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. 2016 Sep;161(1):62-71.
doi: 10.1002/ajpa.23008. Epub 2016 May 18.

Genetic Variation in Tunisia in the Context of Human Diversity Worldwide

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Free PMC article

Genetic Variation in Tunisia in the Context of Human Diversity Worldwide

Lotfi Cherni et al. Am J Phys Anthropol. .
Free PMC article

Abstract

Objectives: North Africa has a complex demographic history of migrations from within Africa, Europe, and the Middle East. However, population genetic studies, especially for autosomal genetic markers, are few relative to other world regions. We examined autosomal markers for eight Tunisian and Libyan populations in order to place them in a global context.

Materials and methods: Data were collected by TaqMan on 399 autosomal single nucleotide polymorphisms on 331 individuals from Tunisia and Libya. These data were combined with data on the same SNPs previously typed on 2585 individuals from 57 populations from around the world. Where meaningful, close by SNPs were combined into multiallelic haplotypes. Data were evaluated by clustering, principal components, and population tree analyses. For a subset of 102 SNPs, data from the literature on seven additional North African populations were included in analyses.

Results: Average heterozygosity of the North African populations is high relative to our global samples, consistent with a complex demographic history. The Tunisian and Libyan samples form a discrete cluster in the global and regional views and can be separated from sub-Sahara, Middle East, and Europe. Within Tunisia the Nebeur and Smar are outlier groups. Across North Africa, pervasive East-West geographical patterns were not found.

Discussion: Known historical migrations and invasions did not displace or homogenize the genetic variation in the region but rather enriched it. Even a small region like Tunisia contains considerable genetic diversity. Future studies across North Africa have the potential to increase our understanding of the historical demographic factors influencing the region. Am J Phys Anthropol 161:62-71, 2016. © 2016 The Authors American Journal of Physical Anthropology Published by Wiley Periodicals, Inc.

Keywords: North Africa; SNP; haplotype; population genetics.

Figures

Figure 1
Figure 1
Map showing sampling locations of Tunisian and Libyan populations.
Figure 2
Figure 2
Principal components analysis. Plot of results for first two principal components. PCA is based on pairwise Tau genetic distances for 65 populations.
Figure 3
Figure 3
STRUCTURE individual bar plots—65 populations, 299 markers study—displaying results for runs with highest likelihood out of 20 runs in each cluster K = 5 to 8. Each individual has a separate column in the bar plot and the individuals in a population are clustered together in the display but the STRUCTURE analysis was unsupervised, i.e. not informed about an individual's population membership. Black vertical lines identify the population boundaries. The height extent of each color within an individual's color bar corresponds to the estimated membership of the individual in one of the clusters; each cluster is assigned a separate color. The bars with multiple colors can be interpreted as genetic admixture or as relative probabilities of belonging to the different clusters. Since there is a separate color bar for each of the more than 2900 individuals, the interval width covered by a population varies and corresponds to the number of individuals in the population.
Figure 4
Figure 4
STRUCTURE population bar plot showing average estimated cluster membership in each of 65 populations for the runs with highest likelihood out of 20 runs for cluster K = 8. There are 65 population bars and each population bar has the same width. The height extent of each color within a population bar corresponds to the average estimated cluster membership for all the individuals in the population.
Figure 5
Figure 5
STRUCTURE individual bar plots—40 populations, 299 markers study—displaying results for the most common cluster pattern out of 20 runs in each cluster for K = 2–6. This analysis omits the 25 populations from East Asia, the Pacific, and the Americas. The highest likelihood run in this more focused analysis is usually found among the runs of the most common cluster pattern.
Figure 6
Figure 6
Best least squares population tree for the 65 populations based on the pairwise genetic distances between the populations. Some of the highest bootstrap values (based on 1,000 iterations) are indicated on the image by symbols Δ (100%) and + (90 to 99.9%).

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