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MBE Advance Access originally published online on May 21, 2009
Molecular Biology and Evolution 2009 26(9):1963-1973; doi:10.1093/molbev/msp106
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© The Author 2009. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org

Research Articles

Spatial Inference of Admixture Proportions and Secondary Contact Zones

Eric Durand*, Flora Jay*, Oscar E. Gaggiotti{dagger} and Olivier François*

* Faculty of Medicine, Laboratoire des Techniques de 1'Ingénierie Médicale et de la Complexité, University Joseph Fourier, Grenoble IT, Group of Mathematical Biology, La Tronche, France
{dagger} Laboratoire d'Ecologie Alpine, Unité Mixte de Recherche Centre National de la Recherche Scientifique 5553, University Joseph Fourier, Grenoble, France

E-mail: olivier.francois{at}imag.fr.

Accepted for publication May 13, 2009.

Genetic admixture of distinct gene pools is the consequence of complex spatiotemporal processes that could have involved massive migration and local mating during the history of a species. However, current methods for estimating individual admixture proportions lack the incorporation of such a piece of information. Here, we extend Bayesian clustering algorithms by including global trend surfaces and spatial autocorrelation in the prior distribution on individual admixture coefficients. We test our algorithm by using spatially explicit and realistic coalescent simulations of colonization followed by secondary contact. By coupling our multiscale spatial analyses with a Bayesian evaluation of model complexity and fit, we show that the algorithm provides a correct description of smooth clinal variation, while still detecting zones of sharp variation when they are present in the data. We also apply our approach to understand the population structure of the killifish, Fundulus heteroclitus, for which the algorithm uncovers a presumed contact zone in the Atlantic coast of North America.

Key Words: admixture • Bayesian inference • spatial trends • spatial autocorrelation • secondary contact zones

Jonathan Pritchard, Associate Editor


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