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

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  • Authors: Laurent Abi-Rached1, Didier Raoult2
  • Editors: Michel Drancourt3, Didier Raoult4
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    Affiliations: 1: Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; 2: Aix Marseille Université, URMITE, UMR CNRS 7278, IRD 198, INSERM 1095, Faculté de Médecine, Institut Hospitalo-Universitaire Méditerranée-Infection, Marseille, France; 3: Aix Marseille Université Faculté de Médecine, Marseille, France; 4: Aix Marseille Université Faculté de Médecine, Marseille, France
    • Source: microbiolspec May 2016 vol. 4 no. 3 doi:10.1128/microbiolspec.PoH-0018-2015
  • Received 08 March 2016 Accepted 14 March 2016 Published 20 May 2016
  • Didier Raoult, [email protected]
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  • Abstract:

    With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes. Although these contributions are modest, they played a major role in shaping immune gene families, such as the HLA class I genes, for which the archaic alleles now represent more than 50% of the alleles in Europe and Asia. Such a high frequency is consistent with these archaic HLA class I variants having been positively selected because of their protective effect against contagious and devastating epidemics, such as those due to the plague agent or to , which is responsible for deadly tuberculosis. While the exact nature of the infectious agents that contributed to the selection of the archaic variants is unknown, we are entering an exciting period in which paleogenetics and paleomicrobiology data can be integrated to generate a clearer picture of how the immune system of modern populations was shaped and the role admixture and epidemics have played in such evolutions.

  • Citation: Abi-Rached L, Raoult D. 2016. Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution. Microbiol Spectrum 4(3):PoH-0018-2015. doi:10.1128/microbiolspec.PoH-0018-2015.

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2016-05-20
2019-11-12

Abstract:

With the advent of next-generation sequencing, paleogenetics has considerably expanded over the past few years and notably encompassed the characterization of the genomes of archaic humans who lived more than 30,000 years ago. These paleogenetics investigations have revealed that admixture between modern and archaic humans occurred, with Neanderthals having contributed to 1.5% to 2.1% of modern Eurasian genomes, and Denisovans to 3% to 6% of modern Melanesian genomes and to approximately 0.2% of modern Asian genomes. Although these contributions are modest, they played a major role in shaping immune gene families, such as the HLA class I genes, for which the archaic alleles now represent more than 50% of the alleles in Europe and Asia. Such a high frequency is consistent with these archaic HLA class I variants having been positively selected because of their protective effect against contagious and devastating epidemics, such as those due to the plague agent or to , which is responsible for deadly tuberculosis. While the exact nature of the infectious agents that contributed to the selection of the archaic variants is unknown, we are entering an exciting period in which paleogenetics and paleomicrobiology data can be integrated to generate a clearer picture of how the immune system of modern populations was shaped and the role admixture and epidemics have played in such evolutions.

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Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution
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Citation: Abi-Rached L, Raoult D. 2016. Paleogenetics and past infections: the two faces of the coin of human immune evolution. microbiolspec 4(3): doi:10.1128/microbiolspec.PoH-0018-2015
/content/microbiolspec/10.1128/microbiolspec.PoH-0018-2015.fig1
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 ( 8 ).

microbiolspec/4/3/PoH-0018-2015-fig1_thmb.gif
microbiolspec/4/3/PoH-0018-2015-fig1.gif
Image of FIGURE 1

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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 ( 8 ).

Source: microbiolspec May 2016 vol. 4 no. 3 doi:10.1128/microbiolspec.PoH-0018-2015
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