Apparent mutational hotspots and long distance linkage disequilibrium resulting from a bottleneck



    1. UMR8120 de Génétique Végétale, INRA/Univ. Paris-Sud/CNRS/AgroParisTech, Ferme du Moulon, Gif-sur-Yvette, France
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    1. Laboratoire Ecologie Systématique et Evolution, UMR 8079, CNRS/Univ. Paris-Sud/AgroParisTech, Orsay, France
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    1. Institut National de la Santé et de la Recherche Médicale (INSERM) U722, Faculté de Médecine Xavier Bichat, Paris, France
    2. Laboratoire Ecologie et Evolution des Microorganismes, Université Denis Diderot-Paris VII, Paris, France
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Maud Tenaillon, INRA Univ. Paris-Sud/CNRS/AgroParisTech, UMR8120, Station de Génétique Végétale, Ferme du Moulon, 91190 Gif-sur-Yvette, France.
Tel.: 33 (0) 1 69 33 23 34; fax: 33 (0) 1 69 33 23 80; e-mail:


Genome wide patterns of nucleotide diversity and recombination reveal considerable variation including hotspots. Some studies suggest that these patterns are primarily dictated by individual locus history related at a broader scale to the population demographic history. Because bottlenecks have occurred in the history of numerous species, we undertook a simulation approach to investigate their impact on the patterns of aggregation of polymorphic sites and linkage disequilibrium (LD). We developed a new index (Polymorphism Aggregation Index) to characterize this aggregation and showed that variation in the density of polymorphic sites results from an interplay between the bottleneck scenario and the recombination rate. Under particular conditions, aggregation is maximized and apparent mutation hotspots resulting in a 50-fold increase in polymorphic sites density can occur. In similar conditions, long distance LD can be detected.