Brief communication: Patterns of linkage disequilibrium and haplotype diversity at Xq13 in six Native American populations

Abstract

Comparative studies of linkage disequilibrium (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 colonization of the New World by a differentiated East Asian population, followed by extensive genetic drift in the Americas.

X‐chromosomal genetic diversity and linkage disequilibrium patterns in Amerindians and non‐Amerindian populations

“…Thus, the lower genetic diversity and the higher level of LD observed in the Native populations, as compared to the CVCR and Gaucho samples, might be associated with these phenomena. Similar results were obtained in previous independent studies involving South Amerindian (Leite et al, 2009;Wang et al, 2010) and other small and isolated populations such as the Khoton from Mongolia (Katoh et al, 2002), the Saami (Laan and Pä ä bo, 1997), and Kuusamo (Varilo et al, 2000) from Finland.…”

“…Notwithstanding linkage disequilibrium investigations among them are scarce. We therefore developed an investigation design, which is an extension of previous and recent investigations on X-STR LD in distinct pools of Amerindian and non-Amerindian samples (Leite et al, 2009;Wang et al, 2010). In our study three relatively isolated Native American populations and two non-native communities were tested for a fast-evolving genetic system, with the following questions in mind: (a) since genetic variability clearly influences the power to detect LD, do the populations investigated here show differences in this characteristic that could influence the patterns obtained?…”

Contrasting Patterns of Nuclear and mtDNA Diversity in Native American Populations

“…In another application, a recent study of autosomal and X chromosome data has led to the proposal of a more severe male than female bottleneck during the initial migration of anatomically modern humans out of Africa (Keinan et al, 2009). In the Americas, continent‐wide Native population surveys have been carried out independently with mtDNA (Torroni et al, 1993; Merriwether et al, 1995; Forster et al, 1996; Bonatto & Salzano, 1997; Fagundes et al, 2008), Y‐chromosome (Lell et al, 2002; Bortolini et al, 2003), autosomal (Salzano & Callegari‐Jacques, 1988; Cavalli‐Sforza et al, 1994; Wang et al, 2007) and, more recently, X‐chromosome markers (Bourgeois et al, 2009; Wang et al, 2010). However, other than regional studies (Mesa et al, 2000) or continental studies combining data for different population samples (Bortolini et al, 2003) there has not been a systematic, continent‐wide, analysis of genetic diversity across marker systems on the same Native American population samples.…”

Reconciling migration models to the Americas with the variation of North American native mitogenomes

“…The ancestral Beringian populations probably retreated into refugia during the Ice Age, where their genetic variation was reshaped not only because of drift, but also because of admixture with population groups newly arrived from regions located west of Beringia. Thus, pre-LGM haplotypes of Asian ancestry were differently preserved, modified, and lost in Beringian enclaves (8)(9)(10)(11)(12)(13).…”