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Forensic and phylogeographic characterisation of mtDNA lineages from Somalia

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Abstract

The African mitochondrial (mt) phylogeny is coarsely resolved but the majority of population data generated so far is limited to the analysis of the first hypervariable segment (HVS-1) of the control region (CR). Therefore, this study aimed on the investigation of the entire CR of 190 unrelated Somali individuals to enrich the severely underrepresented African mtDNA pool. The majority (60.5 %) of the haplotypes were of sub-Saharan origin with L0a1d, L2a1h and L3f being the most frequently observed haplogroups. This is in sharp contrast to previous data reported from the Y-chromosome, where only about 5 % of the observed haplogroups were of sub-Saharan provenance. We compared the genetic distances based on population pairwise F st values between 11 published East, Central and North African as well as western Asian populations and the Somali sequences and displayed them in a multi-dimensional scaling plot. Genetic proximity evidenced by clustering roughly reflected the relative geographic location of the populations. The sequences will be included in the EMPOP database (www.empop.org) under accession number EMP00397 upon publication (Parson and Dür Forensic Sci Int Genet 1:88–92, 2007).

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References

  1. Walter RC, Buffler RT, Bruggemann JH, Guillaume MM, Berhe SM, Negassi B, Libsekal Y, Cheng H, Edwards RL, von Cosel R, Néraudeau D, Gagnon M (2000) Early human occupation of the Red Sea coast of Eritrea during the last interglacial. Nature 405:65–69. doi:10.1038/35011048

    Article  PubMed  CAS  Google Scholar 

  2. Kivisild T, Bamshad MJ, Kaldma K, Metspalu M, Metspalu E, Reidla M, Laos S, Parik J, Watkins WS, Dixon ME, Papiha SS, Mastana SS, Mir MR, Ferak V, Villems R (1999) Deep common ancestry of Indian and western-Eurasian mitochondrial DNA lineages. Curr Biol 9:1331–1334. doi:10.1016/S0960-9822(00)80057-3

    Article  PubMed  CAS  Google Scholar 

  3. Macaulay V, Hill C, Achilli A, Rengo C, Clarke D, Meehan W, Blackburn J, Semino O, Scozzari R, Cruciani F, Taha A, Shaari NK, Raja JM, Ismail P, Zainuddin Z, Goodwin W, Bulbeck D, Bandelt HJ, Oppenheimer S, Torroni A, Richards M (2005) Single, rapid coastal settlement of Asia revealed by analysis of complete mitochondrial genomes. Science 308:1034–1036. doi:10.1126/science.1109792

    Article  PubMed  CAS  Google Scholar 

  4. Stringer CB, Grün R, Schwarcz HP, Goldberg P (1989) ESR dates for the hominid burial site of Es Skhul in Israel. Nature 338:756–758. doi:10.1038/338756a0

    Article  PubMed  CAS  Google Scholar 

  5. Lahr MM, Foley R (1994) Multiple dispersals and modern human origins. Evol Anthropol Issues News Rev 3:48–60. doi:10.1002/evan.1360030206

    Article  Google Scholar 

  6. Derenko M, Malyarchuk B, Grzybowski T, Denisova G, Dambueva I, Perkova M, Dorzhu C, Luzina F, Lee HK, Vanecek T, Villems R, Zakharov I (2007) Phylogeographic analysis of mitochondrial DNA in northern Asian Populations. Am J Hum Genet 81:1025–1041. doi:10.1086/522933

    Article  PubMed  CAS  Google Scholar 

  7. Mellars P (2006) Going east: new genetic and archaeological perspectives on the modern human colonization of Eurasia. Science 313:796–800. doi:10.1126/science.1128402

    Article  PubMed  CAS  Google Scholar 

  8. Stoneking M, Delfin F (2010) The human genetic history of East Asia: weaving a complex tapestry. Curr Biol 20:R188–R193. doi:10.1016/j.cub.2009.11.052

    Article  PubMed  CAS  Google Scholar 

  9. Levinson D (1998) Ethnic groups worldwide: a ready reference handbook. Greenwood Publishing Group, Conneticut

    Google Scholar 

  10. Pateman R (2006) Denmark (cultures of the world). Benchmark Books, New York

    Google Scholar 

  11. Sanchez JJ, Hallenberg C, Børsting C, Hernandez A, Morling N (2005) High frequencies of Y chromosome lineages characterized by E3b1, DYS19-11, DYS392-12 in Somali males. Eur J Hum Genet 13:856–866. doi:10.1038/sj.ejhg.5201390

    Article  PubMed  CAS  Google Scholar 

  12. Sanchez JJ, Monaghan G, Børsting C, Norbury G, Morling N, Gaspar HB (2007) Carrier frequency of a nonsense mutation in the adenosine deaminase (ADA) gene implies a high incidence of ADA-deficient severe combined immunodeficiency (SCID) in Somalia and a single, common haplotype indicates common ancestry. Ann Hum Genet 71:336–347. doi:10.1111/j.1469-1809.2006.00338.x

    Article  PubMed  CAS  Google Scholar 

  13. Zhivotovsky LA, Underhill PA, Cinnioğlu C, Kayser M, Morar B, Kivisild T, Scozzari R, Cruciani F, Destro-Bisol G, Spedini G, Chambers GK, Herrera RJ, Yong KK, Gresham D, Tournev I, Feldman MW, Kalaydjieva L (2004) The effective mutation rate at Y chromosome short tandem repeats, with application to human population-divergence time. Am J Hum Genet 74:50–61. doi:10.1086/380911

    Article  PubMed  CAS  Google Scholar 

  14. Newman JL (1997) The peopling of Africa: a geographic interpretation. Yale University Press, London

    Google Scholar 

  15. Passarino G, Semino O, Quintana-Murci L, Excoffier L, Hammer M, Santachiara-Benerecetti AS (1998) Different genetic components in the Ethiopian population, identified by mtDNA and Y-chromosome polymorphisms. Am J Hum Genet 62:420–434. doi:10.1086/301702

    Article  PubMed  CAS  Google Scholar 

  16. Tishkoff SA, Williams SM (2002) Genetic analysis of African populations: human evolution and complex disease. Nat Rev Genet 3:611–621. doi:10.1038/nrg865

    Article  PubMed  CAS  Google Scholar 

  17. Semino O, Santachiara-Benerecetti AS, Falaschi F, Cavalli-Sforza LL, Underhill PA (2002) Ethiopians and Khoisan share the deepest clades of the human Y-chromosome phylogeny. Am J Hum Genet 70:265–268. doi:10.1086/338306

    Article  PubMed  CAS  Google Scholar 

  18. Watson E, Forster P, Richards M, Bandelt HJ (1997) Mitochondrial footprints of human expansions in Africa. Am J Hum Genet 61:691–704. doi:10.1086/515503

    Article  PubMed  CAS  Google Scholar 

  19. Comas D, Reynolds R, Sajantila A (1999) Analysis of mtDNA HVRII in several human populations using an immobilised SSO probe hybridisation assay. Eur J Hum Genet 7:459–468. doi:10.1038/sj.ejhg.5200326

    Article  PubMed  CAS  Google Scholar 

  20. Stangegaard M, Frøslev TG, Frank-Hansen R, Laursen SS, Jørgensen M, Hansen AJ, Morling N (2009) Automated extraction of DNA and PCR setup using a Tecan Freedom EVO® liquid handler. Forensic Sci Int Genet Suppl Ser 2:74–76. doi:10.1016/j.fsigss.2009.07.002

    Article  Google Scholar 

  21. Parson W, Bandelt HJ (2007) Extended guidelines for mtDNA typing of population data in forensic science. Forensic Sci Int Genet 1:13–19. doi:10.1016/j.fsigen.2006.11.003

    Article  PubMed  CAS  Google Scholar 

  22. Parson W, Roewer L (2010) Publication of population data of linearly inherited DNA markers in the International Journal of Legal Medicine. Int J Legal Med 124:505–509. doi:10.1007/s00414-010-0492-y

    Article  PubMed  Google Scholar 

  23. Bandelt HJ, Parson W (2008) Consistent treatment of length variants in the human mtDNA control region: a reappraisal. Int J Legal Med 122:11–21. doi:10.1007/s00414-006-0151-5

    Article  PubMed  Google Scholar 

  24. van Oven M, Kayser M (2009) Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 30:E386–E394. doi:10.1002/humu.20921

    Article  PubMed  Google Scholar 

  25. Bodner M, Irwin JA, Coble MD, Parson W (2011) Inspecting close maternal relatedness: towards better mtDNA population samples in forensic databases. Forensic Sci Int Genet 5:138–141. doi:10.1016/j.fsigen.2010.10.001

    Article  PubMed  CAS  Google Scholar 

  26. Evett IW, Weir BS (1999) Interpreting DNA evidence: statistical genetics for forensic scientists. Heredity 82:585–586. doi:10.1038/sj.hdy.6885562

    Google Scholar 

  27. Excoffier L, Lischer HEL (2010) Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows. Mol Ecol Resour 10:564–567. doi:10.1111/j.1755-0998.2010.02847.x

    Article  PubMed  Google Scholar 

  28. Abu-Amero KK, Larruga JM, Cabrera VM, González AM (2008) Mitochondrial DNA structure in the Arabian Peninsula. BMC Evol Biol 8:45. doi:10.1186/1471-2148-8-45

    Article  PubMed  Google Scholar 

  29. Cerný V, Mulligan CJ, Rídl J, Zaloudková M, Edens CM, Hájek M, Pereira L (2008) Regional differences in the distribution of the sub-Saharan, West Eurasian, and South Asian mtDNA lineages in Yemen. Am J Phys Anthropol 136:128–137. doi:10.1002/ajpa.20784

    Article  PubMed  Google Scholar 

  30. Cerný V, Pereira L, Kujanová M, Vasíková A, Hájek M, Morris M, Mulligan CJ (2009) Out of Arabia-the settlement of island Soqotra as revealed by mitochondrial and Y chromosome genetic diversity. Am J Phys Anthropol 138:439–447. doi:10.1002/ajpa.20960

    Article  PubMed  Google Scholar 

  31. Ottoni C, Martínez-Labarga C, Loogväli EL, Pennarun E, Achilli A, De Angelis F, Trucchi E, Contini I, Biondi G, Rickards O (2009) First genetic insight into Libyan Tuaregs: a maternal perspective. Ann Hum Genet 73:438–448. doi:10.1111/j.1469-1809.2009.00526.x

    Article  PubMed  Google Scholar 

  32. Saunier JL, Irwin JA, Strouss KM, Ragab H, Sturk KA, Parsons TJ (2009) Mitochondrial control region sequences from an Egyptian population sample. Forensic Sci Int Genet 3:e97–e103. doi:10.1016/j.fsigen.2008.09.004

    Article  PubMed  CAS  Google Scholar 

  33. Quintana-Murci L, Quach H, Harmant C, Luca F, Massonnet B, Patin E, Sica L, Mouguiama-Daouda P, Comas D, Tzur S, Balanovsky O, Kidd KK, Kidd JR, van der Veen L, Hombert JM, Gessain A, Verdu P, Froment A, Bahuchet S, Heyer E, Dausset J, Salas A, Behar DM (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. doi:10.1073/pnas.0711467105

    Article  PubMed  CAS  Google Scholar 

  34. Poloni ES, Naciri Y, Bucho R, Niba R, Kervaire B, Excoffier L, Langaney A, Sanchez-Mazas A (2009) Genetic evidence for complexity in ethnic differentiation and history in East Africa. Ann Hum Genet 73:582–600. doi:10.1111/j.1469-1809.2009.00541.x

    Article  PubMed  CAS  Google Scholar 

  35. Brandstätter A, Peterson CT, Irwin JA, Mpoke S, Koech DK, Parson W, Parsons TJ (2004) Mitochondrial DNA control region sequences from Nairobi (Kenya): inferring phylogenetic parameters for the establishment of a forensic database. Int J Legal Med 118:294–306. doi:10.1007/s00414-004-0466-z

    Article  PubMed  Google Scholar 

  36. Irwin JA, Saunier JL, Niederstätter H, Strouss KM, Sturk KA, Diegoli TM, Brandstätter A, Parson W, Parsons TJ (2009) Investigation of heteroplasmy in the human mitochondrial DNA control region: a synthesis of observations from more than 5000 global population samples. J Mol Evol 68:516–527. doi:10.1007/s00239-009-9227-4

    Article  PubMed  CAS  Google Scholar 

  37. Cruciani F, La Fratta R, Trombetta B, Santolamazza P, Sellitto D, Colomb EB, Dugoujon JM, Crivellaro F, Benincasa T, Pascone R, Moral P, Watson E, Melegh B, Barbujani G, Fuselli S, Vona G, Zagradisnik B, Assum G, Brdicka R, Kozlov AI, Efremov GD, Coppa A, Novelletto A, Scozzari R (2007) Tracing past human male movements in northern/eastern Africa and western Eurasia: new clues from Y-chromosomal haplogroups E-M78 and J-M12. Mol Biol Evol 24:1300–1311. doi:10.1093/molbev/msm049

    Article  PubMed  CAS  Google Scholar 

  38. Stenersen M, Perchla D, Søvik E, Flønes AG, Dupuy BM (2004) Kurdish (Iraq) and Somalian population data for 15 autosomal and 9 Y-chromosomal STR loci. Int Congr Ser 1261:185–187. doi:10.1016/s0531-5131(03)01823-5

    Article  CAS  Google Scholar 

  39. Kivisild T, Reidla M, Metspalu E, Rosa A, Brehm A, Pennarun E, Parik J, Geberhiwot T, Usanga E, Villems R (2004) Ethiopian mitochondrial DNA heritage: tracking gene flow across and around the gate of tears. Am J Hum Genet 75:752–770. doi:10.1086/425161

    Article  PubMed  CAS  Google Scholar 

  40. Stevanovitch A, Gilles A, Bouzaid E, Kefi R, Paris F, Gayraud RP, Spadoni JL, El-Chenawi F, Beraud-Colomb E (2004) Mitochondrial DNA sequence diversity in a sedentary population from Egypt. Ann Hum Genet 68:23–39. doi:10.1046/j.1529-8817.2003.00057.x

    Article  PubMed  CAS  Google Scholar 

  41. Salas A, Richards M, De la Fe T, Lareu MV, Sobrino B, Sánchez-Diz P, Macaulay V, Carracedo A (2002) The making of the African mtDNA landscape. Am J Hum Genet 71:1082–1111. doi:10.1086/344348

    Article  PubMed  CAS  Google Scholar 

  42. Olivieri A, Achilli A, Pala M, Battaglia V, Fornariono S, Al-Zaheri N, Scozzari R, Cruciani F, Behar DM, Dugoujon JM, Coudray C, Santachiara-Benerecetti S, Semino O, Bandelt HJ, Torroni A (2006) The mtDNA legacy of the Levantine early upper Palaeolithic in Africa. Science 314:1767. doi:10.1126/science.1135566

    Article  PubMed  CAS  Google Scholar 

  43. González AM, Larruga JM, Abu-Amero KK, Shi Y, Pestano J, Cabrera VM (2007) Mitochondrial lineage M1 traces an early human backflow to Africa. BMC Genomics 8:223. doi:10.1186/1471-2164-8-223

    Article  PubMed  Google Scholar 

  44. Scheible M, Alenizi M, Sturk-Andreaggi K, Coble MD, Ismael S, Irwin JA (2011) Mitochondrial DNA control region variation in a Kuwaiti population sample. Forensic Sci Int Genet 5:e112–e113. doi:10.1016/j.fsigen.2011.04.001

    Article  PubMed  CAS  Google Scholar 

  45. Alshamali F, Alkhayat AQ, Budowle B, Watson ND (2005) STR population diversity in nine ethnic populations living in Dubai. Forensic Sci Int 152:267–279. doi:10.1016/j.forsciint.2004.09.133

    Article  PubMed  CAS  Google Scholar 

  46. Côrte-Real HB, Macaulay VA, Richards MB, Hariti G, Issad MS, Cambon-Thomsen A, Papiha S, Bertranpetit J, Sykes BC (1996) Genetic diversity in the Iberian Peninsula determined from mitochondrial sequence analysis. Ann Hum Genet 60:331–350. doi:10.1111/j.1469-1809.1996.tb01196.x

    Article  PubMed  Google Scholar 

  47. Fendt L, Röck AW, Zimmermann B, Bodner M, Thye T, Tschentscher F, Owusu-Dabo E, Göbel TMK, Schneider PM, Parson W (2011) MtDNA diversity of Ghana: a forensic and phylogeographic view. Forensic Sci Int Genet. doi:10.1016/j.fsigen.2011.12.007

  48. Maca-Meyer N, González AM, Pestano J, Flores C, Larruga JM, Cabrera VM (2003) Mitochondrial DNA transit between West Asia and North Africa inferred from U6 phylogeography. BMC Genet 4:15. doi:10.1186/1471-2156-4-15

    Article  PubMed  Google Scholar 

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Acknowledgements

We would like to thank Trine L. Hansen and Nadia Jochumsen (Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen) for excellent technical support.

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Authors and Affiliations

  1. Section of Forensic Genetics, Department of Forensic Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark

    Martin Mikkelsen, Eszter Rockenbauer, Anders J. Hansen & Niels Morling

  2. Institute of Legal Medicine, Innsbruck Medical University, Innsbruck, Austria

    Liane Fendt, Alexander W. Röck, Bettina Zimmermann & Walther Parson

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  1. Martin Mikkelsen
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  2. Liane Fendt
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Correspondence to Walther Parson.

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Mikkelsen, M., Fendt, L., Röck, A.W. et al. Forensic and phylogeographic characterisation of mtDNA lineages from Somalia. Int J Legal Med 126, 573–579 (2012). https://doi.org/10.1007/s00414-012-0694-6

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  • DOI: https://doi.org/10.1007/s00414-012-0694-6

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