281..402P. doi:10.1126/science.281.5375.402. PMID 9665881.
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  23. ↑ Kuch M; Rohland N; Betancourt JL; Latorre C; Steppan S; Poinar HN (May 2002). "Molecular analysis of an 11,700-year-old rodent midden from the Atacama Desert, Chile". Mol. Ecol. 11 (5): 913–24. doi:10.1046/j.1365-294X.2002.01492.x. PMID 11975707.
  24. ↑ Willerslev E; Cooper A (January 2005). "Ancient DNA". Proceedings of the Royal Society B 272 (1558): 3–16. doi:10.1098/rspb.2004.2813. PMC 1634942. PMID 15875564.
  25. ↑ Erika Check Hayden (26 June 2013). "First horses arose 4 million years ago". Nature. doi:10.1038/nature.2013.13261.
  26. ↑ Dabney; et al. (2013). "Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments". PNAS 110 (39): 15758–15763. Bibcode:2013PNAS..11015758D. doi:10.1073/pnas.1314445110. Retrieved 18 January 2014.
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  28. ↑ Zimmer, Carl (16 November 2015). "In a Tooth, DNA From Some Very Old Cousins, the Denisovans". New York Times. Retrieved 16 November 2015.
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  31. ↑ Jackson PJ, Hugh-Jones ME, Adair DM, et al. (February 1998). "PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: The presence of multiple Bacillus anthracis strains in different victims". Proceedings of the National Academy of Sciences of the United States of America 95 (3): 1224–9. Bibcode:1998PNAS...95.1224J. doi:10.1073/pnas.95.3.1224. PMC 18726. PMID 9448313.
  32. ↑ Basler CF, Reid AH, Dybing JK, et al. (February 2001). "Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes". Proceedings of the National Academy of Sciences of the United States of America 98 (5): 2746–51. Bibcode:2001PNAS...98.2746B. doi:10.1073/pnas.031575198. PMC 30210. PMID 11226311.
  33. ↑ Taubenberger JK; Reid AH; Krafft AE; Bijwaard KE; Fanning TG (March 1997). "Initial genetic characterization of the 1918 "Spanish" influenza virus". Science 275 (5307): 1793–6. doi:10.1126/science.275.5307.1793. PMID 9065404.

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