Polymorphic Alu insertions and the genetic structure of Iberian Basques

Journal of Human Genetics

Volumn 52, Issue 4, 2007, Pages 317-327

  Garcia Obregon S ^a   Alfonso Sanchez M A ^a   Perez Miranda A M ^a   De Pancorbo, M M ^a   Pena J A ^a  

^a UNIVERSITY OF THE BASQUE COUNTRY UPV EHU   (Spain)

Author keywords

Alu insertions; Basques; Gene flow; Genetic heterogeneity; Wright's FST

Indexed keywords

ALU SEQUENCE; ARTICLE; DNA POLYMORPHISM; EUROPE; GENE INSERTION; GENETIC HETEROGENEITY; GENETIC VARIABILITY; GEOGRAPHY; HUMAN; SHORT TANDEM REPEAT; SPAIN;

ALU ELEMENTS; ETHNIC GROUPS; EUROPEAN CONTINENTAL ANCESTRY GROUP; GENE FREQUENCY; HUMANS; POLYMORPHISM, GENETIC; SPAIN;

EID: 33947626991     PISSN: 14345161     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10038-007-0114-9     Document Type: Article

References (64)

1. Aguirre AI, Vicario A, Mazón LI, Estomba A, de Pancorbo MM, Arrieta-Pico V, Pérez-Elortondo F, Lostao CM (1991) Are the Basques a single and unique population? Am J Hum Genet 49:450-458
2. Alfonso-Sánchez MA, Peña JA, Aresti U, Calderón R (2001) An insight into recent consanguinity within the Basque area in Spain. Effects of autochthony, industrialization and demographic changes. Ann Hum Biol 28:505-521
3. Alfonso-Sánchez MA, Aresti U, Peña JA, Calderón R (2005) Inbreeding levels and consanguinity structure in the Basque province of Guipú zcoa (1862-1980). Am J Phys Anthropol 127:240-252
4. Alfonso-Sánchez MA, Mart?́nez-Bouzas C, Castro A, Peña JA, Fernández-Fernández I, Herrera RJ, de Pancorbo MM (2006) Sequence polymorphisms of the mtDNA control region in a human isolate: the Georgians from Swanetia. J Hum Genet 51:429-439
5. Arnaiz-Villena A, Martinez-Laso J, Gomez-Casado E, Diaz-Campos N, Santos P, Martinho A, Breda-Coimbra H (1997) Relatedness among Basques, Portuguese, Spaniards, and Algerians studied by HLA allelic frequencies and haplotypes. Immunogenetics 47:37-43
6. Barbujani G (1997) DNA variation and language affinities. Am J Hum Genet 61:1011-1014
7. Barbujani G, Sokal RR (1990) Zones of abrupt genetic change in Europe are also linguistic boundaries. Proc Natl Acad Sci USA 87:1816-1819
8. Batzer MA, Deininger PL (2002) Alu repeats and human genomic diversity. Nature 3:370-379
9. Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, Shaikh TH, Novick GE, Ioannou PA, Scheer WD, Herrera RJ, Deininger PL (1994) African origin of human specific polymorphic Alu insertions. Proc Natl Acad Sci USA 91:12288-12292
10. Batzer MA, Arcot SS, Phinney JW, Alegria-Hartman M, Kass DH, Milligan SM, Kimpton C, Gill P, Hochmeister M, Ioannou PA, Herrera RJ, Boudreau DA, Scheer WD, Keats BJ, Deininger PL, Stoneking M (1996) Genetic variation of recent Alu insertions in human populations. J Mol Evol 42:22-29
11. Bertorelle G, Bertranpetit J, Calafell F, Nasidze IS, Barbujani G (1995) Do Basque- and Caucasian-speaking populations share non-Indo-European ancestors? Eur J Hum Genet 3:256-263
12. Bosch E, Calafell F, Pérez-Lezaun A, Comas D, Mateu E, Bertranpetit J (1997) A population history of Northern Africa: Evidence from classical genetic markers. Hum Biol 69:295-311
13. Bosch E, Calafell F, Santos FR, Pérez-Lezaun A, Comas D, Benchemsi N, Tyler-Smith C, Bertranpetit J (1999) Variation in short tandem repeats is deeply structured by genetic background on the human Y chromosome. Am J Hum Genet 65:1623-1638
14. Bosch E, Calafell F, Pérez-Lezaun A, Clarimón J, Comas D, Mateu E, Mart?́nez-Arias R, Morera B, Brakez Z, Akhayat O, Sefiani A, Hariti G, Cambon-Thomsen A, Bertranpetit J (2000) Genetic structure of North-West Africa revealed by STR analysis. Eur J Hum Genet 8:360-366
15. Boyd WC, Boyd LG (1937) New data on blood groups and other inherited factors in Europe and Egypt. Am J Phys Anthropol 23:49-70
16. Calafell F, Bertranpetit J (1994) Principal component analysis of gene frequencies and the origin of Basques. Am J Phys Anthropol 93:201-215
17. Calderón R, Vidales C, Peña JA, Pérez-Miranda A, Dugoujon JM (1998) Immunoglobulin allotypes (GM and KM) in Basques from Spain: Approach to the origin of the Basque population. Hum Biol 70:667-698
18. Cavalli-Sforza LL, Menozzi P, Piazza A (1994) The history and geography of human genes. Princeton University Press, Princeton
19. Chen J, Sokal RR, Ruhlen M (1995) Worldwide analysis of genetic and linguistic relationships of human populations. Hum Biol 67:595-612
20. Comas D, Calafell F, Mateu E, Pérez-Lezaun A, Bertranpetit J (1998) HLA evidence for the lack of genetic heterogeneity in Basques. Ann Hum Genet 62:123-132
21. Comas D, Calafell F, Benchemsi N, Helal A, Lefranc G, Stoneking M, Batzer M Bertranpetit J, Sajantila A (2000) Alu insertion polymorphisms in NW Africa and the Iberian Peninsula: Evidence for a strong genetic boundary through the Gibraltar Straits. Hum Genet 107:312-319
22. Comas D, Plaza S, Calafell F, Sajantila A, Bertranpetit J (2001) Recent insertion of an Alu element within a polymorphic human-specific Alu insertion. Mol Biol Evol 18:85-88
23. Comas D, Schmid H, Braeuer S, Flaiz C, Busquets A, Calafell F, Bertranpetit J, Scheil HG, Huckenbeck W, Efremovska L, Schmidt H (2004) Alu insertion polymorphisms in the Balkans and the origins of the Aromuns. Ann Hum Genet 68:120-127
24. Cordaux R, Jungnam L, Dinoso L, Batzer MA (2006) Recently integrated Alu retrotransposons are essentially neutral residents of the human genome. Gene 373:138-144
25. Etcheverry MA (1945) El factor rhesus en genetica e importancia clinica. Diagn Med 17:1237-1251
26. Excoffier L, Laval G, Schneider S (2005) ARLEQUIN ver. 3.0: an integrated software package for population genetics data analysis. Evol Bioinf Online 1:47-50
27. Forster P, Rohl A, Lunnemann P, Brinkmann C, Zerjal T, Tyler-Smith C, Brinkmann B (2000) A short tandem repeat-based phylogeny for the human Y chromosome. Am J Hum Genet 67:182-196
28. Gamkrelidze T, Ivanov V (1990) The early history of Indo-European languages. Sci Am 262:110-116
29. Garc?́a-Obregó n S, Alfonso-Sánchez MA, Pérez-Miranda AM, Vidales C, Arroyo D, Peña JA (2006) Genetic position of Valencia (Spain) in the Mediterranean basin according to Alu insertions. Am J Hum Biol 18:187-195
30. Goedde HW, Hirth L, Benkmann HG, Pellicer A, Pellicer T, Stahn M, Singh S (1972) Population genetic studies of red cell enzyme polymorphisms in four Spanish populations. Hum Hered 22:552-560
31. Goedde HW, Hirth L, Benkmann HG, Pellicer A, Pellicer T, Stahn M, Singh S (1973) Population genetic studies of serum protein polymorphisms in four Spanish populations. Hum Hered 23:135-146
32. Guo SW, Thompson EA (1992) Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48:361-372
33. Jorde L, Bamshad M, Watkins W, Zenger R, Fraley A, Krakowiak P, Carpenter K, Soodyall H, Jenkins T, Rogers A (1995) Origins and affinities of modern humans: A comparison of mitochondrial and nuclear data. Am J Hum Genet 57:523-538
34. Jorde L, Rogers A, Bamshad M, Watkins W, Krakowiak P, Sung S, Kere J, Harpending H (1997) Microsatellite diversity and the demographic history of modern humans. Proc Natl Acad Sci USA 94:3100-3103
35. Kidd KK, Kidd JR, Pakstis AJ, Bonné-Tamir B, Grigorenko E (2000) Nuclear genetic variation of European populations in a global context. In: Renfrew C, Boyle K (eds) Archaeogenetics: DNA and the population prehistory of Europe. The McDonald Institute for Archaeological Research, Cambridge, pp 109-117
36. Kruskal JB (1964) Nonmetric multidimensional scaling: a numerical method. Psychometrika 29:115-129
37. Lalouel JM (1973) Topology of population structure. In: NE Morton (ed) Genetic structure of populations. University of Hawaii Press, Honolulu, pp 139-149
38. Lell JT, Wallace DC (2000) The peopling of Europe from the maternal and paternal perspectives. Am J Hum Genet 67:1376-1381
39. Levine MH, Von Hagen V, Ruffié J, Darrasse H (1977) A hematological approach to basque isolation in two french Basque villages. Ann NY Acad Sci 293:185-193
40. Liu K, Muse S (2004) POWERMARKER: New genetic data analysis software. Version 3.0. Free program distributed by the author over the internet from http://www.powermarker.net Lucotte G, Hazout S (1996) Y-chromosome DNA haplotypes in Basques. J Mol Evol 42:472-475
41. Maca-Meyer N, Villar J, Pérez-Méndez L, Cabrera de León A, Flores C (2004) A tale of aborigines, conquerors and slaves: Alu insertion polymorphisms and the peopling of Canary Islands. Ann Hum Genet 68:600-605
42. Manni F, Leonardi P, Barakat A, Rouba H, Heyer E, Klintschar M, McElreavey K, Quintana-Murci L (2002) Y-chromosome analysis in Egypt suggests a genetic regional continuity in Northeastern Africa. Hum Biol 74:645-658
43. Nasidze I, Risch GM, Robichaux M, Sherry ST, Batzer MA, Stoneking M (2001) Alu insertion polymorphisms and the genetic structure of human populations from the Caucasus. Eur J Hum Genet 9:267-272
44. de Pancorbo MM, Ló pez-Martinez M, Martinez-Bouzas C, Castro A, Fernández-Fernández I, Antú nez de Mayolo G, Antú nez de Manolo A, Antú nez de Manolo P, Rowold DJ, Herrera RJ (2001) The Basques according to polymorphic Alu insertions. Hum Genet 109:224-233
45. Peña JA, Morales B, Calderón R (1997) New method for comparing levels of microdifferentiation: application to migration matrices of two populations from the Basque Country (Spain). Hum Biol 69:329-344
46. Peña JA, Calderón R, Pérez-Miranda A, Vidales C, Dugoujon JM, Carrión M, Crouau-Roy B (2002) Microsatellite DNA markers from HLA region (D6S105, D6S265 and TNFa) in autochthonous Basques from Northern Navarre (Spain). Ann Hum Biol 29:176-191
47. Peña JA, Garc?́a-Obregón S, Pérez-Miranda AM, De Pancorbo MM, Alfonso-Sánchez MA (2006) Gene flow in the Iberian Peninsula determined from Y-chromosome STR loci. Am J Hum Biol 18:532-539
48. Pérez-Miranda AM, Alfonso-Sánchez MA, Peña JA, Calderón R (2003) HLA-DQA1 polymorphism in autochthonous Basques from Navarre (Spain): Genetic position within European and Mediterranean scopes. Tissue Antigens 61:465-474
49. Pérez-Miranda AM, Alfonso-Sánchez MA, Vidales C, Calderó n R, Peña JA (2004) Genetic polymorphism and linkage disequilibrium of the HLA-DP region in Basques from Navarre (Spain). Tissue Antigens 64:264-275
50. Pérez-Miranda AM, Alfonso-Sánchez MA, Kalantar A, Garc?́a-Obregón S, de Pancorbo MM, Peña JA, Herrera RJ (2005) Microsatellite data support subpopulation structuring among Basques. J Hum Genet 50:403-414
51. Renfrew C (1991) Before Babel, speculations on the origins of linguistic diversity. Cambridge Archaeol J 1:3-23
52. Reynolds J, Weir BS, Cockerman CC (1983) Estimation of the coancestry coefficient: bases for a short term genetic distance. Genetics 105:767-779
53. Richards M (2003) The neolithic invasion of Europe. Annu Rev Anthropol 32:135-162
54. Romualdi C, Balding D, Nasidze IS, Risch G, Robichaux M, Sherry ST, Stoneking M, Batzer MA, Barbujani G (2002) Patterns of human diversity, within and among continents, inferred from biallelic DNA polymorphisms. Genome Res 12:602-612
55. Ruhlen M (1991) A guide to the world's languages (2nd edn). Stanford University Press, Stanford
56. Semino O, Magri C, Benuzzi G, Lin AA, Al-Zahery N, Battaglia V, Maccioni L, Triantaphyllidis C, Shen P, Oefner PJ, Zhivotovsky LA, King R, Torroni A, Cavalli-Sforza LL, Underhill PA, Santachiara-Benerecetti AS (2004) Origin, diffusion, and differentiation of Y-chromosome haplogroups E and J: inferences on the neolithization of Europe and later migratory events in the Mediterranean area. Am J Hum Genet 74:1023-1034
57. Simoni L, Gueresi P, Pettener D, Barbujani G (1999) Patterns of gene flow inferred from genetic distances in the Mediterranean region. Hum Biol 71:399-415
58. Sokal RR, Rohlf FJ (1997) Biometry. The principles and practice of statistics in biological research, 3rd edn. WH Freeman, New York
59. Stoneking M, Fontius J, Clifford S, Soodyall H, Arcot S, Saha N, Jenkins T, Tahir M, Deininger P, Batzer MA (1997) Alu insertion polymorphisms and human evolution: Evidence for a larger population size in Africa. Genome Res 7:1061-1071
60. Torroni A, Bandelt HJ, D'Urbano L, Lahermo P, Moral P, Sellitto D, Rengo C, Forster P, Savontaus ML, Bonné-Tamir B, Scozzari R (1998) MtDNA analysis reveals a major late paleolithic population expansion from southwestern to northeastern Europe. Am J Hum Genet 62:1137-1152
61. Torroni A, Bandelt HJ, Macaulay V, Richards M, Cruciani F, Rengo C, Martinez-Cabrera V, Villems R, Kivisild T, Metspalu E, Parik J, Tolk HV, Tambets K, Forster P, Karger B, Francalacci P, Rudan P, Janicijevic B, Rickards O, Savontaus ML, Huoponen K, Laitinen V, Koivumaki S, Sykes B, Hickey E, Novelletto A, Moral P, Sellitto D, Coppa A, Al-Zaheri N, Santachiara-Benerecetti AS, Semino O, Scozzari R (2001) A signal from human mtDNA of postglacial recolonization in Europe. Am J Hum Genet 69:844-852
62. Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending HC, Rogers AR, Jorde LB (2001) Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms. Am J Hum Genet 68:738-752
63. Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AE, Carroll ML, Nguyen SV, Walker JA, Prasad BVR, Reddy PG, Das PK, Batzer MA, Jorde LB (2003) Genetic variation among world populations: Inferences from 100 Alu insertion polymorphisms. Genome Res 13:1607-1618
64. Zhivotovsky LA, Underhill PA, Cinnioglu 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