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Genetics. 2008 Nov;180(3):1767-71. doi: 10.1534/genetics.108.091850. Epub 2008 Sep 14.

Controlling type-I error of the McDonald-Kreitman test in genomewide scans for selection on noncoding DNA.

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  • Department of Ecology and Evolutionary Biology, Princeton University, Princeton, New Jersey 08544, USA. pandolfa@princeton.edu


Departures from the assumption of homogenously interdigitated neutral and putatively selected sites in the McDonald-Kreitman test can lead to false rejections of the neutral model in the presence of intermediate levels of recombination. This problem is exacerbated by small sample sizes, nonequilibrium demography, recombination rate variation, and in comparisons involving more recently diverged species. I propose that establishing significance levels by coalescent simulation with recombination can improve the fidelity of the test in genomewide scans for selection on noncoding DNA.

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