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Human Population Genetic Structure

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Fax +41 61 306 12 34E-Mail [email protected] Original Paper Hum Hered 2006;62:30–46 DOI: 10.1159/000095851 Human Population Genetic Structureand 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 B a c k g r o u n d / A i m s : 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, Room 7225 Salt Lake City, UT 84112-5330 (USA) Tel. +1 801 587 3094, Fax +1 801 585 9148, E-Mail [email protected] © 2006 S. Karger AG, Basel 0001–5652/06/0621–0030$23.50/0 Accessible online at: www.karger.com/hhe © Free Author Copy - for per-sonal use onlyPLEASE NOTE THAT ANY DISTRIBUTION OF THIS AR-TICLE WITHOUT WRITTEN CONSENT FROM S. KARGER AG, BASEL IS A VIOLATION OF THE COPYRIGHT. Upon request a written per-mission to distribute the PDF fi le will be granted against payment of a permission fee depending on the number of accesses required. Please contact Karger Publishers, Basel, Switzerland at [email protected] L1 and Alu Diversity Hum Hered 2006;62:30–46 31ly truncated upon insertion, rendering them incapable of catalyzing their own replication. Fewer than one hundred L1 s, mostly of the L1Hs Ta and L1 preTa subfamilies, con-tinue to replicate and thereby create polymorphic inser-tions in the human population [6–12] . A l u elements are the most common SINE s (short in-terspersed elements) in the human genome. They are di-meric 300-bp sequences that evolved from the 7SL RNA component of the signal-recognition particle  65 mya and became extremely successful parasites of L1 s. They rely on retrotransposition proteins encoded by active L1 elements in order to replicate [13] . The human genome now contains more than one million Alu insertions, ac-counting for about a tenth of the genome [2] . As with L1 s, some young Alu elements continue to replicate and have spawned subfamilies of Alu insertions, many of which are polymorphic for their presence or absence [14] . Like the numerous and highly polymorphic canine SINEC_Cf re-peats [15] , the L1 and Alu families of mobile elements have had a significant impact on the composition and structure of their host genome. L1 and Alu elements con-tinue to generate mutations by triggering ectopic recom-bination events and chromosomal rearrangements and by insertional disruption of genes [16] . L I N E and SINE insertions have two uniquely valuable properties as markers for phylogenetic and population genetic analyses. First, they are virtually free of homo-plasy: every observed insertion at a specific locus is iden-tical by descent to the insertion created by a single trans-position event. The probability that two insertions of the same element sequence will occur at the same site and then drift to any appreciable frequency is extremely small due to the low rate of insertion relative to the vast number of potential insertion sites [11, 17–22] . Since insertions are almost never precisely deleted [23] , homoplasy due to reversion is also extremely rare [18] . The second advantage of LINE and SINE insertion markers is that the ancestral state of the locus is known to be the absence of the insertion [24] . Other often-used genetic marker types, such as single nucleotide polymor-phisms (SNPs), restriction site polymorphisms (RSPs) and short tandem repeat polymorphisms (STRPs) suffer from


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