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Alu insertion polymorphisms and other SINE elements are robust markers for evolutionary and phylogenetic studies because they have a unique mutational mechanism, an absence of back mutation, and a lack of recurrent forward mutation (Okada 1991; Batzer et al. 1994; Hamdi et al. 1999; Roy-Engel et al. 2001). Aspecific Alu insertion and nearby flanking sequence will be identical by descent in all individuals in whom they occur (Batzer et al. 1994). Thus, sets of related chromosome regions marked by an Alu insertion event can be distinguished from a pool of ancestral chromosomes that lack the element. These features give each locus genetic polarity that allows the independent assignment of an ancestral state and a root for phylogenetic analyses. Previous studies of human genetic variation have utilized polymorphic Alu insertions to gain insight into population history. Studies using multiple Alu loci or a single Alu locus with flanking markers show high African diversity and a greater effective population size for Africans (Batzer et al. 1994; Stoneking et al. 1997; Tishkoff et al. 1998; Watkins et al. 2001). When a large number of Alu elements are analyzed, individuals can usually be classified according to their continent of origin (Bamshad et al. 2003). Alu insertions are also useful for resolving genetic relationships in more limited locales such as NW Africa and the Caucasus region (Comas et al. 2000; Nasidze et al. 2001). Here, we examine population variation using 100 Alu insertion polymorphisms. Most of these Alu elements are recently identified insertions from the human genome sequence (Carroll et al. 2001; Roy-Engel et al. 2001) and are examined in broadly dispersed world populations for the first time. RESULTS For the 31 world populations (Fig. 1) combined, Alu insertion frequencies for the 100 loci are distributed from 0.001–0.999. The average Alu insertion frequencies for four major human population groups are similar among E. Asians (0.557), Indians (0.544), and Europeans (0.559), but lower in African

Year: 2013
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