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Genetics. Published Articles Ahead of Print: November 19, 2005, Copyright © 2005
doi:10.1534/genetics.105.048223
doi:10.1534/genetics.105.048223
A more recent version of this article appeared on March 1, 2006.
REGULAR RESEARCH PAPERS |
Approximate Bayesian Inference reveals evidence for a recent, severe, bottleneck in non-African populations of Drosophila melanogaster
Kevin R. Thornton 1* and Peter Andolfatto 2
1 Cornell University
2 University of California, San Diego
* To whom correspondence should be addressed. E-mail: kt234{at}cornell.edu.
Submitted on July 13, 2005
Revised on September 29, 2005
Accepted on 27 October 2005
Abstract
Genome wide nucleotide variation in non-African populations of Drosophila melanogaster is a subset of variation found in East sub-Saharan African populations, suggesting a bottleneck in the history of the former. We implement an approximate Bayesian approach to infer the timing, duration and severity of this putative bottleneck and ask whether this inferred model is sufficient to account for patterns of variability observed at 115 loci scattered across the X chromosome. We estimate a recent bottleneck 0.006Ne generations ago, somewhat further in the past than suggested by biogeographical evidence. Using various proposed statistical tests, no significant outliers were detected among 115 loci when the estimated bottleneck was used as a null model. Thus, while precise estimates of bottleneck parameters (like inferences of selection) are sensitive to model assumptions, our results imply that it is unnecessary to invoke frequent selective sweeps associated with the dispersal of D. melanogaster from Africa to explain patterns of variability in non-African populations.
Key Words: Drosophila, bottlenecks, hitchhiking, linkage disequilibrium, selective sweeps
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