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Yoruba speakers living in Enugu, Nigeria, have been shown to have significantly different patterns of genetic variation than an African American population from Baltimore, but not so dissimilar to other Yoruba groups (Southwest, Northeast, and Benin) suggesting that they are a distinct subpopulation within this broad geographic area [@pone.0003592-Bigham1].
We have been able to show that a significant proportion of the gene variation within the Yoruba in Nigeria is associated with geography. While other global populations have a much lower proportion, Yoruba is still larger than many but not all geographically stratified groups. The Nigerian Yoruba cluster is clearly related to a specific region. In North America, several groups, like the French Canadians, display as much or more continental structure than the Yoruba.
Signatures of population movements of course will have a significant effect in modifying the structure of the mitochondrial and Y chromosomes. This is reflected in the fact that the Y is found to have much less variation in parts of Africa than in other populations [@pone.0003592-Bigham1], [@pone.0003592-Lao1], [@pone.0003592-Mishmar1]. This difference could be due to a founder effect on a small portion of the X chromosome [@pone.0003592-Perelle1].
Recent demographic history is commonly assumed to have a major impact on a genome, but is difficult to detect because of the large timescale over which population diversity is generated (e.g. [@pone.0003592-Tishkoff1], [@pone.0003592-Lao1]). Thus, there are clear differences between our data and the genome-wide data. These differences may be due to the different assumptions of underlying demographic history in the two approaches. In our approach, the population structure is represented by markers and is assumed to be correlated with historical structure. Thus, differences between our data and those from genome-wide data are most likely due to the different nature of the data and its structure.
We detect a significant geographic effect on the genome that is independent of the genealogy of the different regions. This observation is consistent with a recent study of a multi-ethnic group of Jerusalemis,
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