Copyright © 1998 The American Society of Human Genetics. All rights reserved.
The American Journal of Human Genetics, Volume 62, Issue 6, 1389-1402, 1 June 1998
doi:10.1086/301861
S.A. Tishkoff1, *, A. Goldman2, F. Calafell1, W.C. Speed1, A.S. Deinard1, B. Bonne-Tamir3, J.R. Kidd1, A.J. Pakstis1, T. Jenkins2 and K.K. Kidd1,
, 
1 Department of Genetics, Yale University School of Medicine, New Haven;
2 Department of Human Genetics, School of Pathology, South African Institute for Medical Research, University of the Witwatersrand, Johannesburg
3 Sackler Faculty of Medicine, Tel Aviv University, Ramat Aviv, Tel Aviv
Address for correspondence and reprints: Dr. Kenneth K. Kidd, Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, CT 06520-8005Abstract
Haplotypes consisting of the (CTG)n repeat, as well as several flanking markers at the myotonic dystrophy (DM) locus, were analyzed in normal individuals from 25 human populations (5 African, 2 Middle Eastern, 3 European, 6 East Asian, 3 Pacific/Australo-Melanesian, and 6 Amerindian) and in five nonhuman primate species. Non-African populations have a subset of the haplotype diversity present in Africa, as well as a shared pattern of allelic association. (CTG)18–35 alleles (large normal) were observed only in northeastern African and non-African populations and exhibit strong linkage disequilibrium with three markers flanking the (CTG)n repeat. The pattern of haplotype diversity and linkage disequilibrium observed supports a recent African-origin model of modern human evolution and suggests that the original mutation event that gave rise to DM-causing alleles arose in a population ancestral to non-Africans prior to migration of modern humans out of Africa.
| Short Tandem-Repeat Polymorphism/Alu Haplotype Variation at the PLAT Locus: Implications for Modern Human Origins The American Journal of Human Genetics, Volume 67, Issue 4, 1 October 2000, Pages 901-925 S.A. Tishkoff, A.J. Pakstis, M. Stoneking, J.R. Kidd, G. Destro-Bisol, A. Sanjantila, R.-b. Lu, A.S. Deinard, G. Sirugo, T. Jenkins, K.K. Kidd and A.G. Clark Abstract Two dinucleotide short tandem-repeat polymorphisms (STRPs) and a polymorphic Alu element spanning a 22-kb region of the PLAT locus on chromosome 8p12-q11.2 were typed in 1,287–1,420 individuals originating from 30 geographically diverse human populations, as well as in 29 great apes. These data were analyzed as haplotypes consisting of each of the dinucleotide repeats and the flanking Alu insertion/deletion polymorphism. The global pattern of STRP/Alu haplotype variation and linkage disequilibrium (LD) is informative for the reconstruction of human evolutionary history. Sub-Saharan African populations have high levels of haplotype diversity within and between populations, relative to non-Africans, and have highly divergent patterns of LD. Non-African populations have both a subset of the haplotype diversity present in Africa and a distinct pattern of LD. The pattern of haplotype variation and LD observed at the PLAT locus suggests a recent common ancestry of non-African populations, from a small population originating in eastern Africa. These data indicate that, throughout much of modern human history, sub-Saharan Africa has maintained both a large effective population size and a high level of population substructure. Additionally, Papua New Guinean and Micronesian populations have rare haplotypes observed otherwise only in African populations, suggesting ancient gene flow from Africa into Papua New Guinea, as well as gene flow between Melanesian and Micronesian populations. Abstract | | |
| Haplotypes and Linkage Disequilibrium at the Phenylalanine Hydroxylase Locus, PAH, in a Global Representation of Populations The American Journal of Human Genetics, Volume 66, Issue 6, 1 June 2000, Pages 1882-1899 Judith R. Kidd, Andrew J. Pakstis, Hongyu Zhao, Ru-Band Lu, Friday E. Okonofua, Adekunle Odunsi, Elena Grigorenko, Batsheva Bonne- Tamir, Jonathan Friedlaender, Leslie O. Schulz, Josef Parnas and Kenneth K. Kidd Abstract Because defects in the phenylalanine hydroxylase gene (PAH) cause phenylketonuria (PKU), PAH was studied for normal polymorphisms and linkage disequilibrium soon after the gene was cloned. Studies in the 1980s concentrated on European populations in which PKU was common and showed that haplotype-frequency variation exists between some regions of the world. In European populations, linkage disequilibrium generally was found not to exist between RFLPs at opposite ends of the gene but was found to exist among the RFLPs clustered at each end. We have now undertaken the first global survey of normal variation and disequilibrium across the PAH gene. Four well-mapped single-nucleotide polymorphisms (SNPs) spanning ∼75 kb, two near each end of the gene, were selected to allow linkage disequilibrium across most of the gene to be examined. These SNPs were studied as PCR-RFLP markers in samples of, on average, 50 individuals for each of 29 populations, including, for the first time, multiple populations from Africa and from the Americas. All four sites are polymorphic in all 29 populations. Although all but 5 of the 16 possible haplotypes reach frequencies >5% somewhere in the world, no haplotype was seen in all populations. Overall linkage disequilibrium is highly significant in all populations, but disequilibrium between the opposite ends is significant only in Native American populations and in one African population. This study demonstrates that the physical extent of linkage disequilibrium can differ substantially among populations from different regions of the world, because of both ancient genetic drift in the ancestor common to a large regional group of modern populations and recent genetic drift affecting individual populations. Abstract | | |
| A Back Migration from Asia to Sub-Saharan Africa Is Supported by High-Resolution Analysis of Human Y-Chromosome Haplotypes The American Journal of Human Genetics, Volume 70, Issue 5, 1 May 2002, Pages 1197-1214 Fulvio Cruciani, Piero Santolamazza, Peidong Shen, Vincent Macaulay, Pedro Moral, Antonel Olckers, David Modiano, Susan Holmes, Giovanni Destro-Bisol, Valentina Coia, Douglas C. Wallace, Peter J. Oefner, Antonio Torroni, L. Luca Cavalli-Sforza, Rosaria Scozzari and Peter A. Underhill Abstract The variation of 77 biallelic sites located in the nonrecombining portion of the Y chromosome was examined in 608 male subjects from 22 African populations. This survey revealed a total of 37 binary haplotypes, which were combined with microsatellite polymorphism data to evaluate internal diversities and to estimate coalescence ages of the binary haplotypes. The majority of binary haplotypes showed a nonuniform distribution across the continent. Analysis of molecular variance detected a high level of interpopulation diversity (ΦST=0.342), which appears to be partially related to the geography (ΦCT=0.230). In sub-Saharan Africa, the recent spread of a set of haplotypes partially erased pre-existing diversity, but a high level of population (ΦST=0.332) and geographic (ΦCT=0.179) structuring persists. Correspondence analysis shows that three main clusters of populations can be identified: northern, eastern, and sub-Saharan Africans. Among the latter, the Khoisan, the Pygmies, and the northern Cameroonians are clearly distinct from a tight cluster formed by the Niger-Congo–speaking populations from western, central western, and southern Africa. Phylogeographic analyses suggest that a large component of the present Khoisan gene pool is eastern African in origin and that Asia was the source of a back migration to sub-Saharan Africa. Haplogroup IX Y chromosomes appear to have been involved in such a migration, the traces of which can now be observed mostly in northern Cameroon. Abstract | | |