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

Journal of Evolutionary Biology
M I TenaillonO Tenaillon

Abstract

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.

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Citations

Jul 16, 2008·Proceedings of the National Academy of Sciences of the United States of America·Rob J KulathinalMohamed A F Noor
Mar 28, 2012·Genomics, Proteomics & Bioinformatics·Peng CuiJun Yu
Jun 19, 2016·Computational Biology and Chemistry·Chang-Yong Lee
Apr 17, 2018·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Markus Boenn
Jun 8, 2014·Genetics·Alan R Rogers
Feb 19, 2021·Evolution; International Journal of Organic Evolution·Donald M Waller

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