Recent Acquisition of by Baka Pygmies
Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors.
Vyšlo v časopise:
Recent Acquisition of by Baka Pygmies. PLoS Genet 9(9): e32767. doi:10.1371/journal.pgen.1003775
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pgen.1003775
Souhrn
Both anatomically modern humans and the gastric pathogen Helicobacter pylori originated in Africa, and both species have been associated for at least 100,000 years. Seven geographically distinct H. pylori populations exist, three of which are indigenous to Africa: hpAfrica1, hpAfrica2, and hpNEAfrica. The oldest and most divergent population, hpAfrica2, evolved within San hunter-gatherers, who represent one of the deepest branches of the human population tree. Anticipating the presence of ancient H. pylori lineages within all hunter-gatherer populations, we investigated the prevalence and population structure of H. pylori within Baka Pygmies in Cameroon. Gastric biopsies were obtained by esophagogastroduodenoscopy from 77 Baka from two geographically separated populations, and from 101 non-Baka individuals from neighboring agriculturalist populations, and subsequently cultured for H. pylori. Unexpectedly, Baka Pygmies showed a significantly lower H. pylori infection rate (20.8%) than non-Baka (80.2%). We generated multilocus haplotypes for each H. pylori isolate by DNA sequencing, but were not able to identify Baka-specific lineages, and most isolates in our sample were assigned to hpNEAfrica or hpAfrica1. The population hpNEAfrica, a marker for the expansion of the Nilo-Saharan language family, was divided into East African and Central West African subpopulations. Similarly, a new hpAfrica1 subpopulation, identified mainly among Cameroonians, supports eastern and western expansions of Bantu languages. An age-structured transmission model shows that the low H. pylori prevalence among Baka Pygmies is achievable within the timeframe of a few hundred years and suggests that demographic factors such as small population size and unusually low life expectancy can lead to the eradication of H. pylori from individual human populations. The Baka were thus either H. pylori-free or lost their ancient lineages during past demographic fluctuations. Using coalescent simulations and phylogenetic inference, we show that Baka almost certainly acquired their extant H. pylori through secondary contact with their agriculturalist neighbors.
Zdroje
1. KustersJG, van VlietAH, KuipersEJ (2006) Pathogenesis of Helicobacter pylori infection. Clin Microbiol Rev 19: 449–490.
2. SchwarzS, MorelliG, KusecekB, ManicaA, BallouxF, et al. (2008) Horizontal versus familial transmission of Helicobacter pylori. PLoS Pathog 4: e1000180.
3. Magalhaes QueirozDM, LuzzaF (2006) Epidemiology of Helicobacter pylori infection. Helicobacter 11 Suppl 1: 1–5.
4. MoodleyY, LinzB, BondRP, NieuwoudtM, SoodyallH, et al. (2012) Age of the association between Helicobacter pylori and man. PLoS Pathog 8: e1002693.
5. NdipRN, Malange TakangAE, OjongokpokoJE, LumaHN, MalongueA, et al. (2008) Helicobacter pylori isolates recovered from gastric biopsies of patients with gastro-duodenal pathologies in Cameroon: current status of antibiogram. Trop Med Int Health 13: 848–854.
6. GuissetM, CotonT, ReyP, DebonneJM (1997) Helicobacter pylori infection in developing countries. Med Trop 57: 77–82.
7. FrenckRWJr, ClemensJ (2003) Helicobacter in the developing world. Microbes Infect 5: 705–713.
8. LinzB, BallouxF, MoodleyY, HuaL, ManicaA, et al. (2007) An African origin for the intimate association between humans and Helicobacter pylori. Nature 445: 915–918.
9. FalushD, WirthT, LinzB, PritchardJK, StephensM, et al. (2003) Traces of human migrations in Helicobacter pylori populations. Science 299: 1582–1585.
10. MoodleyY, LinzB, YamaokaY, WindsorHM, BreurecS, et al. (2009) The peopling of the Pacific from a bacterial perspective. Science 323: 527–530.
11. Latifi-NavidS, GhorashiSA, SiavoshiF, LinzB, MassarratS, et al. (2010) Ethnic and geographic differentiation of Helicobacter pylori within Iran. PLoS One 5: e9645.
12. WirthT, WangX, LinzB, NovickRP, LumJK, et al. (2004) Distinguishing human ethnic groups by means of sequences from Helicobacter pylori: lessons from Ladakh. Proc Natl Acad Sci U S A 101: 4746–4751.
13. TayCY, MitchellH, DongQ, GohKL, DawesIW, et al. (2009) Population structure of Helicobacter pylori among ethnic groups in Malaysia: recent acquisition of the bacterium by the Malay population. BMC Microbiol 9: 126.
14. BreurecS, GuillardB, HemS, BrisseS, DieyeFB, et al. (2011) Evolutionary history of Helicobacter pylori sequences reflect past human migrations in Southeast Asia. PLoS One 6: e22058.
15. KawaiM, FurutaY, YaharaK, TsuruT, OshimaK, et al. (2011) Evolution in an oncogenic bacterial species with extreme genome plasticity: Helicobacter pylori East Asian genomes. BMC Microbiol 11: 104.
16. DelportW, CunninghamM, OlivierB, PreisigO, van der MerweSW (2006) A population genetics pedigree perspective on the transmission of Helicobacter pylori. Genetics 174: 2107–2118.
17. BeharDM, VillemsR, SoodyallH, Blue-SmithJ, PereiraL, et al. (2008) The dawn of human matrilineal diversity. Am J Hum Genet 82: 1130–1140.
18. GonderMK, MortensenHM, ReedFA, de SousaA, TishkoffSA (2007) Whole-mtDNA genome sequence analysis of ancient African lineages. Mol Biol Evol 24: 757–768.
19. HellenthalG, AutonA, FalushD (2008) Inferring human colonization history using a copying model. PLoS Genet 4: e1000078.
20. TishkoffSA, ReedFA, FriedlaenderFR, EhretC, RanciaroA, et al. (2009) The genetic structure and history of Africans and African Americans. Science 324: 1035–1044.
21. ZhivotovskyLA, RosenbergNA, FeldmanMW (2003) Features of evolution and expansion of modern humans, inferred from genomewide microsatellite markers. Am J Hum Genet 72: 1171–1186.
22. SchusterSC, MillerW, RatanA, TomshoLP, GiardineB, et al. (2010) Complete Khoisan and Bantu genomes from southern Africa. Nature 463: 943–947.
23. JakobssonM, ScholzSW, ScheetP, GibbsJR, VanLiereJM, et al. (2008) Genotype, haplotype and copy-number variation in worldwide human populations. Nature 451: 998–1003.
24. LiJZ, AbsherDM, TangH, SouthwickAM, CastoAM, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319: 1100–1104.
25. PatinE, LavalG, BarreiroLB, SalasA, SeminoO, et al. (2009) Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set. PLoS Genet 5: e1000448.
26. Quintana-MurciL, QuachH, HarmantC, LucaF, MassonnetB, et al. (2008) Maternal traces of deep common ancestry and asymmetric gene flow between Pygmy hunter-gatherers and Bantu-speaking farmers. Proc Natl Acad Sci U S A 105: 1596–1601.
27. SchlebuschCM, LombardM, SoodyallH (2013) MtDNA control region variation affirms diversity and deep sub-structure in populations from southern Africa. BMC Evol Biol 13: 56.
28. DrakeNA, BlenchRM, ArmitageSJ, BristowCS, WhiteKH (2011) Ancient watercourses and biogeography of the Sahara explain the peopling of the desert. Proc Natl Acad Sci U S A 108: 458–462.
29. Phillipson DW (2005) African Archeology. Cambridge: Cambridge University Press. 389 p.
30. Newman JL (1995) The Peopling of Africa: A Geographic Interpretation. New Haven: Yale University Press. 235 p.
31. PakendorfB, BostoenK, de FilippoC (2011) Molecular perspectives on the Bantu expansion: a synthesis. Language Dynam Change 1: 50–88.
32. EhretC (2001) Bantu expansions: re-envisioning a central problem of early African history. Int J Afr Hist Stud 34: 5–41.
33. MontanoV, FerriG, MarcariV, BatiniC, AnyaeleO, et al. (2011) The Bantu expansion revisited: a new analysis of Y chromosome variation in Central Western Africa. Mol Ecol 20: 2693–2708.
34. SchoenbrunD (2001) Representing the Bantu Expansions: What's at Stake? Int J Afr Hist Stud 34: 1–4.
35. Bahuchet S (2011) Languages of African rainforest « pygmy » hunter-gatherers: language shifts without cultural admixture. In: Guldemann T, McConvell P, Rhodes R, editors. Historical linguistics and hunter-gatherers populations in global perspective. Available: http://hal.archives-ouvertes.fr/docs/00/54/82/07/PDF/Bahuchet_2006-Leipzig_Version1.pdf Accessed July 19, 2013.
36. PalmerDD, WatsonKR, AllenMJ (1994) Helicobacter pylori infection and peptic ulcer disease in Cameroon, West Africa. J Clin Gastroenterol 18: 162–164.
37. NdipRN, MalangeAE, AkoachereJF, MacKayWG, TitanjiVP, et al. (2004) Helicobacter pylori antigens in the faeces of asymptomatic children in the Buea and Limbe health districts of Cameroon: a pilot study. Trop Med Int Health 9: 1036–1040.
38. AchtmanM, AzumaT, BergDE, ItoY, MorelliG, et al. (1999) Recombination and clonal groupings within Helicobacter pylori from different geographic regions. Mol Microbiol 32: 459–470.
39. FalushD, StephensM, PritchardJK (2003) Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Genetics 164: 1567–1587.
40. NaduvilezhathL, RoseLE, MetzlerD (2011) Jaatha: a fast composite-likelihood approach to estimate demographic parameters. Mol Ecol 20: 2709–2723.
41. RupnowMF, ShachterRD, OwensDK, ParsonnetJ (2000) A dynamic transmission model for predicting trends in Helicobacter pylori and associated diseases in the United States. Emerg Infect Dis 6: 228–237.
42. PounderRE, NgD (1995) The prevalence of Helicobacter pylori infection in different countries. Aliment Pharmacol Ther 9 Suppl 2: 33–39.
43. ChenY, SegersS, BlaserMJ (2013) Association between Helicobacter pylori and mortality in the NHANES III study. Gut 62: 1262–9 doi:10.1136/gutjnl-2012-303018
44. RupnowMF, ShachterRD, OwensDK, ParsonnetJ (2001) Quantifying the population impact of a prophylactic Helicobacter pylori vaccine. Vaccine 20: 879–885.
45. RupnowMF, ChangAH, ShachterRD, OwensDK, ParsonnetJ (2009) Cost-effectiveness of a potential prophylactic Helicobacter pylori vaccine in the United States. J Infect Dis 200: 1311–1317.
46. Ndameu B (2003) Case Study 7: Cameroon - Boumba Bek - Protected areas and indigenous peoples: The paradox of conservation and survival of the Baka in Moloundou region (south-east Cameroon). In: Nelson J, Hossack L, editors. Indigenous Peoples and Protected Areas in Africa: From Principles to Practice. Moreton-in-Marsh: Forest Peoples Programme. pp. 215–241.
47. BatiniC, LopesJ, BeharDM, CalafellF, JordeLB, et al. (2011) Insights into the demographic history of African Pygmies from complete mitochondrial genomes. Mol Biol Evol 28: 1099–1110.
48. Dornan S (1925) Pygmies & Bushmen of the Kalahari. London: C. Struik. 318 p.
49. ExcoffierL, SchneiderS (1999) Why hunter-gatherer populations do not show signs of pleistocene demographic expansions. Proc Natl Acad Sci U S A 96: 10597–10602.
50. HamiltonMJ, MilneBT, WalkerRS, BurgerO, BrownJH (2007) The complex structure of hunter-gatherer social networks. Proc Biol Sci 274: 2195–2202.
51. Trevilla L (2009) Ethnologue: Languages of the World. Dallas: SIL International. 1248 p.
52. MiglianoAB, ViniciusL, LahrMM (2007) Life history trade-offs explain the evolution of human pygmies. Proc Natl Acad Sci U S A 104: 20216–20219.
53. KueteV (2010) Potential of Cameroonian plants and derived products against microbial infections: a review. Planta Med 76: 1479–1491.
54. BrusottiG, CesariI, FrassaG, GrisoliP, DacarroC, et al. (2011) Antimicrobial properties of stem bark extracts from Phyllanthus muellerianus (Kuntze) Excell. J Ethnopharmacol 135: 797–800.
55. AssobJC, KamgaHL, NsaghaDS, NjundaAL, NdePF, et al. (2011) Antimicrobial and toxicological activities of five medicinal plant species from Cameroon traditional medicine. BMC Complement Altern Med 11: 70.
56. GrahamDY, YamaokaY, MalatyHM (2007) Thoughts about populations with unexpected low prevalences of Helicobacter pylori infection. Trans R Soc Trop Med Hyg 101: 849–851.
57. FaragTH, StoltzfusRJ, KhalfanSS, TielschJM (2007) Unexpectedly low prevalence of Helicobacter pylori infection among pregnant women on Pemba Island, Zanzibar. Trans R Soc Trop Med Hyg 101: 915–922.
58. LibradoP, RozasJ (2009) DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25: 1451–1452.
59. HudsonRR, BoosDD, KaplanNL (1992) A statistical test for detecting geographic subdivision. Mol Biol Evol 9: 138–151.
60. RosenbergNA (2004) DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4: 137–138.
61. DidelotX, FalushD (2007) Inference of bacterial microevolution using multilocus sequence data. Genetics 175: 1251–1266.
62. JobbG, von HaeselerA, StrimmerK (2004) TREEFINDER: a powerful graphical analysis environment for molecular phylogenetics. BMC Evol Biol 4: 18.
63. HudsonRR (2002) Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 18: 337–338.
64. MorelliG, DidelotX, KusecekB, SchwarzS, BahlawaneC, et al. (2010) Microevolution of Helicobacter pylori during prolonged infection of single hosts and within families. PLoS Genet 6: e1001036.
65. BeckerNS, VerduP, HewlettB, PavardS (2010) Can life history trade-offs explain the evolution of short stature in human pygmies? A response to Migliano et al. (2007). Hum Biol 82: 17–27.
66. JolleyKA, MaidenMC (2010) BIGSdb: Scalable analysis of bacterial genome variation at the population level. BMC Bioinformatics 11: 595.
67. CampbellMC, TishkoffSA (2010) The evolution of human genetic and phenotypic variation in Africa. Curr Biol 20: R166–R173.
Štítky
Genetika Reprodukčná medicínaČlánok vyšiel v časopise
PLOS Genetics
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