Ancient DNA (aDNA) is DNA isolated from ancient specimens. Due to degradation processes (including cross-linking, deamination and fragmentation) ancient DNA is of lower quality in comparison with modern genetic material. 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 contemporary sequencing technologies. Genetic material has been recovered from archaeological and historical skeletal material, mummified tissues, archival collections of non-frozen medical specimens, preserved plant remains, ice and permafrost cores as well as marine and lake sediments.
- 1 History of ancient DNA studies
- 2 Problems and errors
- 3 Non-human aDNA
- 4 Human aDNA
- 5 Researchers specializing in ancient DNA
- 6 See also
- 7 References
- 8 Further reading
- 9 External links
History of ancient DNA studiesEdit
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. 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.
The laborious processes that were required at that time to sequence such DNA (through bacterial cloning) were an effective brake on the development of the field of ancient DNA (aDNA). However, with the development of the Polymerase Chain Reaction (PCR) in the late 1980s, the field began to progress rapidly. 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.
The post-PCR era heralded a wave of publications as numerous research groups tried their hands at aDNA. Soon a series of incredible findings had been published, claiming authentic DNA could be extracted from specimens that were millions of years old, into the realms of what Lindahl (1993b) has labelled Antediluvian DNA. The majority of such claims were based on the retrieval of DNA from organisms preserved in amber. Insects such as stingless bees, termites,[full citation needed][full citation needed] and wood gnats,[full citation needed] as well as plant and bacterial sequences were extracted from Dominican amber dating to the Oligocene epoch. Still older sources of Lebanese amber-encased weevils, dating to within the Cretaceous epoch, reportedly also yielded authentic DNA.[full citation needed] DNA retrieval was not limited to amber.
Several sediment-preserved plant remains dating to the Miocene were successfully investigated. Then, in 1994 and to international acclaim, Woodward et al. reported the most exciting results to date — mitochondrial cytochrome b sequences that had apparently been extracted from dinosaur bones dating to more than 80 million years ago. When in 1995 two further studies reported dinosaur DNA sequences extracted from a Cretaceous 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 halite.
Single primer extension (abr. SPEX) amplification was introduced in 2007 to address postmortem DNA modification damage.
Ancient DNA revolutionEdit
Since 2009 the field of aDNA-studies has been revolutionzed, with the introduction of much cheaper research-techniques, leading to new insights in human migrations.
Problems and errorsEdit
Due to degradation processes (including cross-linking, deamination and fragmentation) ancient DNA is of lower quality in comparison with 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 Allentoft et al. (2012). There is a theoretical correlation between time and DNA degradation, although differences in environmental conditions complicates things. 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 0.4–1.5 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. 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. As such, early studies that reported recovery of much older DNA, for example from Cretaceous dinosaur remains, may have stemmed from contamination of the sample.
A critical review of ancient DNA literature through the development of the field highlights that few studies after about 2002 have succeeded in amplifying DNA from remains older than several hundred thousand years. A greater appreciation for the risks of environmental contamination and studies on the chemical stability of DNA have resulted in concerns being raised over previously reported results. The dinosaur DNA was later revealed to be human Y-chromosome, while the DNA reported from encapsulated halobacteria has been criticized based on its similarity to modern bacteria, which hints at contamination. A 2007 study also suggests that these bacterial DNA samples may not have survived from ancient times, but may instead be the product of long-term, low-level metabolic activity.
aDNA may contain a large number of postmortem mutations, increasing with time. Some regions of polynucleotite are more susceptible to this degradation, so sequence data can bypass statistical filters used to check the validity of data. Due to sequencing errors, great caution should be applied to interpretation of population size. Substitutions resulting from deamination 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.
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 special adapters to identify endogenous molecules of the sample (over ones that may have been introduced during analysis), and applying bioinformatics to resulting sequences based on known reads in order approximate rates of contamination.
Despite the problems associated with 'antediluvian' DNA, a wide and ever-increasing range of aDNA sequences have now been published from a range of animal and plant taxa. Tissues examined include artificially or naturally mummified animal remains, bone, paleofaeces, alcohol preserved specimens, rodent middens, dried plant remains, and recently, extractions of animal and plant DNA directly from soil samples.
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.
In 2013, a German team reconstructed the mitochondrial genome of an Ursus deningeri more than 300,000 years old, proving that authentic ancient DNA can be preserved for hundreds of thousand years outside of permafrost.
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 about 100 thousand years, at which point it followed a slower, power-law decay rate.
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, for example, those preserved in ice, such as the Ötzi the Iceman, or through rapid desiccation, such as high-altitude mummies from the Andes,, as well as various sources of artificially preserved tissue (such as the chemically treated 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 that are much more common in the archaeological record – bone and teeth. Several other sources have also yielded DNA, including paleofaeces, and hair. 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, tissue embedded in paraffin, and formalin-fixed tissue. Efficient computational tools have been developed for pathogen and microorganism aDNA analyses in a small (QIIME) and large scale (FALCON ).
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. 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.
The research has added new complexity to the peopling of Eurasia. 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.
Researchers specializing in ancient DNAEdit
- Ancient protein
- Archaeogenetics of the Near East
- Dinosaur mummy
- Earliest known life forms
- Genetics and archaeogenetics of South Asia
- Genetic history of Africa (disambiguation)
- Genetic history of Europe
- Genetic history of indigenous peoples of the Americas
- Genetic history of Italy
- Genetic history of North Africa
- Genetic history of the Iberian Peninsula
- Genetic history of the British Isles
- Human mitochondrial DNA haplogroups
- Human timeline
- Human Y-chromosome DNA haplogroup
- Life timeline
- List of DNA tested mummies
- List of genetic results derived from historical figures
- Molecular paleontology
- Phylogenetic tree
- Tyrannosaurus#Soft tissue
- Pevsner, Jonathan (2015), Bioinformatics and Functional Genomics (3rd ed.), Wiley-Blackwell, ISBN 978-1118581780
- Jones, Martin (2016), Unlocking the Past: How Archaeologists Are Rewriting Human History with Ancient DNA, Arcade, ISBN 978-1628724479
- Allentoft ME; Collins M; Harker D; Haile J; Oskam CL; Hale ML; Campos PF; Samaniego JA; Gilbert MTP; Willerslev E; Zhang G; Scofield RP; Holdaway RN; Bunce M (2012). "The half-life of DNA in bone: measuring decay kinetics in 158 dated fossils". Proceedings of the Royal Society B. 279 (1748): 4724–33. doi:10.1098/rspb.2012.1745. PMC 3497090. PMID 23055061.
- Willerslev, E. et al., 2004. Long-term persistence of bacterial DNA. Current biology: CB, 14(1), pp. 9–10.
- Higuchi R; Bowman B; Freiberger M; Ryder OA; Wilson AC (1984). "DNA sequences from the quagga, an extinct member of the horse family". Nature. 312 (5991): 282–84. Bibcode:1984Natur.312..282H. doi:10.1038/312282a0. PMID 6504142.
- Pääbo S (1985a). "Preservation of DNA in ancient Egyptian mummies". J. Archaeol. Sci. 12 (6): 411–17. doi:10.1016/0305-4403(85)90002-0.
- Pääbo S (1985b). "Molecular cloning of ancient Egyptian mummy DNA". Nature. 314 (6012): 644–45. Bibcode:1985Natur.314..644P. doi:10.1038/314644a0. PMID 3990798.
- Pääbo S. 1986. Molecular genetic investigations of ancient human remains. Cold Spring Harbour Symp Quant Biol. 51:441–46
- Mullis KB; Faloona FA (1987). Specific synthesis of DNA in vitro via a polymerase-catalyzed chain reaction. Meth. Enzymol. Methods in Enzymology. 155. pp. 335–50. doi:10.1016/0076-6879(87)55023-6. ISBN 978-0-12-182056-5. PMID 3431465.
- Saiki RK, Gelfand DH, Stoffel S, et al. (January 1988). "Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase". Science. 239 (4839): 487–91. Bibcode:1988Sci...239..487S. doi:10.1126/science.2448875. PMID 2448875.
- Lindahl T (1993). "Recovery of antediluvian DNA". Nature. 365 (6448): 700. Bibcode:1993Natur.365..700L. doi:10.1038/365700a0. PMID 8413647.
- 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.
- 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.
- De Salle et al. 1992
- De Salle et al. 1993
- De Salle and Grimaldi 1994
- Poinar H; Cano R; Poinar G (1993). "DNA from an extinct plant". Nature. 363 (6431): 677. Bibcode:1993Natur.363..677P. doi:10.1038/363677a0.
- Cano RJ; Borucki MK; Higby-Schweitzer M; Poinar HN; Poinar GO Jr.; Pollard KJ (1994). "Bacillus DNA in fossil bees: an ancient symbiosis?". Appl Environ Microbiol. 60: 2164–67.
- Cano et al. 1993
- Golenberg EM (1991). "Amplification and analysis of Miocene plant fossil DNA". Philos Trans R Soc Lond B. 333 (1268): 419–26. doi:10.1098/rstb.1991.0092. PMID 1684052.
- Golenberg EM; Giannasi DE; Clegg MT; Smiley CJ; Durbin M; Henderson D; Zurawski G (1990). "Chloroplast DNA sequence from a Miocene Magnolia species". Nature. 344 (6267): 656–58. Bibcode:1990Natur.344..656G. doi:10.1038/344656a0. PMID 2325772.
- Woodward SR; Weyand NJ; Bunnell M (November 1994). "DNA sequence from Cretaceous period bone fragments". Science. 266 (5188): 1229–32. Bibcode:1994Sci...266.1229W. doi:10.1126/science.7973705. PMID 7973705.
- An C-C, Li Y, Zhu Y-X. 1995. Molecular cloning and sequencing of the 18S rDNA from specialized dinosaur egg fossil found in Xixia Henan, China. Acta Sci Nat Univ Pekinensis 31:140–47
- 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.
- 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. PMID 11057666.
- Fish SA; Shepherd TJ; McGenity TJ; Grant WD (May 2002). "Recovery of 16S ribosomal RNA gene fragments from ancient halite". Nature. 417 (6887): 432–36. Bibcode:2002Natur.417..432F. doi:10.1038/417432a. PMID 12024211.
- Brotherton, P; Endicott, P; Sanchez, Jj; Beaumont, M; Barnett, R; Austin, J; Cooper, A (2007). "Novel high-resolution characterization of ancient DNA reveals C > U-type base modification events as the sole cause of post-mortem miscoding lesions" (Free full text). Nucleic Acids Research. 35 (17): 5717–28. doi:10.1093/nar/gkm588. ISSN 0305-1048. PMC 2034480. PMID 17715147.
- Reich 2018.
- Hebsgaard, M.B., Phillips, M.J. & Willerslev, E., 2005. Geologically ancient DNA: fact or artefact? Trends in microbiology, 13(5), pp. 212–20.
- Hansen, A.J. et al., 2006. Crosslinks rather than strand breaks determine access to ancient DNA sequences from frozen sediments. Genetics, 173(2), pp. 1175–79.
- Pruvost, M. et al., 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), pp. 739–44.
- Burger, J. et al., 1999. DNA preservation: a microsatellite-DNA study on ancient skeletal remains. Electrophoresis, 20(8), pp. 1722–28.
- Grass, R.N.; Heckel, R.; Puddu, M.; Paunescu, D.; Stark, W.J. (2015). "Robust Chemical Preservation of Digital Information on DNA in Silica with Error-Correcting Codes". Angewandte Chemie International Edition. 54 (8): 2552–55. doi:10.1002/anie.201411378. PMID 25650567.
- Willerslev E, Hansen AJ, Binladen J, et al. (May 2003). "Diverse plant and animal genetic records from Holocene and Pleistocene sediments". Science. 300 (5620): 791–95. Bibcode:2003Sci...300..791W. doi:10.1126/science.1084114. PMID 12702808.
- Zischler H; Höss M; Handt O; von Haeseler A; van der Kuyl AC; Goudsmit J (May 1995). "Detecting dinosaur DNA". Science. 268 (5214): 1192–93, author reply 1194. doi:10.1126/science.7605504. PMID 7605504.
- Nicholls H (February 2005). "Ancient DNA Comes of Age". PLOS Biology. 3 (2): e56. doi:10.1371/journal.pbio.0030056. PMC 548952. PMID 15719062.
- Johnson SS; Hebsgaard MB; Christensen TR; Mastepanov M; Nielsen R; Munch K; Brand T; Gilbert MT; Zuber MT; Bunce M; Rønn R; Gilichinsky D; Froese D; Willerslev E (September 2007). "Ancient bacteria show evidence of DNA repair". PNAS. 104 (36): 14401–05. Bibcode:2007PNAS..10414401J. doi:10.1073/pnas.0706787104. PMC 1958816. PMID 17728401.
- Pääbo, Svante; Poinar, Hendrik; Serre, David; Jaenicke-Després, Viviane; Hebler, Juliane; Rohland, Nadin; Kuch, Melanie; Krause, Johannes; Vigilant, Linda; Hofreiter, Michael (2004). "Genetic Analyses from Ancient DNA" (PDF). Annual Review of Genetics. 38 (1): 645–79. doi:10.1146/annurev.genet.37.110801.143214. ISSN 0066-4197. PMID 15568989. Archived from the original (PDF) on December 17, 2008. Retrieved December 1, 2008.
- Johnson, Pl; Slatkin, M (Jan 2008). "Accounting for bias from sequencing error in population genetic estimates" (Free full text). Molecular Biology and Evolution. 25 (1): 199–206. doi:10.1093/molbev/msm239. ISSN 0737-4038. PMID 17981928.
- Briggs, Aw; Stenzel, U; Johnson, Pl; Green, Re; Kelso, J; Prüfer, K; Meyer, M; Krause, J; Ronan, Mt; et al. (Sep 2007). "Patterns of damage in genomic DNA sequences from a Neandertal". Proceedings of the National Academy of Sciences of the United States of America. 104 (37): 14616–21. Bibcode:2007PNAS..10414616B. doi:10.1073/pnas.0704665104. ISSN 0027-8424. PMC 1976210. PMID 17715061.
- Gansauge, Marie-Theres; Meyer, Matthias (2014). "Selective enrichment of damaged DNA molecules for ancient genome sequencing". Genome Research. 24 (9): 1543–49. doi:10.1101/gr.174201.114. PMC 4158764. PMID 25081630.
- Pratas, Diogo; Hosseini, Morteza; Grilo, Goncalo; Pinho, Armando; Silva, Raquel; Caetano, Tania; Carneiro, Joao; Pereira, Filipe (2018). "Metagenomic Composition Analysis of an Ancient Sequenced Polar Bear Jawbone from Svalbard". Genes. 9 (9): 445. doi:10.3390/genes9090445. PMC 6162538. PMID 30200636.
- Slatkin, Montgomery; Racimo, Fernando (2016-06-07). "Ancient DNA and human history". Proceedings of the National Academy of Sciences. 113 (23): 6380–87. doi:10.1073/pnas.1524306113. ISSN 0027-8424. PMC 4988579. PMID 27274045.
- Thomas RH; Schaffner W; Wilson AC; Pääbo S (August 1989). "DNA phylogeny of the extinct marsupial wolf". Nature. 340 (6233): 465–67. Bibcode:1989Natur.340..465T. doi:10.1038/340465a0. PMID 2755507.
- Hagelberg E; Sykes B; Hedges R (1989). "Ancient bone DNA amplified". Nature. 342 (6249): 485. Bibcode:1989Natur.342..485H. doi:10.1038/342485a0. PMID 2586623.
- Cooper A; Mourer-Chauviré C; Chambers GK; von Haeseler A; Wilson A; Pääbo S (1992). "Independent origins of New Zealand moas and kiwis". Proceedings of the National Academy of Sciences of the United States of America. 89 (18): 8741–44. Bibcode:1992PNAS...89.8741C. doi:10.1073/pnas.89.18.8741. PMC 49996. PMID 1528888.
- Hagelberg E; Thomas MG; Cook Jr. CE; Sher AV; Baryshnikov GF; Lister AM (1994). "DNA from ancient mammoth bones". Nature. 370 (6488): 333–334. Bibcode:1994Natur.370R.333H. doi:10.1038/370333b0. PMID 8047136.
- Hänni C; Laudet V; Stehelin D; Taberlet P (December 1994). "Tracking the origins of the cave bear (Ursus spelaeus) by mitochondrial DNA sequencing". Proceedings of the National Academy of Sciences of the United States of America. 91 (25): 12336–40. Bibcode:1994PNAS...9112336H. doi:10.1073/pnas.91.25.12336. PMC 45432. PMID 7991628.
- Poinar HN, Hofreiter M, Spaulding WG, et al. (July 1998). "Molecular coproscopy: dung and diet of the extinct ground sloth Nothrotheriops shastensis". Science. 281 (5375): 402–06. Bibcode:1998Sci...281..402P. doi:10.1126/science.281.5375.402. PMID 9665881.
- Hofreiter M, Poinar HN, Spaulding WG, et al. (December 2000). "A molecular analysis of ground sloth diet through the last glaciation". Mol. Ecol. 9 (12): 1975–84. doi:10.1046/j.1365-294X.2000.01106.x. PMID 11123610.
- Junqueira ACM; Lessinger AC; Azeredo-Espin AML (2002). "Methods for the recovery of mitochondrial DNA sequences from museum specimens of myiasis-causing flies". Med Vet Entomol. 16 (1): 39–45. doi:10.1046/j.0269-283x.2002.00336.x. PMID 11963980.
- Kuch M; Rohland N; Betancourt JL; Latorre C; Steppan S; Poinar HN (May 2002). "Molecular analysis of an 11,700-year-old rodent midden from the Atacama Desert, Chile". Mol. Ecol. 11 (5): 913–24. doi:10.1046/j.1365-294X.2002.01492.x. PMID 11975707.
- Goloubinoff P; Pääbo S; Wilson AC (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. PMC 46007. PMID 8446621.
- Dumolin-Lapegue S; Pemonge H-M; Gielly L; Taberlet P; Petit RJ (1999). "Amplification of oak DNA from ancient and modern wood". Mol. Ecol. 8 (12): 2137–40. doi:10.1046/j.1365-294x.1999.00788.x. PMID 10632865.
- Willerslev E; Cooper A (January 2005). "Ancient DNA". Proceedings of the Royal Society B. 272 (1558): 3–16. doi:10.1098/rspb.2004.2813. PMC 1634942. PMID 15875564.
- Erika Check Hayden (26 June 2013). "First horses arose 4 million years ago". Nature. doi:10.1038/nature.2013.13261.
- Jane J. Lee (November 7, 2017). "World's Oldest Genome Sequenced From 700,000-Year-Old Horse DNA". National Geographic. Retrieved May 19, 2019.
- Willerslev, Eske; Wang, Jun; Shapiro, Beth; Ludovic, Orlando; et al. (1 July 2013). "Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse". Nature. 499 (7456): 74–78. doi:10.1038/nature12323. Retrieved 18 May 2019 – via www.nature.com.
- Dabney; et al. (2013). "Complete mitochondrial genome sequence of a Middle Pleistocene cave bear reconstructed from ultrashort DNA fragments". PNAS. 110 (39): 15758–15763. Bibcode:2013PNAS..11015758D. doi:10.1073/pnas.1314445110. PMC 3785785. PMID 24019490. Retrieved 18 January 2014.
- Kirkpatrick, John B.; Walsh, Emily A.; D’Hondt, Steven (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. doi:10.1130/g37933.1. ISSN 0091-7613.
- Handt O, Richards M, Trommsdorf M, Kilger C, Simanainen J, Georgiev O, Bauer K, Stone A, Hedges R (1994b). "Molecular genetic analyses of the Tyrolean Ice Man". Science. 264 (5166): 1775–1778. Bibcode:1994Sci...264.1775H. doi:10.1126/science.8209259. PMID 8209259.
- Montiel R; Malgosa A; Francalacci P (2001). "Authenticating ancient human mitochondrial DNA". Hum Biol. 73 (5): 689–713. doi:10.1353/hub.2001.0069.
- 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. PMID 7806242.
- Poinar HN, Küch M, Sobolik KD, Barnes I, Stankiewicz AB, Kuder T, Spaulding WG, Bryant VM, Cooper A (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. PMC 31832. PMID 11296282.
- Baker LE. 2001. Mitochondrial DNA haplotype and sequence analysis of historic Choctaw and Menominee hair shaft samples. PhD Thesis. University of Tennessee, Knoxville.
- 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 (2004). "Ancient mitochondrial DNA from hair". Current Biology. 14 (12): R463–64. doi:10.1016/j.cub.2004.06.008. PMID 15203015.
- Donoghue HD, Spigelman M, Zias J, Gernaey-Child AM, Minnikin DE. 1998. Mycobacterium tuberculosis complex DNA in calcified pleura from remains 1400 years old. Lett Appl Microbiol 27:265–69
- Jackson PJ, Hugh-Jones ME, Adair DM, et al. (February 1998). "PCR analysis of tissue samples from the 1979 Sverdlovsk anthrax victims: The presence of multiple Bacillus anthracis strains in different victims". Proceedings of the National Academy of Sciences of the United States of America. 95 (3): 1224–29. Bibcode:1998PNAS...95.1224J. doi:10.1073/pnas.95.3.1224. PMC 18726. PMID 9448313.
- Basler CF, Reid AH, Dybing JK, et al. (February 2001). "Sequence of the 1918 pandemic influenza virus nonstructural gene (NS) segment and characterization of recombinant viruses bearing the 1918 NS genes". Proceedings of the National Academy of Sciences of the United States of America. 98 (5): 2746–51. Bibcode:2001PNAS...98.2746B. doi:10.1073/pnas.031575198. PMC 30210. PMID 11226311.
- Taubenberger JK; Reid AH; Krafft AE; Bijwaard KE; Fanning TG (March 1997). "Initial genetic characterization of the 1918 "Spanish" influenza virus". Science. 275 (5307): 1793–96. doi:10.1126/science.275.5307.1793. PMID 9065404.
- Pratas D; Pinho AJ; Silva RM; Rodrigues JMOS; Hosseini M; Caetano T; Ferreira PJSG (February 2018). "FALCON: a method to infer metagenomic composition of ancient DNA". bioRxiv. doi:10.1101/267179.
- Lalueza-Fox, Carles; Rosas, Antonio; Rasilla, Marco de la (2012-01-20). "Palaeogenetic research at the El Sidrón Neanderthal site". Annals of Anatomy - Anatomischer Anzeiger. Special Issue: Ancient DNA. 194 (1): 133–37. doi:10.1016/j.aanat.2011.01.014. hdl:10261/79609. PMID 21482084.
- Zimmer, Carl (16 November 2015). "In a Tooth, DNA From Some Very Old Cousins, the Denisovans". The New York Times. Retrieved 16 November 2015.
- Sawyer, Susanna; Renaud, Gabriel; Viola, Bence; Hublin, Jean-Jacques; Gansauge, Marie-Theres; Shunkov, Michael V.; Derevianko, Anatoly P.; Prüfer, Kay; Kelso, Janet; Pääbo, Svante (11 November 2015). "Nuclear and mitochondrial DNA sequences from two Denisovan individuals". PNAS. 112 (51): 15696–700. Bibcode:2015PNAS..11215696S. doi:10.1073/pnas.1519905112. PMC 4697428. PMID 26630009. Retrieved 16 November 2015.
- Zimmer, Carl (21 September 2017). "Clues to Africa's Mysterious Past Found in Ancient Skeletons". The New York Times. Retrieved 21 September 2017.
- "Ancient DNA". Ancestral journeys. Archived from the original on October 3, 2016.
- Famous mtDNA, isogg wiki
- Ancient mtDNA, isogg wiki
- Ancient DNA, y-str.org
- Evidence of the Past: A Map and Status of Ancient Remains – samples from USA no sequence data here.
- "Unravelling the mummy mystery – using DNA". Archived from the original on December 14, 2009 – no data on YDNA only mtDNA