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Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference


While it is widely recognized that DNA patterns vary across world-wide human populations, the primary features that drive these differences are less well understood. As an example, the Ari peoples of Ethiopia are presently socially divided according to occupation, with Ari Blacksmiths marginalised relative to Ari Cultivators. Two competing theories proposed by anthropologists to explain the existence of these occupational groupings suggest very different histories: (i) the Cultivators reflect migrants who moved into the region occupied by ancestors of the Blacksmiths perhaps many thousands of years ago, versus (ii) the Blacksmiths and Cultivators comprised the same ancestral group before the former was marginalised due solely to their trade. Recent genetic studies showed that Blacksmiths and Cultivators are distinguishable by their DNA, and suggested that overall DNA patterns among the two groups were consistent with (i). However, we demonstrate here that interpreting the results of currently popular algorithms that compare DNA is not always straight-forward. Instead we use a variety of analyses to show that (ii) seems a more likely explanation, perhaps illustrating how social marginalisation can lead to groups becoming genetically distinguishable over a relatively short time period.


Vyšlo v časopise: Evidence for a Common Origin of Blacksmiths and Cultivators in the Ethiopian Ari within the Last 4500 Years: Lessons for Clustering-Based Inference. PLoS Genet 11(8): e32767. doi:10.1371/journal.pgen.1005397
Kategorie: Research Article
prolekare.web.journal.doi_sk: https://doi.org/10.1371/journal.pgen.1005397

Souhrn

While it is widely recognized that DNA patterns vary across world-wide human populations, the primary features that drive these differences are less well understood. As an example, the Ari peoples of Ethiopia are presently socially divided according to occupation, with Ari Blacksmiths marginalised relative to Ari Cultivators. Two competing theories proposed by anthropologists to explain the existence of these occupational groupings suggest very different histories: (i) the Cultivators reflect migrants who moved into the region occupied by ancestors of the Blacksmiths perhaps many thousands of years ago, versus (ii) the Blacksmiths and Cultivators comprised the same ancestral group before the former was marginalised due solely to their trade. Recent genetic studies showed that Blacksmiths and Cultivators are distinguishable by their DNA, and suggested that overall DNA patterns among the two groups were consistent with (i). However, we demonstrate here that interpreting the results of currently popular algorithms that compare DNA is not always straight-forward. Instead we use a variety of analyses to show that (ii) seems a more likely explanation, perhaps illustrating how social marginalisation can lead to groups becoming genetically distinguishable over a relatively short time period.


Zdroje

1. Pankhurst A (1999) ‘Caste’ in Africa: The Evidence from South-Western Ethiopia Reconsidered. Africa: 485–509.

2. Pagani L, Kivisild T, Tarekegn A, Ekong R, Plaster C, et al. (2012) Ethiopian Genetic Diversity Reveals Linguistic Stratification and Complex Influences on the Ethiopian Gene Pool. The American Journal of Human Genetics 91: 83–96. doi: 10.1016/j.ajhg.2012.05.015 22726845

3. Freeman D, Pankhurst A (2003) Peripheral People: The Excluded Minorities of Ethiopia. London: Hurst and Company.

4. Gebre Y (1995) The Ari of Southwestern Ethiopia: An Exploratory Study of Production Practices. Social Anthropology Dissertation Series.

5. Biasutti R (1905) Pastori, agricoltori e cacciatori nell ’Africa Orientale’. Bolletino del Reale Societa geografica italiana 6: 155–179.

6. Lewis H (1962) Historical Problems in Ethiopia and the Horn of Africa. Annals of the New York Academy of Sciences 96: 504–511. doi: 10.1111/j.1749-6632.1962.tb50145.x

7. Todd D (1978) The Origins of Outcastes in Ethiopia: Reflections on an Evolutionary Theory. Abbay 9: 145–158.

8. Haberland E (1965) Untersuchungen zum äthiopischen Königtum, volume 18. F. Steiner.

9. Lange W (1982) History of the Southern Gonga (Southwestern Ethiopia). Wiesbaden: Franz Steiner Verlag.

10. Alexander D, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Res 19: 1655–1664. doi: 10.1101/gr.094052.109 19648217

11. Hodgson J, Mulligan C, Al-Meeri A, Raaum R (2014) Early Back-to-Africa Migration in the Horn of Africa. PLoS Genetics 10: e1004393. doi: 10.1371/journal.pgen.1004393 24921250

12. Pritchard J, Stephens M, Donnelly P (2000) Inference of Population Structure Using Multilocus Genotype Data. Genetics 155: 945–959. 10835412

13. Falush D, Stephens M, Pritchard J (2003) Inference of Population Structure From Multilocus Genotype Data: Linked Loci and Correlated Allele Frequencies. Genetics 164: 1567–1587. 12930761

14. Tang H, Peng J, Wang P, Risch N (2005) Estimation of Individual Admixture: Analytical and Study Design Considerations. Genetic Epidemiology 28: 289–301. doi: 10.1002/gepi.20064 15712363

15. Li J, Absher D, Tang H, Southwick A, Casto A, et al. (2008) Worldwide human relationships inferred from genome-wide patterns of variation. Science 319: 1100–1104. doi: 10.1126/science.1153717 18292342

16. Tishkoff S, Reed F, Friedlaender F, Ehret C, Ranciaro A, et al. (2009) The Genetic Structure and History of Africans and African Americans. Science 324: 1035–1044. doi: 10.1126/science.1172257 19407144

17. Patterson N, Price A, Reich D (2006) Population Structure and Eigenanalysis. PLoS Genetics 2: e190. doi: 10.1371/journal.pgen.0020190 17194218

18. McVean G (2009) A Genealogical Interpretation of Principal Components. PLoS Genetics 5: e1000686. doi: 10.1371/journal.pgen.1000686 19834557

19. International HapMap 3 Consortium (2010) Integrating common and rare genetic variation in diverse human populations. Nature 467: 52–58. doi: 10.1038/nature09298 20811451

20. Delaneau O, Marchini J, Zagury JF (2012) A linear complexity phasing method for thousands of genomes. Nature methods 9: 179–181. doi: 10.1038/nmeth.1785

21. Lawson D, Hellenthal G, Myers S, Falush D (2012) Inference of Population Structure using Dense Haplotype Data. PLoS Genetics 8: e1002453. doi: 10.1371/journal.pgen.1002453 22291602

22. Conrad D, Jakobsson M, Coop G, Wen X, Wall J, et al. (2006) A worldwide survey of haplotype variation and linkage disequilibrium in the human genome. Nature Genetics 38: 1251–1260. doi: 10.1038/ng1911 17057719

23. Hellenthal G, Auton A, Falush D (2008) Inferring Human Colonization History Using a Copying Model. PLoS Genetics 4: e1000078. doi: 10.1371/journal.pgen.1000078 18497854

24. Li N, Stephens M (2003) Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism data. Genetics 165: 2213–33. 14704198

25. Leslie S, Winney B, Hellenthal G, Davison D, Boumertit A, et al. (2015) The fine-scale genetic structure of the british population. Nature 519: 309–314. doi: 10.1038/nature14230 25788095

26. Chen G, Marjoram P, Wall J (2009) Fast and flexible simulation of DNA sequence data. Genome Res 19: 136–142. doi: 10.1101/gr.083634.108 19029539

27. Valente C, Alvarez L, Marks SJ, Lopez-Parra AM, Parson W, et al. (2015) Exploring the relationship between lifestyles, diets and genetic adaptations in humans. BMC genetics 16: 55. doi: 10.1186/s12863–015-0212–1 26018448

28. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira M, et al. (2007) PLINK: a toolset for whole-genome association and population-based linkage analysis. Am J Hum Genet 81: 559–575. doi: 10.1086/519795 17701901

29. Sajantila A, Salem AH, Savolainen P, Bauer K, Gierig C, et al. (1996) Paternal and maternal dna lineages reveal a bottleneck in the founding of the finnish population. Proceedings of the National Academy of Sciences 93: 12035–12039. doi: 10.1073/pnas.93.21.12035

30. Melé M, Javed A, Pybus M, Zalloua P, Haber M, et al. (2012) Recombination gives a new insight in the effective population size and the history of the old world human populations. Molecular biology and evolution 29: 25–30. doi: 10.1093/molbev/msr213 21890475

31. Prugnolle F, Manica A, Balloux F (2005) Geography predicts neutral genetic diversity of human populations. Current Biology 15: R159–R160. doi: 10.1016/j.cub.2005.02.038 15753023

32. Pickrell JK, Patterson N, Loh PR, Lipson M, Berger B, et al. (2014) Ancient west Eurasian ancestry in southern and eastern Africa. Proceedings of the National Academy of Sciences 111: 2632–2637. doi: 10.1073/pnas.1313787111

33. Hellenthal G, Busby G, Band G, Wilson J, Capelli C, et al. (2014) A genetic atlas of human admixture history. Science 343: 747–751. doi: 10.1126/science.1243518 24531965

34. Patterson N, Moorjani P, Luo Y, Mallick S, Rohland N, et al. (2012) Ancient Admixture in Human History. Genetics 192: 1065–1093. doi: 10.1534/genetics.112.145037 22960212

35. Li H, Durbin R (2011) Inference of human population history from individual whole-genome sequences. Nature 475: 493–496. doi: 10.1038/nature10231 21753753

36. Gronau I, Hubisz M, Gulko B, Danko C, Siepel A (2011) Bayesian inference of ancient human demography from individual genome sequences. Nature Genetics 43: 1031–1034. doi: 10.1038/ng.937 21926973

37. Schiffels S, Durbin R (2014) Inferring human population size and separation history from multiple genome sequences. Nature Genetics 46: 919–925. doi: 10.1038/ng.3015 24952747

38. Pagani L, Schiffels S, Gurdasani D, Danecek P, Scally A, et al. (2015) Tracing the route of modern humans out of africa by using 225 human genome sequences from ethiopians and egyptians. The American Journal of Human Genetics. doi: 10.1016/j.ajhg.2015.04.019

39. de Contenson H (1981) Pre-aksumite culture. UNESCO general history of Africa 2: 341–361.

40. Phillipson DW, Phillips JS, Tarekegn A (2000) Archaeology at Aksum, Ethiopia, 1993–7, volume 2. British Institute in Eastern Africa.

41. Rosenberg N, Pritchard J, Weber J, Cann H, Kidd K, et al. (2002) Genetic Structure of Human Populations. Science 298: 2981–2985. doi: 10.1126/science.1078311

42. Thornton T, Conomos MP, Sverdlov S, Blue EM, Cheung CY, et al. (2014) Estimating and adjusting for ancestry admixture in statistical methods for relatedness inference, heritability estimation, and association testing. In: BMC Proceedings. BioMed Central Ltd, volume 8, p. S5.

43. Reich D, Thangaraj K, Patterson N, Price A, Singh L (2009) Reconstructing Indian population history. Nature 461: 489–494. doi: 10.1038/nature08365 19779445

44. McVean GA, et al. (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 1. doi: 10.1038/nature11632

45. The 1000 Genomes Project Consortium (2012) An integrated map of genetic variation from 1,092 human genomes. Nature 491: 55–65.

46. Ralph P, Coop G (2013) The Geography of Recent Genetic Ancestry across Europe. PLoS Biology 11: e1001555. doi: 10.1371/journal.pbio.1001555 23667324

47. Busing F, Meijer E, Van Der Leeden R (1999) Delete-m Jackknife for Unequal m. Statistics and Computing 9: 3–8. doi: 10.1023/A:1008800423698

48. Hudson R, Slatkin M, Maddison W (1992) Estimation of Levels of Gene Flow from DNA Sequence Data. Genetics 132: 583–589. 1427045

49. Gamerman D, Lopes HF (2006) Markov Chain Monte Carlo: Stochastic Simulation for Bayesian Inference. CRC Press.

50. Price L, Tandon A, Patterson N, Barnes K, Rafaels N, et al. (2009) Sensitive Detection of Chromosomal Segments of Distinct Ancestry in Admixed Populations. PLoS Genetics 5: e1000519. doi: 10.1371/journal.pgen.1000519 19543370

51. Moorjani P, Patterson N, Hirschhorn J, Keinan A, Hao L, et al. (2011) The History of African Gene Flow into Southern Europeans, Levantines, and Jews. PLoS Genetics 7: e1001373. doi: 10.1371/journal.pgen.1001373 21533020

52. Loh P, Lipson M, Patterson N, Moorjani P, Pickrell J, et al. (2013) Inferring Admixture Histories of Human Populations Using Linkage Disequilibrium. Genetics 193: 1233–1254. doi: 10.1534/genetics.112.147330 23410830

53. Gutenkunst R, Hernandez R, Williamson S, Bustamante C (2009) Inferring the Joint Demographic History of Multiple Populations from Multidimensional SNP Frequency Data. PLoS Genetics 5: e1000695. doi: 10.1371/journal.pgen.1000695 19851460

54. Keinan A, Mullikin J, Patterson N, Reich D (2007) Measurement of the human allele frequency spectrum demonstrates greater genetic drift in East Asians than in Europeans. Nature Genetics 39: 1251–1255. doi: 10.1038/ng2116 17828266

55. Marth G, Czabarka E, Murvai J, Sherry S (2004) The allele frequency spectrum in genome-wide human variation data reveals signals of differential demographic history in three large world populations. Genetics 166: 351–372. doi: 10.1534/genetics.166.1.351 15020430

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