A comparison of the variability spectra of two genomic loci in a European group of individuals reveals fundamental differences pointing to selection or a population bottleneck

Annals of Human Genetics

Volumn 71, Issue 3, 2007, Pages 370-378

  Schmegner, C ^a   Hoegel, J ^a   Vogel, W ^a   Assum, Guenter ^a  

^a UNIVERSITY OF ULM   (Germany)

Author keywords

Ancient European subpopulations; Genetic variability; Long range LD; Population genetics

Indexed keywords

ARTICLE; BOTTLENECK POPULATION; CHROMOSOME 17; CHROMOSOME 22; CLINICAL ARTICLE; COMPARATIVE STUDY; CONTROLLED STUDY; DEMOGRAPHY; EUROPE; GENE FREQUENCY; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC RECOMBINATION; GENETIC VARIABILITY; HAPLOTYPE; HUMAN; NATURAL SELECTION; PRIORITY JOURNAL; SEQUENCE ANALYSIS;

CHROMOSOMES, HUMAN, PAIR 17; CHROMOSOMES, HUMAN, PAIR 22; DNA; EUROPEAN CONTINENTAL ANCESTRY GROUP; EVOLUTION, MOLECULAR; GENETICS, POPULATION; GERMANY; HAPLOTYPES; HUMANS; LINKAGE DISEQUILIBRIUM; MODELS, GENETIC; PHYLOGENY; POLYMORPHISM, SINGLE NUCLEOTIDE; SELECTION (GENETICS); VARIATION (GENETICS);

EID: 34247124140     PISSN: 00034800     EISSN: 14691809     Source Type: Journal    
DOI: 10.1111/j.1469-1809.2006.00342.x     Document Type: Article

References (38)

1. Akey, J. M., Eberle, M. A., Rieder, M. J., Carlson, C. S., Shriver, M. D., Nickerson, D. A. & Kruglyak, L. (2004) Population history and natural selection shape patterns of genetic variation in 132 genes. PLoS Biol 2, e286.
2. Alonso, S. & Armour, J. A. (2004) Compound haplotypes at Xp11. 23 and human population growth in Eurasia. Ann Hum Genet 68, 428-437.
3. Balciuniene, J., Syvanen, A. C., McLeod, H. L., Pettersson, U. & Jazin, E. E. (2001) The geographic distribution of monoamine oxidase haplotypes supports a bottleneck during the dispersion of modern humans from Africa. J Mol Evol 52, 157-163.
4. Barbujani, G. & Bertorelle, G. (2001) Genetics and the population history of Europe. Proc Natl Acad Sci USA 98, 22-25.
5. Chikhi, L., Nichols, R. A., Barbujani, G. & Beaumont, M. A. (2002) Y genetic data support the Neolithic demic diffusion model. Proc Natl Acad Sci USA 99, 11008-11013.
6. Clark, A. G., Weiss, K. M., Nickerson, D. A., Taylor, S. L., Buchanan, A., Stengard, J., Salomaa, V., Vartiainen, E., Perola, M., Boerwinkle, E. & Sing, C. F. (1998) Haplotype structure and population genetic inferences from nucleotide-sequence variation in human lipoprotein lipase. Am J Hum Genet 63, 595-612.
7. Devlin, B. & Risch, N. (1995) A comparison of linkage disequilibrium measures for fine-scale mapping. Genomics 29, 311-322.
8. Dupanloup, I., Bertorelle, G., Chikhi, L. & Barbujani, G. (2004) Estimating the impact of prehistoric admixture on the genome of Europeans. Mol Biol Evol 21, 1361-1372.
9. Eisenbarth, I., Striebel, A. M., Moschgath, E., Vogel, W. & Assum, G. (2001) Long-range sequence composition mirrors linkage disequilibrium pattern in a 1.13 Mb region of human chromosome 22. Hum Mol Genet 10, 2833-2839.
10. Evans, P. D., Gilbert, S. L., Mekel-Bobrov, N., Vallender, E. J., Anderson, J. R., Vaez-Azizi, L. M., Tishkoff, S. A., Hudson, R. R. & Lahn, B. T. (2005) Microcephalin, a gene regulating brain size, continues to evolve adaptively in humans. Science 309, 1717-1720.
11. Fay, J. C. & Wu, C. I. (2000) Hitchhiking under positive Darwinian selection. Genetics 155, 1405-1413.
12. Fu, Y. X. & Li, W. H. (1993) Statistical tests of neutrality of mutations. Genetics 133, 693-709.
13. Griffiths, R. C. & Tavare, S. (1994) Simulating Probability Distributions in the Coalescent. Theoretical Population Biology 46, 131-159.
14. Haak, W., Forster, P., Bramanti, B., Matsumura, S., Brandt, G., Tanzer, M., Villems, R., Renfrew, C., Gronenborn, D., Alt, K. W. & Burger, J. (2005) Ancient DNA from the first European farmers in 7500-year-old Neolithic sites. Science 310, 1016-1018.
15. Hammer, M. F., Garrigan, D., Wood, E., Wilder, J. A., Mobasher, Z., Bigham, A., Krenz, J. G. & Nachman, M. W. (2004) Heterogeneous patterns of variation among multiple human x-linked Loci: The possible role of diversity-reducing selection in non-africans. Genetics 167, 1841-1853.
16. Harding, R. M., Fullerton, S. M., Griffiths, R. C., Bond, J., Cox, M. J., Schneider, J. A., Moulin, D. S. & Clegg, J. B. (1997) Archaic African and Asian lineages in the genetic ancestry of modern humans. Am J Hum Genet 60, 772-789.
17. Harpending, H. & Rogers, A. (2000) Genetic perspectives on human origins and differentiation. Annu Rev Genomics Hum Genet 1, 361-385.
18. Kayser, M., Brauer, S. & Stoneking, M. (2003) A genome scan to detect candidate regions influenced by local natural selection in human populations. Mol Biol Evol 20, 893-900.
19. Marth, G. T., Czabarka, E., Murvai, J. & Sherry, S. T. (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.
20. Mekel-Bobrov, N., Gilbert, S. L., Evans, P. D., Vallender, E. J., Anderson, J. R., Hudson, R. R., Tishkoff, S. A. & Lahn, B. T. (2005) Ongoing adaptive evolution of ASPM, a brain size determinant in Homo sapiens. Science 309, 1720-1722.
21. Plagnol, V. & Wall, J. D. (2006) Possible Ancestral Structure in Human Populations. PloS Genet 2, e105.
22. Richards, M., Macaulay, V., Hickey, E., Vega, E., Sykes, B., Guida, V., Rengo, C., Sellitto, D., Cruciani, F., Kivisild, T., Villems, R., Thomas, M., Rychkov, S., Rychkov, O., Rychkov, Y., Golge, M., Dimitrov, D., Hill, E., Bradley, D., Romano, V., Cali, F., Vona, G., Demaine, A., Papiha, S., Triantaphyllidis, C., Stefanescu, G., Hatina, J., Belledi, M., Di Rienzo, A., Novelletto, A., Oppenheim, A., Norby, S., Al Zaheri, N., Santachiara-Benerecetti, S., Scozari, R., Torroni, A. & Bandelt, H. J. (2000) Tracing European founder lineages in the Near Eastern mtDNA pool. Am J Hum Genet 67, 1251-1276.
23. Rozas, J., Sanchez-DelBarrio, J. C., Messeguer, X. & Rozas, R. (2003) DnaSP, DNA polymorphism analyses by the coalescent and other methods. Bioinformatics 19, 2496-2497.
24. Sabeti, P. C., Reich, D. E., Higgins, J. M., Levine, H. Z., Richter, D. J., Schaffner, S. F., Gabriel, S. B., Platko, J. V., Patterson, N. J., McDonald, G. J., Ackerman, H. C., Campbell, S. J., Altshuler, D., Cooper, R., Kwiatkowski, D., Ward, R. & Lander, E. S. (2002) Detecting recent positive selection in the human genome from haplotype structure. Nature 419, 832-837.
25. Schmegner, C., Hoegel, J., Vogel, W. & Assum, G. (2005) Genetic variability in a genomic region with long-range linkage disequilibrium reveals traces of a bottleneck in the history of the European population. Hum Genet 118, 276-286.
26. Semino, O., Passarino, G., Oefner, P. J., Lin, A. A., Arbuzova, S., Beckman, L. E., De Benedictis, G., Francalacci, P., Kouvatsi, A., Limborska, S., Marcikiae, M., Mika, A., Mika, B., Primorac, D., Santachiara-Benerecetti, A. S., Cavalli-Sforza, L. L. & Underhill, P. A. (2000) The genetic legacy of Paleolithic Homo sapiens sapiens in extant Europeans: A Y chromosome perspective. Science 290, 1155-1159.
27. Soejima, M., Tachida, H., Ishida, T., Sano, A. & Koda, Y. (2006) Evidence for recent positive selection at the human AIM1 locus in a European population. Mol Biol Evol 23, 179-188.
28. Stajich, J. E. & Hahn, M. W. (2005) Disentangling the effects of demography and selection in human history. Mol Biol Evol 22, 63-73.
29. Stephens, J. C., Schneider, J. A., Tanguay, D. A., Choi, J., Acharya, T., Stanley, S. E., Jiang, R., Messer, C. J., Chew, A., Han, J. H., Duan, J., Carr, J. L., Lee, M. S., Koshy, B., Kumar, A. M., Zhang, G., Newell, W. R., Windemuth, A., Xu, C., Kalbfleisch, T. S., Shaner, S. L., Arnold, K., Schulz, V., Drysdale, C. M., Nandabalan, K., Judson, R. S., Ruano, G. & Vovis, G. F. (2001) Haplotype variation and linkage disequilibrium in 313 human genes. Science 293, 489-493.
30. Stephens, M. & Donnelly, P. (2003) A comparison of bayesian methods for haplotype reconstruction from population genotype data. Am J Hum Genet 73, 1162-1169.
31. Storz, J. F., Payseur, B. A. & Nachman, M. W. (2004) Genome scans of DNA variability in humans reveal evidence for selective sweeps outside of Africa. Mol Biol Evol 21, 1800-1811.
32. Tajima, F. (1989) Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585-595.
33. The International HapMap Consortium (2005) A haplotype map of the human genome. Nature 437, 1299-1320.
34. Voight, B. F., Adams, A. M., Frisse, L. A., Qian, Y., Hudson, R. R. & Di Rienzo, A. (2005) Interrogating multiple aspects of variation in a full resequencing data set to infer human population size changes. Proc Natl Acad Sci USA 102, 18508-18513.
35. Voight, B. F., Kudaravalli, S., Wen, X. & Pritchard, J. K. (2006) A map of recent positive selection in the human genome. PLoS Biol 4, e72.
36. Walsh, E. C., Sabeti, P., Hutcheson, H. B., Fry, B., Schaffner, S. F., de Bakker, P. I., Varilly, P., Palma, A. A., Roy, J., Cooper, R., Winkler, C., Zeng, Y., de The, G., Lander, E. S., O'Brien, S. & Altshuler, D. (2006) Searching for signals of evolutionary selection in 168 genes related to immune function. Hum Genet 119, 92-102.
37. Yu, N., Zhao, Z., Fu, Y. X., Sambuughin, N., Ramsay, M., Jenkins, T., Leskinen, E., Patthy, L., Jorde, L. B., Kuromori, T. & Li, W. H. (2001) Global patterns of human DNA sequence variation in a 10-kb region on chromosome 1. Mol Biol Evol 18, 214-222.
38. Zhao, Z., Jin, L., Fu, Y. X., Ramsay, M., Jenkins, T., Leskinen, E., Pamilo, P., Trexler, M., Patthy, L., Jorde, L. B., Ramos-Onsins, S., Yu, N. & Li, W. H. (2000) Worldwide DNA sequence variation in a 10-kilobase noncoding region on human chromosome 22. Proc Natl Acad Sci USA 97, 11354-11358.