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Genetic Variation Among World Populations: Inferences from 100 Alu Insertion Polymorphisms W Letter Genetic Variation Among World Populations: Inferences From 100 Alu Insertion Polymorphisms W. Scott Watkins,1 Alan R. Rogers,2 Christopher T. Ostler,1 Steve Wooding,1 Michael J. Bamshad,1,3 Anna-Marie E. Brassington,1 Marion L. Carroll,4 Son V. Nguyen,5 Jerilyn A. Walker,5 B.V. Ravi Prasad,6 P. Govinda Reddy,7 Pradipta K. Das,8 Mark A. Batzer,5 and Lynn B. Jorde1,9 1Department of Human Genetics, 2Department of Anthropology, and 3Department of Pediatrics, University of Utah, Salt Lake City, Utah 84112, USA; 4Department of Chemistry, Xavier University of Louisiana, New Orleans, Louisiana 70125, USA; 5Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana 70803, USA; 6Department of Anthropology, Andhra University, Visakhapatnam, Andhra Pradesh 530 003, India; 7Department of Anthropology, University of Madras, Chennai 600-005, Tamil Nadu 600 005, India; 8Department of Anthropology, Utkal University, Bhubaneswar 751004, India We examine the distribution and structure of human genetic diversity for 710 individuals representing 31 populations from Africa, East Asia, Europe, and India using 100 Alu insertion polymorphisms from all 22 autosomes. Alu diversity is highest in Africans (0.349) and lowest in Europeans (0.297). Alu insertion frequency is lowest in Africans (0.463) and higher in Indians (0.544), E. Asians (0.557), and Europeans (0.559). Large genetic distances are observed among African populations and between African and non-African populations. The root of a neighbor-joining network is located closest to the African populations. These findings are consistent with an African origin of modern humans and with a bottleneck effect in the human populations that left Africa to colonize the rest of the world. Genetic distances among all pairs of populations show a significant product-moment correlation with geographic distances (r = 0.69, P < 0.00001). FST, the proportion of genetic diversity attributable to population subdivision is 0.141 for Africans/E. Asians/Europeans, 0.047for E. Asians/Indians/Europeans, and 0.090 for all 31 populations. Resampling analyses show that ∼50 Alu polymorphisms are sufficient to obtain accurate and reliable genetic distance estimates. These analyses also demonstrate that markers with higher FST values have greater resolving power and produce more consistent genetic distance estimates. [Supplemental material is available online at www.genome.org. The following individuals kindly provided reagents, samples, or unpublished information as indicated in the paper: J.M. Naidu, B.B. Rao, T. Jenkins, J. Kidd, K. Kidd, and H. Soodyall.] The study of human genetic variation provides opportunities 2002). Although the distribution and organization of human to examine population history and genetic structure. From genetic variation bears directly upon the diverse fields of link- early work characterizing blood groups and protein polymor- age and association mapping, haplotype and recombination phisms, the field has progressed to include studies of mtDNA studies, and human evolutionary history, its assessment re- (Cann et al. 1987; Vigilant et al. 1991; Stoneking and Soodyall mains incomplete. 1996; Ingman et al. 2000; Bamshad et al. 2001), Y- Alu insertion elements are the most abundant class of chromosome variation (Hammer et al. 1998; Seielstad et al. short interspersed elements (SINEs) in the human genome, 1999; Forster et al. 2000), genome-wide polymorphic autoso- numbering >1 million per haploid genome (Rubin et al. 1980; mal microsatellite variation (Bowcock et al. 1994; Deka et al. International Human Genome Consortium 2001). Alu ele- 1995; Goldstein et al. 1995; Jorde et al. 1997; Perez-Lezaun et ments are dimeric 300-bp sequences that propagate by retro- al. 1997) and single-nucleotide variation (Sachidanandam et position into new chromosomal locations, probably by using al. 2001; Stephens et al. 2001; Gabriel et al. 2002; Marth et al. a target-site primed mechanism (Vanin 1985; Weiner et al. 2003). Assessing individual and population level variation is 1986; Eickbush 1992; Luan et al. 1993; Feng et al. 1996; Jurka becoming commonplace for gene mapping, association 1997; Esnault et al. 2000; Kajikawa and Okada 2002). Germ- analysis for complex traits, and analysis of population history line and somatic Alu retroposition is ongoing, and de novo (Jorde et al. 2000; Risma et al. 2002; Tang et al. 2002; Yu et al. insertions into genes are responsible for cases of neurofibro- matosis type-1, Apert syndrome, and various cancers (Wallace et al. 1991; Miki et al. 1996; Deininger and Batzer 1999; Ol- 9 Corresponding author. dridge et al. 1999). Members of the Y, Ya5, Ya8, Yb8, Yb9, Yc1, E-MAIL [email protected]; FAX (801) 585-9148. Article and publication are at http://www.genome.org/cgi/doi/10.1101/ Yc2, and Yd subfamilies all produce new Alu insertions that gr.894603. Article published online before print in June 2003. are polymorphic in the human population (Batzer and Dein- 13:1607–1618 ©2003 by Cold Spring Harbor Laboratory Press ISSN 1088-9051/03 $5.00; www.genome.org Genome Research 1607 www.genome.org Watkins et al. inger 1991, 2002; Batzer et al. 1995; Carroll et al. 2001; Roy- 1994; Stoneking et al. 1997; Tishkoff et al. 1998; Watkins et al. Engel et al. 2001; Xing et al. 2003). 2001). When a large number of Alu elements are analyzed, Alu insertion polymorphisms and other SINE elements individuals can usually be classified according to their conti- are robust markers for evolutionary and phylogenetic studies nent of origin (Bamshad et al. 2003). Alu insertions are also because they have a unique mutational mechanism, an ab- useful for resolving genetic relationships in more limited lo- sence of back mutation, and a lack of recurrent forward mu- cales such as NW Africa and the Caucasus region (Comas et al. tation (Okada 1991; Batzer et al. 1994; Hamdi et al. 1999; 2000; Nasidze et al. 2001). Here, we examine population Roy-Engel et al. 2001). Aspecific Alu insertion and nearby variation using 100 Alu insertion polymorphisms. Most of flanking sequence will be identical by descent in all individu- these Alu elements are recently identified insertions from the als in whom they occur (Batzer et al. 1994). Thus, sets of human genome sequence (Carroll et al. 2001; Roy-Engel et al. related chromosome regions marked by an Alu insertion event 2001) and are examined in broadly dispersed world popula- can be distinguished from a pool of ancestral chromosomes tions for the first time. that lack the element. These features give each locus genetic polarity that allows the independent assignment of an ances- tral state and a root for phylogenetic analyses. RESULTS Previous studies of human genetic variation have utilized For the 31 world populations (Fig. 1) combined, Alu insertion polymorphic Alu insertions to gain insight into population frequencies for the 100 loci are distributed from 0.001–0.999. history. Studies using multiple Alu loci or a single Alu locus The average Alu insertion frequencies for four major human with flanking markers show high African diversity and a population groups are similar among E. Asians (0.557), Indi- greater effective population size for Africans (Batzer et al. ans (0.544), and Europeans (0.559), but lower in Africans Figure 1 A map showing the locations of the 31 populations sampled in the study. 1608 Genome Research www.genome.org Alu Variation in World Populations values, we repeated the analysis using artificial data generated Table 1. Alu Diversity for Major Groups and by randomly reassigning alleles to genotypes while maintain- 31 Populations alleles in each sample. The ”מ“ ing the counts of the “+” and Alu diversity results (Fig. 2, right) show the pattern expected under the hypothesis of HWE. The left and right panels are indistin- Africans 0.3487 guishable. Thus, the observed deficit of samples with large P (0.3189–0.3785) values is consistent with the expected distribution of F and Alur 0.3544 Biaka Pygmy 0.3073 shows that these data are in HWE. Hema 0.3503 The genetic distance estimates reported here are based on !Kung 0.3390 Nei’s D method (Nei 1987). These estimates are highly similar Mbuti Pygmy (Coriell) 0.3221 to those produced by alternative methods (squared Euclidean, Mbuti Pygmy 0.3135 Cavalli-Sforza’s chord measure, and Reynold’s distance), with Nande 0.3393 all distance matrix correlations exceeding 0.985 (P < 0.0001) Nguni 0.3445 Sotho/Tswana 0.3411 for our data. The genetic distances between Africans and the Tsonga 0.3510 non-African groups are significantly larger than those among E. Asians, Europeans, and Indians (Table 2). In a neighbor- E. Asians 0.3104 (0.2729–0.3480) joining network, African, E. Asian, and European populations Cambodian 0.2947 form distinct clusters, with bootstrap values of 99.8%, 98.2%, Chinese 0.3178 and 96.7%, respectively (Fig. 3). The South Indian caste and Japanese 0.3064 tribal populations are located in the same portion of the net- Malay 0.3256 work, between the European and E. Asian clusters. The boot- Vietnamese 0.2965 strap value for a branch that includes the Indian populations Europeans 0.2973 with the E. Asian populations is only 45.2%, which reflects (0.2616–0.3331) the fact that the genetic distance between the Indian and E. Finns 0.2927 Asian population groups is almost identical to the genetic French 0.3009 N. European 0.2964 distance between the Indian and European population groups Poles 0.2798 (Table 2). The overall topology of the network shows similarity to Indians 0.3159 the geographic distribution of these populations. The net- (0.2803–0.3514) Brahmin 0.3128 work is rooted by an ancestral outgroup that was created using Irula 0.3068 an Alu insertion frequency of 0 for each locus. The actual Kapu 0.3117 genetic distance between the hypothetical root and any Afri- Khonda Dora 0.3050 can population is smaller than the distance between the root Kshatriya 0.3031 and any non-African population.
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