A spatial statistical model for landscape genetics

• Published in: Genetics
• Main Authors: Guillot, Gilles, Estoup, Arnaud, Mortier, Fréderic, Cosson, Jean-Francois, J.-F.
• Other Authors: Mathématiques et Informatique Appliquées (MIA-Paris), Ecole Nationale du Génie Rural, des Eaux et des Forêts (ENGREF)-Institut National de la Recherche Agronomique (INRA)-Institut National Agronomique Paris-Grignon (INA P-G), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD France-Sud )-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Forêt (Cirad-FORET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)
• Format: Article in Journal/Newspaper
• Language: English
• Published: HAL CCSD 2005
• Subjects: GENETIQUE DES POPULATIONS; STRUCTURE GENETIQUE DES POPULATIONS; [SDV.GEN]Life Sciences [q-bio]/Genetics; Gulo gulo
• Online Access: https://hal.inrae.fr/hal-02683491; https://doi.org/10.1534/genetics.104.033803

International audience Landscape genetics is a new discipline that aims to provide information oil 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 georeferenced 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., F-ST < 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.