Inferences of African evolutionary history from genomic data

Current Opinion in Genetics and Development

Volumn 41, Issue , 2016, Pages 159-166

  Beltrame, Marcia Holsbach ^a   Rubel, Meagan A ^a   Tishkoff, Sarah A ^a  

^a UNIVERSITY OF PENNSYLVANIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AFRICA; AFRICA SOUTH OF THE SAHARA; AFRICAN; CULTURAL FACTOR; DNA DETERMINATION; DNA MODIFICATION; ENVIRONMENTAL FACTOR; EVOLUTION; EVOLUTIONARY ADAPTATION; FOSSIL; GENETIC ANALYSIS; GENETIC VARIABILITY; GENOMICS; HUMAN; LINGUISTICS; METABOLOMICS; PHENOTYPE; PRIORITY JOURNAL; PROTEIN ANALYSIS; REVIEW; BLACK PERSON; GENETIC VARIATION; GENETICS; MOLECULAR EVOLUTION; PHYLOGENY; POPULATION GENETICS;

AFRICA; AFRICAN CONTINENTAL ANCESTRY GROUP; EVOLUTION, MOLECULAR; GENETIC VARIATION; GENETICS, POPULATION; GENOMICS; HUMANS; PHYLOGENY;

EID: 84994236541     PISSN: 0959437X     EISSN: 18790380     Source Type: Journal    
DOI: 10.1016/j.gde.2016.10.002     Document Type: Review

References (78)

1. 1 Reyes-Centeno, H., Out of Africa and into Asia: fossil and genetic evidence on modern human origins and dispersals [Internet]. Quat Int, 2016, 10.1016/j.quaint.2015.11.063.
2. 2 Campbell, M.C., Tishkoff, S.A., African genetic diversity: implications for human demographic history, modern human origins, and complex disease mapping. Annu Rev Genomics Hum Genet 9 (2008), 403–433.
3. 3 The 1000 Genomes Project Consortium, A global reference for human genetic variation. Nature 526 (2015), 68–74.
4. 4 Campbell, M.C., Tishkoff, S.A., The evolution of human genetic and phenotypic variation in Africa. Curr Biol 20 (2010), R166–R173.
5. 5•• Vernot, B., Akey, J.M., Resurrecting surviving Neandertal lineages from modern human genomes. Science 343 (2014), 1017–1021 In this paper authors identified Neandertal lineages that persist in the DNA of modern humans and suggested that there were fitness costs to hybridization, that admixture occurred both before and after divergence of non-African modern humans, and that Neandertals were a source of adaptive variation for loci involved in skin phenotypes.
6. 6 Kim, B.Y., Lohmueller, K.E., Selection and reduced population size cannot explain higher amounts of Neandertal ancestry in East Asian than in European human populations. Am J Hum Genet 96 (2015), 454–461.
7. 7 Vernot, B., Akey, J.M., Complex history of admixture between modern humans and Neandertals. Am J Hum Genet 96 (2015), 448–453.
8. 8 Sankararaman, S., Patterson, N., Li, H., Pääbo, S., Reich, D., The date of interbreeding between Neandertals and modern humans. PLOS Genet, 8, 2012, e1002947.
9. 9 Green, R.E., Krause, J., Briggs, A.W., Maricic, T., Stenzel, U., Kircher, M., Patterson, N., Li, H., Zhai, W., Fritz, M.H.-Y., et al. A draft sequence of the Neandertal genome. Science 328 (2010), 710–722.
10. 10 Reich, D., Green, R.E., Kircher, M., Krause, J., Patterson, N., Durand, E.Y., Viola, B., Briggs, A.W., Stenzel, U., Johnson, P.L.F., et al. Genetic history of an archaic hominin group from Denisova Cave in Siberia. Nature 468 (2010), 1053–1060.
11. 11 Clark, J.D., Beyene, Y., WoldeGabriel, G., Hart, W.K., Renne, P.R., Gilbert, H., Defleur, A., Suwa, G., Katoh, S., Ludwig, K.R., et al. Stratigraphic, chronological and behavioural contexts of Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature 423 (2003), 747–752.
12. 12 White, T.D., Asfaw, B., DeGusta, D., Gilbert, H., Richards, G.D., Suwa, G., Howell, F.C., Pleistocene Homo sapiens from Middle Awash, Ethiopia. Nature 423 (2003), 742–747.
13. 13 McDougall, I., Brown, F.H., Fleagle, J.G., Stratigraphic placement and age of modern humans from Kibish, Ethiopia. Nature 433 (2005), 733–736.
14. 14 Rightmire, G.P., Out of Africa: modern human origins special feature: middle and later Pleistocene hominins in Africa and Southwest Asia. Proc Natl Acad Sci U S A 106 (2009), 16046–16050.
15. 15 Harvati, K., Stringer, C., Grün, R., Aubert, M., Allsworth-Jones, P., Folorunso, C.A., The Later Stone Age Calvaria from Iwo Eleru, Nigeria: morphology and chronology. PLoS One, 6, 2011, e24024.
16. 16 Bräuer, G., The origin of modern anatomy: by speciation or intraspecific evolution?. Evol Anthropol Issues News Rev 17 (2008), 22–37.
17. 17 Plagnol, V., Wall, J.D., Possible ancestral structure in human populations. PLoS Genet, 2, 2006, e105.
18. 18 Wall, J.D., Lohmueller, K.E., Plagnol, V., Detecting ancient admixture and estimating demographic parameters in multiple human populations. Mol Biol Evol 26 (2009), 1823–1827.
19. 19 Hammer, M.F., Woerner, A.E., Mendez, F.L., Watkins, J.C., Wall, J.D., Genetic evidence for archaic admixture in Africa. Proc Natl Acad Sci U S A 108 (2011), 15123–15128.
20. 20 Lachance, J., Vernot, B., Elbers, C.C., Ferwerda, B., Froment, A., Bodo, J.-M., Lema, G., Fu, W., Nyambo, T.B., Rebbeck, T.R., et al. Evolutionary history and adaptation from high-coverage whole-genome sequences of diverse African hunter-gatherers. Cell 150 (2012), 457–469.
21. 21 Stringer, C., Harvati, K., Allsworth-Jones, P., Grün, R., Folorunso, C., New research on the Iwo Eleru cranium from Nigeria. Am J Phys Anthr, S50, 2010, 292.
22. 22 Wall, J.D., Yang, M.A., Jay, F., Kim, S.K., Durand, E.Y., Stevison, L.S., Gignoux, C., Woerner, A., Hammer, M.F., Slatkin, M., Higher levels of Neanderthal ancestry in East Asians than in Europeans. Genetics 194 (2013), 199–209.
23. 23• Hsieh, P., Woerner, A.E., Wall, J.D., Lachance, J., Tishkoff, S.A., Gutenkunst, R.N., Hammer, M.F., Model-based analyses of whole-genome data reveal a complex evolutionary history involving archaic introgression in Central African Pygmies [Internet]. Genome Res, 2016, 10.1101/gr.196634.115 Using inference methods, the authors rejected the hypothesis that the ancestors of AMH were genetically isolated in Africa and provided evidence or archaic admixture.
24. 24 Llorente, M.G., Jones, E.R., Eriksson, A., Siska, V., Arthur, K.W., Arthur, J.W., Curtis, M.C., Stock, J.T., Coltorti, M., Pieruccini, P., et al. Ancient Ethiopian genome reveals extensive Eurasian admixture in Eastern Africa. Science 350 (2015), 820–822.
25. 25 Mathieson, I., Lazaridis, I., Rohland, N., Mallick, S., Patterson, N., Roodenberg, S.A., Harney, E., Stewardson, K., Fernandes, D., Novak, M., et al. Genome-wide patterns of selection in 230 ancient Eurasians. Nature 528 (2015), 499–503.
26. 26 Tishkoff, S.A., Reed, F.A., Friedlaender, F.R., Ehret, C., Ranciaro, A., Froment, A., Hirbo, J.B., Awomoyi, A.A., Bodo, J.-M., Doumbo, O., et al. The genetic structure and history of Africans and African Americans. Science 324 (2009), 1035–1044.
27. 27 Gibbs, R.A., Belmont, J.W., Hardenbol, P., Willis, T.D., Yu, F., Yang, H., Ch'ang, L.-Y., Huang, W., Liu, B., Shen, Y., et al. The International HapMap Project. Nature 426 (2003), 789–796.
28. 28 Cann, H.M., Toma, C. de, Cazes, L., Legrand, M.-F., Morel, V., Piouffre, L., Bodmer, J., Bodmer, W.F., Bonne-Tamir, B., Cambon-Thomsen, A., et al. A human genome diversity cell line panel. Science 296 (2002), 261–262.
29. 29 Gurdasani, D., Carstensen, T., Tekola-Ayele, F., Pagani, L., Tachmazidou, I., Hatzikotoulas, K., Karthikeyan, S., Iles, L., Pollard, M.O., Choudhury, A., et al. The African Genome Variation Project shapes medical genetics in Africa. Nature 517 (2015), 327–332.
30. 30 Hirbo, J., Ranciaro, A., Tishkoff, S., Population structure and migration in Africa: correlations between archeological, linguistic, and genetic data. Campbell, B., Crawford, M.H., (eds.) Causes and Consequences of Migration, 2012, Cambridge University Press.
31. 31 Bryc, K., Auton, A., Nelson, M.R., Oksenberg, J.R., Hauser, S.L., Williams, S., Froment, A., Bodo, J.-M., Wambebe, C., Tishkoff, S.A., et al. Genome-wide patterns of population structure and admixture in West Africans and African Americans. Proc Natl Acad Sci U S A 107 (2010), 786–791.
32. 32• Busby, G., Band, G., Si Le, Q., Jallow, M., Bougama, E., Mangano, V., Amenga-Etego, L., Emil, A., Apinjoh, T., Ndila, C., et al. Admixture into and within sub-Saharan Africa. bioRxiv, 2016, 10.1101/038406 The authors used haplotype-based population genetics inference to describe gene-flow and admixture mainly in SSA, showing haplotype sharing across different geographic groups and subtle population structure.
33. 33• Uren, C., Kim, M., Martin, A.R., Bobo, D., Gignoux, C.R., Helden, D.V., Möller, M., Hoal, E.G., Henn, B.M., Fine-scale human population structure in southern Africa reflects ecological boundaries. Genetics 204 (2016), 303–314, 10.1101/038729 This study used SNP arrays and whole mitochondrial genomes of southern African populations to examine fine-scale population structure in and around the Kalahari desert reflecting geographic barriers and ecology. This structure did not always correspond with linguistic and subsistence categories.
34. 34 Montinaro, F., Busby, G.B.J., Gonzalez-santos, M., Oosthuitzen, O., Complex ancient genetic structure and cultural transitions in southern African populations [Internet]. bioRxiv, 2016, 10.1101/043562.
35. 35 Veeramah, K.R., Wegmann, D., Woerner, A., Mendez, F.L., Watkins, J.C., Destro-Bisol, G., Soodyall, H., Louie, L., Hammer, M.F., 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 (2012), 617–630.
36. 36• Hellenthal, G., Busby, G.B.J., Band, G., Wilson, J.F., Capelli, C., Falush, D., Myers, S., A genetic atlas of human admixture history. Science 343 (2014), 747–751 This study used chromosome painting methods to trace worldwide human genetic admixture over the last 4000 years. They identify genetic admixture events that correlate with the timing of the Mongol empire, Arab slave trade, and Bantu expansion.
37. 37 Pedro Soares, Rito, T., Pereira, L., Richards, M.B., A genetic perspective on African prehistory. Africa from MIS 6-2: Population Dynamics and Paleoenvironments, Vertebrate, 2016, 383–405.
38. 38 Li, S., Schlebusch, C., Jakobsson, M., Genetic variation reveals large-scale population expansion and migration during the expansion of Bantu-speaking peoples. Proc R Soc B Biol Sci, 281, 2014, 20141448.
39. 39 Schlebusch, C.M., Skoglund, P., Sjödin, P., Gattepaille, L.M., Hernandez, D., Jay, F., Li, S., De Jongh, M., Singleton, A., Blum, M.G.B., et al. Genomic variation in seven Khoe-San groups reveals adaptation and complex African history. Science 338 (2012), 374–379.
40. 40 Veeramah, K.R., Hammer, M.F., The impact of whole-genome sequencing on the reconstruction of human population history. Nat Rev Genet 15 (2014), 149–162.
41. 41 Pickrell, J.K., Patterson, N., Barbieri, C., Berthold, F., Gerlach, L., Güldemann, T., Kure, B., Mpoloka, S.W., Nakagawa, H., Naumann, C., et al. The genetic prehistory of southern Africa. Nat Commun, 3, 2012, 1143.
42. 42 Patin, E., Laval, G., Barreiro, L.B., Salas, A., Semino, O., Santachiara-Benerecetti, S., Kidd, K.K., Kidd, J.R., Veen, L.V. der, Hombert, J.-M., et al. Inferring the demographic history of African farmers and pygmy hunter-gatherers using a multilocus resequencing data set. PLOS Genet, 5, 2009, e1000448.
43. 43 Tishkoff, S.A., Gonder, M.K., Henn, B.M., Mortensen, H., Knight, A., Gignoux, C., Fernandopulle, N., Lema, G., Nyambo, T.B., Ramakrishnan, U., et al. History of click-speaking populations of Africa inferred from mtDNA and Y chromosome genetic variation. Mol Biol Evol 24 (2007), 2180–2195.
44. 44 Scheinfeldt, L.B., Tishkoff, S.A., Recent human adaptation: genomic approaches, interpretation and insights. Nat Rev Genet 14 (2013), 692–702.
45. 45 Fan, S., Hansen, M.E.B., Lo, Y., Tishkoff, S.A., Going global by adapting local: a review of recent human adaptation. Science, 2016, 354.
46. 46 Lamason, R.L., Mohideen, M.-A.P.K., Mest, J.R., Wong, A.C., Norton, H.L., Aros, M.C., Jurynec, M.J., Mao, X., Humphreville, V.R., Humbert, J.E., et al. SLC24A5, a exchanger, affects putative cation pigmentation in zebrafish and humans. Science 310 (2005), 1782–1786.
47. 47 Campbell, M.C., Ranciaro, A., Froment, A., Hirbo, J., Omar, S., Bodo, J.-M., Nyambo, T., Lema, G., Zinshteyn, D., Drayna, D., et al. Evolution of functionally diverse alleles associated with PTC bitter taste sensitivity in Africa. Mol Biol Evol 29 (2012), 1141–1153.
48. 48 Perry, G.H., Dominy, N.J., Claw, K.G., Lee, A.S., Fiegler, H., Redon, R., Werner, J., Villanea, F.A., Mountain, J.L., Misra, R., et al. Diet and the evolution of human amylase gene copy number variation. Nat Genet 39 (2007), 1256–1260.
49. 49 Breton, G., Schlebusch, C.M., Lombard, M., Sjödin, P., Soodyall, H., Jakobsson, M., Lactase persistence alleles reveal partial East African ancestry of southern African Khoe pastoralists. Curr Biol 24 (2014), 852–858.
50. 50• Ranciaro, A., Campbell, M.C., Hirbo, J.B., Ko, W.-Y., Froment, A., Anagnostou, P., Kotze, M.J., Ibrahim, M., Nyambo, T., Omar, S.A., et al. Genetic origins of lactase persistence and the spread of Pastoralism in Africa. Am J Hum Genet 94 (2014), 496–510 Authors identified two new LP-associated SNPs and detected strong signatures of recent positive selection in eastern African populations and Fulani pastoralists from central Africa. Their results supported an eastern African origin of the C-14010 LP-associated mutation in southern Africa.
51. 51 Scheinfeldt, L.B., Soi, S., Thompson, S., Ranciaro, A., Woldemeskel, D., Beggs, W., Lambert, C., Jarvis, J.P., Abate, D., Belay, G., et al. Genetic adaptation to high altitude in the Ethiopian highlands. Genome Biol, 13, 2012, R1.
52. 52 Alkorta-Aranburu, G., Beall, C.M., Witonsky, D.B., Gebremedhin, A., Pritchard, J.K., Di Rienzo, A., The genetic architecture of adaptations to high altitude in Ethiopia [Internet]. PLoS Genet, 2012, 8.
53. 53 Jarvis, J.P., Scheinfeldt, L.B., Soi, S., Lambert, C., Omberg, L., Ferwerda, B., Froment, A., Bodo, J.-M., Beggs, W., Hoffman, G., et al. Patterns of ancestry, signatures of natural selection, and genetic association with stature in Western African pygmies. PLoS Genet, 8, 2012, e1002641.
54. 54• Perry, G.H., Foll, M., Grenier, J.-C., Patin, E., Nédélec, Y., Pacis, A., Barakatt, M., Gravel, S., Zhou, X., Nsobya, S.L., et al. Adaptive, convergent origins of the pygmy phenotype in African rainforest hunter-gatherers. Proc. Natl Acad Sci 111 (2014), E3596–E3603 This study suggested that the origin of the ‘pygmy’ phenotype in African hunter-gatherers was adaptive and at least partially convergent between geographically distant eastern and western populations, supporting the hypothesis that small body size confers a selective advantage in tropical rainforest environments.
55. 55 Genovese, G., Friedman, D.J., Ross, M.D., Lecordier, L., Uzureau, P., Freedman, B.I., Bowden, D.W., Langefeld, C.D., Oleksyk, T.K., Knob, A.L.U., et al. Association of trypanolytic ApoL1 variants with kidney disease in African Americans. Science 329 (2010), 841–845.
56. 56 Lachance, J., Disease-associated alleles in genome-wide association studies are enriched for derived low frequency alleles relative to HapMap and neutral expectations. BMC Med Genomics, 3, 2010, 57.
57. 57 Jallow, M., Teo, Y.Y., Small, K.S., Rockett, K.A., Deloukas, P., Clark, T.G., Kivinen, K., Bojang, K.A., Conway, D.J., Pinder, M., et al. Genome-wide and fine-resolution association analysis of malaria in West Africa. Nat Genet 41 (2009), 657–665.
58. 58 Timmann, C., Thye, T., Vens, M., Evans, J., May, J., Ehmen, C., Sievertsen, J., Muntau, B., Ruge, G., Loag, W., et al. Genome-wide association study indicates two novel resistance loci for severe malaria. Nature 489 (2012), 443–446.
59. 59 Tishkoff, S.A., Varkonyi, R., Cahinhinan, N., Abbes, S., Argyropoulos, G., Destro-Bisol, G., Drousiotou, A., Dangerfield, B., Lefranc, G., Loiselet, J., et al. Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293 (2001), 455–462.
60. 60 Ko, W.-Y., Kaercher, K.A., Giombini, E., Marcatili, P., Froment, A., Ibrahim, M., Lema, G., Nyambo, T.B., Omar, S.A., Wambebe, C., et al. Effects of natural selection and gene conversion on the evolution of human glycophorins coding for MNS blood polymorphisms in malaria-endemic African populations. Am J Hum Genet 88 (2011), 741–754.
61. 61 Bersaglieri, T., Sabeti, P.C., Patterson, N., Vanderploeg, T., Schaffner, S.F., Drake, J.A., Rhodes, M., Reich, D.E., Hirschhorn, J.N., Genetic signatures of strong recent positive selection at the lactase gene. Am J Hum Genet 74 (2004), 1111–1120.
62. 62 Voight, B.F., Kudaravalli, S., Wen, X., Pritchard, J.K., A map of recent positive selection in the human genome [Internet]. PLoS Biol, 2006, 4.
63. 63 Hassan, H.Y., van Erp, A., Jaeger, M., Tahir, H., Oosting, M., Joosten, L.A.B., Netea, M.G., Genetic diversity of lactase persistence in East African populations [Internet]. BMC Res Notes, 2016, 9.
64. 64•• Labrie, V., Buske, O.J., Oh, E., Jeremian, R., Ptak, C., Gasiūnas, G., Maleckas, A., Petereit, R., Žvirbliene, A., Adamonis, K., et al. Lactase nonpersistence is directed by DNA-variation-dependent epigenetic aging. Nat Struct Mol Biol 23 (2016), 566–573 The authors investigated LP phenotypes in human and mouse small intestines by using chromosome-wide DNA-modification profiling and targeted bisulfite sequencing. This research showed that genetic factors enable a gradual accumulation of epigenetic changes in the LCT regulatory region with increased age, with marked differences separating LP and Lactase Non-persistent (LNP) haplotypes. The impact of the regulatory elements was confirmed using CRISPR– Cas9-induced deletions.
65. 65 Ingram, C.J.E., Elamin, M.F., Mulcare, C.A., Weale, M.E., Tarekegn, A., Raga, T.O., Bekele, E., Elamin, F.M., Thomas, M.G., Bradman, N., et al. A novel polymorphism associated with lactose tolerance in Africa: multiple causes for lactase persistence?. Hum Genet 120 (2007), 779–788.
66. 66 Tishkoff, S.A., Reed, F.A., Ranciaro, A., Voight, B.F., Babbitt, C.C., Silverman, J.S., Powell, K., Mortensen, H.M., Hirbo, J.B., Osman, M., et al. Convergent adaptation of human lactase persistence in Africa and Europe. Nat Genet 39 (2007), 31–40.
67. 67• Macholdt, E., Slatkin, M., Pakendorf, B., Stoneking, M., New insights into the history of the C-14010 lactase persistence variant in Eastern and Southern Africa. Am J Phys Anthr 156 (2015), 661–664 Authors confirmed the hypothesis of the Eastern African origin of the LP-associated allele C-14010 in Southern African Khoisan-speaking groups.
68. 68 Migliano, A.B., Romero, I.G., Leavesley, M., Pagani, L., Evolution of the pygmy phenotype: Evidence of positive selection from genome-wide scans in African, Asian, and Melanesian pygmies. Hum Biol 85 (2013), 251–284.
69. 69 Hsieh, P., Veeramah, K.R., Lachance, J., Tishkoff, S.A., Wall, J.D., Hammer, M.F., Gutenkunst, R.N., Whole-genome sequence analyses of Western Central African Pygmy hunter-gatherers reveal a complex demographic history and identify candidate genes under positive natural selection [Internet]. Genome Res, 2016, 10.1101/gr.192971.115.
70. 70 Pickrell, J.K., Coop, G., Novembre, J., Kudaravalli, S., Li, J.Z., Absher, D., Srinivasan, B.S., Barsh, G.S., Myers, R.M., Feldman, M.W., et al. Signals of recent positive selection in a worldwide sample of human populations. Genome Res 19 (2009), 826–837.
71. 71•• Fagny, M., Patin, E., MacIsaac, J.L., Rotival, M., Flutre, T., Jones, M.J., Siddle, K.J., Quach, H., Harmant, C., McEwen, L.M., et al. The epigenomic landscape of African rainforest hunter-gatherers and farmers. Nat Commun, 6, 2015, 10047 Authors investigated DNA methylation profiles of farmers and hunter-gatherers and found that both current habitat and traditional subsistence have critical impacts on the methylome, but in different ways. Methylation variation associated with recent changes in habitat are mostly related to immune and cellular functions, whereas methylation associated with traditional subsistence affects developmental processes.
72. 72 Gopalan, S., Carja, O., Fagny, M., Patin, E., Myrick, J.W., McEwen, L., Mah, S.M., Kobor, M.S., Froment, A., Feldman, M.W., et al. Trends in DNA methylation with age replicate across diverse human populations. bioRxiv, 2016, 10.1101/073171.
73. 73 De Filippo, C., Cavalieri, D., Di Paola, M., Ramazzotti, M., Poullet, J.B., Massart, S., Collini, S., Pieraccini, G., Lionetti, P., Impact of diet in shaping gut microbiota revealed by a comparative study in children from Europe and rural Africa. Proc Natl Acad Sci U S A 107 (2010), 14691–14696.
74. 74 Yatsunenko, T., Rey, F.E., Manary, M.J., Trehan, I., Dominguez-Bello, M.G., Contreras, M., Magris, M., Hidalgo, G., Baldassano, R.N., Anokhin, A.P., et al. Human gut microbiome viewed across age and geography. Nature 486 (2012), 222–227.
75. 75• Schnorr, S.L., Candela, M., Rampelli, S., Centanni, M., Consolandi, C., Basaglia, G., Turroni, S., Biagi, E., Peano, C., Severgnini, M., et al. Gut microbiome of the Hadza hunter-gatherers [Internet]. Nat Commun, 2014, 5 The gut microbiomes of Hadza hunter-gatherers from Tanzania were compared with other rural Africans (Malawi and Burkina Faso populations) and urban Italians. The Hadza possessed more biodiverse and rich gut microbiomes than Italians, lacked Bifidobacteria (a prevalent taxa in western gut microbiomes), and were enriched with several taxa (Treponema, unclassified Bacteroidetes, and Prevotella) that may help extract nutrients from fibrous foods characteristic of a hunting and gathering lifestyle.
76. 76 Rampelli, S., Schnorr, S.L., Consolandi, C., Turroni, S., Severgnini, M., Peano, C., Brigidi, P., Crittenden, A.N., Henry, A.G., Candela, M., Metagenome sequencing of the Hadza hunter-gatherer gut microbiota. Curr Biol 25 (2015), 1682–1693.
77. 77 Morton, E.R., Lynch, J., Froment, A., Lafosse, S., Heyer, E., Przeworski, M., Blekhman, R., Ségurel, L., Variation in rural African gut microbiota is strongly correlated with colonization by entamoeba and subsistence. PLOS Genet, 11, 2015, e1005658.
78. 78• Gomez, A., Petrzelkova, K.J., Burns, M.B., Yeoman, C.J., Amato, K.R., Vlckova, K., Modry, D., Todd, A., Jost Robinson, C.A., Remis, M.J., et al. Gut microbiome of coexisting BaAka pygmies and bantu reflects gradients of traditional subsistence patterns [Internet]. Cell Rep, 2016, 0 This study highlights the adaptability of the human gut microbiome to local ecology. The researchers investigate the gut bacterial communities of Bantu agriculturalists and neighboring BaAka rainforest hunter-gatherers. Although both groups are broadly similar in microbial composition, the BaAka had gut microbiomes that were abundant in some taxa not found at high frequencies in the Bantu, which could be a byproduct of their hunter-gatherer subsistence and diet. Microbiome composition in both Bantu and BaAka follows a gradient that correlates with the degree of traditional lifestyle, with Bantu gut microbiomes possessing more western (US)-like features than the BaAka.