Brief Communication: Patterns of Linkage Disequilibrium and Haplotype Diversity at Xq13 in Six Native American Populations Sijia Wang, 1 * Gabriel Bedoya, 2 Damian Labuda, 3 and Andres Ruiz-Linares 1 * 1 Department of Genetics, Evolution and Environment, University College London, 4 Stephenson Way, London NW1 2HE, UK 2 Laboratorio de Gene ´tica Molecular, Universidad de Antioquia, Medellı´n, Colombia 3 CHU Sainte-Justine, De ´partement de Pe ´diatrie, Universite ´ de Montre ´al, Montre ´al, PQ, Canada KEY WORDS linkage disequilibrium; Xq13; Native Americans; haplotype ABSTRACT Comparative studies of linkage disequili- brium (LD) can provide insights into human demographic history. Here, we characterize LD in six Native American populations using seven microsatellite markers in Xq13, a region of the genome extensively studied in populations around the world. Native Americans show relatively low diversity and high LD, in agreement with recent genome- wide survey and a scenario of sequential founder effects accompanying human population dispersal around the globe. LD in Native Americans is similar to that observed in some recently described small population isolates and higher than in large European isolates (e.g., Finns), which have been extensively analyzed in medical genetics studies. Haplotype analyses are consistent with a coloni- zation of the New World by a differentiated East Asian population, followed by extensive genetic drift in the Americas. Am J Phys Anthropol 142:476–480, 2010. V V C 2009 Wiley-Liss, Inc. Patterns of linkage disequilibrium (LD) across the ge- nome are influenced by a range of factors, including vari- able mutation and recombination rates, natural selection, and population demography (Ardlie et al., 2002). Genome- wide comparisons of LD in different human populations have been carried out in the CEPH-HGDP panel and the HapMap reference set. Other extensive population surveys have been performed for a few regions of the genome, including a 13 Mb segment on Xq13, which has been examined in a range of populations across the world (Laan and Paabo, 1997; Zavattari et al., 2000; Angius et al., 2001; Kaessmann et al., 2002; Katoh et al., 2002; Latini et al., 2004; Laan et al., 2005; Marroni et al., 2006; Branco et al., 2008; Bellis et al., 2008, Leite et al., 2009). So far, comparative studies of LD including Native Americans are fairly scant, often limited to the five populations of the CEPH-HGDP panel (Sawyer et al., 2005; Conrad et al., 2006; Jakobsson et al., 2008; Li et al., 2008; Bosch et al., 2009). To further the analysis of LD in Native Americans here we examine the Xq13 region, previously studied around the world, in six Native American populations. MATERIALS AND METHODS Samples DNA samples (isolated from peripheral blood) were obtained from consenting individuals representing six Native American populations: Wayuu (n 5 66 chromo- somes), Ingano (n 5 38), Kogi (n 5 44), Zenu (n 5 46), and Ticuna (n 5 30), from Colombia, and Cree (n 5 25) from Saskatchewan, Canada. Following the linguistic classification of Ruhlen (1991), Wayuu and Ticuna both belong to the Equatorial-Tucanoan linguistic stock. Wayuu is one of the largest Native American groups in Colombia, with an estimated population size of 135,000, whereas the Ticuna have a population size of 8,000. The Ingano is an Andean population, with a population size of 18,000. Kogi and Zenu are Chibchan-Paezan populations, with estimated population sizes of 3,000 and 34,000, respectively. See Mesa et al. (2000) for more information of the Native Americans in Colombia. Cree belongs to a large population (200,000 in Canada) organized into many smaller groups. The Cree in Sas- katchewan have a census of roughly 73,500. Our genotyping data were combined with published datasets using the same markers on seven East Asian (Katoh et al., 2002; Laan et al., 2005) (Buriat, n 5 78; Evenki, n 5 71; Japanese, n 5 100, Khalkha, n 5 83; Khoton, n 5 40; Uriankhai, n 5 55; and Zahkchin, n 5 59), five Volga-Ural (Laan et al., 2005) (Chuvashi, n 5 40; Komi, n 5 46; Mari, n 5 44; Mordva, n 5 48; and Udmurt, n 5 49), and eight Western European populations (Laan and Paabo, 1997; Zavattari et al., 2000; Laan et al., 2005) (Dutch, n 5 70; Estonian, n 5 45; Finnish, n 5 80; German, n 5 41; Italian, n 5 92; Russian, n 5 66; Saami, n 5 54; and Swedish, n 5 41). See Supporting Information Table 1 for census size for all 26 populations. Additional supporting information may be found in the online version of this article. *Correspondence to: Sijia Wang, FAS Center for Systems Biology, Harvard University, 52 Oxford Street, Cambridge, MA 02138. E-mail: swang@oeb.harvard.edu; Andres Ruiz-Linares, Department of Genetics, Evolution and Environment, University College London, 4 StephensonWay, London NW1 2HE, UK. E-mail: a.ruizlin@ucl.ac.uk Received 22 July 2009; accepted 23 October 2009 DOI 10.1002/ajpa.21234 Published online 23 December 2009 in Wiley InterScience (www.interscience.wiley.com). V V C 2009 WILEY-LISS, INC. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 142:476–480 (2010)