Ancient DNA

File:Equus quagga quagga, coloured.jpg (Equus quagga quagga), an extinct subspecies of the plains zebra.]]

The first study of what would come to be called aDNA was conducted in 1984, when Russ Higuchi and colleagues at the University of California, 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.{{cite journal | vauthors = Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC | title = DNA sequences from the quagga, an extinct member of the horse family | journal = Nature | volume = 312 | issue = 5991 | pages = 282–4 | date = 1984 | pmid = 6504142 | doi = 10.1038/312282a0 | bibcode = 1984Natur.312..282H | s2cid = 4313241 }} 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.{{cite journal | vauthors = Pääbo S | year = 1985a | title = Preservation of DNA in ancient Egyptian mummies | journal = J. Archaeol. Sci. | volume = 12 | issue = 6| pages = 411–17 | doi = 10.1016/0305-4403(85)90002-0 | bibcode = 1985JArSc..12..411P }}{{cite journal | vauthors = Pääbo S | title = Molecular cloning of Ancient Egyptian mummy DNA | journal = Nature | volume = 314 | issue = 6012 | pages = 644–5 | year = 1985b | pmid = 3990798 | doi = 10.1038/314644a0 | bibcode = 1985Natur.314..644P | s2cid = 1358295 }}{{cite journal | vauthors = Pääbo S | title = Molecular genetic investigations of ancient human remains | journal = Cold Spring Harbor Symposia on Quantitative Biology | volume = 51 | issue = Pt 1 | pages = 441–6 | date = 1986 | pmid = 3107879 | doi = 10.1101/SQB.1986.051.01.053 }}

The laborious processes that were required at that time to sequence such DNA (through bacterial cloning) were an effective brake on the study of ancient DNA (aDNA) and the field of museomics. However, with the development of the Polymerase Chain Reaction (PCR) in the late 1980s, the field began to progress rapidly.{{cite book | vauthors = Mullis KB, Faloona FA | chapter = Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction | title = Recombinant DNA Part F | series = Methods in Enzymology | volume = 155 | pages = 335–50 | date = 1987 | pmid = 3431465 | doi = 10.1016/0076-6879(87)55023-6 | chapter-url = https://archive.org/details/recombinantdna0000unse/page/335 | isbn = 978-0-12-182056-5 }}{{cite journal | vauthors = Raxworthy CJ, Smith BT | title = Mining museums for historical DNA: advances and challenges in museomics | journal = Trends in Ecology & Evolution | volume = 36 | issue = 11 | pages = 1049–1060 | date = November 2021 | pmid = 34456066 | doi = 10.1016/j.tree.2021.07.009 | s2cid = 239687836 | bibcode = 2021TEcoE..36.1049R | doi-access = free }}{{cite journal | vauthors = Saiki RK, Gelfand DH, Stoffel S, Scharf SJ, Higuchi R, Horn GT, Mullis KB, Erlich HA | title = Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase | journal = Science | volume = 239 | issue = 4839 | pages = 487–491 | date = January 1988 | pmid = 2448875 | doi = 10.1126/science.239.4839.487 | bibcode = 1988Sci...239..487S }} 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.

File:Baltic Amber.jpg

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 labelled Antediluvian DNA.{{cite journal | vauthors = Lindahl T | title = Recovery of antediluvian DNA | journal = Nature | volume = 365 | issue = 6448 | pages = 700 | date = October 1993 | pmid = 8413647 | doi = 10.1038/365700a0 | s2cid = 4365447 | doi-access = free | bibcode = 1993Natur.365..700L }} The majority of such claims were based on the retrieval of DNA from organisms preserved in amber. Insects such as stingless bees,{{cite journal | vauthors = Cano RJ, Poinar H, Poinar Jr GO | year = 1992a | title = Isolation and partial characterisation of DNA from the bee Problebeia dominicana (Apidae:Hymenoptera) in 25–40 million year old amber | journal = Med Sci Res | volume = 20 | pages = 249–51 }}{{cite journal | vauthors = Cano RJ, Poinar HN, Roubik DW, Poinar Jr GO | year = 1992b | title = 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 | journal = Med Sci Res | volume = 20 | pages = 619–22 }} termites,{{cite journal | vauthors = Matson E, Ottesen E, Leadbetter J | title = Extracting DNA from the gut microbes of the termite (Zootermopsis nevadensis) | journal = Journal of Visualized Experiments | volume = | issue = 4 | pages = 195 | date = 2007 | pmid = 18979000 | pmc = 2556161 | doi = 10.3791/195 }} and wood gnats,{{cite journal | vauthors = DeSalle R, Grimaldi D | title = Very old DNA | journal = Current Opinion in Genetics & Development | volume = 4 | issue = 6 | pages = 810–5 | date = December 1994 | pmid = 7888749 | doi = 10.1016/0959-437x(94)90064-7 }} as well as plant{{cite journal | vauthors = Poinar H, Cano R, Poinar G | date = 1993 | title = DNA from an extinct plant | journal = Nature | volume = 363 | issue = 6431| page = 677|doi=10.1038/363677a0 |bibcode = 1993Natur.363..677P | s2cid = 4330200 | doi-access = free }} and bacterial{{cite journal | vauthors = Cano RJ, Borucki MK, Higby-Schweitzer M, Poinar HN, Poinar GO, Pollard KJ | title = Bacillus DNA in fossil bees: an ancient symbiosis? | journal = Applied and Environmental Microbiology | volume = 60 | issue = 6 | pages = 2164–2167 | date = June 1994 | pmid = 8031102 | pmc = 201618 | doi = 10.1128/aem.60.6.2164-2167.1994 | bibcode = 1994ApEnM..60.2164C | doi-access = free }} sequences were said to have been 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.{{cite journal | vauthors = Cano RJ, Poinar HN, Pieniazek NJ, Acra A, Poinar GO | title = Amplification and sequencing of DNA from a 120-135-million-year-old weevil | journal = Nature | volume = 363 | issue = 6429 | pages = 536–538 | date = June 1993 | pmid = 8505978 | doi = 10.1038/363536a0 | bibcode = 1993Natur.363..536C | s2cid = 4243196 }} Claims of DNA retrieval were not limited to amber.

Reports of several sediment-preserved plant remains dating to the Miocene were published.{{cite journal | vauthors = Golenberg EM | title = Amplification and analysis of Miocene plant fossil DNA | journal = Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences | volume = 333 | issue = 1268 | pages = 419–26; discussion 426–7 | date = September 1991 | pmid = 1684052 | doi = 10.1098/rstb.1991.0092 }}{{cite journal | vauthors = Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M, Henderson D, Zurawski G | title = Chloroplast DNA sequence from a miocene Magnolia species | journal = Nature | volume = 344 | issue = 6267 | pages = 656–8 | date = April 1990 | pmid = 2325772 | doi = 10.1038/344656a0 | bibcode = 1990Natur.344..656G | s2cid = 26577394 }} Then in 1994, Woodward et al. reported what at the time was called the most exciting results to date{{cite journal | vauthors = Woodward SR, Weyand NJ, Bunnell M | title = DNA sequence from Cretaceous period bone fragments | journal = Science | volume = 266 | issue = 5188 | pages = 1229–32 | date = November 1994 | pmid = 7973705 | doi = 10.1126/science.7973705 | bibcode = 1994Sci...266.1229W }} — 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,{{cite journal | vauthors = An CC, Li Y, Zhu YX | year = 1995 | title = Molecular cloning and sequencing of the 18S rDNA from specialized dinosaur egg fossil found in Xixia Henan, China | journal = Acta Sci Nat Univ Pekinensis | volume = 31 | pages = 140–47 }}{{cite journal |vauthors=Li Y, An CC, Zhu YX | year = 1995 | title = DNA isolation and sequence analysis of dinosaur DNA from Cretaceous dinosaur egg in Xixia Henan, China | journal = Acta Sci Nat Univ Pekinensis | volume = 31 | pages = 148–52 }} 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 from halite.{{cite journal | vauthors = Vreeland RH, Rosenzweig WD, Powers DW | title = Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal | journal = Nature | volume = 407 | issue = 6806 | pages = 897–900 | date = October 2000 | pmid = 11057666 | doi = 10.1038/35038060 | bibcode = 2000Natur.407..897V | s2cid = 9879073 }}{{cite journal | vauthors = Fish SA, Shepherd TJ, McGenity TJ, Grant WD | title = Recovery of 16S ribosomal RNA gene fragments from ancient halite | journal = Nature | volume = 417 | issue = 6887 | pages = 432–6 | date = May 2002 | pmid = 12024211 | doi = 10.1038/417432a | bibcode = 2002Natur.417..432F | s2cid = 4423309 }}

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.{{cite journal | vauthors = Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, Kuch M, Krause J, Vigilant L, Hofreiter M | title = Genetic analyses from ancient DNA | journal = Annual Review of Genetics | volume = 38 | issue = 1 | pages = 645–79 | year = 2004 | pmid = 15568989 | doi = 10.1146/annurev.genet.37.110801.143214 | url = http://www.454genomics.net/downloads/news-events/geneticanalysisfromancientdna.pdf | url-status = dead | archive-url = https://web.archive.org/web/20081217110352/http://www.454genomics.net/downloads/news-events/geneticanalysisfromancientdna.pdf | archive-date = December 17, 2008 }}

Single primer extension amplification was introduced in 2007 to address postmortem DNA modification damage.{{cite journal | vauthors = Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, Cooper A | title = Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions | journal = Nucleic Acids Research | volume = 35 | issue = 17 | pages = 5717–28 | date = 2007 | pmid = 17715147 | pmc = 2034480 | doi = 10.1093/nar/gkm588 | url = }} Since 2009 the field of aDNA studies has been revolutionized with the introduction of much cheaper research techniques,{{sfn|Reich|2018|pp=30-31}} and since 2010 been able to sequence ancient human DNA, recovering complete genomes.{{cite news |last1=Forbes |first1=Peter |title=Who We Are and How We Got Here by David Reich review – new findings from ancient DNA |url=https://www.theguardian.com/books/2018/mar/29/who-we-are-how-got-here-david-reich-ancient-dna-review |access-date=6 May 2018|work=The Guardian|date=29 March 2018}} The use of high-throughput Next 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.{{cite journal | vauthors = Wales N, Carøe C, Sandoval-Velasco M, Gamba C, Barnett R, Samaniego JA, Madrigal JR, Orlando L, Gilbert MT | title = New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA | journal = BioTechniques | volume = 59 | issue = 6 | pages = 368–71 | date = December 2015 | pmid = 26651516 | doi = 10.2144/000114364 | doi-access = free }}{{cite journal | vauthors = Bennett EA, Massilani D, Lizzo G, Daligault J, Geigl EM, Grange T | title = Library construction for ancient genomics: single strand or double strand? | journal = BioTechniques | volume = 56 | issue = 6 | pages = 289–90, 292–6, 298, passim | date = June 2014 | pmid = 24924389 | doi = 10.2144/000114176 | doi-access = free }}

File:Svante Paabo and Fumio Kishida 20230201 1.jpg

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.{{cite journal | vauthors = Nicholls H | title = Ancient DNA comes of age | journal = PLOS Biology | volume = 3 | issue = 2 | pages = e56 | date = February 2005 | pmid = 15719062 | pmc = 548952 | doi = 10.1371/journal.pbio.0030056 | doi-access = free }}

The 2022 Nobel Prize in Physiology or Medicine was awarded to Svante Pääbo "for his discoveries concerning the genomes of extinct hominins and human evolution".{{cite web|access-date=2024-10-31 |language=en-US |title=The Nobel Prize in Physiology or Medicine 2022 |url=https://www.nobelprize.org/prizes/medicine/2022/press-release/}} A few days later, on the 7th of December 2022, a study in Nature reported that two-million year old genetic material was found in Greenland, and is currently considered the oldest DNA discovered so far.{{cite news | vauthors = Zimmer C |authorlink=Carl Zimmer |title=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. |url=https://www.nytimes.com/2022/12/07/science/oldest-dna-greenland-species.html |date=7 December 2022 |work=The New York Times |access-date=7 December 2022 }}{{cite journal | vauthors = Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, Sand KK, Jelavić S, Ruter AH, Schmidt AM, Kjeldsen KK, Tesakov AS, Snowball I, Gosse JC, Alsos IG, Wang Y, Dockter C, Rasmussen M, Jørgensen ME, Skadhauge B, Prohaska A, Kristensen JÅ, Bjerager M, Allentoft ME, Coissac E, Rouillard A, Simakova A, Fernandez-Guerra A, Bowler C, Macias-Fauria M, Vinner L, Welch JJ, Hidy AJ, Sikora M, Collins MJ, Durbin R, Larsen NK, Willerslev E | title = A 2-million-year-old ecosystem in Greenland uncovered by environmental DNA | journal = Nature | volume = 612 | issue = 7939 | pages = 283–291 | date = December 2022 | pmid = 36477129 | pmc = 9729109 | doi = 10.1038/s41586-022-05453-y | bibcode = 2022Natur.612..283K }}

Due to degradation processes (including cross-linking, deamination and fragmentation), ancient DNA is of lower quality than modern genetic material. 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. There is a theoretical correlation between time and DNA degradation,{{cite journal | vauthors = Hebsgaard MB, Phillips MJ, Willerslev E | title = Geologically ancient DNA: fact or artefact? | journal = Trends in Microbiology | volume = 13 | issue = 5 | pages = 212–20 | date = May 2005 | pmid = 15866038 | doi = 10.1016/j.tim.2005.03.010 }} although differences in environmental conditions complicate matters. Samples subjected to different conditions are unlikely to predictably align to a uniform age-degradation relationship.{{cite journal | vauthors = Hansen AJ, Mitchell DL, Wiuf C, Paniker L, Brand TB, Binladen J, Gilichinsky DA, Rønn R, Willerslev E | title = Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments | journal = Genetics | volume = 173 | issue = 2 | pages = 1175–9 | date = June 2006 | pmid = 16582426 | pmc = 1526502 | doi = 10.1534/genetics.106.057349 }} The environmental effects may even matter after excavation, as DNA decay-rates may increase,{{cite journal | vauthors = Pruvost M, Schwarz R, Correia VB, Champlot S, Braguier S, Morel N, Fernandez-Jalvo Y, Grange T, Geigl EM | title = Freshly excavated fossil bones are best for amplification of ancient DNA | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 3 | pages = 739–44 | date = January 2007 | pmid = 17210911 | pmc = 1783384 | doi = 10.1073/pnas.0610257104 | bibcode = 2007PNAS..104..739P | doi-access = free }} particularly under fluctuating storage conditions.{{cite journal | vauthors = Burger J, Hummel S, Hermann B, Henke W | title = DNA preservation: a microsatellite-DNA study on ancient skeletal remains | journal = Electrophoresis | volume = 20 | issue = 8 | pages = 1722–8 | date = June 1999 | pmid = 10435438 | doi = 10.1002/(sici)1522-2683(19990101)20:8<1722::aid-elps1722>3.0.co;2-4 | s2cid = 7325310 }} 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.

Research into the decay of mitochondrial and nuclear DNA in moa bones has modelled mitochondrial DNA degradation to an average length of 1 base pair after 6,830,000 years at −5 °C.{{cite journal | vauthors = Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, Campos PF, Samaniego JA, Gilbert MT, Willerslev E, Zhang G, Scofield RP, Holdaway RN, Bunce M | title = The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils | journal = Proceedings. Biological Sciences | volume = 279 | issue = 1748 | pages = 4724–33 | date = December 2012 | pmid = 23055061 | pmc = 3497090 | doi = 10.1098/rspb.2012.1745 }} The decay kinetics have been measured by accelerated aging experiments, further displaying the strong influence of storage temperature and humidity on DNA decay.

{{cite journal | vauthors = Grass RN, Heckel R, Puddu M, Paunescu D, Stark WJ | title = Robust chemical preservation of digital information on DNA in silica with error-correcting codes | journal = Angewandte Chemie | volume = 54 | issue = 8 | pages = 2552–5 | date = February 2015 | pmid = 25650567 | doi = 10.1002/anie.201411378 }} Nuclear DNA degrades at least twice as fast as mtDNA. Early studies that reported recovery of much older DNA, for example from Cretaceous dinosaur remains, may have stemmed from contamination of the sample.

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.{{cite journal | vauthors = Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MT, Shapiro B, Bunce M, Wiuf C, Gilichinsky DA, Cooper A | title = Diverse plant and animal genetic records from Holocene and Pleistocene sediments | journal = Science | volume = 300 | issue = 5620 | pages = 791–5 | date = May 2003 | pmid = 12702808 | doi = 10.1126/science.1084114 | bibcode = 2003Sci...300..791W | s2cid = 1222227 | doi-access = free }} A greater appreciation for the risks of environmental contamination and studies on the chemical stability of DNA have raised concerns over previously reported results. The alleged dinosaur DNA was later revealed to be human Y-chromosome.{{cite journal | vauthors = Zischler H, Höss M, Handt O, von Haeseler A, van der Kuyl AC, Goudsmit J | title = Detecting dinosaur DNA | journal = Science | volume = 268 | issue = 5214 | pages = 1192–3; author reply 1194 | date = May 1995 | pmid = 7605504 | doi = 10.1126/science.7605504 | doi-access = free | bibcode = 1995Sci...268.1191B }} The DNA reported from encapsulated halobacteria has been criticized based on its similarity to modern bacteria, which hints at contamination, or they may be the product of long-term, low-level metabolic activity.{{cite journal | vauthors = 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 | title = Ancient bacteria show evidence of DNA repair | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 36 | pages = 14401–5 | date = September 2007 | pmid = 17728401 | pmc = 1958816 | doi = 10.1073/pnas.0706787104 | bibcode = 2007PNAS..10414401J | doi-access = free }}

aDNA may contain a large number of postmortem mutations, 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. Due to sequencing errors, great caution should be applied to interpretation of population size.{{cite journal | vauthors = Johnson PL, Slatkin M | title = Accounting for bias from sequencing error in population genetic estimates | journal = Molecular Biology and Evolution | volume = 25 | issue = 1 | pages = 199–206 | date = January 2008 | pmid = 17981928 | doi = 10.1093/molbev/msm239 | format = Free full text | doi-access = free }} Substitutions resulting from deamination of cytosine residues are vastly over-represented in the ancient DNA sequences. Miscoding of C to T and G to A accounts for the majority of errors.{{cite journal | vauthors = Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, Meyer M, Krause J, Ronan MT, Lachmann M, Pääbo S | title = Patterns of damage in genomic DNA sequences from a Neandertal | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 104 | issue = 37 | pages = 14616–21 | date = September 2007 | pmid = 17715061 | pmc = 1976210 | doi = 10.1073/pnas.0704665104 | bibcode = 2007PNAS..10414616B | doi-access = free }}

Another problem with ancient DNA samples is contamination by modern human DNA and by microbial DNA (most of which is also ancient).{{cite journal | vauthors = Gansauge MT, Meyer M | title = Selective enrichment of damaged DNA molecules for ancient genome sequencing | journal = Genome Research | volume = 24 | issue = 9 | pages = 1543–9 | date = September 2014 | pmid = 25081630 | pmc = 4158764 | doi = 10.1101/gr.174201.114 }}{{cite journal | vauthors = Pratas D, Hosseini M, Grilo G, Pinho AJ, Silva RM, Caetano T, Carneiro J, Pereira F | title = Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard | journal = Genes | volume = 9 | issue = 9 | pages = 445 | date = September 2018 | pmid = 30200636 | pmc = 6162538 | doi = 10.3390/genes9090445 | doi-access = free }} 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.{{cite journal | vauthors = Slatkin M, Racimo F | title = Ancient DNA and human history | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 113 | issue = 23 | pages = 6380–7 | date = June 2016 | pmid = 27274045 | pmc = 4988579 | doi = 10.1073/pnas.1524306113 | bibcode = 2016PNAS..113.6380S | doi-access = free }}{{cite journal | vauthors = Borry M, Hübner A, Rohrlach AB, Warinner C | title = PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA de novo assembly | journal = PeerJ | volume = 9 | pages = e11845 | date = 2021-07-27 | pmid = 34395085 | pmc = 8323603 | doi = 10.7717/peerj.11845 | doi-access = free }}

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.{{cite journal | vauthors = Dabney J, Meyer M, Pääbo S | title = Ancient DNA damage | journal = Cold Spring Harbor Perspectives in Biology | volume = 5 | issue = 7 | pages = a012567 | date = July 2013 | pmid = 23729639 | pmc = 3685887 | doi = 10.1101/cshperspect.a012567 }} 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 {{cite journal | vauthors = Jónsson H, Ginolhac A, Schubert M, Johnson PL, Orlando L | title = mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters | journal = Bioinformatics | volume = 29 | issue = 13 | pages = 1682–1684 | date = July 2013 | pmid = 23613487 | pmc = 3694634 | doi = 10.1093/bioinformatics/btt193 }}{{cite journal | vauthors = Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S, Krause J, Jakobsson M | title = Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 111 | issue = 6 | pages = 2229–2234 | date = February 2014 | pmid = 24469802 | pmc = 3926038 | doi = 10.1073/pnas.1318934111 | doi-access = free | bibcode = 2014PNAS..111.2229S }} and interactively on metaDMG.{{cite bioRxiv| vauthors = Michelsen C, Pedersen MW, Fernandez-Guerra A, Zhao L, Petersen TC, Korneliussen TS |title=metaDMG – A Fast and Accurate Ancient DNA Damage Toolkit for Metagenomic Data |date=9 December 2022 |biorxiv=10.1101/2022.12.06.519264 }} 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.{{cite journal | vauthors = Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, Pääbo S | title = A complete mtDNA genome of an early modern human from Kostenki, Russia | journal = Current Biology | volume = 20 | issue = 3 | pages = 231–236 | date = February 2010 | pmid = 20045327 | doi = 10.1016/j.cub.2009.11.068 | s2cid = 16440465 | doi-access = free | bibcode = 2010CBio...20..231K }}{{cite journal | vauthors = Pochon Z, Bergfeldt N, Kırdök E, Vicente M, Naidoo T, van der Valk T, Altınışık NE, Krzewińska M, Dalén L, Götherström A, Mirabello C, Unneberg P, Oskolkov N | title = aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow | journal = Genome Biology | volume = 24 | issue = 1 | pages = 242 | date = October 2023 | pmid = 37872569 | doi = 10.1186/s13059-023-03083-9|doi-access=free|biorxiv=10.1101/2022.10.03.510579 | pmc = 10591440 | s2cid = 252763827 }}

Despite the problems associated with aDNA, 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,{{cite journal | vauthors = Thomas RH, Schaffner W, Wilson AC, Pääbo S | title = DNA phylogeny of the extinct marsupial wolf | journal = Nature | volume = 340 | issue = 6233 | pages = 465–7 | date = August 1989 | pmid = 2755507 | doi = 10.1038/340465a0 | bibcode = 1989Natur.340..465T | s2cid = 4310500 }} bone,{{cite journal | vauthors = Hagelberg E, Sykes B, Hedges R | title = Ancient bone DNA amplified | journal = Nature | volume = 342 | issue = 6249 | pages = 485 | date = November 1989 | pmid = 2586623 | doi = 10.1038/342485a0 | bibcode = 1989Natur.342..485H | s2cid = 13434992 | doi-access = free }}{{cite journal | vauthors = Cooper A, Mourer-Chauviré C, Chambers GK, von Haeseler A, Wilson AC, Pääbo S | title = Independent origins of New Zealand moas and kiwis | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 89 | issue = 18 | pages = 8741–4 | date = September 1992 | pmid = 1528888 | pmc = 49996 | doi = 10.1073/pnas.89.18.8741 | bibcode = 1992PNAS...89.8741C | doi-access = free }}{{cite journal | vauthors = Hagelberg E, Thomas MG, Cook CE, Sher AV, Baryshnikov GF, Lister AM | title = DNA from ancient mammoth bones | journal = Nature | volume = 370 | issue = 6488 | pages = 333–4 | date = August 1994 | pmid = 8047136 | doi = 10.1038/370333b0 | bibcode = 1994Natur.370R.333H | s2cid = 8694387 }}{{cite journal | vauthors = Hänni C, Laudet V, Stehelin D, Taberlet P | title = Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 91 | issue = 25 | pages = 12336–40 | date = December 1994 | pmid = 7991628 | pmc = 45432 | doi = 10.1073/pnas.91.25.12336 | bibcode = 1994PNAS...9112336H | doi-access = free }} shells,{{cite journal | vauthors = Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, Funder S, Gotfredsen AB, Gregersen KM, Hansen CH, Ilsøe PC, Klassen L, Kristensen IK, Ravnholt GB, Marin F, Der Sarkissian C | title = Advancing responsible genomic analyses of ancient mollusc shells | journal = PLOS ONE | volume = 19 | issue = 5 | pages = e0302646 | date = 2024-05-06 | pmid = 38709766 | pmc = 11073703 | doi = 10.1371/journal.pone.0302646 | doi-access = free | bibcode = 2024PLoSO..1902646M | veditors = Fernández Robledo JA }} paleofaeces,{{cite journal | vauthors = Poinar HN, Hofreiter M, Spaulding WG, Martin PS, Stankiewicz BA, Bland H, Evershed RP, Possnert G, Pääbo S | title = Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis | journal = Science | volume = 281 | issue = 5375 | pages = 402–6 | date = July 1998 | pmid = 9665881 | doi = 10.1126/science.281.5375.402 | bibcode = 1998Sci...281..402P }}{{cite journal | vauthors = Hofreiter M, Poinar HN, Spaulding WG, Bauer K, Martin PS, Possnert G, Pääbo S | title = A molecular analysis of ground sloth diet through the last glaciation | journal = Molecular Ecology | volume = 9 | issue = 12 | pages = 1975–84 | date = December 2000 | pmid = 11123610 | doi = 10.1046/j.1365-294X.2000.01106.x | bibcode = 2000MolEc...9.1975H | s2cid = 22685601 }} alcohol preserved specimens,{{cite journal | vauthors = Junqueira AC, Lessinger AC, Azeredo-Espin AM | title = Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis-causing flies | journal = Medical and Veterinary Entomology | volume = 16 | issue = 1 | pages = 39–45 | date = March 2002 | pmid = 11963980 | doi = 10.1046/j.0269-283x.2002.00336.x | doi-access = free }} rodent middens,{{cite journal | vauthors = Kuch M, Rohland N, Betancourt JL, Latorre C, Steppan S, Poinar HN | title = Molecular analysis of an 11,700-year-old rodent midden from the Atacama Desert, Chile | journal = Molecular Ecology | volume = 11 | issue = 5 | pages = 913–24 | date = May 2002 | pmid = 11975707 | doi = 10.1046/j.1365-294X.2002.01492.x | bibcode = 2002MolEc..11..913K | s2cid = 10538371 }} dried plant remains,{{cite journal | vauthors = Goloubinoff P, Pääbo S, Wilson AC | title = Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 90 | issue = 5 | pages = 1997–2001 | date = March 1993 | pmid = 8446621 | pmc = 46007 | doi = 10.1073/pnas.90.5.1997 | bibcode = 1993PNAS...90.1997G | doi-access = free }}{{cite journal | vauthors = Dumolin-Lapègue S, Pemonge MH, Gielly L, Taberlet P, Petit RJ | title = Amplification of oak DNA from ancient and modern wood | journal = Molecular Ecology | volume = 8 | issue = 12 | pages = 2137–40 | date = December 1999 | pmid = 10632865 | doi = 10.1046/j.1365-294x.1999.00788.x | bibcode = 1999MolEc...8.2137D | s2cid = 41967121 }} and recently, extractions of animal and plant DNA directly from soil samples.{{cite journal | vauthors = Willerslev E, Cooper A | title = Ancient DNA | journal = Proceedings. Biological Sciences | volume = 272 | issue = 1558 | pages = 3–16 | date = January 2005 | pmid = 15875564 | pmc = 1634942 | doi = 10.1098/rspb.2004.2813 }}

In June 2013, a group of researchers including Eske Willerslev, Marcus Thomas Pius Gilbert and Orlando Ludovic of the Centre for Geogenetics, Natural History Museum of Denmark at the University 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 in permafrost in Canada's Yukon territory.{{cite news|url= http://www.nature.com/news/first-horses-arose-4-million-years-ago-1.13261 |title=First horses arose 4 million years ago |author=Erika Check Hayden |journal=Nature |date=26 June 2013 |doi=10.1038/nature.2013.13261}}{{cite web |url= https://www.nationalgeographic.co.uk/history-and-civilisation/2017/11/worlds-oldest-genome-sequenced-700000-year-old-horse-dna |title=World's Oldest Genome Sequenced From 700,000-Year-Old Horse DNA |work=National Geographic |date=November 7, 2017 |access-date=May 19, 2019 | vauthors = Lee JL }}{{cite journal | vauthors = Orlando L, Ginolhac A, Zhang G, Froese D, Albrechtsen A, Stiller M, Schubert M, Cappellini E, Petersen B, Moltke I, Johnson PL, Fumagalli M, Vilstrup JT, Raghavan M, Korneliussen T, Malaspinas AS, Vogt J, Szklarczyk D, Kelstrup CD, Vinther J, Dolocan A, Stenderup J, Velazquez AM, Cahill J, Rasmussen M, Wang X, Min J, Zazula GD, Seguin-Orlando A, Mortensen C, Magnussen K, Thompson JF, Weinstock J, Gregersen K, Røed KH, Eisenmann V, Rubin CJ, Miller DC, Antczak DF, Bertelsen MF, Brunak S, Al-Rasheid KA, Ryder O, Andersson L, Mundy J, Krogh A, Gilbert MT, Kjær K, Sicheritz-Ponten T, Jensen LJ, Olsen JV, Hofreiter M, Nielsen R, Shapiro B, Wang J, Willerslev E | title = Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse | journal = Nature | volume = 499 | issue = 7456 | pages = 74–8 | date = July 2013 | pmid = 23803765 | doi = 10.1038/nature12323 | bibcode = 2013Natur.499...74O | s2cid = 4318227 }} A German team also reported in 2013 the reconstructed mitochondrial genome of 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.{{cite journal | vauthors = Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, Valdiosera C, García N, Pääbo S, Arsuaga JL, Meyer M | title = Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 110 | issue = 39 | pages = 15758–63 | date = September 2013 | pmid = 24019490 | pmc = 3785785 | doi = 10.1073/pnas.1314445110 | bibcode = 2013PNAS..11015758D | doi-access = free }} The DNA sequence of even older nuclear DNA was reported in 2021 from the permafrost-preserved teeth of two Siberian mammoths, both over a million years old.{{cite journal | vauthors = Callaway E | title = Million-year-old mammoth genomes shatter record for oldest ancient DNA | journal = Nature | volume = 590 | issue = 7847 | pages = 537–538 | date = February 2021 | pmid = 33597786 | doi = 10.1038/d41586-021-00436-x| bibcode = 2021Natur.590..537C |issn=0028-0836 | doi-access = free }}

Researchers in 2016 measured chloroplast DNA in marine sediment cores, and found diatom DNA dating back to 1.4 million years.{{Cite journal | vauthors = Kirkpatrick JB, Walsh EA, D'Hondt S |date=2016-07-08 |title=Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales |journal=Geology |language=en |volume=44 |issue=8 |pages=615–18 |doi=10.1130/g37933.1 |bibcode=2016Geo....44..615K |issn=0091-7613|url= https://digitalcommons.uri.edu/cgi/viewcontent.cgi?article=1606&context=gsofacpubs |doi-access=free}} 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.

File:Map of human fossils with an age of at least ~40,000 years that yielded genome-wide data and location of the Zlatý kůň fossil.webp

Due to the considerable anthropological, archaeological, and public interest directed 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.

Due to the morphological preservation 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 the Ötzi the Iceman frozen in a glacier{{cite journal | vauthors = Handt O, Richards M, Trommsdorff M, Kilger C, Simanainen J, Georgiev O, Bauer K, Stone A, Hedges R, Schaffner W | title = Molecular genetic analyses of the Tyrolean Ice Man | journal = Science | volume = 264 | issue = 5166 | pages = 1775–8 | date = June 1994 | pmid = 8209259 | doi = 10.1126/science.8209259 | bibcode = 1994Sci...264.1775H }} and bodies preserved through rapid desiccation at high altitude in the Andes,{{cite journal | vauthors = Montiel R, Malgosa A, Francalacci P | title = Authenticating ancient human mitochondrial DNA | journal = Human Biology | volume = 73 | issue = 5 | pages = 689–713 | date = October 2001 | pmid = 11758690 | doi = 10.1353/hub.2001.0069 | s2cid = 39302526 }} as well as various chemically treated preserved tissue such as the mummies of ancient Egypt.{{cite journal | vauthors = Hänni C, Laudet V, Coll J, Stehelin D | title = An unusual mitochondrial DNA sequence variant from an Egyptian mummy | journal = Genomics | volume = 22 | issue = 2 | pages = 487–9 | date = July 1994 | pmid = 7806242 | doi = 10.1006/geno.1994.1417 }} 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 the archaeological record: bones and teeth. The bone that is most often used for DNA extraction is the petrous ear bone, since its dense structure provides good conditions for DNA preservation.{{cite journal | vauthors = Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, Gerritsen F, Moiseyev V, Gromov A, Raczky P, Anders A, Pietrusewsky M, Rollefson G, Jovanovic M, Trinhhoang H, Bar-Oz G, Oxenham M, Matsumura H, Hofreiter M | title = Optimal Ancient DNA Yields from the Inner Ear Part of the Human Petrous Bone | journal = PLOS ONE | volume = 10 | issue = 6 | pages = e0129102 | date = 2015-06-18 | pmid = 26086078 | pmc = 4472748 | doi = 10.1371/journal.pone.0129102 | bibcode = 2015PLoSO..1029102P | doi-access = free }} Several other sources have also yielded DNA, including paleofaeces,{{cite journal | vauthors = Poinar HN, Kuch M, Sobolik KD, Barnes I, Stankiewicz AB, Kuder T, Spaulding WG, Bryant VM, Cooper A, Pääbo S | title = A molecular analysis of dietary diversity for three archaic Native Americans | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 8 | pages = 4317–22 | date = April 2001 | pmid = 11296282 | pmc = 31832 | doi = 10.1073/pnas.061014798 | bibcode = 2001PNAS...98.4317P | doi-access = free }} and hair.{{cite thesis | vauthors = Baker LE | date = 2001 | title = Mitochondrial DNA haplotype and sequence analysis of historic Choctaw and Menominee hair shaft samples. | degree = PhD | publisher = University of Tennessee, Knoxville }}{{cite journal | vauthors = Gilbert MT, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, Higham TF, Richards MP, O'Connell TC, Tobin DJ, Janaway RC, Cooper A | title = Ancient mitochondrial DNA from hair | journal = Current Biology | volume = 14 | issue = 12 | pages = R463-4 | date = June 2004 | pmid = 15203015 | doi = 10.1016/j.cub.2004.06.008 | doi-access = free | bibcode = 2004CBio...14.R463G }} Contamination remains a major problem when working on ancient human material.

Ancient pathogen DNA 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 calcified pleura,{{cite journal | vauthors = Donoghue HD, Spigelman M, Zias J, Gernaey-Child AM, Minnikin DE | year = 1998 | title = Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old | journal = Lett Appl Microbiol | volume = 27 | issue = 5| pages = 265–69 | doi = 10.1046/j.1472-765x.1998.t01-8-00449.x | doi-broken-date = 24 December 2024 | pmid = 9830142 }} tissue embedded in paraffin,{{cite journal | vauthors = Jackson PJ, Hugh-Jones ME, Adair DM, Green G, Hill KK, Kuske CR, Grinberg LM, Abramova FA, Keim P | title = PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: the presence of multiple Bacillus anthracis strains in different victims | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 95 | issue = 3 | pages = 1224–9 | date = February 1998 | pmid = 9448313 | pmc = 18726 | doi = 10.1073/pnas.95.3.1224 | bibcode = 1998PNAS...95.1224J | doi-access = free }}{{cite journal | vauthors = Basler CF, Reid AH, Dybing JK, Janczewski TA, Fanning TG, Zheng H, Salvatore M, Perdue ML, Swayne DE, García-Sastre A, Palese P, Taubenberger JK | title = Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 98 | issue = 5 | pages = 2746–51 | date = February 2001 | pmid = 11226311 | pmc = 30210 | doi = 10.1073/pnas.031575198 | bibcode = 2001PNAS...98.2746B | doi-access = free }} and formalin-fixed tissue.{{cite journal | vauthors = Taubenberger JK, Reid AH, Krafft AE, Bijwaard KE, Fanning TG | title = Initial genetic characterization of the 1918 "Spanish" influenza virus | journal = Science | volume = 275 | issue = 5307 | pages = 1793–6 | date = March 1997 | pmid = 9065404 | doi = 10.1126/science.275.5307.1793 | s2cid = 8976173 | url = https://zenodo.org/record/1231104 }} Efficient computational tools have been developed for pathogen and microorganism aDNA analyses in a small (QIIME[http://qiime.org/ QIIME]) and large scale (FALCON {{cite bioRxiv | vauthors = Pratas D, Pinho AJ, Silva RM, Rodrigues JM, Hosseini M, Caetano T, Ferreira PJ |title=FALCON: a method to infer metagenomic composition of ancient DNA |date=February 2018 |biorxiv= 10.1101/267179}}).

Taking preventative measures in their procedure against such contamination though, a 2012 study analyzed bone samples of a Neanderthal group in the El Sidrón cave, finding new insights on potential kinship and genetic diversity from the aDNA.{{cite journal | vauthors = Lalueza-Fox C, Rosas A, de la Rasilla M | title = Palaeogenetic research at the El Sidrón Neanderthal site | journal = Annals of Anatomy - Anatomischer Anzeiger | volume = 194 | issue = 1 | pages = 133–7 | date = January 2012 | pmid = 21482084 | doi = 10.1016/j.aanat.2011.01.014 | series = Special Issue: Ancient DNA | hdl = 10261/79609 }} In November 2015, scientists reported finding a 110,000-year-old tooth containing DNA from the Denisovan hominin, an extinct species of human in the genus Homo.{{cite news | vauthors = Zimmer C |author-link=Carl Zimmer |title=In a Tooth, DNA From Some Very Old Cousins, the Denisovans |url= https://www.nytimes.com/2015/11/17/science/in-a-tooth-dna-from-some-very-old-cousins-the-denisovans.html |date=16 November 2015 |work=The New York Times |access-date=16 November 2015 }}{{cite journal | vauthors = Sawyer S, Renaud G, Viola B, Hublin JJ, Gansauge MT, Shunkov MV, Derevianko AP, Prüfer K, Kelso J, Pääbo S | title = Nuclear and mitochondrial DNA sequences from two Denisovan individuals | journal = Proceedings of the National Academy of Sciences of the United States of America | volume = 112 | issue = 51 | pages = 15696–700 | date = December 2015 | pmid = 26630009 | pmc = 4697428 | doi = 10.1073/pnas.1519905112 | bibcode = 2015PNAS..11215696S | doi-access = free }}

The research has added new complexity to the peopling of Eurasia. A study from 2018 {{cite journal | vauthors = Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, Rohland N, Mallick S, Szécsényi-Nagy A, Mittnik A, Altena E, Lipson M, Lazaridis I, Harper TK, Patterson N, Broomandkhoshbacht N, Diekmann Y, Faltyskova Z, Fernandes D, Ferry M, Harney E, de Knijff P, Michel M, Oppenheimer J, Stewardson K, Barclay A, Alt KW, Liesau C, Ríos P, Blasco C, Miguel JV, García RM, Fernández AA, Bánffy E, Bernabò-Brea M, Billoin D, Bonsall C, Bonsall L, Allen T, Büster L, Carver S, Navarro LC, Craig OE, Cook GT, Cunliffe B, Denaire A, Dinwiddy KE, Dodwell N, Ernée M, Evans C, Kuchařík M, Farré JF, Fowler C, Gazenbeek M, Pena RG, Haber-Uriarte M, Haduch E, Hey G, Jowett N, Knowles T, Massy K, Pfrengle S, Lefranc P, Lemercier O, Lefebvre A, Martínez CH, Olmo VG, Ramírez AB, Maurandi JL, Majó T, McKinley JI, McSweeney K, Mende BG, Modi A, Kulcsár G, Kiss V, Czene A, Patay R, Endrődi A, Köhler K, Hajdu T, Szeniczey T, Dani J, Bernert Z, Hoole M, Cheronet O, Keating D, Velemínský P, Dobeš M, Candilio F, Brown F, Fernández RF, Herrero-Corral AM, Tusa S, Carnieri E, Lentini L, Valenti A, Zanini A, Waddington C, Delibes G, Guerra-Doce E, Neil B, Brittain M, Luke M, Mortimer R, Desideri J, Besse M, Brücken G, Furmanek M, Hałuszko A, Mackiewicz M, Rapiński A, Leach S, Soriano I, Lillios KT, Cardoso JL, Pearson MP, Włodarczak P, Price TD, Prieto P, Rey PJ, Risch R, Rojo Guerra MA, Schmitt A, Serralongue J, Silva AM, Smrčka V, Vergnaud L, Zilhão J, Caramelli D, Higham T, Thomas MG, Kennett DJ, Fokkens H, Heyd V, Sheridan A, Sjögren KG, Stockhammer PW, Krause J, Pinhasi R, Haak W, Barnes I, Lalueza-Fox C, Reich D | title = The Beaker phenomenon and the genomic transformation of northwest Europe | journal = Nature | volume = 555 | issue = 7695 | pages = 190–196 | date = March 2018 | pmid = 29466337 | pmc = 5973796 | doi = 10.1038/nature25738 | bibcode = 2018Natur.555..190O }} showed that a Bronze Age mass migration had greatly impacted the genetic makeup of the British Isles, bringing with it the Bell Beaker culture 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,{{sfn|Reich|2018|pp=219-220}} although, in September 2017, ancient DNA samples, as old as 8,100 years old, have been reported.{{cite news | vauthors = Zimmer C |author-link=Carl Zimmer |title=Clues to Africa's Mysterious Past Found in Ancient Skeletons |url=https://www.nytimes.com/2017/09/21/science/africa-dna-migration.html |date=21 September 2017|work=The New York Times |access-date=21 September 2017 }}

Moreover, ancient DNA has helped researchers to estimate modern human divergence.{{cite journal | vauthors = Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A, Edlund H, Munters AR, Vicente M, Steyn M, Soodyall H, Lombard M, Jakobsson M | title = Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago | journal = Science | volume = 358 | issue = 6363 | pages = 652–655 | date = November 2017 | pmid = 28971970 | doi = 10.1126/science.aao6266 | bibcode = 2017Sci...358..652S | doi-access = free }} 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.{{cite news |title=Neanderthal ancestry identifies oldest modern human genome |url=https://phys.org/news/2021-04-neanderthal-ancestry-oldest-modern-human.html |access-date=10 May 2021 |work=phys.org |language=en}}{{cite journal | vauthors = Prüfer K, Posth C, Yu H, Stoessel A, Spyrou MA, Deviese T, Mattonai M, Ribechini E, Higham T, Velemínský P, Brůžek J, Krause J | title = A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia | journal = Nature Ecology & Evolution | volume = 5 | issue = 6 | pages = 820–825 | date = June 2021 | pmid = 33828249 | pmc = 8175239 | doi = 10.1038/s41559-021-01443-x | doi-access = free | bibcode = 2021NatEE...5..820P }} 50px Available under [https://creativecommons.org/licenses/by/4.0/ CC BY 4.0]. Such genetic data provides insights into the migration and genetic history – e.g. of Europe – including about interbreeding between archaic and modern humans like a common admixture between initial European modern humans and Neanderthals.{{cite news |title=Europe's oldest known humans mated with Neandertals surprisingly often |url=https://www.sciencenews.org/article/europe-oldest-known-humans-mated-neandertals-dna-fossils |access-date=10 May 2021 |work=Science News |date=7 April 2021}}{{cite journal | vauthors = Hajdinjak M, Mafessoni F, Skov L, Vernot B, Hübner A, Fu Q, Essel E, Nagel S, Nickel B, Richter J, Moldovan OT, Constantin S, Endarova E, Zahariev N, Spasov R, Welker F, Smith GM, Sinet-Mathiot V, Paskulin L, Fewlass H, Talamo S, Rezek Z, Sirakova S, Sirakov N, McPherron SP, Tsanova T, Hublin JJ, Peter BM, Meyer M, Skoglund P, Kelso J, Pääbo S | title = Initial Upper Palaeolithic humans in Europe had recent Neanderthal ancestry | journal = Nature | volume = 592 | issue = 7853 | pages = 253–257 | date = April 2021 | pmid = 33828320 | pmc = 8026394 | doi = 10.1038/s41586-021-03335-3 | bibcode = 2021Natur.592..253H | doi-access = free }} 50px Available under [https://creativecommons.org/licenses/by/4.0/ CC BY 4.0].

{{div col|colwidth=30em}}

• Erika Hagelberg
• Alan Cooper
• Kirsten Bos
• Joachim Burger
• M. Thomas P. Gilbert
• Johannes Krause
• Svante Pääbo
• Hendrik Poinar
• David Reich
• Beth Shapiro
• Mark G. Thomas
• Eske Willerslev
• Carles Lalueza-Fox

{{div col end}}

{{div col|colwidth=30em}}

• Ancient pathogen genomics
• Ancient protein
• Archaeogenetics
• Environmental DNA (eDNA)
• List of DNA tested mummies
• List of haplogroups of historic people
• Molecular paleontology
• Paleogenetics
• Sedimentary ancient DNA (sedaDNA)

{{div col end}}

{{Reflist}}

{{refbegin}}

• {{cite book |title=Who We Are And How We Got Here – Ancient DNA and the New Science of the Human Past | vauthors = Reich D | author-link =David Reich (geneticist) |publisher=Pantheon Books |year=2018 |isbn=978-1101870327 }}
• {{cite news | vauthors = Diamond J | author-link = Jared Diamond|title=A Brand-New Version of Our Origin Story |url=https://www.nytimes.com/2018/04/20/books/review/david-reich-who-we-are-how-we-got-here.html |date=April 20, 2018 |newspaper=The New York Times |access-date=April 23, 2018 }}
• {{cite journal | vauthors = Orlando L | title = A 400,000-year-old mitochondrial genome questions phylogenetic relationships amongst archaic hominins: using the latest advances in ancient genomics, the mitochondrial genome sequence of a 400,000-year-old hominin has been deciphered | journal = BioEssays | volume = 36 | issue = 6 | pages = 598–605 | date = June 2014 | pmid = 24706482 | doi = 10.1002/bies.201400018 | s2cid = 35786511 }}
• {{cite book |title=Ancient DNA: The Making of a Celebrity Science | vauthors = Jones E | author-link =|publisher=Yale University Press |date=2022 |isbn=978-0-300-24012-2}}

{{refend}}

• {{cite web |archive-url=https://web.archive.org/web/20161003201826/http://www.ancestraljourneys.org/palaeolithicdna.shtml |archive-date=October 3, 2016 |url=http://www.ancestraljourneys.org/palaeolithicdna.shtml |title=Ancient DNA |work=Ancestral journeys }}
• [https://isogg.org/wiki/Y-DNA_famous_people Famous mtDNA], isogg wiki
• [https://isogg.org/wiki/Ancient_DNA Ancient mtDNA], isogg wiki
• [https://www.y-str.org/p/ancient-dna.html Ancient DNA] {{Webarchive|url=https://web.archive.org/web/20200306201227/http://www.y-str.org/p/ancient-dna.html |date=2020-03-06 }}, y-str.org
• [https://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.
• {{cite web |archive-url=https://web.archive.org/web/20091214080708/http://www.egyptologyonline.com/using_dna.htm |archive-date=December 14, 2009 |url=http://www.egyptologyonline.com/using_dna.htm |title=Unravelling the mummy mystery – using DNA |postscript=none }} – no data on YDNA only mtDNA

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