Human Population Genetic Structure


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Fax +41 61 306 12 34 E-Mail [email protected] www.karger.com Original Paper Hum Hered 2006;62:30–46 DOI: 10.1159/000095851 Human Population Genetic Structure and Diversity Inferred from Polymorphic L1 (LINE-1) and Alu Insertions D.J. Witherspoon a E.E. Marchani a W.S. Watkins a C.T. Ostler a S.P. Wooding a B.A. Anders b J.D. Fowlkes b S. Boissinot c A.V. Furano d D.A. Ray b A.R. Rogers e M.A. Batzer b L.B. Jorde a a Department of Human Genetics, University of Utah Health Sciences Center, Salt Lake City, Utah , b Department of Biological Sciences, Louisiana State University, Baton Rouge, La. , c Department of Biology, Queens College, Flushing, N.Y. , d Laboratory of Molecular and Cellular Biology, NIDDK, National Institutes of Health, Bethesda, Md. , e Department of Anthropology, University of Utah, Salt Lake City, Utah , USA than 50 typical loci, structure cannot be reliably discerned in these populations. The inclusion of geographically interme- diate populations (from India) reduces the distinctness of clustering. Our results indicate that human genetic variation is neither perfectly correlated with geographic distance (purely clinal) nor independent of distance (purely clus- tered), but a combination of both: stepped clinal. Copyright © 2006 S. Karger AG, Basel Introduction The LINE-1 (long interspersed element 1, or L1 ) ret- rotransposable element family is by far the most success- ful and enduring self-replicating genomic parasite of the human genome. L1 s became established in the ancestors of mammals  120 million years ago (mya), and today remnants of over half a million L1 s constitute one-fifth of the human genome [1–4] . Intact L1 s are  6 kb in length and encode the proteins required for their own replica- tion, which proceeds through a target-primed reverse transcription (TPRT) mechanism [5] . As a result of this mode of retrotransposition, many L1 elements are severe- Key Words Genetics/population genetics  Evolution  Bioinformatics/ computational biology Abstract Background/Aims: The L1 retrotransposable element family is the most successful self-replicating genomic parasite of the human genome. L1 elements drive replication of Alu ele- ments, and both have had far-reaching impacts on the hu- man genome. We use L1 and Alu insertion polymorphisms to analyze human population structure. Methods: We geno- typed 75 recent, polymorphic L1 insertions in 317 individuals from 21 populations in sub-Saharan Africa, East Asia, Europe and the Indian subcontinent. This is the first sample of L1 loci large enough to support detailed population genetic infer- ence. We analyzed these data in parallel with a set of 100 polymorphic Alu insertion loci previously genotyped in the same individuals. Results and Conclusion: The data sets yield congruent results that support the recent African ori- gin model of human ancestry. A genetic clustering algorithm detects clusters of individuals corresponding to continental regions. The number of loci sampled is critical: with fewer Received: April 18, 2006 Accepted after revision: July 25, 2006 Published online: September 21, 2006 David J. Witherspoon Department of Human Genetics, Eccles Institute of Human Genetics University of Utah, 15 North 2030 East, ...

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