Adaptation to infectious disease exposure in indigenous Southern African populations

Proceedings of the Royal Society B: Biological Sciences

Volumn 284, Issue 1852, 2017, Pages

  Owers, Katharine A ^a,b   Sjödin, Per ^a   Schlebusch, Carina M ^a   Skoglund, Pontus ^a   Soodyall, Himla ^c   Jakobsson, Mattias ^a,d  

^a UPPSALA UNIVERSITY   (Sweden)

^b YALE UNIVERSITY   (United States)

^c UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^d UPPSALA UNIVERSITY   (Sweden)

Author keywords

Adaptation; Human migrations; Immune genes; Introduced diseases; Population genetics

Indexed keywords

ADAPTATION; DISEASE INCIDENCE; EVOLUTIONARY BIOLOGY; GENE; GENE EXPRESSION; GENETIC ANALYSIS; GENOME; GENOMICS; IMMIGRANT POPULATION; INFECTIOUS DISEASE; MIGRATORY POPULATION; POPULATION GENETICS; SELECTION;

SOUTH AFRICA;

ADAPTATION; BLACK PERSON; COMMUNICABLE DISEASE; ENVIRONMENTAL EXPOSURE; ETHNIC GROUP; GENETIC SELECTION; GENETICS; GENOMICS; HUMAN; IMMUNITY; POPULATION GENETICS; SOUTH AFRICA;

ADAPTATION, PHYSIOLOGICAL; AFRICAN CONTINENTAL ANCESTRY GROUP; COMMUNICABLE DISEASES; ENVIRONMENTAL EXPOSURE; ETHNIC GROUPS; GENETICS, POPULATION; GENOMICS; HUMANS; IMMUNITY; SELECTION, GENETIC; SOUTH AFRICA;

EID: 85017269175     PISSN: 09628452     EISSN: 14712954     Source Type: Journal    
DOI: 10.1098/rspb.2017.0226     Document Type: Article

References (44)

1. Dobyns HF. 1993 Disease transfer at contact. Annu. Rev. Anthropol. 22, 273–291. (doi:10.1146/annurev.an.22.100193.001421)
2. Crosby AW. 1976 Virgin soil epidemics as a factor in the aboriginal depopulation in America. William Mary Q. 33, 289–299. (doi:10.2307/1922166)
3. Breton G, Schlebusch CM, Lombard M, Sjödin P, Soodyall H, Jakobsson M. 2014 Lactase persistence alleles reveal partial east African ancestry of southern African Khoe pastoralists. Curr. Biol. 24, 852–858. (doi:10.1016/j.cub.2014.02.041)
4. Macholdt E, Lede V, Barbieri C, Mpoloka SW, Chen H, Slatkin M, Pakendorf B, Stoneking M. 2014 Tracing pastoralist migrations to southern Africa with lactase persistence alleles. Curr. Biol. 24, 875–879. (doi:10.1016/j.cub.2014.03.027)
5. Pickrell JK, Patterson N, Loh P-R, Lipson M, Berger B, Stoneking M, Pakendorf B, Reich D. 2014 Ancient west Eurasian ancestry in southern and eastern Africa. Proc. Natl Acad. Sci. USA 111, 2632–2637. (doi:10.1073/pnas.1313787111)
6. Smith AB. 2008 Pastoral origins at the Cape, South Africa: influences and arguments. South Afr. Humanit. 20, 49–60.
7. Sadr K. 2015 Livestock first reached Southern Africa in two separate events. PLoS ONE 10, e0134215. (doi:10.1371/journal.pone.0134215)
8. Schlebusch CM et al. 2012 Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338, 374–379. (doi:10.1126/science.1227721)
9. Li S, Schlebusch C, Jakobsson M. 2014 Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples. Proc. R. Soc. B 281, 20141448. (doi:10.1098/rspb. 2014.1448)
10. Phillipson DW. 2005 African archaeology. Cambridge, UK: Cambridge University Press.
11. Coelho M, Sequeira F, Luiselli D, Beleza S, Rocha J. 2009 On the edge of Bantu expansions: mtDNA, Y chromosome and lactase persistence genetic variation in southwestern Angola. BMC Evol. Biol. 9, 80. (doi:10.1186/1471-2148-9-80)
12. Nurse GT, Weiner JS, Jenkins T. 1986 The peoples of Southern Africa and their affinities. New York, NY: Oxford University Press.
13. Sabeti PC et al. 2006 Positive natural selection in the human lineage. Science 312, 1614–1620. (doi:10.1126/science.1124309)
14. Voight BF, Kudaravalli S, Wen X, Pritchard JK. 2006 A map of recent positive selection in the human genome. PLoS Biol. 4, 0446–0458. (doi:10.1371/journal.pbio.0040446)
15. Sabeti PC et al. 2007 Genome-wide detection and characterization of positive selection in human populations. Nature 449, 913–918. (doi:10.1038/nature06250)
16. Yi X et al. 2010 Sequencing of 50 human exomes reveals adaptation to high altitude. Science 329, 75–78. (doi:10.1126/science.1190371)
17. Gronau I, Hubisz MJ, Gulko B, Danko CG, Siepel A. 2011 Bayesian inference of ancient human demography from individual genome sequences. Nat. Genet. 43, 1031–1034. (doi:10. 1038/ng.937)
18. Veeramah KR, Wegmann D, Woerner A, Mendez FL, Watkins JC, Destro-Bisol G, Soodyall H, Louie L, Hammer MF. 2012 An early divergence of KhoeSan ancestors from those of other modern humans is supported by an ABC-based analysis of autosomal resequencing data. Mol. Biol. Evol. 29, 617–630. (doi:10.1093/molbev/msr212)
19. Pickrell JK et al. 2009 Signals of recent positive selection in a worldwide sample of human populations. Genome Res. 19, 826–837. (doi:10. 1101/gr.087577.108)
20. Barnard A. 1992 Hunters and herders of Southern Africa - a comparative ethnography of the Khoisan peoples. Cambridge, UK: Cambridge University Press.
21. Teshima KM, Coop G, Przeworski M. 2006 How reliable are empirical genomic scans for selective sweeps? Genome Res. 16, 702–712. (doi:10.1101/gr.5105206)
22. de Bakker PIW et al. 2006 A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat. Genet. 38, 1166–1172. (doi:10.1038/ng1885)
23. Guernier V, Hochberg ME, Guégan JF. 2004 Ecology drives the worldwide distribution of human diseases. PLoS Biol. 2, e141. (doi:10.1371/journal.pbio.0020141)
24. + thymocytes. Eur. J. Immunol. 39, 956–964. (doi:10.1002/eji.200839175)
25. Abeler-Dörner L, Swamy M, Williams G, Hayday AC, Bas A. 2012 Butyrophilins: an emerging family of immune regulators. Trends Immunol. 33, 34–41. (doi:10.1016/j.it.2011.09.007)
26. Dement-Brown J, Newton CS, Ise T, Damdinsuren B, Nagata S, Tolnay M. 2012 Fc receptor-like 5 promotes B cell proliferation and drives the development of cells displaying switched isotypes. J. Leukoc. Biol. 91, 59–67. (doi:10.1189/jlb. 0211096)
27. Kaiser L, Fritz RS, Straus SE, Gubareva L, Hayden FG. 2001 Symptom pathogenesis during acute influenza: Interleukin-6 and other cytokine responses. J. Med. Virol. 64, 262–268. (doi:10. 1002/jmv.1045)
28. Cheung CY, Poon LLM, Lau AS, Luk W, Lau YL, Shortridge KF, Gordon S, Guan Y, Peiris JSM. 2002 Induction of proinflammatory cytokines in human macrophages by influenza A (H5N1) viruses: a mechanism for the unusual severity of human disease? Lancet. 360, 1831–1837. (doi:10.1016/S0140-6736(02)11772-7)
29. Huang KJ, Su IJ, Theron M, Wu YC, Lai SK, Liu CC, Lei HY. 2005 An interferon-gamma-related cytokine storm in SARS patients. J. Med. Virol. 75, 185–194. (doi:10.1002/jmv.20255)
30. Stanford MM, McFadden G, Karupiah G, Chaudhri G. 2007 Immunopathogenesis of poxvirus infections: forecasting the impending storm. Immunol. Cell Biol. 85, 93–102. (doi:10.1038/sj.icb.7100033)
31. Bowie A, Kiss-Toth E, Symons JA, Smith GL, Dower SK, O’Neill LA. 2000 A46R and A52R from vaccinia virus are antagonists of host IL-1 and toll-like receptor signaling. Proc. Natl Acad. Sci. USA 97, 10 162–10 167. (doi:10.1073/pnas. 160027697)
32. DiPerna G et al. 2004 Poxvirus protein N1 L targets the I-kB kinase complex, inhibits signaling to NF-kB by the tumor necrosis factor superfamily of receptors, and inhibits NF-kB and IRF3 signaling by toll-like receptors. J. Biol. Chem. 279, 36 570–36 578. (doi:10.1074/jbc.M400567200)
33. Dunlop LR, Oehlberg KA, Reid JJ, Avci D, Rosengard AM. 2003 Variola virus immune evasion proteins. Microbes Infect. 5, 1049–1056. (doi:10.1016/S1286-4579(03)00194-1)
34. Seet BT et al. 2003 Poxviruses and immune evasion. Annu. Rev. Immunol. 21, 377–423. (doi:10.1146/annurev.immunol.21.120601.141049)
35. Hilton HG, Norman PJ, Nemat-Gorgani N, Goyos A, Hollenbach JA, Henn BM, Gignoux CR, Guethlein LA, Parham P. 2015 Loss and gain of natural killer cell receptor function in an African hunter-gatherer population. PLoS Genet. 11, e1005439. (doi:10.1371/journal.pgen.1005439)
36. Data from Schlebusch et al. 2012 See http://jakobssonlab.iob.uu.se/data/.
37. Ortutay C, Siermala M, Vihinen M. 2007 Molecular characterization of the immune system: emergence of proteins, processes, and domains. Immunogenetics 59, 333–348. (doi:10.1007/s00251-007-0191-0)
38. Immunome. 2012 See http://structure.bmc.lu.se/idbase/Immunome/index.php (accessed 15 May 2012).
39. Weir BS, Cockerham CC. 1984 Estimating F-statistics for the analysis of population structure. Evolution 38, 1358–1370 (doi:10.2307/2408641)
40. Busing F, Meijer E, Leeden R. 1999 Delete-m jackknife for unequal m. Stat. Comput. 9, 3–8. (doi:10.1023/A:1008800423698)
41. Safran M et al. 2010 GeneCards Version 3 the human gene integrator. Database 2010, baq020. (doi:10.1093/database/baq020)
42. Genecards: The Human Gene Database. 2012 See http://www.genecards.org (accessed 30 May 2012).
43. Fujita PA et al. 2011 The UCSC genome browser database: Update 2011. Nucleic Acids Res. 39(Suppl 1), 876–882. (doi:10.1093/nar/gkq963)
44. UCSC Genome Bioinformatics. 2012 See http://genome.ucsc.edu (accessed 30 May 2012).