Distinguishing migration from isolation using genes with intragenic recombination: detecting introgression in the Drosophila simulans species complex.
2014
Navascués, Miguel | Legrand, Delphine | Campagne, Cécile | Cariou, Marie-Louise | Depaulis, Frantz | 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 [Occitanie])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro) | Laboratoire Ecologie et évolution ; École normale supérieure - Paris (ENS-PSL) ; Université Paris Sciences et Lettres (PSL)-Université Paris Sciences et Lettres (PSL)-Université Pierre et Marie Curie - Paris 6 (UPMC)-Centre National de la Recherche Scientifique (CNRS) | Station d’Ecologie Expérimentale du CNRS à Moulis (SEEM) ; Université Toulouse III - Paul Sabatier (UT3) ; Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS) | Laboratoire Evolution, Génomes et Spéciation (LEGS) ; Centre National de la Recherche Scientifique (CNRS) | Agence Nationale de la Recherche [ANR-06-BDIV-003.DL]; TULIP [ANR-10-LABX-41]; INRA 2010
BACKGROUND: Determining the presence or absence of gene flow between populations is the target of some statistical methods in population genetics. Until recently, these methods either avoided the use of recombining genes, or treated recombination as a nuisance parameter. However, genes with recombination contribute additional information for the detection of gene flow (i.e. through linkage disequilibrium).METHODS: We present three summary statistics based on the spatial arrangement of fixed differences, and shared and exclusive polymorphisms that are sensitive to the presence and direction of gene flow. Power and false positive rate for tests based on these statistics are studied by simulation.RESULTS: The application of these tests to populations from the Drosophila simulans species complex yielded results consistent with migration between D. simulans and its two endemic sister species D. mauritiana and D. sechellia, and between populations D. mauritiana on the islands of the Mauritius and Rodrigues.CONCLUSIONS: We demonstrate the sensitivity of the developed statistics to the presence and direction of gene flow, and characterize their power as a function of differentiation level and recombination rate. The properties of these statistics make them especially suitable for analyzing high-throughput sequencing data or for their integration within the approximate Bayesian computation framework.
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