Wikipedia

Ancient DNA

Ancient DNA(aDNA) isDNAisolated from ancient sources (typicallyspecimens,but alsoenvironmental DNA).[1][2]Due to degradation processes (includingcross-linking,deaminationandfragmentation)[3]ancient DNA is more degraded in comparison with contemporary genetic material.[4]Genetic material has been recovered from paleo/archaeological and historical skeletal material,mummifiedtissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and frompermafrostcores, marine and lake sediments andexcavationdirt.

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

Even under the best preservation conditions, there is an upper boundary of 0.4–1.5 million years for a sample to contain sufficient DNA for sequencing technologies.[5]The oldest DNA sequenced from physical specimens are frommammothmolars in Siberia over 1 million years old.[6]In 2022, two-million year old genetic material was recovered from sediments inGreenland,and is currently considered the oldest DNA discovered so far.[7][8]

History of ancient DNA studies

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1980s

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Quagga (Equus quagga quagga), an extinct sub-species of zebra.

The first study of what would come to be called aDNA was conducted in 1984, when Russ Higuchi and colleagues at theUniversity of California, Berkeleyreported that traces of DNA from a museum specimen of theQuagganot only remained in the specimen over 150 years after the death of the individual, but could be extracted and sequenced.[9]Over the next two years, through investigations into natural and artificially mummified specimens,Svante Pääboconfirmed that this phenomenon was not limited to relatively recent museum specimens but could apparently be replicated in a range ofmummifiedhuman samples that dated as far back as several thousand years.[10][11][12]

The laborious processes that were required at that time to sequence such DNA (throughbacterial cloning) were an effective brake on the study of ancient DNA (aDNA) and the field ofmuseomics.However, with the development of thePolymerase Chain Reaction(PCR) in the late 1980s, the field began to progress rapidly.[13][14][15]Double primer PCR amplification of aDNA (jumping-PCR) can produce highly skewed and non-authentic sequence artifacts. Multiple primer,nested PCRstrategy was used to overcome those shortcomings.

1990s

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A diptera (Mycetophilidae) from the Eocene (40-50 million years ago) in a piece of transparent Baltic amber along with other smaller inclusions. Shown under daylight (big photograph) and under UV light (small photograph).

The post-PCR era heralded a wave of publications as numerous research groups claimed success in isolating 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 labelledAntediluvianDNA.[16]The majority of such claims were based on the retrieval of DNA from organisms preserved inamber.Insects such as stingless bees,[17][18]termites,[19]and wood gnats,[20]as well as plant[21]and bacterial[22]sequences were said to have been extracted fromDominicanamber dating to theOligoceneepoch. Still older sources of Lebanese amber-encasedweevils,dating to within theCretaceousepoch, reportedly also yielded authentic DNA.[23]Claims of DNA retrieval were not limited to amber.

Reports of several sediment-preserved plant remains dating to theMiocenewere published.[24][25]Then in 1994, Woodwardet al.reported what at the time was called the most exciting results to date[26]— mitochondrial cytochrome b sequences that had apparently been extracted from dinosaur bones dating to more than 80 million years ago. When in 1995 two further studies reported dinosaur DNA sequences extracted from a Cretaceous egg,[27][28]it seemed that the field would 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 fromhalite.[29][30]

The development of a better understanding of the kinetics of DNA preservation, the risks of sample contamination and other complicating factors led the field to view these results more skeptically. Numerous careful attempts failed to replicate many of the findings, and all of the decade's claims of multi-million year old aDNA would come to be dismissed as inauthentic.[31]

2000s

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Single primer extension amplification was introduced in 2007 to address postmortem DNA modification damage.[32]Since 2009 the field of aDNA studies has been revolutionized with the introduction of much cheaper research techniques.[33]The use of high-throughputNext Generation Sequencing(NGS) techniques in the field of ancient DNA research has been essential for reconstructing the genomes of ancient or extinct organisms. A single-stranded DNA (ssDNA) library preparation method has sparked great interest among ancient DNA (aDNA) researchers.[34][35]

Svante Pääbo (left) with his medal for the Nobel Prize on Physiology or Medicine.

In addition to these technical innovations, the start of the decade saw the field begin to develop better standards and criteria for evaluating DNA results, as well as a better understanding of the potential pitfalls.[31][36]

2020s

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Autumn of 2022, the Nobel Prize of Physiology or Medicine was awarded to Svante Pääbo "for his discoveries concerning the genomes of extinct hominins and human evolution".[37]A few days later, on the 7th of December 2022, a study inNaturereported that two-million year old genetic material was found in Greenland, and is currently considered the oldest DNA discovered so far.[7][8]

Problems and errors

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Degradation processes

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Due to degradation processes (including cross-linking, deamination and fragmentation),[3]ancient DNA is of lower quality than modern genetic material.[4]The damage characteristics and ability of aDNA to survive through time restricts possible analyses and places an upper limit on the age of successful samples.[4]There is a theoretical correlation between time and DNA degradation,[38]although differences in environmental conditions complicate matters. Samples subjected to different conditions are unlikely to predictably align to a uniform age-degradation relationship.[39]The environmental effects may even matter after excavation, as DNA decay-rates may increase,[40]particularly under fluctuating storage conditions.[41]Even under the best preservation conditions, there is an upper boundary of 0.4 to 1.5 million years for a sample to contain sufficient DNA for contemporary sequencing technologies.[5]

Research into the decay ofmitochondrialandnuclear DNAinmoabones has modelled mitochondrial DNA degradation to an average length of 1base pairafter 6,830,000 years at −5 °C.[4]The decay kinetics have been measured by accelerated aging experiments, further displaying the strong influence of storage temperature and humidity on DNA decay.[42]Nuclear DNA degrades at least twice as fast as mtDNA. Early studies that reported recovery of much older DNA, for example fromCretaceousdinosaurremains, may have stemmed from contamination of the sample.

Age limit

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A critical review of ancient DNA literature through the development of the field highlights that few studies have succeeded in amplifying DNA from remains older than several hundred thousand years.[43]A greater appreciation for the risks of environmental contamination and studies on thechemical stabilityof DNA have raised concerns over previously reported results. The alleged dinosaur DNA was later revealed to be humanY-chromosome.[44]The DNA reported from encapsulatedhalobacteriahas been criticized based on its similarity to modern bacteria, which hints at contamination,[36]or they may be the product of long-term, low-levelmetabolicactivity.[45]

aDNA may contain a large number of postmortemmutations,increasing with time. Some regions of polynucleotide are more susceptible to this degradation, allowing erroneous sequence data to bypass statistical filters used to check the validity of data.[31]Due to sequencing errors, great caution should be applied to interpretation of population size.[46]Substitutions resulting fromdeaminationofcytosineresidues are vastly over-represented in the ancient DNA sequences. Miscoding ofCtoTandGtoAaccounts for the majority of errors.[47]

Contamination

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Another problem with ancient DNA samples is contamination by modern human DNA and by microbial DNA (most of which is also ancient).[48][49]New methods have emerged in recent years to prevent possible contamination of aDNA samples, including conducting extractions under extreme sterile conditions, using special adapters to identify endogenous molecules of the sample (distinguished from those introduced during analysis), and applying bioinformatics to resulting sequences based on known reads in order to approximate rates of contamination.[50][51]

Authentication of aDNA

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Development in the aDNA field in the 2000s increased the importance of authenticating recovered DNA to confirm that it is indeed ancient and not the result of recent contamination. As DNA degrades over time, the nucleotides that make up the DNA may change, especially at the ends of the DNA molecules. The deamination of cytosine to uracil at the ends of DNA molecules has become a way of authentication. During DNA sequencing, the DNA polymerases will incorporate an adenine (A) across from the uracil (U), leading to cytosine (C) to thymine (T) substitutions in the aDNA data.[52]These substitutions increase in frequency as the sample gets older. Frequency measurement of the C-T level, ancient DNA damage, can be made using various software such as mapDamage2.0 or PMDtools[53][54]and interactively on metaDMG.[55]Due to hydrolytic depurination, DNA fragments into smaller pieces, leading to single-stranded breaks. Combined with the damage pattern, this short fragment length can also help differentiate between modern and ancient DNA.[56][57]

Non-human aDNA

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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 planttaxa.Tissues examined include artificially or naturally mummified animal remains,[9][58]bone,[59][60][61][62]shells,[63]paleofaeces,[64][65]alcohol preserved specimens,[66]rodent middens,[67]dried plant remains,[68][69]and recently, extractions of animal and plant DNA directly fromsoilsamples.[70]

In June 2013, a group of researchers includingEske Willerslev,Marcus Thomas Pius Gilbertand Orlando Ludovic of theCentre for Geogenetics,Natural History Museum of Denmarkat theUniversity of Copenhagen,announced that they had sequenced the DNA of a 560–780 thousand year old horse, using material extracted from a leg bone found buried inpermafrostin Canada'sYukonterritory.[71][72][73]A German team also reported in 2013 the reconstructedmitochondrial genomeof a bear,Ursus deningeri,more than 300,000 years old, proving that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost.[74]The DNA sequence of even older nuclear DNA was reported in 2021 from the permafrost-preserved teeth of two Siberianmammoths,both over a million years old.[6][75]

Researchers in 2016 measured chloroplast DNA in marine sediment cores, and found diatom DNA dating back to 1.4 million years.[76]This DNA had a half-life significantly longer than previous research, of up to 15,000 years. Kirkpatrick's team also found that DNA only decayed along a half-life rate until about 100 thousand years, at which point it followed a slower, power-law decay rate.[76]

Human aDNA

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Map of human fossils with an age of at least ~40,000 years that yielded genome-wide data[77]

Due to the considerableanthropological,archaeological,andpublic interestdirected toward human remains, they have received considerable attention from the DNA community. There are also more profound contamination issues, since the specimens belong to the same species as the researchers collecting and evaluating the samples.

Sources

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Due to themorphologicalpreservation in mummies, many studies from the 1990s and 2000s used mummified tissue as a source of ancient human DNA. Examples include both naturally preserved specimens, such as theÖtzi the Icemanfrozen in a glacier[78]and bodies preserved through rapiddesiccationat high altitude in the Andes,[12][79]as well as various chemically treated preserved tissue such as the mummies of ancient Egypt.[80]However, mummified remains are a limited resource. The majority of human aDNA studies have focused on extracting DNA from two sources much more common in thearchaeological record:bonesandteeth.The bone that is most often used for DNA extraction is thepetrousear bone, since its dense structure provides good conditions for DNA preservation.[81]Several other sources have also yielded DNA, includingpaleofaeces,[82]andhair.[83][84]Contamination remains a major problem when working on ancient human material.

AncientpathogenDNA has been successfully retrieved from samples dating to more than 5,000 years old in humans and as long as 17,000 years ago in other species. In addition to the usual sources of mummified tissue, bones and teeth, such studies have also examined a range of other tissue samples, including calcifiedpleura,[85]tissue embedded inparaffin,[86][87]andformalin-fixed tissue.[88]Efficient computational tools have been developed for pathogen and microorganism aDNA analyses in a small (QIIME[89]) and large scale (FALCON[90]).

Results

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Taking preventative measures in their procedure against such contamination though, a 2012 study analyzed bone samples of aNeanderthalgroup in the El Sidrón cave, finding new insights on potential kinship and genetic diversity from the aDNA.[91]In November 2015, scientists reported finding a 110,000-year-old tooth containing DNA from theDenisovan hominin,anextinctspeciesofhumanin the genusHomo.[92][93]

The research has added new complexity to the peopling of Eurasia. A study from 2018[94]showed that aBronze Agemass migration had greatly impacted the genetic makeup of the British Isles, bringing with it theBell Beakerculture from mainland Europe.

It has also revealed new information about links between the ancestors of Central Asians and the indigenous peoples of the Americas. In Africa, older DNA degrades quickly due to the warmer tropical climate, although, in September 2017, ancient DNA samples, as old as 8,100 years old, have been reported.[95]

Moreover, ancient DNA has helped researchers to estimate modern human divergence.[96]By sequencing African genomes from three Stone Age hunter gatherers (2000 years old) and four Iron Age farmers (300 to 500 years old), Schlebusch and colleagues were able to push back the date of the earliest divergence between human populations to 350,000 to 260,000 years ago.

As of 2021, the oldest completely reconstructed human genomes are~45,000 years old.[97][77]Such genetic data provides insights into the migration and genetic history – e.g.of Europe– including aboutinterbreeding between archaic and modern humanslike a common admixture between initial European modern humans and Neanderthals.[98][77][99]

Researchers specializing in ancient DNA

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See also

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References

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  1. ^Pevsner J (2015).Bioinformatics and Functional Genomics(3rd ed.). Wiley-Blackwell.ISBN978-1118581780.
  2. ^Jones M (2016).Unlocking the Past: How Archaeologists Are Rewriting Human History with Ancient DNA.Arcade.ISBN978-1628724479.
  3. ^abAnderson LA (May 2023)."A chemical framework for the preservation of fossil vertebrate cells and soft tissues".Earth-Science Reviews.240:104367.Bibcode:2023ESRv..24004367A.doi:10.1016/j.earscirev.2023.104367.S2CID257326012.
  4. ^abcdAllentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, et al. (December 2012)."The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils".Proceedings. Biological Sciences.279(1748): 4724–33.doi:10.1098/rspb.2012.1745.PMC3497090.PMID23055061.
  5. ^abWillerslev E, Hansen AJ, Rønn R, Brand TB, Barnes I, Wiuf C, et al. (January 2004)."Long-term persistence of bacterial DNA"(PDF).Current Biology.14(1): R9-10.Bibcode:2004CBio...14...R9W.doi:10.1016/j.cub.2003.12.012.PMID14711425.S2CID12227538.
  6. ^abvan der Valk T, Pečnerová P, Díez-Del-Molino D, Bergström A, Oppenheimer J, Hartmann S, et al. (March 2021)."Million-year-old DNA sheds light on the genomic history of mammoths".Nature.591(7849): 265–269.Bibcode:2021Natur.591..265V.doi:10.1038/s41586-021-03224-9.PMC7116897.PMID33597750.
  7. ^abZimmer C(7 December 2022)."Oldest Known DNA Offers Glimpse of a Once-Lush Arctic - In Greenland's permafrost, scientists discovered two-million-year-old genetic material from scores of plant and animal species, including mastodons, geese, lemmings and ants".The New York Times.Retrieved7 December2022.
  8. ^abKjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, et al. (December 2022)."A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA".Nature.612(7939): 283–291.Bibcode:2022Natur.612..283K.doi:10.1038/s41586-022-05453-y.PMC9729109.PMID36477129.
  9. ^abHiguchi 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.PMID6504142.S2CID4313241.
  10. ^Pääbo S (1985a). "Preservation of DNA in ancient Egyptian mummies".J. Archaeol. Sci.12(6): 411–17.Bibcode:1985JArSc..12..411P.doi:10.1016/0305-4403(85)90002-0.
  11. ^Pääbo S (1985b). "Molecular cloning of Ancient Egyptian mummy DNA".Nature.314(6012): 644–5.Bibcode:1985Natur.314..644P.doi:10.1038/314644a0.PMID3990798.S2CID1358295.
  12. ^abPääbo S (1986). "Molecular genetic investigations of ancient human remains".Cold Spring Harbor Symposia on Quantitative Biology.51(Pt 1): 441–6.doi:10.1101/SQB.1986.051.01.053.PMID3107879.
  13. ^Mullis KB, Faloona FA (1987)."Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction".Recombinant DNA Part F.Methods in Enzymology. Vol. 155. pp. 335–50.doi:10.1016/0076-6879(87)55023-6.ISBN978-0-12-182056-5.PMID3431465.
  14. ^Raxworthy CJ, Smith BT (November 2021)."Mining museums for historical DNA: advances and challenges in museomics".Trends in Ecology & Evolution.36(11): 1049–1060.Bibcode:2021TEcoE..36.1049R.doi:10.1016/j.tree.2021.07.009.PMID34456066.S2CID239687836.
  15. ^Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, et al. (January 1988). "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase".Science.239(4839): 487–491.Bibcode:1988Sci...239..487S.doi:10.1126/science.239.4839.487.PMID2448875.
  16. ^Lindahl T (October 1993)."Recovery of antediluvian DNA".Nature.365(6448): 700.Bibcode:1993Natur.365..700L.doi:10.1038/365700a0.PMID8413647.S2CID4365447.
  17. ^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.20:249–51.
  18. ^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.20:619–22.
  19. ^Matson E, Ottesen E, Leadbetter J (2007)."Extracting DNA from the gut microbes of the termite (Zootermopsis nevadensis)".Journal of Visualized Experiments(4): 195.doi:10.3791/195.PMC2556161.PMID18979000.
  20. ^DeSalle R, Grimaldi D (December 1994). "Very old DNA".Current Opinion in Genetics & Development.4(6): 810–5.doi:10.1016/0959-437x(94)90064-7.PMID7888749.
  21. ^Poinar H, Cano R, Poinar G (1993)."DNA from an extinct plant".Nature.363(6431): 677.Bibcode:1993Natur.363..677P.doi:10.1038/363677a0.S2CID4330200.
  22. ^Cano RJ, Borucki MK, Higby-Schweitzer M, Poinar HN, Poinar GO, Pollard KJ (June 1994)."Bacillus DNA in fossil bees: an ancient symbiosis?".Applied and Environmental Microbiology.60(6): 2164–2167.Bibcode:1994ApEnM..60.2164C.doi:10.1128/aem.60.6.2164-2167.1994.PMC201618.PMID8031102.
  23. ^Cano RJ, Poinar HN, Pieniazek NJ, Acra A, Poinar GO (June 1993). "Amplification and sequencing of DNA from a 120-135-million-year-old weevil".Nature.363(6429): 536–538.Bibcode:1993Natur.363..536C.doi:10.1038/363536a0.PMID8505978.S2CID4243196.
  24. ^Golenberg EM (September 1991). "Amplification and analysis of Miocene plant fossil DNA".Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.333(1268): 419–26, discussion 426–7.doi:10.1098/rstb.1991.0092.PMID1684052.
  25. ^Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M, Henderson D, et al. (April 1990). "Chloroplast DNA sequence from a miocene Magnolia species".Nature.344(6267): 656–8.Bibcode:1990Natur.344..656G.doi:10.1038/344656a0.PMID2325772.S2CID26577394.
  26. ^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.PMID7973705.
  27. ^An CC, Li Y, Zhu YX (1995). "Molecular cloning and sequencing of the 18S rDNA from specialized dinosaur egg fossil found in Xixia Henan, China".Acta Sci Nat Univ Pekinensis.31:140–47.
  28. ^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.31:148–52.
  29. ^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.Bibcode:2000Natur.407..897V.doi:10.1038/35038060.PMID11057666.S2CID9879073.
  30. ^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.PMID12024211.S2CID4423309.
  31. ^abcPääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, et al. (2004)."Genetic analyses from ancient DNA"(PDF).Annual Review of Genetics.38(1): 645–79.doi:10.1146/annurev.genet.37.110801.143214.PMID15568989.Archived fromthe original(PDF)on December 17, 2008.
  32. ^Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, et al. (2007)."Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions".Nucleic Acids Research.35(17): 5717–28.doi:10.1093/nar/gkm588.PMC2034480.PMID17715147.
  33. ^Reich 2018.
  34. ^Wales N, Carøe C, Sandoval-Velasco M, Gamba C, Barnett R, Samaniego JA, et al. (December 2015)."New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA".BioTechniques.59(6): 368–71.doi:10.2144/000114364.PMID26651516.
  35. ^Bennett EA, Massilani D, Lizzo G, Daligault J, Geigl EM, Grange T (June 2014)."Library construction for ancient genomics: single strand or double strand?".BioTechniques.56(6): 289–90, 292–6, 298, passim.doi:10.2144/000114176.PMID24924389.
  36. ^abNicholls H (February 2005)."Ancient DNA comes of age".PLOS Biology.3(2): e56.doi:10.1371/journal.pbio.0030056.PMC548952.PMID15719062.
  37. ^"The Nobel Prize in Physiology or Medicine 2022".Retrieved2024-10-31.
  38. ^Hebsgaard MB, Phillips MJ, Willerslev E (May 2005). "Geologically ancient DNA: fact or artefact?".Trends in Microbiology.13(5): 212–20.doi:10.1016/j.tim.2005.03.010.PMID15866038.
  39. ^Hansen AJ, Mitchell DL, Wiuf C, Paniker L, Brand TB, Binladen J, et al. (June 2006)."Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments".Genetics.173(2): 1175–9.doi:10.1534/genetics.106.057349.PMC1526502.PMID16582426.
  40. ^Pruvost M, Schwarz R, Correia VB, Champlot S, Braguier S, Morel N, et al. (January 2007)."Freshly excavated fossil bones are best for amplification of ancient DNA".Proceedings of the National Academy of Sciences of the United States of America.104(3): 739–44.Bibcode:2007PNAS..104..739P.doi:10.1073/pnas.0610257104.PMC1783384.PMID17210911.
  41. ^Burger J, Hummel S, Hermann B, Henke W (June 1999). "DNA preservation: a microsatellite-DNA study on ancient skeletal remains".Electrophoresis.20(8): 1722–8.doi:10.1002/(sici)1522-2683(19990101)20:8<1722::aid-elps1722>3.0.co;2-4.PMID10435438.S2CID7325310.
  42. ^ Grass RN, Heckel R, Puddu M, Paunescu D, Stark WJ (February 2015). "Robust chemical preservation of digital information on DNA in silica with error-correcting codes".Angewandte Chemie.54(8): 2552–5.doi:10.1002/anie.201411378.PMID25650567.
  43. ^Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MT, Shapiro B, 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.PMID12702808.S2CID1222227.
  44. ^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.Bibcode:1995Sci...268.1191B.doi:10.1126/science.7605504.PMID7605504.
  45. ^Johnson SS, Hebsgaard MB, Christensen TR, Mastepanov M, Nielsen R, Munch K, et al. (September 2007)."Ancient bacteria show evidence of DNA repair".Proceedings of the National Academy of Sciences of the United States of America.104(36): 14401–5.Bibcode:2007PNAS..10414401J.doi:10.1073/pnas.0706787104.PMC1958816.PMID17728401.
  46. ^Johnson PL, Slatkin M (January 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.PMID17981928.
  47. ^Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, et al. (September 2007)."Patterns of damage in genomic DNA sequences from a Neandertal".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.PMC1976210.PMID17715061.
  48. ^Gansauge MT, Meyer M (September 2014)."Selective enrichment of damaged DNA molecules for ancient genome sequencing".Genome Research.24(9): 1543–9.doi:10.1101/gr.174201.114.PMC4158764.PMID25081630.
  49. ^Pratas D, Hosseini M, Grilo G, Pinho AJ, Silva RM, Caetano T, et al. (September 2018)."Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard".Genes.9(9): 445.doi:10.3390/genes9090445.PMC6162538.PMID30200636.
  50. ^Slatkin M, Racimo F (June 2016)."Ancient DNA and human history".Proceedings of the National Academy of Sciences of the United States of America.113(23): 6380–7.Bibcode:2016PNAS..113.6380S.doi:10.1073/pnas.1524306113.PMC4988579.PMID27274045.
  51. ^Borry M, Hübner A, Rohrlach AB, Warinner C (2021-07-27)."PyDamage: automated ancient damage identification and estimation for contigs in ancient DNAde novoassembly ".PeerJ.9:e11845.doi:10.7717/peerj.11845.PMC8323603.PMID34395085.
  52. ^Dabney J, Meyer M, Pääbo S (July 2013)."Ancient DNA damage".Cold Spring Harbor Perspectives in Biology.5(7): a012567.doi:10.1101/cshperspect.a012567.PMC3685887.PMID23729639.
  53. ^Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L (July 2013)."mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters".Bioinformatics.29(13): 1682–1684.doi:10.1093/bioinformatics/btt193.PMC3694634.PMID23613487.
  54. ^Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S, Krause J, et al. (February 2014)."Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal".Proceedings of the National Academy of Sciences of the United States of America.111(6): 2229–2234.Bibcode:2014PNAS..111.2229S.doi:10.1073/pnas.1318934111.PMC3926038.PMID24469802.
  55. ^Michelsen C, Pedersen MW, Fernandez-Guerra A, Zhao L, Petersen TC, Korneliussen TS (9 December 2022). "metaDMG – A Fast and Accurate Ancient DNA Damage Toolkit for Metagenomic Data".bioRxiv:2022.12.06.519264.doi:10.1101/2022.12.06.519264.S2CID254536966.
  56. ^Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, et al. (February 2010)."A complete mtDNA genome of an early modern human from Kostenki, Russia".Current Biology.20(3): 231–236.Bibcode:2010CBio...20..231K.doi:10.1016/j.cub.2009.11.068.PMID20045327.S2CID16440465.
  57. ^Pochon Z, Bergfeldt N, Kırdök E, Vicente M, Naidoo T, van der Valk T, et al. (October 2023)."aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow".Genome Biology.24(1): 242.doi:10.1101/2022.10.03.510579.PMC10591440.PMID37872569.S2CID252763827.
  58. ^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.PMID2755507.S2CID4310500.
  59. ^Hagelberg E, Sykes B, Hedges R (November 1989)."Ancient bone DNA amplified".Nature.342(6249): 485.Bibcode:1989Natur.342..485H.doi:10.1038/342485a0.PMID2586623.S2CID13434992.
  60. ^Cooper A, Mourer-Chauviré C, Chambers GK, von Haeseler A, Wilson AC, Pääbo S (September 1992)."Independent origins of New Zealand moas and kiwis".Proceedings of the National Academy of Sciences of the United States of America.89(18): 8741–4.Bibcode:1992PNAS...89.8741C.doi:10.1073/pnas.89.18.8741.PMC49996.PMID1528888.
  61. ^Hagelberg E, Thomas MG, Cook CE, Sher AV, Baryshnikov GF, Lister AM (August 1994). "DNA from ancient mammoth bones".Nature.370(6488): 333–4.Bibcode:1994Natur.370R.333H.doi:10.1038/370333b0.PMID8047136.S2CID8694387.
  62. ^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.PMC45432.PMID7991628.
  63. ^Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, et al. (2024-05-06). Fernández Robledo JA (ed.)."Advancing responsible genomic analyses of ancient mollusc shells".PLOS ONE.19(5): e0302646.Bibcode:2024PLoSO..1902646M.doi:10.1371/journal.pone.0302646.PMC11073703.PMID38709766.
  64. ^Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA, Bland H, 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.PMID9665881.
  65. ^Hofreiter M, Poinar HN, Spaulding WG, Bauer K, Martin PS, Possnert G, et al. (December 2000). "A molecular analysis of ground sloth diet through the last glaciation".Molecular Ecology.9(12): 1975–84.Bibcode:2000MolEc...9.1975H.doi:10.1046/j.1365-294X.2000.01106.x.PMID11123610.S2CID22685601.
  66. ^Junqueira AC, Lessinger AC, Azeredo-Espin AM (March 2002)."Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis-causing flies".Medical and Veterinary Entomology.16(1): 39–45.doi:10.1046/j.0269-283x.2002.00336.x.PMID11963980.
  67. ^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".Molecular Ecology.11(5): 913–24.Bibcode:2002MolEc..11..913K.doi:10.1046/j.1365-294X.2002.01492.x.PMID11975707.S2CID10538371.
  68. ^Goloubinoff P, Pääbo S, Wilson AC (March 1993)."Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens".Proceedings of the National Academy of Sciences of the United States of America.90(5): 1997–2001.Bibcode:1993PNAS...90.1997G.doi:10.1073/pnas.90.5.1997.PMC46007.PMID8446621.
  69. ^Dumolin-Lapègue S, Pemonge MH, Gielly L, Taberlet P, Petit RJ (December 1999). "Amplification of oak DNA from ancient and modern wood".Molecular Ecology.8(12): 2137–40.Bibcode:1999MolEc...8.2137D.doi:10.1046/j.1365-294x.1999.00788.x.PMID10632865.S2CID41967121.
  70. ^Willerslev E, Cooper A (January 2005)."Ancient DNA".Proceedings. Biological Sciences.272(1558): 3–16.doi:10.1098/rspb.2004.2813.PMC1634942.PMID15875564.
  71. ^Erika Check Hayden (26 June 2013)."First horses arose 4 million years ago".Nature.doi:10.1038/nature.2013.13261.
  72. ^Lee JL (November 7, 2017)."World's Oldest Genome Sequenced From 700,000-Year-Old Horse DNA".National Geographic.RetrievedMay 19,2019.
  73. ^Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, et al. (July 2013). "Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse".Nature.499(7456): 74–8.Bibcode:2013Natur.499...74O.doi:10.1038/nature12323.PMID23803765.S2CID4318227.
  74. ^Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, et al. (September 2013)."Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments".Proceedings of the National Academy of Sciences of the United States of America.110(39): 15758–63.Bibcode:2013PNAS..11015758D.doi:10.1073/pnas.1314445110.PMC3785785.PMID24019490.
  75. ^Callaway E (February 2021)."Million-year-old mammoth genomes shatter record for oldest ancient DNA".Nature.590(7847): 537–538.Bibcode:2021Natur.590..537C.doi:10.1038/d41586-021-00436-x.ISSN0028-0836.PMID33597786.
  76. ^abKirkpatrick JB, Walsh EA, D'Hondt S (2016-07-08)."Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales".Geology.44(8): 615–18.Bibcode:2016Geo....44..615K.doi:10.1130/g37933.1.ISSN0091-7613.
  77. ^abcPrüfer K, Posth C, Yu H, Stoessel A, Spyrou MA, Deviese T, et al. (June 2021)."A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia".Nature Ecology & Evolution.5(6): 820–825.Bibcode:2021NatEE...5..820P.doi:10.1038/s41559-021-01443-x.PMC8175239.PMID33828249.Available underCC BY 4.0.
  78. ^Handt O, Richards M, Trommsdorff M, Kilger C, Simanainen J, Georgiev O, et al. (June 1994). "Molecular genetic analyses of the Tyrolean Ice Man".Science.264(5166): 1775–8.Bibcode:1994Sci...264.1775H.doi:10.1126/science.8209259.PMID8209259.
  79. ^Montiel R, Malgosa A, Francalacci P (October 2001). "Authenticating ancient human mitochondrial DNA".Human Biology.73(5): 689–713.doi:10.1353/hub.2001.0069.PMID11758690.S2CID39302526.
  80. ^Hänni C, Laudet V, Coll J, Stehelin D (July 1994). "An unusual mitochondrial DNA sequence variant from an Egyptian mummy".Genomics.22(2): 487–9.doi:10.1006/geno.1994.1417.PMID7806242.
  81. ^Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015-06-18)."Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone".PLOS ONE.10(6): e0129102.Bibcode:2015PLoSO..1029102P.doi:10.1371/journal.pone.0129102.PMC4472748.PMID26086078.
  82. ^Poinar HN, Kuch M, Sobolik KD, Barnes I, Stankiewicz AB, Kuder T, et al. (April 2001)."A molecular analysis of dietary diversity for three archaic Native Americans".Proceedings of the National Academy of Sciences of the United States of America.98(8): 4317–22.Bibcode:2001PNAS...98.4317P.doi:10.1073/pnas.061014798.PMC31832.PMID11296282.
  83. ^Baker LE (2001).Mitochondrial DNA haplotype and sequence analysis of historic Choctaw and Menominee hair shaft samples(PhD thesis). University of Tennessee, Knoxville.
  84. ^Gilbert MT, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, et al. (June 2004)."Ancient mitochondrial DNA from hair".Current Biology.14(12): R463-4.Bibcode:2004CBio...14.R463G.doi:10.1016/j.cub.2004.06.008.PMID15203015.
  85. ^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(5): 265–69.doi:10.1046/j.1472-765x.1998.t01-8-00449.x.PMID9830142.
  86. ^Jackson PJ, Hugh-Jones ME, Adair DM, Green G, Hill KK, Kuske CR, 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.PMC18726.PMID9448313.
  87. ^Basler CF, Reid AH, Dybing JK, Janczewski TA, Fanning TG, Zheng H, 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.PMC30210.PMID11226311.
  88. ^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.PMID9065404.S2CID8976173.
  89. ^QIIME
  90. ^Pratas D, Pinho AJ, Silva RM, Rodrigues JM, Hosseini M, Caetano T, et al. (February 2018)."FALCON: a method to infer metagenomic composition of ancient DNA".bioRxiv.doi:10.1101/267179.
  91. ^Lalueza-Fox C, Rosas A, de la Rasilla M (January 2012). "Palaeogenetic research at the El Sidrón Neanderthal site".Annals of Anatomy - Anatomischer Anzeiger.Special Issue: Ancient DNA.194(1): 133–7.doi:10.1016/j.aanat.2011.01.014.hdl:10261/79609.PMID21482084.
  92. ^Zimmer C(16 November 2015)."In a Tooth, DNA From Some Very Old Cousins, the Denisovans".The New York Times.Retrieved16 November2015.
  93. ^Sawyer S, Renaud G, Viola B, Hublin JJ, Gansauge MT, Shunkov MV, et al. (December 2015)."Nuclear and mitochondrial DNA sequences from two Denisovan individuals".Proceedings of the National Academy of Sciences of the United States of America.112(51): 15696–700.Bibcode:2015PNAS..11215696S.doi:10.1073/pnas.1519905112.PMC4697428.PMID26630009.
  94. ^Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, et al. (March 2018)."The Beaker phenomenon and the genomic transformation of northwest Europe".Nature.555(7695): 190–196.Bibcode:2018Natur.555..190O.doi:10.1038/nature25738.PMC5973796.PMID29466337.
  95. ^Zimmer C(21 September 2017)."Clues to Africa's Mysterious Past Found in Ancient Skeletons".The New York Times.Retrieved21 September2017.
  96. ^Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A, Edlund H, et al. (November 2017)."Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago".Science.358(6363): 652–655.Bibcode:2017Sci...358..652S.doi:10.1126/science.aao6266.PMID28971970.
  97. ^"Neanderthal ancestry identifies oldest modern human genome".phys.org.Retrieved10 May2021.
  98. ^"Europe's oldest known humans mated with Neandertals surprisingly often".Science News.7 April 2021.Retrieved10 May2021.
  99. ^Hajdinjak M, Mafessoni F, Skov L, Vernot B, Hübner A, Fu Q, et al. (April 2021)."Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry".Nature.592(7853): 253–257.Bibcode:2021Natur.592..253H.doi:10.1038/s41586-021-03335-3.PMC8026394.PMID33828320.Available underCC BY 4.0.

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