Paleogenetics

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Paleogenetics is the study of the past through the examination of preserved genetic material from the remains of ancient organisms.[1][2] Emile Zuckerkandl and Linus Pauling introduced the term in 1963, long before the sequencing of DNA, in reference to the possible reconstruction of the corresponding polypeptide sequences of past organisms.[3] The first sequence of ancient DNA, isolated from a museum specimen of the extinct quagga, was published in 1984 by a team led by Allan Wilson.[4]

Paleogeneticists do not recreate actual organisms, but piece together ancient DNA sequences using various analytical methods.[5] Fossils are "the only direct witnesses of extinct species and of evolutionary events"[6] and finding DNA within those fossils exposes tremendously more information about these species, potentially their entire physiology and anatomy.

The most ancient DNA sequence to date was reported in February 2021, from the tooth of a Siberian mammoth frozen for over a million years.[7][8]

Applications[edit]

Evolution[edit]

Similar sequences are often found along DNA (and the derived protein polypetide chains) in different species. This similarity is directly linked to the sequence of the DNA (the genetic material of the organism). Due to the improbability of this being random chance, and its consistency too long to be attributed to convergence by natural selection, these similarities can be plausibly linked to the existence of a common ancestor with common genes. This allows DNA sequences to be compared between species. Comparing an ancient genetic sequence to later or modern ones can be used to determine ancestral relations, while comparing two modern genetic sequences can determine, within error, the time since their last common ancestor.[3]

Human evolution[edit]

Using the thigh bone of a Neanderthal female, 63% of the Neanderthal genome was recovered and 3.7 billion bases of DNA were decoded.[9][10] It showed that Homo neanderthalensis was the closest living relative of Homo sapiens, until the former lineage died out 30,000 years ago. The Neanderthal genome was shown to be within the range of variation of those of anatomically modern humans, although at the far periphery of that range of variation. Paleogenetic analysis also suggests that Neanderthals shared slightly more DNA with chimpanzees than homo sapiens.[10] It was also found that Neanderthals were less genetically diverse than modern humans, which indicates that Homo neanderthalensis grew from a group composed of relatively few individuals.[10] DNA sequences suggest that Homo sapiens first appeared between about 130,000 and 250,000 years ago in Africa.[10]

Paleogenetics opens up many new possibilities for the study of hominid evolution and dispersion. By analyzing the genomes of hominid remains, their lineage can be traced back to from where they came, or from where they share a common ancestor. The Denisova hominid, a species of hominid found in Siberia from which DNA was able to be extracted, may show signs of having genes that are not found in any Neanderthal nor Homo sapiens genome, possibly representing a new lineage or species of hominid.[11]

Evolution of culture[edit]

Looking at DNA can give insight into lifestyles of people of the past. Neandertal DNA shows that they lived in small temporary communities.[10] DNA analysis can also show dietary restrictions and mutations, such as the fact that Homo neanderthalensis was lactose-intolerant.[10]

Archaeology[edit]

Ancient disease[edit]

Studying DNA of the deceased also allows us to look at the medical history of the human species. By looking back we can discover when certain diseases first appeared and began to afflict humans.

Ötzi[edit]

The oldest case of Lyme disease was discovered in the genome[clarification needed] on Ötzi the Iceman.[12] Ötzi died around 3,300 B.C., and his remains were discovered frozen in the Eastern Alps in the early 1990s, and his genetic material was analyzed in the 2010s.[12] Genetic remains of the bacterium that causes Lyme disease, Borrelia burgdorferi, were discovered in the body.[12]

Domestication of animals[edit]

Not only can past humans be investigated through paleogenetics, but the organisms they had an effect on can also be examined. Through examination of the divergence found in domesticated species such as cattle and the archaeological record from their wild counterparts; the effect of domestication can be studied, which could tell us a lot about the behaviors of the cultures that domesticated them. The genetics of these animals also reveals traits not shown in the paleontological remains, such as certain clues as to the behavior, development, and maturation of these animals. The diversity in genes can also tell where the species were domesticated, and how these domesticates migrated from these locations elsewhere.[6]

Challenges[edit]

Ancient remains usually contain only a small fraction of the original DNA of an organism.[3][13] This is due to the degradation of DNA in dead tissue by biotic and abiotic decay. DNA preservation depends on a number of environmental characteristics, including temperature, humidity, oxygen and sunlight. Remains from regions with high heat and humidity typically contain less intact DNA than those from permafrost or caves, where remains may persist in cold, low oxygen conditions for several hundred thousand years.[14] In addition, DNA degrades much more quickly following excavation of materials, and freshly excavated bone has a much higher chance of containing viable genetic material.[6] After excavation, bone may also become contaminated with modern DNA (i.e. from contact with skin or unsterilized tools), which can create false-positive results.[6]

See also[edit]

References[edit]

  1. ^ Brown TA, Brown KA (October 1994). "Ancient DNA: using molecular biology to explore the past". BioEssays. 16 (10): 719–726. doi:10.1002/bies.950161006. PMID 7980476. S2CID 27567988.
  2. ^ Pääbo S, Poinar H, Serre D, Jaenicke-Despres V, Hebler J, Rohland N, et al. (2004). "Genetic analyses from ancient DNA". Annual Review of Genetics. 38: 645–679. doi:10.1146/annurev.genet.37.110801.143214. PMID 15568989.
  3. ^ a b c Pauling L, Zuckerkand E, Henriksen T, Lövstad R (1963). "Chemical Paleogenetics: Molecular "Restoration Studies" of Extinct Forms of Life". Acta Chemica Scandinavica. 17 (supl): 9–16. doi:10.3891/acta.chem.scand.17s-0009.
  4. ^ 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): 282–284. Bibcode:1984Natur.312..282H. doi:10.1038/312282a0. PMID 6504142. S2CID 4313241.
  5. ^ Gibbons A (December 2010). "Tiny time machines revisit ancient life". Science. 330 (6011): 1616. Bibcode:2010Sci...330.1616G. doi:10.1126/science.330.6011.1616. PMID 21163988. "Paleogenetics: Unlocking the secrets from DNA of long ago". SciTechStory. March 6, 2011. Archived from the original on 2015-10-18.
  6. ^ a b c d Geigl EM (2008). "Palaeogenetics of cattle domestication: Methodological challenges for the study of fossil bones preserved in the domestication centre in Southwest Asia". Comptes Rendus Palevol. 7 (2–3): 99–112. doi:10.1016/j.crpv.2008.02.001.
  7. ^ Hunt K (17 February 2021). "World's oldest DNA sequenced from a mammoth that lived more than a million years ago". CNN News. Retrieved 17 February 2021.
  8. ^ Callaway E (February 2021). "Million-year-old mammoth genomes shatter record for oldest ancient DNA". Nature. 590 (7847): 537–538. doi:10.1038/d41586-021-00436-x. PMID 33597786.
  9. ^ Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, et al. (May 2010). "A draft sequence of the Neandertal genome". Science. 328 (5979): 710–722. Bibcode:2010Sci...328..710G. doi:10.1126/science.1188021. PMC 5100745. PMID 20448178.
  10. ^ a b c d e f Saey TH (2009). "Story one: Team decodes neanderthal DNA: Genome draft may reveal secrets of human evolution". Science News. 175 (6): 5–7. doi:10.1002/scin.2009.5591750604.
  11. ^ Zorich Z (2010). "Neanderthal Genome Decoded". Archaeology. Archaeological Institute of America. 63 (4).
  12. ^ a b c Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, et al. (February 2012). "New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing". Nature Communications. 3 (2): 698. Bibcode:2012NatCo...3..698K. doi:10.1038/ncomms1701. PMID 22426219.
  13. ^ Kaplan M (10 October 2012). "DNA has a 521-year half-life". Nature News.
  14. ^ Wickman F (5 February 2013). "What's the Shelf-Life of DNA?". Slate.