Ancient DNA - Knowledge

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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. 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 and interactively on metaDMG. 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.

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samples. There is a theoretical correlation between time and DNA degradation, although differences in environmental conditions complicate matters. Samples subjected to different conditions are unlikely to predictably align to a uniform age-degradation relationship. The environmental effects may even matter after excavation, as DNA decay-rates may increase, particularly under fluctuating storage conditions. 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.

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Moreover, ancient DNA has helped researchers to estimate modern human divergence. 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

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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.

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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

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Researchers in 2016 measured chloroplast DNA in marine sediment cores, and found diatom DNA dating back to 1.4 million years. 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

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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

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reported what at the time was called the most exciting results to date — 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

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after 6,830,000 years at −5 °C. The decay kinetics have been measured by accelerated aging experiments, further displaying the strong influence of storage temperature and humidity on DNA decay. Nuclear DNA degrades at least twice as fast as mtDNA. Early studies that reported recovery of much

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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

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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)

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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). New methods have emerged in recent years to prevent possible contamination of aDNA samples, including conducting extractions under extreme sterile conditions, using

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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

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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. A greater appreciation for the risks of environmental contamination and studies on the

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at high altitude in the Andes, as well as various chemically treated preserved tissue such as the mummies of ancient Egypt. 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

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Orlando L (June 2014). "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".

199:(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. 194:

Single primer extension amplification was introduced in 2007 to address postmortem DNA modification damage. Since 2009 the field of aDNA studies has been revolutionized with the introduction of much cheaper research techniques. The use of high-throughput

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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.

382:, more than 300,000 years old, proving that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost. The DNA sequence of even older nuclear DNA was reported in 2021 from the permafrost-preserved teeth of two Siberian 1470:

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".

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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.

337:. Tissues examined include artificially or naturally mummified animal remains, bone, shells, paleofaeces, alcohol preserved specimens, rodent middens, dried plant remains, and recently, extractions of animal and plant DNA directly from 985:"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" 75:

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. The oldest DNA sequenced from physical specimens are from

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not only remained in the specimen over 150 years after the death of the individual, but could be extracted and sequenced. Over the next two years, through investigations into natural and artificially mummified specimens,

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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.

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egg, 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

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group in the El Sidrón cave, finding new insights on potential kinship and genetic diversity from the aDNA. In November 2015, scientists reported finding a 110,000-year-old tooth containing DNA from the

129:(PCR) in the late 1980s, the field began to progress rapidly. Double primer PCR amplification of aDNA (jumping-PCR) can produce highly skewed and non-authentic sequence artifacts. Multiple primer, 3576:

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".

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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".

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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

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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".

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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".

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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".

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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".

60:) ancient DNA is more degraded in comparison with contemporary genetic material. Genetic material has been recovered from paleo/archaeological and historical skeletal material, 3619:

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".

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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".

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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".

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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 plant

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Donoghue HD, Spigelman M, Zias J, Gernaey-Child AM, Minnikin DE (1998). "Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old".

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Golenberg EM, Giannasi DE, Clegg MT, Smiley CJ, Durbin M, Henderson D, et al. (April 1990). "Chloroplast DNA sequence from a miocene Magnolia species".

484:-fixed tissue. Efficient computational tools have been developed for pathogen and microorganism aDNA analyses in a small (QIIME) and large scale (FALCON ). 5553: 2054:"Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post mortem miscoding lesions" 4269:

Handt O, Richards M, Trommsdorff M, Kilger C, Simanainen J, Georgiev O, et al. (June 1994). "Molecular genetic analyses of the Tyrolean Ice Man".

4682:"Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes" 4623:"PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: the presence of multiple Bacillus anthracis strains in different victims" 4607: 1858:

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".

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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

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Vreeland RH, Rosenzweig WD, Powers DW (October 2000). "Isolation of a 250 million-year-old halotolerant bacterium from a primary salt crystal".

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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".

2405: 4873: 364:, 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 150:. Insects such as stingless bees, termites, and wood gnats, as well as plant and bacterial sequences were said to have been extracted from 456:

ear bone, since its dense structure provides good conditions for DNA preservation. Several other sources have also yielded DNA, including

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reported that two-million year old genetic material was found in Greenland, and is currently considered the oldest DNA discovered so far.

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Dumolin-Lapègue S, Pemonge MH, Gielly L, Taberlet P, Petit RJ (December 1999). "Amplification of oak DNA from ancient and modern wood".

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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".

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Higuchi R, Bowman B, Freiberger M, Ryder OA, Wilson AC (1984). "DNA sequences from the quagga, an extinct member of the horse family".

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confirmed that this phenomenon was not limited to relatively recent museum specimens but could apparently be replicated in a range of

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Martin-Roy R, Thyrring J, Mata X, Bangsgaard P, Bennike O, Christiansen G, et al. (2024-05-06). Fernández Robledo JA (ed.).

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Burger J, Hummel S, Hermann B, Henke W (June 1999). "DNA preservation: a microsatellite-DNA study on ancient skeletal remains".

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Fish SA, Shepherd TJ, McGenity TJ, Grant WD (May 2002). "Recovery of 16S ribosomal RNA gene fragments from ancient halite".

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Hänni C, Laudet V, Coll J, Stehelin D (July 1994). "An unusual mitochondrial DNA sequence variant from an Egyptian mummy".

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Taking preventative measures in their procedure against such contamination though, a 2012 study analyzed bone samples of a

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molars in Siberia over 1 million years old. In 2022, two-million year old genetic material was recovered from sediments in

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of DNA have raised concerns over previously reported results. The alleged dinosaur DNA was later revealed to be human

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Hagelberg E, Thomas MG, Cook CE, Sher AV, Baryshnikov GF, Lister AM (August 1994). "DNA from ancient mammoth bones".

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Lalueza-Fox C, Rosas A, de la Rasilla M (January 2012). "Palaeogenetic research at the El Sidrón Neanderthal site".

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Kjær KH, Winther Pedersen M, De Sanctis B, De Cahsan B, Korneliussen TS, Michelsen CS, et al. (December 2022).

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The first study of what would come to be called aDNA was conducted in 1984, when Russ Higuchi and colleagues at the

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van der Valk T, Pečnerová P, Díez-Del-Molino D, Bergström A, Oppenheimer J, Hartmann S, et al. (March 2021).

6450: 5949: 5462: 984: 5096: 4148:"Fossil DNA persistence and decay in marine sediment over hundred-thousand-year to million-year time scales" 3922: 6460: 6445: 6326: 5971: 5681: 5568: 3764:"Evolution of maize inferred from sequence diversity of an Adh2 gene segment from archaeological specimens" 2576:

Johnson SS, Hebsgaard MB, Christensen TR, Mastepanov M, Nielsen R, Munch K, et al. (September 2007).

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Thomas RH, Schaffner W, Wilson AC, Pääbo S (August 1989). "DNA phylogeny of the extinct marsupial wolf".

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Woodward SR, Weyand NJ, Bunnell M (November 1994). "DNA sequence from Cretaceous period bone fragments".

3672:"Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis-causing flies" 6455: 6398: 6074: 5457: 5020: 650: 575: 349: 196: 4510:

Mitochondrial DNA haplotype and sequence analysis of historic Choctaw and Menominee hair shaft samples

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Pinhasi R, Fernandes D, Sirak K, Novak M, Connell S, Alpaslan-Roodenberg S, et al. (2015-06-18).

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Montiel R, Malgosa A, Francalacci P (October 2001). "Authenticating ancient human mitochondrial DNA".

2286:"Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments" 6230: 6215: 5791: 5779: 5645: 5585: 5538: 5415: 2113:

Wales N, Carøe C, Sandoval-Velasco M, Gamba C, Barnett R, Samaniego JA, et al. (December 2015).

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tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and from

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Schlebusch CM, Malmström H, Günther T, Sjödin P, Coutinho A, Edlund H, et al. (November 2017).

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Skoglund P, Northoff BH, Shunkov MV, Derevianko AP, Pääbo S, Krause J, et al. (February 2014).

6235: 6054: 5813: 5706: 5655: 5605: 5595: 5221: 5049:"Southern African ancient genomes estimate modern human divergence to 350,000 to 260,000 years ago" 2249:

Hebsgaard MB, Phillips MJ, Willerslev E (May 2005). "Geologically ancient DNA: fact or artefact?".

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The research has added new complexity to the peopling of Eurasia. A study from 2018 showed that a

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mass migration had greatly impacted the genetic makeup of the British Isles, bringing with it the

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

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epoch, reportedly also yielded authentic DNA. Claims of DNA retrieval were not limited to amber.

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Pratas D, Pinho AJ, Silva RM, Rodrigues JM, Hosseini M, Caetano T, et al. (February 2018).

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Basler CF, Reid AH, Dybing JK, Janczewski TA, Fanning TG, Zheng H, et al. (February 2001).

2115:"New insights on single-stranded versus double-stranded DNA library preparation for ancient DNA" 146:

DNA. The majority of such claims were based on the retrieval of DNA from organisms preserved in

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Cooper A, Mourer-Chauviré C, Chambers GK, von Haeseler A, Wilson AC, Pääbo S (September 1992).

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Krause J, Briggs AW, Kircher M, Maricic T, Zwyns N, Derevianko A, et al. (February 2010).

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Pruvost M, Schwarz R, Correia VB, Champlot S, Braguier S, Morel N, et al. (January 2007).

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Sawyer S, Renaud G, Viola B, Hublin JJ, Gansauge MT, Shunkov MV, et al. (December 2015).

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Jackson PJ, Hugh-Jones ME, Adair DM, Green G, Hill KK, Kuske CR, et al. (February 1998).

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Dabney J, Knapp M, Glocke I, Gansauge MT, Weihmann A, Nickel B, et al. (September 2013).

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Willerslev E, Hansen AJ, Binladen J, Brand TB, Gilbert MT, Shapiro B, et al. (May 2003).

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Gilbert MT, Wilson AS, Bunce M, Hansen AJ, Willerslev E, Shapiro B, et al. (June 2004).

4202:"A genome sequence from a modern human skull over 45,000 years old from Zlatý kůň in Czechia" 2899:"PyDamage: automated ancient damage identification and estimation for contigs in ancient DNA 2679:

Briggs AW, Stenzel U, Johnson PL, Green RE, Kelso J, Prüfer K, et al. (September 2007).

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Olalde I, Brace S, Allentoft ME, Armit I, Kristiansen K, Booth T, et al. (March 2018).

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Pratas D, Hosseini M, Grilo G, Pinho AJ, Silva RM, Caetano T, et al. (September 2018).

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Allentoft ME, Collins M, Harker D, Haile J, Oskam CL, Hale ML, et al. (December 2012).

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Brotherton P, Endicott P, Sanchez JJ, Beaumont M, Barnett R, Austin J, et al. (2007).

2023: 1956: 1905: 1824: 1773: 1687: 1632: 1583: 1407: 1360: 1307: 1169: 1134: 1083: 1027: 933: 873: 762: 3052:"Separating endogenous ancient DNA from modern day contamination in a Siberian Neandertal" 2284:

Hansen AJ, Mitchell DL, Wiuf C, Paniker L, Brand TB, Binladen J, et al. (June 2006).

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Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, et al. (2004).

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Golenberg EM (September 1991). "Amplification and analysis of Miocene plant fossil DNA".

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Willerslev E, Hansen AJ, Rønn R, Brand TB, Barnes I, Wiuf C, et al. (January 2004).

524: 428: 49: 41: 5164: 5064: 4976: 4917: 4697: 4638: 4540: 4466: 4407: 4282: 4217: 4163: 4103: 4044: 3989: 3834: 3779: 3724: 3632: 3589: 3553: 3534: 3518: 3475: 3460:"Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing" 3420: 3365: 3308: 3253: 3157: 3067: 2855: 2696: 2593: 2544: 2487: 2350: 1960: 1909: 1828: 1777: 1731:

Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences

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

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Cano RJ, Borucki MK, Higby-Schweitzer M, Poinar HN, Poinar GO, Pollard KJ (June 1994).

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Hajdinjak M, Mafessoni F, Skov L, Vernot B, Hübner A, Fu Q, et al. (April 2021).

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The laborious processes that were required at that time to sequence such DNA (through

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Zischler H, Höss M, Handt O, von Haeseler A, van der Kuyl AC, Goudsmit J (May 1995).

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about 100 thousand years, at which point it followed a slower, power-law decay rate.

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Prüfer K, Posth C, Yu H, Stoessel A, Spyrou MA, Deviese T, et al. (June 2021).

3858: 3748: 3656: 3334: 3183: 3018: 3003:"mapDamage2.0: fast approximate Bayesian estimates of ancient DNA damage parameters" 1801: 1645: 903: 775: 750: 542:. Such genetic data provides insights into the migration and genetic history – e.g. 6346: 6321: 5899: 5834: 5801: 5512: 5497: 5282: 5178: 5168: 5068: 4988: 4980: 4931: 4921: 4843: 4835: 4806: 4772: 4752: 4711: 4701: 4652: 4642: 4581: 4544: 4480: 4470: 4421: 4411: 4364: 4321: 4286: 4231: 4221: 4167: 4107: 4058: 4048: 4013: 3993: 3930: 3893: 3885: 3838: 3793: 3783: 3728: 3683: 3636: 3593: 3548: 3538: 3489: 3479: 3444: 3424: 3379: 3369: 3312: 3277: 3257: 3206: 3161: 3114: 3081: 3071: 3022: 3014: 2973: 2965: 2924: 2914: 2869: 2859: 2810: 2800: 2759: 2751: 2710: 2700: 2651: 2607: 2597: 2548: 2513: 2491: 2444: 2421: 2401: 2364: 2354: 2305: 2297: 2258: 2221: 2211: 2167: 2126: 2073: 2065: 2019: 1984: 1964: 1933: 1913: 1832: 1781: 1738: 1715: 1695: 1650: 1640: 1605: 1591: 1544: 1507: 1499: 1437: 1415: 1368: 1315: 1258: 1223: 1197: 1177: 1142: 1111: 1091: 1043: 1035: 949: 941: 881: 826: 818: 770: 723:

Unlocking the Past: How Archaeologists Are Rewriting Human History with Ancient DNA

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Who We Are And How We Got Here – Ancient DNA and the New Science of the Human Past

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like a common admixture between initial European modern humans and Neanderthals.

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residues are vastly over-represented in the ancient DNA sequences. Miscoding of

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