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Gene Flow from North Africa Affected Genetic Diversity in Southern Europe

NEW YORK (GenomeWeb News) – Gene flow from Northern Africans may be behind the higher levels of genetic diversity seen in Southern Europeans, according to a report published today in the Proceedings of the National Academy of Sciences.

By analyzing SNP data from 43 populations from North Africa, Europe, the Near East, and sub-Saharan Africa, researchers led by Carlos Bustamante, a professor at Stanford University, found that Southwestern Europeans have high levels of recent North African ancestry, levels that decline in more Northern populations. Southeastern Europeans, by contrast, have higher levels of shared ancestry with populations from the Near East. Such genetic diversity, the researchers added, could have implications for calculating disease risk.

"Using genome-wide SNP data from over 2,000 individuals, we characterize broad clinal patterns of recent gene flow between Europe and Africa that have a substantial effect on genetic diversity of European populations," Bustamante and his colleagues reported.

Three main hypotheses —which the researchers noted are not mutually exclusive — have been proposed to address the high levels of genetic diversity in Southern Europeans. In one scenario, when Europeans re-colonized Northern Europe after the glaciers retreated, only a subset of genetic diversity returned to the north. Another hypothesis says that differences in genetic diversity are due to gene flow from the Near East, particularly as agriculture spread. Or, migrations from Africa may have affected genetic diversity levels.

In this study, Bustamante and his colleagues examined the patterns of gene flow between European and African populations.

With published SNP data from seven North African populations, 30 European populations (including Galician, Andalusian, and Canary Island populations), two European Jewish populations, a Near Eastern population, and the HapMap3 sub-Saharan African populations, the researchers used an unsupervised clustering algorithm to estimate allele sharing among those populations.

From this they found that Southern European populations have a high proportion of Near Eastern and North African ancestry. In particular, Southwestern Europeans had a higher proportion of North African ancestry.

Previous reports had suggested that Europeans had relatively low levels of shared ancestry with Africans, though many of those reports relied on data from sub-Saharan populations.

"When North African populations are included as a source, allele frequency-based clustering indicates better assignment to North African than to Sub-Saharan ancestry, and estimates of African ancestry in European populations increase relative to previous studies," the researchers wrote.

By examining identity-by-descent, or IBD, haplotypes, the researchers found high levels of ancestry among Iberian Peninsula populations and North African populations, with the exception of the Basques. In particular, Southwestern European populations, especially the Canary Island population, had high levels of IBD sharing with Northwestern African populations, such as Moroccans, Western Saharans, and Tunisian Berbers.

At the same time, the researchers found that Southeastern European populations had high levels of IBD segments shared with Egyptian and Near Eastern populations.

Further, populations in the Eastern Mediterranean shared more IBD segments with Near Eastern populations than with Western North African populations, while Southwestern Europeans share more IBD segments with populations in the Maghreb than the Near East.

This, the researchers pointed out, rules out the scenario in which allele sharing between European and North African populations is due to gene flow from the Near East into those areas.

"Our results, based on both allele frequencies and long shared haplotypes, support the hypothesis that recent migrations from North Africa contributed substantially to the higher genetic diversity in Southwestern Europe," the researchers said.

Such patterns of genetic diversity, Bustamante and his colleagues noted, could affect disease risk estimates. While they found that most risk alleles contained in a database of genome-wide association studies followed expected divergence patterns, multiple sclerosis did not appear to adhere to a pattern of neutral genetic drift. North African Maghrebi populations — especially West Saharans and North Moroccans —had a higher genetic risk for MS than expected, while Canary Island populations had a low genetic risk of the disease.

"The complexity of these results serves to emphasize the importance of conducting disease associations in many diverse populations," the researchers wrote. "The significant gene flow from North Africa into Southern Europe will result in a miscalculation of genetic disease risk in certain European populations, if North African-specific risk variants are not taken into account."