Cited by 587Forensic and Genetic ResearchGenetic diversity and population structureGenetic Associations and Epidemiology

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Global Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins

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.·1996·Science

DOI 10.1126/science.271.5254.1380

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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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Mitochondrial DNA and human evolution
Cann, R. L., Stoneking, M., & Wilson, A. C. (1987) · Nature · doi:10.1038/325031a0 · Cited by 3,100

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“Over the years haplotype analysis has emerged as a powerful tool for gaining insights into the population dynamics as it gives more meaningful insights both in evolutionary studies and disease-association studies than unlinked markers (Tishkoff et al., 1996; The International HapMap Consortium, 2005; Plagnol and Wall,…”
Influential
Origin of modern humans in East Asia: clues from the Y chromosome
Shi, H., & Su, B. (2009) · Frontiers of Biology in China · doi:10.1007/s11515-009-0010-0 · Cited by 10
“The autosomal (Bowcock et al., 1994; Tishkoff et al., 1996; Chu et al., 1998; Jin et al., 1999) and mtDNA (Harihara et al., 1988; Vigilant et al., 1991; Ballinger et al., 1992; Yao et al., 2000; Yao et al., 2002; Wen et al., 2004b, 2005) evidences support an African ancestry of modern humans in…”
Background
A reanalysis of 409 European‐Ancestry and African American schizophrenia pedigrees reveals significant linkage to 8p23.3 with evidence of locus heterogeneity
Holliday, E., Mowry, B. J., & Nyholt, D. (2008) · American Journal of Medical Genetics Part B: Neuropsychiatric Genetics · doi:10.1002/ajmg.b.30722 · Cited by 10
“…allele frequencies show that individuals of European/Caucasian or African ancestry represent genetically distinct populations [Bowcock et al., 1991; Tishkoff et al., 1996; Perez-Lezaun et al., 1997] and direct comparisons of marker allele frequencies also indicate significant differences between…”
Nonsynonymous SNPs: validation characteristics, derived allele frequency patterns, and suggestive evidence for natural selection
Fredman, D., Sawyer, S., Stromqvist, L., Mottagui-Tabar, S., Kidd, K., Wahlestedt, C., Chanock, S., & Brookes, A. (2006) · Human Mutation · doi:10.1002/humu.20289 · Cited by 10
“Published studies on the question of human genome evolution have begun to identify genes and regions marked by evidence of selection [Tishkoff et al., 1996; Salamon et al., 1999; Huttley et al., 2000; Akey et al., 2002; Osier et al., 2002; Sabeti et al., 2002; Shen et al., 2002; Gilad and Lancet, 2003; Kayser et al.,…”
BackgroundSelf-citation
On the Distribution of K-tuple Matches for Sequence Homology: A Constant Time Exact Calculation of the Variance
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SNPs: why do we care?
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Evolution of a D2 Dopamine Receptor Intron Within the Great Apes and Humans
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Self-citation
Evolution, genetic diversity, and health
Palma-Martínez, M. J., Posadas‐García, Y. S., Shaukat, A., López-Ángeles, B. E., & Sohail, M. (2025) · Nature Medicine · doi:10.1038/s41591-025-03558-1 · Cited by 13
“One example is the Out-of-Africa migration, which caused a bottleneck and decreased the genetic diversity found in humans that populated the rest of the world 17 .”
Multiple haplotype reconstruction from allele frequency data
Pelizzola, M., Behr, M., Li, H., Munk, A., & Futschik, A. (2021) · Nature Computational Science · doi:10.1038/s43588-021-00056-5 · Cited by 13
Recent out of Yemen: new version of the theory of unique and recent origin of modern man
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Migration and transcultural psychiatry in Europe
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“Borra [1] suggest that asking culture-related questions leads to a culturally sensitive therapy, to more empathy and better understanding of a client with a different cultural background and illustrates this hypothesis with a case report [16].”
Background
The genetics of African Americans: Implications for disease gene mapping and identity
Kittles, R., & Royal, C. (2003) · doi:10.1525/9780520929975-015 · Cited by 9
Ethnic divergence and linkage disequilibrium of novel SNPs in the human NLI-IF gene: evidence of human origin and lack of association with tuberculosis susceptibility
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“Accumulating evidence from human mitochondrial DNA (mtDNA) (Cann et al. 1987), Y chromosome DNA (Underhill et al. 2000), and nuclear autosome DNA (Tishkoff et al. 1996) studies has strongly argued for the recent African origin model or the “out-of-Africa” model, and against the multiregional…”
BackgroundInfluential
Interbreeding between farmers and hunter-gatherers along the inland and Mediterranean routes of Neolithic spread in Europe
Fort, J., & Pérez-Losada, J. (2024) · Nature Communications · doi:10.1038/s41467-024-51335-4 · Cited by 8
Genetic Variation in TLR Genes in Ugandan and South African Populations and Comparison with HapMap Data
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“%) is slightly higher than that described for Europeans and North Africans.”
BackgroundMethodResultInfluentialSelf-citation
Genetic Differentiation of the Population of Central Asia Inferred from Autosomal Markers
Khitrinskaya, I., Stepanov, V., Puzyrev, V. P., Spiridonova, M., & Voevoda, M. (2003) · Russian Journal of Genetics · doi:10.1023/a:1026183112690 · Cited by 8
“In contrast to other Alu repeats, the presence of an insertion is primary for CD4 ; primates (chimpanzee, gibbons, and gorillas) are monomorphic for Alu(+) [ 15 ].”
High-throughput analysis of informative CYP2D6 compound haplotypes.
Fletcher, B., Goldstein, D., Bradman, A. L. R., Weale, M., Bradman, N., & Thomas, M. G. (2003) · Genomics · doi:10.1016/s0888-7543(02)00031-9 · Cited by 8
“More recently, compound haplotypes made up of combinations of microsatellites and “simple nucleotide polymorphisms” (SNPs) have been used extensively to differentiate populations [19], study human migration in prehistory [20], date events in prehistory [21], and estimate the age of mutations [22].”
Background
Lipoprotein lipase and APOE/APOC‐I/APOC‐II gene cluster diversity in native Brazilian populations
de Andrade, F. D., Ewald, G., Salzano, F., & Hutz, M. (2002) · American Journal of Human Biology · doi:10.1002/ajhb.10064 · Cited by 8
HumCD4--validation of a STR system for forensic purposes in an Austrian Caucasian population sample.
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Patterns of hemoglobin polymorphism [α-globin (HBA) and β-globin (HBB)] across the contact zone of two distinct phylogeographic lineages of the European rabbit (Oryctolagus cuniculus)
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“There is now a wide range of statistical tests available to assess deviations from the neutral model using nucleotide sequence data (e.g. Hudson et al. 1987; Tajima 1989 ).”
Method
Selection Selection on mitochondrial DNA and the Neanderthal problem
Hawks, J. (2006) · Vertebrate paleobiology and paleoanthroplogy series/Vertebrate paleobiology and paleoanthropology series · doi:10.1007/978-1-4020-5121-0_12 · Cited by 8
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Recombination networks as genetic markers in a human variation study of the Old World
Javed, A., Melé, M., Pybus, M., Zalloua, P., Haber, M., Comas, D., Netea, M. G., Balanovsky, O., Balanovska, E. V., Li, J., et al. (2011) · Human Genetics · doi:10.1007/s00439-011-1104-8 · Cited by 6
Genetic Factors in Reproduction and Their Evolutionary Significance
Gill, T. J. (1997) · American Journal of Reproductive Immunology · doi:10.1111/j.1600-0897.1997.tb00187.x · Cited by 7
Genetic data and the african origin of humans.
Pritchard, J., & Feldman, M. (1996) · Science · doi:10.1126/science.274.5292.1548a · Cited by 7
Analyses of the COGA data set in one ethnic group with examinations of alternative definitions of alcoholism
Sheffield, L., Knauert, M., Pakstis, A., Zhao, H.-Y., & Kidd, K. (1999) · Genetic Epidemiology · doi:10.1002/gepi.1370170754 · Cited by 7
Self-citation
The importance of including ethnically diverse populations in studies of quantitative trait evolution
McQuillan, M. A., Zhang, C., Tishkoff, S. A., & Platt, A. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.05.037 · Cited by 8
Self-citation
[Advances in haplotype analysis technique].
Li, S.-S., Zhang, Y.-X., Fan, C.-M., Chen, Y.-H., Deng, C.-L., & Hu, Z. (2018) · Sheng wu gong cheng xue bao = Chinese journal of biotechnology · doi:10.13345/j.cjb.170451 · Cited by 6
“单倍型技术主要应用领域包括:在医学上探索致病机理,挖掘致病基因,寻找疾病治疗新方法([8-10]); 在群体遗传学上分析等位基因间差异([2,11-12]),追踪个体亲缘关系([13]),了解生物迁徙模式和进化历史([14-16]);”
Population data of six Alu insertions in indigenous groups from Sabah, Malaysia
Kee, B. P., Chua, K. H., Lee, P. C., & Lian, L. H. (2012) · Annals of Human Biology · doi:10.3109/03014460.2012.719548 · Cited by 2
“23, were selected and typed in all samples with primer sets reported in previous studies (Batzer et al. 1994; Arcot et al. 1996; Tishkoff et al. 1996).”
Result
Geographic and Ethnic Differences in the Prevalence of Thrombophilia
Salazar-Sánchez, L. (2011) · doi:10.5772/28405 · Cited by 6
“sapiens ancestor that evolved in Africa approximately 100,000 to 200,000 years ago and then spread and diversified throughout the rest of the world (Tishkoff et al., 1996; Zivellin et al., 1997).”
Background
Anthropological Genetics: Inferring the History of Our Species Through the Analysis of DNA
Hodgson, J. A., & Disotell, T. R. (2010) · Evolution Education and Outreach · doi:10.1007/s12052-010-0262-9 · Cited by 8
“For example, CD4, a gene located on human chromosome 12, shows a pattern very similar to that seen with mitochondria and Y-chromosomes (Tishkoff et al. 1996).”
BackgroundInfluential
A Consensus Tree Approach for Reconstructing Human Evolutionary History and Detecting Population Substructure
Tsai, M.-C., Blelloch, G., Ravi, R., & Schwartz, R. (2010) · IEEE/ACM Transactions on Computational Biology & Bioinformatics · doi:10.1109/tcbb.2011.23 · Cited by 6
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A war-prone tribe migrated out of Africa to populate the world.Preprint
Moreno, E. (2010) · Nature Precedings · doi:10.1038/npre.2010.4303.1 · Cited by 5
Haplotype analysis and phylogeny of ornithine transcarbamylase polymorphisms
Azevedo, L., Calafell, F., Vilarinho, L., & Amorim, A. (2002) · Annals of Human Genetics · doi:10.1046/j.1469-1809.2002.00129.x · Cited by 6
MODELING THE GENETIC ARCHITECTURE OF MODERN POPULATIONS
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Genetic Data and the African Origin of Humans
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Self-citation
Infectious Disease and Host–Pathogen Evolution: G6PD Deficiency and Malarial Resistance in Humans: Insights from Evolutionary Genetic Analyses
Tishkoff, S., & Verrelli, B. (2004) · Cambridge University Press eBooks · doi:10.1017/cbo9780511546259.006 · Cited by 6
Self-citation
Mitochondrial DNA Variation in the Southwest Pacific
Merriwether, D. A., Kaestle, F. A., Zemel, B. S., Koki, G., Mgone, C. S., Alpers, M. P., & Friedlaender, J. S. (1999) · Springer eBooks · doi:10.1007/978-1-4615-4263-6_12 · Cited by 6
Highly Accurate and Efficient Data-Driven Methods for Genotype Imputation
Choudhury, O., Chakrabarty, A., & Emrich, S. (2017) · IEEE Transactions on Computational Biology and Bioinformatics · doi:10.1109/tcbb.2017.2708701 · Cited by 8
“Other downstream analyses include identifying recombinant breakpoints [2], deducing history of human demographics [3], and modeling cisregulation of gene expression [4].”
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.
ORCID: Tishkoff, S. A.
Pakstis, A. J.
Moral, P.
Pääbo, S.
Risch, N.
Jenkins, T.
Venue: Science
Publisher: American Association for the Advancement of Science (AAAS)
Published: 1996-03-08
Volume: 271
Issue: 5254
Pages: 1380-1387
ISSN: 0036-8075 (ISSN-L)
1095-9203
DOI: 10.1126/science.271.5254.1380
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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Global Patterns of Linkage Disequilibrium at the CD4 Locus and Modern Human Origins

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