1887
No metrics data to plot.
The attempt to load metrics for this article has failed.
The attempt to plot a graph for these metrics has failed.

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

MyBook is a cheap paperback edition of the original book and will be sold at uniform, low price.
  • PDF
    577.42 Kb
  • HTML
    42.72 Kb
  • XML
    37.26 Kb
  • Authors: Laurent Abi-Rached1, Didier Raoult2
  • Editors: Michel Drancourt3, Didier Raoult4
  • VIEW AFFILIATIONS HIDE AFFILIATIONS
    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]
image of Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution
    Preview this microbiology spectrum article:
    Preview Magnify
    Zoom in
    Zoomout

    Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution, Page 1 of 2

    | /docserver/preview/fulltext/microbiolspec/4/3/PoH-0018-2015-1.gif /docserver/preview/fulltext/microbiolspec/4/3/PoH-0018-2015-2.gif

  • 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.

References

1. Rasmussen M, Li Y, Lindgreen S, Pedersen JS, Albrechtsen A, Moltke I, Metspalu M, Metspalu E, Kivisild T, Gupta R, Bertalan M, Nielsen K, Gilbert MT, Wang Y, Raghavan M, Campos PF, Kamp HM, Wilson AS, Gledhill A, Tridico S, Bunce M, Lorenzen ED, Binladen J, Guo X, Zhao J, Zhang X, Zhang H, Li Z, Chen M, Orlando L, Kristiansen K, Bak M, Tommerup N, Bendixen C, Pierre TL, Gronnow B, Meldgaard M, Andreasen C, Fedorova SA, Osipova LP, Higham TF, Ramsey CB, Hansen TV, Nielsen FC, Crawford MH, Brunak S, Sicheritz-Ponten T, Villems R, Nielsen R, Krogh A, Wang J, Willerslev E. 2010. Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature 463:757–762. [PubMed][CrossRef]
2. Green RE, Krause J, Briggs AW, Maricic T, Stenzel U, Kricher M, Patterson N, Heng L, Zhai W, Fritz MH, Hansen NF, Durand EY, Malaspinas A, Jensen JD, Marques-Bonet T, Alkan C, Prüger K, Meyer M, Burbano HA, Good JM, Schultz R, Aximu-Petri A, Butthof A, Höber B, Höffner B, Siegemund M, Weihmann A, Nusbaum C, Lander ES, Russ C, Novod N, Affourtit J, Egholm M, Verna C, Rudan P, Brajkovic D, Kucan Z, Gusic I, Doronichev VB, Golovanova LV, Lalueza-Fox C, Rasilla M, Fortea J, Rosas A, Schmitz RW, Johnson PLF, Eichler EE, Falush D, Birney E, Mullikin JC, Slatkin M, Nielsen R, Kelso J, Lachmann M, Reich D, Pääbo S. 2010. A draft sequence of the Neandertal genome. Science 328:710–722. [PubMed][CrossRef]
3. Reich D, Green RE, Kircher M, Krause J, Patterson N, Durand EY, Viola B, Briggs AW, Stenzel U, Johnson PLF, Maricic T, Good JM, Marques-Bonet T, Alkan C, Fu Q, Mallick S, Li H, Meyer M, Eichler EE, Stoneking M, Richards M, Talamo S, Shunkov MV, Derevianko AP, Hublin J, Kelso J, Slatkin M, Pääbo S. 2010. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468:1053–1060. [PubMed][CrossRef]
4. Krause J, Fu Q, Good JM, Viola B, Shunkov MV, Derevianko AP, Pääbo S. 2010. The complete mitochondrial DNA genome of an unknown hominin from southern Siberia. Nature 464:894–897. [PubMed][CrossRef]
5. Chuong EB. 2013. Retroviruses facilitate the rapid evolution of the mammalian placenta. Bioessays 35:853–861. [PubMed][CrossRef]
6. Lee A, Huntley D, Aiewsakun P, Kanda RK, Lynn C, Tristem M. 2014. Novel Denisovan and Neanderthal retroviruses. J Virol 88:12907–12909. [PubMed][CrossRef]
7. Meyer M, Kircher M, Gansauge MT, Li H, Racimo F, Mallick S, Schraiber JG, Jay F, Prüfer K, de Filippo C, Sudmant PH, Alkan C, Fu Q, Do R, Rohland N, Tandon A, Siebauer M, Green RE, Bryc K, Briggs AW, Stenzel U, Dabney J, Shendure J, Kitzman J, Hammer MF, Shunkov MV, Derevianko AP, Patterson N, Andrés AM, Eichler EE, Slatkin M, Reich D, Kelso J, Pääbo S. 2012. A high-coverage genome sequence from an archaic Denisovan individual. Science 338:222–226. [PubMed][CrossRef]
8. Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellman I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. 2014. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505:43–49. [PubMed][CrossRef]
9. Callaway E. 2015. Neanderthals had outsize effect on human biology. Nature 523:512–513. [PubMed][CrossRef]
10. Birney E, Pritchard JK. 2014. Archaic humans four makes a party. Nature 505:32–34. [PubMed][CrossRef]
11. Sankararaman, S. Mallick S, Dannemann M, Prüfer K, Kelso J, Pääbo S, Patterson N, Reich D. 2014. The genomic landscape of Neanderthal ancestry in present-day humans. Nature 507:354–357. [PubMed][CrossRef]
12. Abi-Rached L, Jobin MJ, Kulkarni S, McWhinnie A, Dalva K, Gragert L, Babrzadeh F, Gharizadeh B, Luo M, Plummer FA, Kimani J, Carrington M, Middleton D, Rajalingam R, Beksac M, Marsh SG, Maiers M, Guethlein LA, Tavoularis S, Little AM, Green RE, Norman PJ, Parham P. 2011. The shaping of modern human immune systems by multiregional admixture with archaic humans. Science 334:89–94. [PubMed][CrossRef]
13. Dannemann M, Andres AM, Kelso J. 2016. Introgression of Neandertal- and Denisovan-like haplotypes contributes to adaptive variation in human Toll-like receptors. Am J Hum Genet 98:22–33. [PubMed][CrossRef]
14. Asara JM, Schweitzer MH, Freimark LM, Phillips M, Cantley LC. 2007. Protein sequences from mastodon and Tyrannosaurus rex revealed by mass spectrometry. Science 316:280–285. [PubMed][CrossRef]
15. Schweitzer MH, Zheng W, Organ CL, Avci R, Suo Z, Freimark LM, Lebleu VS, Duncan MB, Vander Heiden MG, Neveu JM, Lane WS, Cottrell JS, Horner JR, Cantley LC, Kalluri R, Asara JM. 2009. Biomolecular characterization and protein sequences of the Campanian hadrosaur B. canadensis. Science 324:626–631. [PubMed][CrossRef]
16. Corthals A, Koller A, Martin DW, Rieger R, Chen EI, Bernaski M, Recagno G, Dávalos LM. 2012. Detecting the immune system response of a 500 year-old Inca mummy. PLoS ONE 7:e41244. doi:10.1371/journal.pone.0041244. [PubMed][CrossRef]
17. Kolman CJ, Centurion-Lara A, Lukehart SA, Owsley DW, Tuross N. 1999. Identification of Treponema pallidum subspecies pallidum in a 200-year-old skeletal specimen. J Infect Dis 180:2060–2063. [PubMed][CrossRef]
18. Norman PJ, Hollenbach JA, Nemat-Gorgani N, Guethlein LA, Hilton HG, Pando MJ, Koram KA, Riley EM, Abi-Rached L, Parham P. 2013. Co-evolution of human leukocyte antigen (HLA) class I ligands with killer-cell immunoglobulin-like receptors (KIR) in a genetically diverse population of sub-Saharan Africans. PLoS Genet 9:e1003938. doi:10.1371/journal.pgen.1003938. [CrossRef]
19. Campos-Lima PO, Gavioli R, Zhang QJ, Wallace LE, Dolcetti R, Rowe M, Rickinson AB, Masucci MG. 1993. HLA-A11 epitope loss isolates of Epstein-Barr virus from a highly A11+ population. Science 260:98–100. [PubMed][CrossRef]
20. Allers K, Schneider T. 2015. CCR5Δ32 mutation and HIV infection: basis for curative HIV therapy. Curr Opin Virol 14:24–29. [PubMed][CrossRef]
21. Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, Gerrard B, Malasky M, Ramos MD, Morlot S, Tzetis M, Oddoux C, di Giovine FS, Nasioulas G, Chandler D, Aseev M, Hanson M, Kalaydjieva L, Glavac D, Gasparini P, Kanavakis E, Claustres M, Kambouris M,Ostrer H, Duff G, Baranov V, Sibul H, Metspalu A, Goldman D, Martin N, Duffy D, Schmidtke J, Estivill X, O’Brien SJ, Dean M. 1998. Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes. Am J Hum Genet 62:1507–1515. [PubMed][CrossRef]
22. Hummel S, Schmidt D, Kremeyer B, Herrmann B, Oppermann M. 2005. Detection of the CCR5-Delta32 HIV resistance gene in Bronze Age skeletons. Genes Immun 6:371–374. [PubMed][CrossRef]
23. Lucotte G. 2002. Frequencies of 32 base pair deletion of the (Delta 32) allele of the CCR5 HIV-1 co-receptor gene in Caucasians: a comparative analysis. Infect Genet Evol 1:201–205. [PubMed][CrossRef]
24. Signoli M. 2012. Reflections on crisis burials related to past plague epidemics. Clin Microbiol Infect 18218–223. [CrossRef]
25. Mecsas J, Franklin G, Kuziel WA, Brubaker RR, Falkow S, Mosier DE. 2004. Evolutionary genetics: CCR5 mutation and plague protection. Nature 427:606. [PubMed][CrossRef]
26. Elvin SJ, Elvin SJ, Williamson ED, Scott JC, Smith JN, Pérez De Lema G, Chilla S, Clapham P, Pfeffer K, Schlöndorff D, Luckow B. 2004. Evolutionary genetics: ambiguous role of CCR5 in Y. pestis infection. Nature 430:417. [PubMed][CrossRef]
27. Styer KL, Click EM, Hopkins GW, Frothingham R, Aballay A. 2007. Study of the role of CCR5 in a mouse model of intranasal challenge with Yersinia pestis. Microbes Infect 9:1135–1138. [PubMed][CrossRef]
28. Galvani AP, Slatkin M. 2003. Evaluating plague and smallpox as historical selective pressures for the CCR5-Delta 32 HIV-resistance allele. Proc Natl Acad Sci U S A 100:15276–15279. [PubMed][CrossRef]
Loading

Article metrics loading...

/content/journal/microbiolspec/10.1128/microbiolspec.PoH-0018-2015
2016-05-20
2020-05-25

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.

Highlighted Text: Show | Hide
Loading full text...

Full text loading...

/deliver/fulltext/microbiolspec/4/3/PoH-0018-2015.html?itemId=/content/journal/microbiolspec/10.1128/microbiolspec.PoH-0018-2015&mimeType=html&fmt=ahah

Figures

Paleogenetics and Past Infections: the Two Faces of the Coin of Human Immune Evolution
[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/microbiolspec/10.1128/microbiolspec.PoH-0018-2015-1,webId=/content/author/microbiolspec/10.1128/microbiolspec.PoH-0018-2015-1,properties={foaf_givenname=Laurent, foaf_name=Laurent Abi-Rached, foaf_surname=Abi-Rached, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/microbiolspec/10.1128/microbiolspec.PoH-0018-2015-aff1]]}], com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/author/microbiolspec/10.1128/microbiolspec.PoH-0018-2015-2,webId=/content/author/microbiolspec/10.1128/microbiolspec.PoH-0018-2015-2,properties={foaf_givenname=Didier, foaf_name=Didier Raoult, foaf_surname=Raoult, pub_isAffiliatedWith=[com.pub2web.rdf.cci.facet.ContentItem[id=http://asm.metastore.ingenta.com/content/affiliation/microbiolspec/10.1128/microbiolspec.PoH-0018-2015-aff2]]}]]
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

Click to view

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
Permissions and Reprints Request Permissions
Download as Powerpoint

Supplemental Material

No supplementary material available for this content.

Back to top
This is a required field
Please enter a valid email address
Please check the format of the address you have entered.
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error