Chapter 3 : Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution

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With the advent of next-generation sequencing, the field of paleogenetics has considerably expanded over the past few years, making investigations that were once considered impossible a reality. A milestone in paleogenetics was reached in the year 2010, which saw for the first time the reconstruction of the nuclear genome of ancient humans who lived thousands of years ago. The genomes characterized that year covered both modern humans, with the approximately 4,000-year-old Saqqaq man ( ), and archaic humans, with the approximately 38,000-year-old Neanderthals from Croatia ( ) and a more than 30,000-year-old Denisovan individual discovered in Siberia ( ). These studies notably uncovered a migration of modern humans from Siberia into the New World some 5,500 years ago ( ) and a new group of archaic humans who lived in Siberia, the Denisovans ( ). With these molecular data, it was also possible to refine the separation between modern and archaic humans to between 272,000 and 435,000 years ago, with a genetic divergence time of 734,000 to 1,087,000 years ago ( ). Consistent with such an ancient genetic divergence between modern and archaic humans, for the human endogenous retrovirus (HERV) that is thought to have promoted the development of the placenta in mammals ( ), archaic individuals have six HERV-K proviruses (three common to Denisovans and Neanderthals, two specific to Neanderthals, and one specific to the Denisovan individual) that are absent in a 402-genome set of modern-day individuals ( ). Following these early characterizations of draft genomes of archaic humans, efforts focused on reconstructing high-quality genome sequences, and this was achieved for the original Denisovan genome ( ) and for the genome of a Neanderthal individual who lived in Altai ( Fig. 1 ) ( ).

Citation: Abi-Rached L, Raoult D. 2016. Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution, p 21-27. In Drancourt M, Raoult D (ed), Paleomicrobiology of Humans. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PoH-0018-2015
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Figure 1

Known complete archaicgenomes and their representation in modern populations. The three complete nuclear genomes of archaic humans that have been reconstructed to date are indicated by red (Denisovan) or blue (Neanderthal) circles at the geographical location where the samples used for these reconstructions were uncovered. The impact of archaic humans on the genomes of modern humans—as measured by the average proportion of the genome that is of archaic origin—is given for four regions of the world in gray circles. Red/blue: proportions of the genome that are of Denisovan (red) or Neanderthal (blue) origin ( ).

Citation: Abi-Rached L, Raoult D. 2016. Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution, p 21-27. In Drancourt M, Raoult D (ed), Paleomicrobiology of Humans. ASM Press, Washington, DC. doi: 10.1128/microbiolspec.PoH-0018-2015
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