Controlling Type-I Error of the McDonald–Kreitman Test in Genomewide Scans for Selection on Noncoding DNA

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.

[1]  P. Andolfatto,et al.  Positive and negative selection on noncoding DNA in Drosophila simulans. , 2008, Molecular biology and evolution.

[2]  Sònia Casillas,et al.  Standard and generalized McDonald–Kreitman test: a website to detect selection by comparing different classes of DNA sites , 2008, Nucleic Acids Res..

[3]  Sean B. Carroll,et al.  The Evolution of Gene Regulation Underlies a Morphological Difference between Two Drosophila Sister Species , 2008, Cell.

[4]  Colin N. Dewey,et al.  Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans , 2007, PLoS biology.

[5]  Zhaohui S. Qin,et al.  A second generation human haplotype map of over 3.1 million SNPs , 2007, Nature.

[6]  J. Mezey,et al.  Adaptive Gene Expression Divergence Inferred from Population Genomics , 2007, PLoS genetics.

[7]  Sònia Casillas,et al.  Purifying selection maintains highly conserved noncoding sequences in Drosophila. , 2007, Molecular biology and evolution.

[8]  Chenhui Zhang,et al.  Adaptive genic evolution in the Drosophila genomes , 2007, Proceedings of the National Academy of Sciences.

[9]  Garrett Hellenthal,et al.  msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots , 2007, Bioinform..

[10]  G. Coop,et al.  An evolutionary view of human recombination , 2007, Nature Reviews Genetics.

[11]  I. Kullo,et al.  Molecular evolution of 5′ flanking regions of 87 candidate genes for atherosclerotic cardiovascular disease , 2006, Genetic epidemiology.

[12]  Zhongming Zhao,et al.  Nucleotide Variation and Haplotype Diversity in a 10-kb Noncoding Region in Three Continental Human Populations , 2006, Genetics.

[13]  N. Derome,et al.  Contrasted Polymorphism Patterns in a Large Sample of Populations From the Evolutionary Genetics Model Drosophila simulans , 2006, Genetics.

[14]  John J Welch,et al.  Estimating the Genomewide Rate of Adaptive Protein Evolution in Drosophila , 2006, Genetics.

[15]  Kevin R. Thornton,et al.  Approximate Bayesian Inference Reveals Evidence for a Recent, Severe Bottleneck in a Netherlands Population of Drosophila melanogaster , 2006, Genetics.

[16]  Kevin R. Thornton,et al.  EXTENSIVE INTROGRESSION OF MITOCHONDRIAL DNA RELATIVE TO NUCLEAR GENES IN THE DROSOPHILA YAKUBA SPECIES GROUP , 2006, Evolution; international journal of organic evolution.

[17]  M. Noor,et al.  Fine-Scale Crossover Rate Heterogeneity in Drosophila pseudoobscura , 2006, Journal of Molecular Evolution.

[18]  R. Nielsen.  Molecular signatures of natural selection. , 2005, Annual review of genetics.

[19]  Ryan D. Hernandez,et al.  Natural selection on protein-coding genes in the human genome , 2005, Nature.

[20]  P. Andolfatto.  Adaptive evolution of non-coding DNA in Drosophila , 2005, Nature.

[21]  A. Long,et al.  Identifying signatures of selection at the enhancer of split neurogenic gene complex in Drosophila. , 2005, Molecular biology and evolution.

[22]  Chung-I Wu,et al.  Inference of positive and negative selection on the 5' regulatory regions of Drosophila genes. , 2004, Molecular biology and evolution.

[23]  Adam Eyre-Walker,et al.  Changing effective population size and the McDonald-Kreitman test. , 2002, Genetics.

[24]  J. Wall,et al.  Testing models of selection and demography in Drosophila simulans. , 2002, Genetics.

[25]  Adam Eyre-Walker,et al.  Adaptive protein evolution in Drosophila , 2002, Nature.

[26]  Richard R. Hudson,et al.  Generating samples under a Wright-Fisher neutral model of genetic variation , 2002, Bioinform..

[27]  J. Pritchard,et al.  Linkage disequilibrium in humans: models and data. , 2001, American journal of human genetics.

[28]  R. Nielsen.  Statistical tests of selective neutrality in the age of genomics , 2001, Heredity.

[29]  P. Andolfatto,et al.  A genome-wide departure from the standard neutral model in natural populations of Drosophila. , 2000, Genetics.

[30]  T. Jukes,et al.  The neutral theory of molecular evolution. , 2000, Genetics.

[31]  M. Kreitman,et al.  Evolutionary dynamics of the enhancer region of even-skipped in Drosophila. , 1995, Molecular biology and evolution.

[32]  D. L. Jenkins,et al.  A test for adaptive change in DNA sequences controlling transcription , 1995, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[33]  D. Hartl,et al.  Population genetics of polymorphism and divergence. , 1992, Genetics.

[34]  M. Kreitman,et al.  Adaptive protein evolution at the Adh locus in Drosophila , 1991, Nature.

[35]  M. Kimura.  The Neutral Theory of Molecular Evolution: Introduction , 1983 .

[36]  R. Hudson.  Properties of a neutral allele model with intragenic recombination. , 1983, Theoretical population biology.