Polymorphic Alu insertions and the genetic structure of Iberian Basques

Abstract

Eight Alu sequences (ACE, TPA25, PV92, APO, FXIIIB, D1, A25 and B65) were analyzed in two samples from Navarre and Guipú zcoa provinces (Basque Country, Spain). Alu data for other European, Caucasus and North African populations were compiled from the literature for comparison purposes to assess the genetic relationships of the Basques in a broader geographic context. Results of both MDS plot and AMOVA revealed spatial heterogeneity among these three population clusters clearly defined by geography. On the contrary, no substantial genetic heterogeneity was found between the Basque samples, or between Basques and other Europeans (excluding Caucasus populations). Moreover, the genetic information obtained from Alu data conflicts with hypotheses linking the origin of Basques with populations from North Africa (Berbers) or from the Caucasus region (Georgia). In order to explain the reduced genetic heterogeneity detected by Alu insertions among Basque subpopulations, values of the Wright's F ST statistic were estimated for both Alu markers and a set of short tandem repeats (STRs) in terms of two geographical scales: (1) the Basque Country, (2) Europe (including Basques). In the Basque area, estimates of Wahlund's effect for both genetic markers showed no statistical difference between Basque subpopulations. However, when this analysis was performed on a European scale, F ST values were significantly higher for Alu insertions than for STR alleles. From these results, we suggest that the spatial heterogeneity of the Basque gene pool identified in previous polymorphism studies is relatively recent and probably caused by a differential process of genetic admixture with nonBasque neighboring populations modulated by the effect of a linguistic barrier to random mating.

Alu insertion polymorphisms and an assessment of the genetic contribution of Central Asia to Anatolia with respect to the Balkans

“…Without affects from mutation and selection, Alu insertions reflect the processes of interaction between gene flow and genetic drift within the past (Garcia-Obregon et al, 2007). Therefore, in the present study, to quantify the Central Asian genetic contribution to Anatolia instead of using the Bertorelle and Excoffier's (1998) admixture method the Chikhi et al's (2001) admixture method was used.…”

“…To calculate the proportion of Anatolians that can be traced to Central Asians, Alu insertion polymorphisms, multiple independent autosomal loci, were employed jointly thus providing a general view of the genomic contribution of the Turkic populations. Because the Alu markers representing unique insertions (Batzer et al, 1991) and being under the effect of pure drift (Garcia-Obregon et al, 2007) satisfied the assumptions of Chikhi et al's (2001) admixture method. Thus Chikhi et al's (2001) method was used to estimate the proportion Finally, to obtain a more detailed perspective about the contribution of Turkic speaking tribes within the Central Asian-Balkan region, as well as Anatolia, Azerbaijan (another Turkic speaking population) and some other non-Turkic speaking neighboring populations were also examined using Chikhi et al's (2001) method.…”

Insights on human evolution: an analysis of Alu insertion polymorphisms

“…[47][48][49] With the aim of interpreting the genetic diversity observed among population clusters, we used two methods to assess its congruency in relation to the geographic and genetic coordinates. First, to obtain a consensus topogenetic map, the first two eigenvectors of the nonmetric MDS analysis were extracted and rotated to maximum congruence with geographic coordinates using methods described by Lalouel.…”

The ins and outs of population relationships in west-Mediterranean islands: data from autosomal Alu polymorphisms and Alu/STR compound systems

“…These samples (see Fig. 1 for geographical location) come from the works of Stoneking et al (1997), Comas et al (2000) and Garcia-Obregon et al (2006, 2007. The consulted population data from CD4, F13B and DM STRs was obtained from the ALFRED database (Rajeevan et al 2005).…”