A Different Kind of Gene Mapping: Comparing Genetic and Geographic Structure in Europe: The Return!

By Chris Gignoux and Brenna HennEarly human history was characterized by many rapid, long-distance migrations. But despite our beginnings as travelers, genetic evidence published online last Sunday in Nature indicates that after expanding to all corners of the earth people (at least those in Europe) tended to stay close to home.Close on the heels of similar research published just a few weeks ago (and covered in The Spittoon), John Novembre and colleagues have created a genetic “map” of Europe that closely mirrors the geographic map. Their results will allow scientists to better understand how geography contributes to genetic variation, which is important for both genome-wide association studies and ancestry analyses.

Figure 1: The genetic map of Europe using PCA, with the geographic map of Europe for reference. Figure 2: The same map, but zoomed in on Switzerland. Swiss individuals tend to cluster with countries that speak the same language. (Courtesy: John Novembre, UCLA)

The researchers used a mathematical technique called principle components analysis (PCA) to collapse large amounts of SNP data for 3,192 people drawn from throughout Europe into a two-dimensional “map” of their genetic distances from one another. (Figure 1)When the researchers looked at the DNA of any two individuals, they found that the number of genetic differences between them was proportional to the geographic distance that separates their respective home countries. Even within countries the researchers saw that groups with similar cultural histories shared similar genetics. For example, Italian-speakers from southern Switzerland tended to cluster together with other Italian-speakers and apart from other Swiss groups. (Figure 2)Using only genetic data, the researchers were able to assign, on average, 50% of European individuals to within 400 kilometers of their correct country of origin. But there was one caveat: all four grandparents of an individual had to come from the same European country for the assignment to be correct. People with mixed European ancestry tended to show up between the locations of their ancestors.The accuracy of assignment varied greatly from country to country: some people, like the Swedes and Portuguese, were placed on the map with less precision than other groups like the Polish and Belgians.As in earlier research that constructed a genetic map of Europe, the results of this study show that genetic variations between people tend to follow a northwest to southeast path. This may reflect an ancient migration after the Last Ice Age when glacial sheets extended down from northern Europe. Human groups (not to mention grasshoppers, hedgehogs, etc.) were forced to take refuge in warm southern locations like the Italian and Iberian Peninsulas. But after the glaciers melted about 15,000 years ago, humans began to re-colonize Europe, moving from south to north.In the past, genome-wide association studies have been hampered by the effects of geography on genetics. For example, a study looking for DNA variants associated with height found spurious evidence of linkage to SNPs that are actually linked to lactose tolerance, because both traits vary along the same NW/SE axis in Europe. The results of this study current study and others like it will help scientists make corrections in their data and increase their ability to detect true associations.
  • Karl

    Why do slovaks cluster so far away from other slavic groups, and close to italians. That doesnt make sense in comparison with other studies done on slovaks.

    • aschops

      Only one single Slovak was put under analysis in that study. Out of sheer luck, it turned out that he had a particularly southern profile. If more Slovaks, and from many parts of their country, had been studied, this would have reduced the influence of outliars with exotic genetic profiles and no doubt the Slovakian position on the plot would more closely resemble its geographic location.

  • 23blog

    We about 40 reference populations in estimating European ancestry. Of those about 10 our public reference databases and the rest come from 23andMe. In total we use about 6,800 samples from those various reference populations.