Global Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins
Abstract
Haplotypes consisting of alleles at a short tandem repeat polymorphism (STRP) and an Alu deletion polymorphism at the CD4 locus on chromosome 12 were analyzed in more than 1600 individuals sampled from 42 geographically dispersed populations (13 African, 2 Middle Eastern, 7 European, 9 Asian, 3 Pacific, and 8 Amerindian). Sub-Saharan African populations had more haplotypes and exhibited more variability in frequencies of haplotypes than the Northeast African or non-African populations. The Alu deletion was nearly always associated with a single STRP allele in non-African and Northeast African populations but was associated with a wide range of STRP alleles in the sub-Saharan African populations. This global pattern of haplotype variation and linkage disequilibrium suggests a common and recent African origin for all non-African human populations.
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The relatively high rate of mutation in microsatellites makes possible the assessment of LD that was created recently.
“The relatively high rate of mutation in microsatellites makes possible the assessment of LD that was created recently115,116.”
From Linkage disequilibrium--understanding the evolutionary past and mapping the medical future. (2008) · cites this paper as [115]
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Hanihara, T. (2008) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20792 · Cited by 191 · see citing works
Mathematical properties of the r2 measure of linkage disequilibrium.
VanLiere, J. M., & Rosenberg, N. (2008) · Theoretical Population Biology · doi:10.1016/j.tpb.2008.05.006 · Cited by 190 · see citing works
“LD finds applications in diverse contexts, including the inference of demographic events in human evolutionary history (Tishkoff et al., 1996; Plagnol and Wall, 2006), the fine-mapping of disease genes after localization via linkage analysis (Devlin and Risch, 1995), and the modeling, selection,…”
Association of inhaled corticosteroid use with cataract extraction in elderly patients.
Garbe, E., Suissa, S., & LeLorier, J. (1998) · Journal of the American Medical Association (JAMA) · doi:10.1001/jama.280.6.539 · Cited by 190 · see citing works
Amini, S., Pushkarev, D., Christiansen, L., Kostem, E., Royce, T., Turk, C., Pignatelli, N., Adey, A., Kitzman, J. O., Vijayan, K., et al. (2014) · Nature Genetics · doi:10.1038/ng.3119 · Cited by 189 · see citing works
The DNA revolution in population genetics.
Cavalli-sforza, L. (1998) · Trends in Genetics · doi:10.1016/s0168-9525(97)01327-9 · Cited by 189 · see citing works
Lactase haplotype diversity in the Old World.
Hollox, E., Poulter, M., Zvarík, M., Ferák, V., Krause, A., Jenkins, T., Saha, N., Kozlov, A., & Swallow, D. (2001) · American Journal of Human Genetics · doi:10.1086/316924 · Cited by 188 · see citing works
“1991; Hammer 1995), and small autosomal regions with no significant recombination (Wainscoat et al. 1986; Tishkoff et al. 1996; Bergstrom et al. 1998; Jaruzelska et al. 1999), but, recently, large regions containing autosomal genes usually associated with diseases have been analyzed in a variety of populations (Clark…”
BackgroundSelf-citationMinisatellite diversity supports a recent African origin for modern humans
Armour, J., Anttinen, T., May, C. A., Vega, E., Sajantila, A., Kidd, J., Kidd, K., Bertranpetit, J., Pääbo, S., & Jeffreys, A. (1996) · Nature Genetics · doi:10.1038/ng0696-154 · Cited by 183 · see citing works
Self-citationAdaptive hitchhiking effects on genome variability.
Andolfatto, P. (2001) · Current Opinion in Genetics and Development · doi:10.1016/s0959-437x(00)00246-x · Cited by 181 · see citing works
Tishkoff, S. A., Goldman, A., Calafell, F., Speed, W. C., Deinard, A., Bonné-Tamir, B., Kidd, J., Pakstis, A., Jenkins, T., & Kidd, K. (1998) · American Journal of Human Genetics · doi:10.1086/301861 · Cited by 181 · see citing works
“Thus, these data are consistent with the “out of Africa” hypothesis of modern human origins, which purports that all human populations descend from an anatomically modern Homo sapiens population that migrated out of Africa »100,000 years ago ( Stringer and Andrews 1988 ).”
ResultSelf-citationMicrohaplotypes in forensic genetics
Oldoni, F., Kídd, K. K., & Podini, D. S. (2018) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2018.09.009 · Cited by 209 · see citing works
Self-citationGenetic dissection of myocilin glaucoma.
Gong, G., Kosoko-Lasaki, O., Haynatzki, G., & Wilson, M. (2004) · Human Molecular Genetics · doi:10.1093/hmg/ddh074 · Cited by 175 · see citing works
“All modern humans are descendants of about 10 000 (effect size) founders (118,119) 100 000–160 000 years ago (84,85).”
BackgroundHaplotype analysis in population genetics and association studies
Zhao, H., Pfeiffer, R. M., & Gail, M. H. (2003) · Pharmacogenomics · doi:10.1517/phgs.4.2.171.22636 · Cited by 167 · see citing works
“Population genetics of haplotypes and linkage disequilibrium Linkage disequilibrium A study of haplotypes consisting of a short tandem repeat polymorphism (STRP) and an Alu deletion polymorphism at the CD4 locus in 42 worldwide populations first demonstrated the usefulness of comparing LD patterns of different populat…”
BackgroundPääbo, S. (2003) · Nature · doi:10.1038/nature01400 · Cited by 174 · see citing works
Self-citationSNP and haplotype variation in the human genome.
Salisbury, B. A., Pungliya, M., Choi, J. Y., Jiang, R., Sun, X., & Stephens, J. (2003) · Mutation research · doi:10.1016/s0027-5107(03)00014-9 · Cited by 170 · see citing works
“These trends are well documented by others [4,11–14].”
Assessing the performance of the haplotype block model of linkage disequilibrium.
Wall, J., & Pritchard, J. (2003) · American Journal of Human Genetics · doi:10.1086/378099 · Cited by 168 · see citing works
“, a temporary sharp reduction in effective population size) (Tishkoff et al. 1996; Reich et al. 2001), and bottlenecks are known to”
BackgroundThe biology of the colonizing ape
Wells, J. C. K., & Stock, J. T. (2007) · American Journal of Physical Anthropology · doi:10.1002/ajpa.20735 · Cited by 198 · see citing works
“There is clear evidence for the controlled use of fire in northern Europe by 400 KYA, associated with Homo heidelbergensis (Gowlett, 2006) suggesting that such technological innovation, if not associated with the dispersal of this species (Foley, 2002), was at least necessary for the colonization of northern latitudes.”
BackgroundInfluentialPassarino, G., Semino, O., Quintana-Murci, L., Excoffier, L., Hammer, M., & Santachiara-Benerecetti, A. (1998) · American Journal of Human Genetics · doi:10.1086/301702 · Cited by 166 · see citing works
“a mismatched primer (see Torroni et al. [1996]).”
BackgroundSelf-citationLuminescence dating in archaeology:from origins to optical
Roberts, R. (1997) · Radiation Measurements · doi:10.1016/s1350-4487(97)00221-7 · Cited by 166 · see citing works
Oota, H., Pakstis, A., Bonné-Tamir, B., Goldman, D., Grigorenko, E., Kajuna, S. L. B., Karoma, N. J., Kungulilo, S., Lu, R., Odunsi, K., et al. (2004) · Annals of Human Genetics · doi:10.1046/j.1529-8817.2003.00060.x · Cited by 165 · see citing works
“Haplotype and linkage disequilibrium (LD) analyses have been widely applied to disease gene mapping and understanding human population history (Castiglione et al. 1995; Jorde, 1995; Tishkoff et al. 1996, 1998; Laan & Pääbo, 1997; Kidd et al. 1998, 2000; Reich et al. 2001; DeMille et al. 2002).”
BackgroundInfluentialSelf-citationEvidence for balancing selection from nucleotide sequence analyses of human G6PD.
Verrelli, B., McDonald, J., Argyropoulos, G., Destro-Bisol, G., Froment, A., Drousiotou, A., Lefranc, G., Helal, A., Loiselet, J., & Tishkoff, S. (2002) · American Journal of Human Genetics · doi:10.1086/344345 · Cited by 160 · see citing works
“These observations support a recent ancestry for the A allele class, which is consistent with the microsatellite and LD analyses by Tishkoff et al. (2001). These results also suggest that the A allele may have recently risen to intermediate frequency as well.”
BackgroundResultSelf-citationEvans, P. D., Mekel-Bobrov, N., Vallender, E. J., Hudson, R. R., & Lahn, B. T. (2006) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0606966103 · Cited by 153 · see citing works
Bhangale, T., Rieder, M., Livingston, R. J., & Nickerson, D. (2005) · Human Molecular Genetics · doi:10.1093/hmg/ddi006 · Cited by 151 · see citing works
“The bottleneck in recent history of non-African populations is often considered as an explanation for the high levels of LD observed in the ED population (57,58).”
Background
- Authors
- Tishkoff, S. A., Dietzsch, E., Speed, W., Pakstis, A. J., Kidd, J. R., Cheung, K., Bonné-Tamir, B., Santachiara-Benerecetti, A. S., Moral, P., Krings, M., Pääbo, S., Watson, E., Risch, N., Jenkins, T., & Kidd, K. K.
- Affiliations
- Yale University (US)
- University of the Witwatersrand (ZA)
- B. Bonné-Tamir is in the Department of Human Genetics, Sackler Faculty of Medicine, Tel Aviv University, 69978 Ramat Aviv, Israel.
- A. S. Santachiara-Benerecetti is in the Buzzati Traverso Department of Genetics and Microbiology, University of Pavia, Via Abbiategrasso 207, 27100 Pavia, Italy.
- Universitat de Barcelona (ES)
- Ludwig-Maximilians-Universität München (DE)
- Massey University (NZ)
- Stanford Medicine (US)
- S. A. Tishkoff, W. Speed, A. J. Pakstis, J. R. Kidd, K. Cheung, and K. K. Kidd are in the Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8005, USA.
- Venue
- Science
- Published
- 1996-03-08
- Volume
- 271
- Issue
- 5254
- Pages
- 1380-1387
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- OpenAlex
- W1971604012
- Cited by
- 587
- References
- 64
- Citations by year
- 2026: 2 · 2025: 5 · 2024: 4 · 2023: 3 · 2022: 2 · 2021: 9 · 2020: 5 · 2019: 1 · 2018: 8 · 2017: 6 · 2016: 5 · 2015: 9 · 2014: 12 · 2013: 10 · 2012: 14
- FWCI
- 27.44
- Type
- journal article
- Language
- en
- Open access
- closed
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- MPG.PuRe (Max Planck Society) (submittedVersion)
- Funders
- National Institutes of Health (5r01hg000348-09)
- National Institute on Alcohol Abuse and Alcoholism (R01AA009379, AA09379)
- National Institute of Mental Health (MH39 239)
- National Human Genome Research Institute (HG00348)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Associations and Epidemiology
- Keywords
- linkage disequilibrium, chromosome 12, short tandem repeat polymorphism, haplotype variation, human origins, African origin of modern humans, sub-Saharan African populations, population genetics
- MeSH terms
- Africa, Alleles, Animals, Base Sequence, Chromosomes, Human, Pair 12, Gene Frequency, Haplotypes, Humans, Molecular Sequence Data, Polymorphism, Genetic, Primates, Repetitive Sequences, Nucleic Acid, Genetic Variation, Hominidae, CD4 Antigens, Linkage Disequilibrium, Sequence Deletion, Evolution, Molecular
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