Paleogenetics

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

Paleogeneticists do not recreate actual organisms, but piece together ancient DNA sequences using various analytical methods.[4] Fossils are "the only direct witnesses of extinct species and of evolutionary events"[5] and finding DNA within those fossils allows for a deeper examination of these events.

Applications

Evolution

Similar sequences are often found along protein polypeptide 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 polypeptide sequences to be compared between species, and the difference between two genetic sequences can be used to determine – within error – the time at which a common ancestor existed.[2]

Human evolution

Using the thigh bone of a Neanderthal female, 63% of the Neanderthal genome was uncovered and 3.7 billion bases of DNA were decoded.[6][7] 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 more DNA with chimpanzees than homo sapiens.[7] It was also found that Neanderthals were less genetically diverse than modern humans are, which indicates that Homo neanderthalensis grew from a group composed of relatively few individuals.[7] DNA sequences suggest that Homo sapiens first appeared between about 130,000 and 250,000 years ago in Africa.[7]

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.[8]

Evolution of culture

Looking at DNA can give insight into lifestyles of people of the past. Neandertal DNA shows that they lived in small temporary communities.[7] DNA analysis can also show dietary restrictions and mutations, such as the fact that Homo neanderthalensis was lactose-intolerant.[7]

Archaeology

Ancient disease

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

The oldest case of Lyme disease was discovered in the genome on a man called Ötzi the Iceman.[9] Ötzi died around 3,300 B.C., and his remains were discovered in the Eastern Alps in the early 1990s.[9] An analysis of his genes was not run until 20 years later. Genetic remains of the bacterium that cause Lyme disease, Borrelia burgdorferi, were discovered in genetic material from Ötzi.[9]

Domestication of animals

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.[5]

Challenges

Ancient remains usually contain only a small fraction of the original DNA present in an organism.[2][10] This is due to the degradation of DNA in dead tissue by biotic and abiotic factors once repair enzymes present in living tissue cease to be functional. DNA preservation is dependent 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.[11] 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.[5] 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.[5]

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See also

References
  1. Benner SA, Sassi SO, Gaucher EA (2007). "Molecular paleoscience: Systems biology from the past". Protein evolution. Advances in Enzymology and Related Areas of Molecular Biology. 75. pp. 1–132, xi. doi:10.1002/9780471224464.ch1. ISBN 9780471224464. PMID 17124866.
  2. 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.
  3. 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): 282–4. doi:10.1038/312282a0. PMID 6504142. Lay summary – Science Magazine.
  4. Gibbons, A (December 2010). "Tiny time machines revisit ancient life". Science. 330 (6011): 1616. doi:10.1126/science.330.6011.1616. PMID 21163988. Lay summary – SciTechStory.
  5. Geigl E-M (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.
  6. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kircher M, Patterson N, Li H, Zhai W, et al. (May 2010). "A draft sequence of the Neanderthal genome". Science. 328 (5979): 710–22. doi:10.1126/science.1188021. PMC 5100745. PMID 20448178.
  7. 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.
  8. Zorich Z (2010). "Neanderthal Genome Decoded". Archaeology. Archaeological Institute of America. 63 (4).
  9. Keller A, Graefen A, Ball M, Matzas M, Boisguerin V, Maixner F, Leidinger P, Backes C, Khairat R, et al. (2012). "New insights into the Tyrolean Iceman's origin and phenotype as inferred by whole-genome sequencing". Nature Communications. 3 (2): 698. doi:10.1038/ncomms1701. PMID 22426219. Lay summary – DiscoveryNews.
  10. Kaplan, Matt. DNA has a 521-year half-life. Nature News, 10 October 2012.
  11. Wickman, Forrest. What’s the Shelf-Life of DNA? Slate, 5 February 2013.
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