Abstract
Algorithms for inferring population structure from genetic data (ie, population assignment methods) have shown to effectively recognize genetic clusters in human populations. However, their performance in identifying groups of genealogically related individuals, especially in scanty-differentiated populations, has not been tested empirically thus far. For this study, we had access to both genealogical and genetic data from two closely related, isolated villages in southern Italy. We found that nearly all living individuals were included in a single pedigree, with multiple inbreeding loops. Despite Fst between villages being a low 0.008, genetic clustering analysis identified two clusters roughly corresponding to the two villages. Average kinship between individuals (estimated from genealogies) increased at increasing values of group membership (estimated from the genetic data), showing that the observed genetic clusters represent individuals who are more closely related to each other than to random members of the population. Further, average kinship within clusters and Fst between clusters increases with increasingly stringent membership threshold requirements. We conclude that a limited number of genetic markers is sufficient to detect structuring, and that the results of genetic analyses faithfully mirror the structuring inferred from detailed analyses of population genealogies, even when Fst values are low, as in the case of the two villages. We then estimate the impact of observed levels of population structure on association studies using simulated data.
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Acknowledgements
We thank the populations of Gioi and Cardile for their kind cooperation. We thank Don Guglielmo Manna and Dr Leopoldo Errico for helping in the interaction with the populations; Raffaella Romano and Teresa Rizzo for the organization of the study in the villages; Valerio Di Vico for providing us with historical information; Agnar Helgason, Giorgio Bertorelle, and Catherine Bourgain for several important suggestions and comments. This study was supported by funds of the Italian Ministry of Universities (PRIN 2006 and FIRB 2008) to G.B, (FIRB -RBIN064YAT) and the Fondazione Banco di Napoli to MC.
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Supplementary Information accompanies the paper on European Journal of Human Genetics website (http://www.nature.com/ejhg)
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Colonna, V., Nutile, T., Ferrucci, R. et al. Comparing population structure as inferred from genealogical versus genetic information. Eur J Hum Genet 17, 1635–1641 (2009). https://doi.org/10.1038/ejhg.2009.97
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DOI: https://doi.org/10.1038/ejhg.2009.97
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