Human population genetic structure and diversity inferred from polymorphic L1 (LINE-1) and Alu insertions

Human Heredity

Volumn 62, Issue 1, 2006, Pages 30-46

  Witherspoon, David J ^a,f   Marchani, E E ^a   Watkins, W S ^a   Ostler, C T ^a   Wooding, S P ^a   Anders, B A ^b   Fowlkes, J D ^b   Boissinot, S ^c   Furano, A V ^d   Ray, D A ^b   Rogers, A R ^e   Batzer, M A ^b   Jorde, L B ^a  

^a UNIVERSITY OF UTAH HEALTH SCIENCES CENTER   (United States)

^b LOUISIANA STATE UNIVERSITY   (United States)

^c CITY UNIVERSITY OF NEW YORK   (United States)

^d NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES   (United States)

^e UNIVERSITY OF UTAH   (United States)

^f UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

Bioinformatics computational biology; Evolution; Genetics population genetics

Indexed keywords

AFRICA; ALGORITHM; ALU SEQUENCE; ARTICLE; ASIA; CORRELATION ANALYSIS; DATA ANALYSIS; DNA POLYMORPHISM; EUROPE; GENE CLUSTER; GENE FREQUENCY; GENE INSERTION; GENE LOCUS; GENETIC DISTANCE; GENETIC VARIABILITY; GENOTYPE; GEOGRAPHIC DISTRIBUTION; HUMAN; INDIA; LONG INTERSPERSED REPEAT; MAJOR CLINICAL STUDY; POPULATION GENETIC STRUCTURE; POPULATION GENETICS; POPULATION RESEARCH; POPULATION STRUCTURE; RETROPOSON;

ALU ELEMENTS; GENE FREQUENCY; GENETIC LINKAGE; GENETIC VARIATION; GENETICS, POPULATION; GENOME, HUMAN; GENOTYPE; HUMANS; LINKAGE (GENETICS); LONG INTERSPERSED NUCLEOTIDE ELEMENTS; PHYLOGENY; POLYMORPHISM, GENETIC; POPULATION GROUPS; VARIATION (GENETICS);

EID: 33750165708     PISSN: 00015652     EISSN: None     Source Type: Journal    
DOI: 10.1159/000095851     Document Type: Article

References (92)

1. Smit AF, Toth G, Riggs AD, Jurka J: Ancestral, mammalian-wide subfamilies of LINE-1 repetitive sequences. J Mol Biol 1995;246:401-417.
2. Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al: Initial sequencing and analysis of the human genome. Nature 2001;409:860-921.
3. Kazazian HH Jr, Moran JV: The impact of L1 retrotransposons on the human genome. Nat Genet 1998;19:19-24.
4. Kazazian HH Jr: Mobile elements: drivers of genome evolution. Science 2004;303:1626-1632.
5. Luan DD, Korman MH, Jakubczak JL, Eickbush TH: Reverse transcription of R2Bm RNA is primed by a nick at the chromosomal target site: A mechanism for non-LTR retrotransposition. Cell 1993;72:595-605.
6. Sassaman DM, Dombroski BA, Moran JV, Kimberland ML, Naas TP, DeBerardinis RJ, Gabriel A, Swergold GD, Kazazian HH Jr: Many human L1 elements are capable of retrotransposition. Nat Genet 1997;16:37-43.
7. Boissinot S, Chevret P, Furano AV: L1 (LINE-1) retrotransposon evolution and amplification in recent human history. Mol Biol Evol 2000;17:915-928.
8. Sheen FM, Sherry ST, Risch GM, Robichaux M, Nasidze I, Stoneking M, Batzer MA, Swergold GD: Reading between the LINEs: Human genomic variation induced by LINE-1 retrotransposition. Genome Res 2000;10:1496-1508.
9. Ovchinnikov I, Rubin A, Swergold GD: Tracing the LINEs of human evolution. Proc Natl Acad Sci USA 2002;99:10522-10527.
10. Badge RM, Alisch RS, Moran JV: ATLAS: a system to selectively identify human-specific L1 insertions. Am J Hum Genet 2003;72:823-838.
11. Salem AH, Myers JS, Otieno AC, Watkins WS, Jorde LB, Batzer MA: LINE-1 preTa elements in the human genome. J Mol Biol 2003;326:1127-1146.
12. Myers JS, Vincent BJ, Udall H, Watkins WS, Morrish TA, Kilroy GE, Swergold GD, Henke J, Henke L, Moran JV, Jorde LB, Batzer MA: A comprehensive analysis of recently integrated human Ta L1 elements. Am J Hum Genet 2002;71:312-326.
13. Dewannieux M, Esnault C, Heidmann T: LINE-mediated retrotransposition of marked Alu sequences. Nat Genet 2003;35:41-48.
14. Batzer MA, Deininger PL: Alu repeats and human genomic diversity. Nat Rev Genet 2002;3:370-379.
15. Wang W, Kirkness EF: Short interspersed elements (SINEs) are a major source of canine genomic diversity. Genome Res 2005;15:1798-1808.
16. Deininger PL, Batzer MA: Alu repeats and human disease. Mol Genet Metab 1999;67:183-193.
17. Batzer MA, Deininger PL: A human-specific subfamily of Alu sequences. Genomics 1991;9:481-487.
18. Ho HJ, Ray DA, Salem AH, Myers JS, Batzer MA: Straightening out the LINEs: LINE-1 orthologous loci. Genomics 2005;85:201-207.
19. Roy-Engel AM, Carroll ML, El-Sawy M, Salem AH, Garber RK, Nguyen SV, Deininger PL, Batzer MA: Non-traditional Alu evolution and primate genomic diversity. J Mol Biol 2002;316:1033-1040.
20. Ray DA, Xing J, Hedges DJ, Hall MA, Laborde ME, Anders BA, White BR, Stoilova N, Fowlkes JD, Landry KE, Chemnick LG, Ryder OA, Batzer MA: Alu insertion loci and platyrrhine primate phylogeny. Mol Phylogenet Evol 2005;35:117-126.
21. Xing J, Wang H, Han K, Ray DA, Huang CH, Chemnick LG, Stewart CB, Disotell TR, Ryder OA, Batzer MA: A mobile element based phylogeny of Old World monkeys. Mol Phylogenet Evol 2005;37:872-880.
22. Salem AH, Kilroy GE, Watkins WS, Jorde LB, Batzer MA: Recently integrated Alu elements and human genomic diversity. Mol Biol Evol 2003;20:1349-1361.
23. van de Lagemaat LN, Gagnier L, Medstrand P, Mager DL: Genomic deletions and precise removal of transposable elements mediated by short identical DNA segments in primates. Genome Res 2005;15:1243-1249.
24. Batzer MA, Stoneking M, Alegria-Hartman M, Bazan H, Kass DH, Shaikh TH, Novick GE, Ioannou PA, Scheer WD, Herrera RJ, et al: African origin of human-specific polymorphic Alu insertions. Proc Natl Acad Sci USA 1994;91:12288-12292.
25. Otieno AC, Carter AB, Hedges DJ, Walker JA, Ray DA, Garber RK, Anders BA, Stoilova N, Laborde ME, Fowlkes JD, Huang CH, Perodeau B, Batzer MA: Analysis of the human Alu Ya-lineage. J Mol Biol 2004;342:109-118.
26. Terai Y, Takezaki N, Mayer WE, Tichy H, Takahata N, Klein J, Okada N: Phylogenetic relationships among East African haplochromine fish as revealed by short interspersed elements (SINEs). J Mol Evol 2004;58:64-78.
27. Okada N, Shedlock AM, Nikaido M: Retroposon mapping in molecular systematics. Methods Mol Biol 2004;260:189-226.
28. Okada N: SINEs: Short interspersed repeated elements of the eukaryotic genome. Trends Ecol Evol (Amst) 1991;6:358-361.
29. Shedlock AM, Okada N: SINE insertions: powerful tools for molecular systematics. Bioessays 2000;22:148-160.
30. Sherry ST, Harpending HC, Batzer MA, Stoneking M: Alu evolution in human populations: using the coalescent to estimate effective population size. Genetics 1997;147:1977-1982.
31. Stoneking M, Fontius JJ, Clifford SL, Soodyall H, Arcot SS, Saha N, Jenkins T, Tahir MA, Deininger PL, Batzer MA: Alu insertion polymorphisms and human evolution: Evidence for a larger population size in Africa. Genome Res 1997;7:1061-1071.
32. Bamshad MJ, Wooding S, Watkins WS, Ostler CT, Batzer MA, Jorde LB: Human population genetic structure and inference of group membership. Am J Hum Genet 2003;72:578-589.
33. Watkins WS, Rogers AR, Ostler CT, Wooding S, Bamshad MJ, Brassington AM, Carroll ML, Nguyen SV, Walker JA, Prasad BV, Reddy PG, Das PK, Batzer MA, Jorde LB: Genetic variation among world populations: inferences from 100 Alu insertion polymorphisms. Genome Res 2003;13:1607-1618.
34. Watkins WS, Ricker CE, Bamshad MJ, Carroll ML, Nguyen SV, Batzer MA, Harpending HC, Rogers AR, Jorde LB: Patterns of ancestral human diversity: an analysis of Alu-insertion and restriction-site polymorphisms. Am J Hum Genet 2001;68:738-752.
35. Boissinot S, Entezam A, Young L, Munson PJ, Furano AV: The insertional history of an active family of L1 retrotransposons in humans. Genome Res 2004;14:1221-1231.
36. Roy AM, Carroll ML, Kass DH, Nguyen SV, Salem AH, Batzer MA, Deininger PL: Recently integrated human Alu repeats: Finding needles in the haystack. Genetica 1999;107:149-161.
37. Batzer MA, Kilroy GE, Richard PE, Shaikh TH, Desselle TD, Hoppens CL, Deininger PL: Structure and variability of recently inserted Alu family members. Nucleic Acids Res 1990;18:6793-6798.
38. Hedges DJ, Cordaux R, Xing J, Witherspoon DJ, Rogers AR, Jorde LB, Batzer MA: Modeling the amplification dynamics of human alu retrotransposons. PLoS Comput Biol 2005;1:e44.
39. Batzer MA, Rubin CM, Hellmann-Blumberg U, Alegria-Hartman M, Leeflang EP, Stern JD, Bazan HA, Shaikh TH, Deininger PL, Schmid CW: Dispersion and insertion polymorphism in two small subfamilies of recently amplified human Alu repeats. J Mol Biol 1995;247:418-427.
40. Boissinot S, Davis J, Entezam A, Petrov D, Furano AV: Fitness cost of LINE-1 (L1) activity in humans. Proc Natl Acad Sci USA 2006;103:9590-9594.
41. Serre D, Paabo S: Evidence for gradients of human genetic diversity within and among continents. Genome Res 2004;14:1679-1685.
42. Rosenberg NA, Mahajan S, Ramachandran S, Zhao C, Pritchard JK, Feldman MW: Clines, Clusters, and the Effect of Study Design on the Inference of Human Population Structure. PLoS Genet 2005;1:e70.
43. Melton T, Peterson R, Redd AJ, Saha N, Sofro AS, Martinson J, Stoneking M: Polynesian genetic affinities with Southeast Asian populations as identified by mtDNA analysis. Am J Hum Genet 1995;57:403-414.
44. Newman WP, Middaugh JP, Propst MT, Rogers DR: Atherosclerosis in Alaska Natives and non-natives. Lancet 1993;341:1056-1057.
45. 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: Genetic variation of recent Alu insertions in human populations. J Mol Evol 1996;42:22-29.
46. Monson KL, Moisan JP, Pascal O, McSween M, Aubert D, Giusti A, Budowle B, Lavergne L: Description and analysis of allele distribution for four VNTR markers in French and French Canadian populations. Hum Hered 1995;45:135-143.
47. Carroll ML, Roy-Engel AM, Nguyen SV, Salem AH, Vogel E, Vincent B, Myers J, Ahmad Z, Nguyen L, Sammarco M, Watkins WS, Henke J, Makalowski W, Jorde LB, Deininger PL, Batzer MA: Large-scale analysis of the Alu Ya5 and Yb8 subfamilies and their contribution to human genomic diversity. J Mol Biol 2001;311:17-40.
48. Roy AM, Carroll ML, Nguyen SV, Salem AH, Oldridge M, Wilkie AO, Batzer MA, Deininger PL: Potential gene conversion and source genes for recently integrated Alu elements. Genome Res 2000;10:1485-1495.
49. Carter AB, Salem AH, Hedges DJ, Keegan CN, Kimball B, Walker JA, Watkins WS, Jorde LB, Batzer MA: Genome-wide analysis of the human Alu Yb-lineage. Hum Genomics 2004;1:167-178.
50. Wang J, Song L, Grover D, Azrak S, Batzer MA: dbRIP: A Highly Integrated Database of Retrotransposon Insertion Polymorphism in Human. Submitted 2006.
51. Nei M: Molecular Evolutionary Genetics-New York, Columbia University Press, 1987.
52. Montoya-Delgado LE, Irony TZ, de B Pereira CA, Whittle MR: An unconditional exact test for the Hardy-Weinberg equilibrium law: Sample-space ordering using the Bayes factor. Genetics 2001;158:875-883.
53. Nei M: Genetic distance between populations. Am Nat 1972;106:283-292.
54. Felsenstein J: PHYLIP: Phylogenetic Inference Package, Version 3.5. 1993.
55. Pritchard JK, Stephens M, Donnelly P: Inference of population structure using multilocus genotype data. Genetics 2000;155:945-959.
56. Falush D, Stephens M, Pritchard JK: Inference of population structure using multilocus genotype data: Linked loci and correlated allele frequencies. Genetics 2003;164:1567-1587.
57. Smouse PE, Chakraborty R: The use of restriction fragment length polymorphisms in paternity analysis. Am J Hum Genet 1986;38:918-939.
58. Rosenberg NA, Pritchard JK, Weber JL, Cann HM, Kidd KK, Zhivotovsky LA, Feldman MW: Genetic structure of human populations. Science 2002;298:2381-2385.
59. Yang N, Li H, Criswell LA, Gregersen PK, Alarcon-Riquelme ME, Kittles R, Shigeta R, Silva G, Patel PI, Belmont JW, Seldin MF: Examination of ancestry and ethnic affiliation using highly informative diallelic DNA markers: Application to diverse and admixed populations and implications for clinical epidemiology and forensic medicine. Hum Genet 2005;118:382-392.
60. Stringer CB, Andrews P: Genetic and fossil evidence for the origin of modern humans. Science 1988;239:1263-1268.
61. Tishkoff SA, Verrelli BC: Patterns of human genetic diversity: implications for human evolutionary history and disease. Annu Rev Genomics Hum Genet 2003;4:293-340.
62. Corbo RM, Scacchi R: Apolipoprotein E (APOE) allele distribution in the world. Is APOE*4 a 'thrifty' allele? Ann Hum Genet 1999;63(Pt 4):301-310.
63. Cavalli-Sforza L, Menozzi P, Piazza A: The History and Geography of Human Genes. Princeton, Princeton University Press, 1994.
64. Torroni A, Rengo C, Guida V, Cruciani F, Sellitto D, Coppa A, Calderon FL, Simionati B, Valle G, Richards M, Macaulay V, Scozzari R: Do the four clades of the mtDNA haplogroup L2 evolve at different rates? Am J Hum Genet 2001;69:1348-1356.
65. Chen YS, Olckers A, Schurr TG, Kogelnik AM, Huoponen K, Wallace DC: mtDNA variation in the South African Kung and Khwe-and their genetic relationships to other African populations. Am J Hum Genet 2000;66:1362-1383.
66. Forster P, Rohl A, Lunnemann P, Brinkmann C, Zerjal T, Tyler-Smith C, Brinkmann B: A short tandem repeat-based phylogeny for the human Y chromosome. Am J Hum Genet 2000;67:182-196.
67. Underhill PA, Shen P, Lin AA, Jin L, Passarino G, Yang WH, Kauffman E, Bonne-Tamir B, Bertranpetit J, Francalacci P, Ibrahim M, Jenkins T, Kidd JR, Mehdi SQ, Seielstad MT, Wells RS, Piazza A, Davis RW, Feldman MW, Cavalli-Sforza LL, Oefner PJ: Y chromosome sequence variation and the history of human populations. Nat Genet 2000;26:358-361.
68. Hammer MF, Karafet TM, Redd AJ, Jarjanazi H, Santachiara-Benerecetti S, Soodyall H, Zegura SL: Hierarchical patterns of global human Y-chromosome diversity. Mol Biol Evol 2001;18:1189-1203.
69. Mountain JL, Cavalli-Sforza LL: Inference of human evolution through cladistic analysis of nuclear DNA restriction polymorphisms. Proc Natl Acad Sci USA 1994;91:6515-6519.
70. Jorde LB, Bamshad MJ, Watkins WS, Zenger R, Fraley AE, Krakowiak PA, Carpenter KD, Soodyall H, Jenkins T, Rogers AR: Origins and affinities of modern humans: A comparison of mitochondrial and nuclear genetic data. Am J Hum Genet 1995;57:523-538.
71. Deka R, Jin L, Shriver MD, Yu LM, DeCroo S, Hundrieser J, Bunker CH, Ferrell RE, Chakraborty R: Population genetics of dinucleotide (dC-dA)n.(dG-dT)n polymorphisms in world populations. Am J Hum Genet 1995;56:461-474.
72. Bowcock AM, Ruiz-Linares A, Tomfohrde J, Minch E, Kidd JR, Cavalli-Sforza LL: High resolution of human evolutionary trees with polymorphic microsatellites. Nature 1994;368:455-457.
73. Jorde LB, Watkins WS, Bamshad MJ, Dixon ME, Ricker CE, Seielstad MT, Batzer MA: The distribution of human genetic diversity: A comparison of mitochondrial, autosomal, and Y-chromosome data. Am J Hum Genet 2000;66:979-988.
74. Jorde LB, Rogers AR, Bamshad M, Watkins WS, Krakowiak P, Sung S, Kere J, Harpending HC: Microsatellite diversity and the demographic history of modern humans. Proc Natl Acad Sci USA 1997;94:3100-3103.
75. Shriver MD, Mei R, Parra EJ, Sonpar V, Halder I, Tishkoff SA, Schurr TG, Zhadanov SI, Osipova LP, Brutsaert TD, Friedlaender J, Jorde LB, Watkins WS, Bamshad MJ, Gutierrez G, Loi H, Matsuzaki H, Kittles RA, Argyropoulos G, Fernandez JR, Akey JM, Jones KW: Large-scale SNP analysis reveals clustered and continuous patterns of human genetic variation. Hum Genomics 2005;2:81-89.
76. Chen J, Sokal RR, Ruhlen M: Worldwide analysis of genetic and linguistic relationships of human populations. Hum Biol 1995;67:595-612.
77. Weber JL, David D, Heil J, Fan Y, Zhao C, Marth G: Human diallelic insertion/deletion polymorphisms. Am J Hum Genet 2002;71:854-862.
78. Watkins WS, Prasad BV, Naidu JM, Rao BB, Bhanu BA, Ramachandran B, Das PK, Gai PB, Reddy PC, Reddy PG, Sethuraman M, Bamshad MJ, Jorde LB: Diversity and divergence among the tribal populations of India. Ann Hum Genet 2005;69:680-692.
79. Barbujani G, Magagni A, Minch E, Cavalli-Sforza LL: An apportionment of human DNA diversity. Proc Natl Acad Sci USA 1997;94:4516-4519.
80. Rogers AR, Jorde LB: Genetic evidence on modern human origins. Hum Biol 1995;67:1-36.
81. Harpending H, Rogers A: Genetic perspectives on human origins and differentiation. Annu Rev Genomics Hum Genet 2000;1:361-385.
82. Relethford JH: Mutation rate and excess African heterozygosity. Hum Biol 1997;69:785-792.
83. Relethford JH, Jorde LB: Genetic evidence for larger African population size during recent human evolution. Am J Phys Anthropol 1999;108:251-260.
84. Eller E: Population substructure and isolation by distance in three continental regions. Am J Phys Anthropol 1999;108:147-159.
85. Rogers AR, Jorde LB: Ascertainment bias in estimates of average heterozygosity. Am J Hum Genet 1996;58:1033-1041.
86. Nei M, Takezaki N: The root of the phylogenetic tree of human populations. Mol Biol Evol 1996;13:170-177.
87. Tishkoff SA, Williams SM: Genetic analysis of African populations: human evolution and complex disease. Nat Rev Genet 2002;3:611-621.
88. Ramachandran S, Deshpande O, Roseman CC, Rosenberg NA, Feldman MW, Cavalli-Sforza LL: Support from the relationship of genetic and geographic distance in human populations for a serial founder effect originating in Africa. Proc Natl Acad Sci USA 2005;102:15942-15947.
89. Barbujani G, Sokal RR: Genetic population structure of Italy. I. Geographic patterns of gene frequencies. Hum Biol 1991;63:253-272.
90. Barbujani G, Sokal RR: Zones of sharp genetic change in Europe are also linguistic boundaries. Proc Natl Acad Sci USA 1990;87:1816-1819.
91. Turakulov R, Easteal S: Number of SNPS loci needed to detect population structure. Hum Hered 2003;55:37-45.
92. Eswaran V, Harpending H, Rogers AR: Genomics refutes an exclusively African origin of humans. J Hum Evol 2005;49:1-18.