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Originally published as Genetics Published Articles Ahead of Print on November 1, 2004.
Genetics, Vol. 170, 1261-1280, July 2005, Copyright © 2005
doi:10.1534/genetics.104.033803
A Spatial Statistical Model for Landscape Genetics
Gilles Guillot*,1,
Arnaud Estoup
,
Frédéric Mortier
and
Jean François Cosson
* Unité de Mathématiques et Informatique Appliquées, INRA-INAPG-ENGREF, Paris, France 75231
Centre de Biologie et de Gestion des Populations, INRA-ENSAM-IRD-CIRAD, Montpellier, France F-34988
CIRAD, Département Forêt, Montpellier, France F-34398
Centre de Biologie et de Gestion des Populations, INRA-ENSAM-IRD-CIRAD, Montpellier, France F-34988
1 Corresponding author: Unité de Mathématiques et Informatiques Appliquées, INRA-INAPG-ENGREF, Institut National Agronomique, 16 rue Claude Bernard, 75231 Paris Cedex 5, France.
E-mail: guillot{at}inapg.inra.fr
Landscape genetics is a new discipline that aims to provide information on how landscape and environmental features influence population genetic structure. The first key step of landscape genetics is the spatial detection and location of genetic discontinuities between populations. However, efficient methods for achieving this task are lacking. In this article, we first clarify what is conceptually involved in the spatial modeling of genetic data. Then we describe a Bayesian model implemented in a Markov chain Monte Carlo scheme that allows inference of the location of such genetic discontinuities from individual geo-referenced multilocus genotypes, without a priori knowledge on populational units and limits. In this method, the global set of sampled individuals is modeled as a spatial mixture of panmictic populations, and the spatial organization of populations is modeled through the colored Voronoi tessellation. In addition to spatially locating genetic discontinuities, the method quantifies the amount of spatial dependence in the data set, estimates the number of populations in the studied area, assigns individuals to their population of origin, and detects individual migrants between populations, while taking into account uncertainty on the location of sampled individuals. The performance of the method is evaluated through the analysis of simulated data sets. Results show good performances for standard data sets (e.g., 100 individuals genotyped at 10 loci with 10 alleles per locus), with high but also low levels of population differentiation (e.g., FST < 0.05). The method is then applied to a set of 88 individuals of wolverines (Gulo gulo) sampled in the northwestern United States and genotyped at 10 microsatellites.
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