Detecting recent positive selection in the human genome from haplotype structure

Nature - Tập 419 Số 6909 - Trang 832-837 - 2002
Pardis C. Sabeti1, David Reich2, John M. Higgins2, Haninah Z P Levine2, Daniel J. Richter2, S. F. Schaffner2, Stacey Gabriel2, Jill Platko2, Nick Patterson2, Gavin J McDonald2, Hans Ackerman3, Sarah J. Pickett3, David Green4,2, Richard Cooper5, Dominic Kwiatkowski3, Ryk Ward6, Eric S. Lander2
1Whitehead Institute / MIT Center for Genome Research, Nine Cambridge Center, Cambridge, Massachusetts 02142, USA.
2Whitehead Institute/MIT Center for Genome Research, Nine Cambridge Center, Cambridge, USA
3Wellcome Trust Centre for Human Genetics, Oxford, UK
4Departments of Genetics and Medicine, Harvard Medical School, Department of Molecular Biology and Diabetes Unit, Massachusetts General Hospital, Boston, USA
5Department of Preventive Medicine and Epidemiology, Loyola University Medical School, Maywood, USA
6Institute of Biological Anthropology, University of Oxford, Oxford, UK

Tóm tắt

Từ khóa


Tài liệu tham khảo

Ruwende, C. & Hill, A. Glucose-6-phosphate dehydrogenase deficiency and malaria. J. Mol. Med. 76, 581–588 (1998)

Sabeti, P. et al. CD40L association with protection from severe malaria. Genes Immun. 3, 286–291 (2002)

Cavalli-Sforza, L. L., Menozzi, P. & Piazza, A. The History and Geography of Human Genes (Princeton Univ. Press, Princeton, 1994)

Kimura, M. The Neutral Theory of Molecular Evolution (Cambridge Univ. Press, Cambridge/New York, 1983)

Stephens, J. C. et al. Dating the origin of the CCR5-Delta32 AIDS-resistance allele by the coalescence of haplotypes. Am. J. Hum. Genet. 62, 1507–1515 (1998)

Hudson, R. R. & Kaplan, N. L. Statistical properties of the number of recombination events in the history of a sample of DNA sequences. Genetics 111, 147–164 (1985)

Lewontin, R. The interaction of selection and linkage. I. General considerations; heterotic models. Genetics 49, 49–67 (1964)

Nei, M. Molecular Evolutionary Genetics Eqn. 8.4 (Columbia Univ. Press, New York, 1987)

Luzatto, L., Mehta, A. & Vulliamy, T. The Metabolic & Molecular Bases of Inherited Disease 4517–4553 (McGraw-Hill, New York, 2001)

Raymond, M. & Rousset, F. An exact test for population differentiation. Evolution 49, 1280–1283 (1995)

Hudson, R. R. Properties of a neutral allele model with intragenic recombination. Theor. Popul. Biol. 23, 183–201 (1983)

Reich, D. E. & Goldstein, D. B. Microsatellites: Evolution and Applications 128–138 (Oxford Univ. Press, Oxford/New York, 1999)

Tishkoff, S. A. et al. Haplotype diversity and linkage disequilibrium at human G6PD: recent origin of alleles that confer malarial resistance. Science 293, 455–462 (2001)

Rozas, J. & Rozas, R. DnaSP version 3: an integrated program for molecular population genetics and molecular evolution analysis. Bioinformatics 15, 174–175 (1999)

Tajima, F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. Genetics 123, 585–595 (1989)

Fu, Y. X. & Li, W. H. Statistical tests of neutrality of mutations. Genetics 133, 693–709 (1993)

Fay, J. C. & Wu, C. I. Hitchhiking under positive Darwinian selection. Genetics 155, 1405–1413 (2000)

Hughes, A. L. & Nei, M. Pattern of nucleotide substitution at major histocompatibility complex class I loci reveals overdominant selection. Nature 335, 167–170 (1988)

McDonald, J. H. & Kreitman, M. Adaptive protein evolution at the Adh locus in Drosophila. Nature 351, 652–654 (1991)

Hudson, R. R., Kreitman, M. & Aguade, M. A test of neutral molecular evolution based on nucleotide data. Genetics 116, 153–159 (1987)

Gabriel, S. B. et al. The structure of haplotype blocks in the human genome. Science 23, 2225–2229 (2002)

Wootton, J. C. et al. Genetic diversity and chloroquine selective sweeps in Plasmodium falciparum. Nature 418, 320–323 (2002)

Tang, K. et al. Chip-based genotyping by mass spectrometry. Proc. Natl Acad. Sci. USA 96, 10016–10020 (1999)

Vulliamy, T. J. et al. Linkage disequilibrium of polymorphic sites in the G6PD gene in African populations and the origin of G6PD A. Gene Geogr. 5, 13–21 (1991)

Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature 409, 928–933 (2001)

Reich, D. E. et al. Linkage disequilibrium in the human genome. Nature 411, 199–204 (2001)