摘要: The McDonald–Kreitman (MK) test is a simple and widely used of selection in which the numbers nonsilent silent substitutions (Dn Ds) are compared with polymorphisms (Pn Ps). neutrality index (NI 5 DsPn/DnPs), odds ratio (OR) MK table, measures direction degree departure from neutral evolution. mean NI values across genes often taken to summarize patterns species. Here, we show that this leads statistical bias both simulated real data extent species, pattern adaptive evolution, can apparently be subject weak purifying vice versa. We removed by using variant Cochran—Mantel–Haenszel procedure for estimating weighted average OR. also several point estimators statistically biased even when cutoff employed. therefore suggest new statistic study sparse, selection: DoS Dn/(Dn þ � Pn/(Pn
oup.com
sussex.ac.uk
oxfordjournals.org
susx.ac.uk 参考文章(38)
M Delgado-Rodriguez, Statistical analysis of epidemiologic data, 3rd ed Journal of Epidemiology and Community Health. ,vol. 59, pp. 1007- 1007 ,(2005)
Carlos D Bustamante, Adi Fledel-Alon, Scott Williamson, Rasmus Nielsen, Melissa Todd Hubisz, Stephen Glanowski, David M Tanenbaum, Thomas J White, John J Sninsky, Ryan D Hernandez, Daniel Civello, Mark D Adams, Michele Cargill, Andrew G Clark, None, Natural selection on protein-coding genes in the human genome Nature. ,vol. 437, pp. 1153- 1157 ,(2005) , 10.1038/NATURE04240
John H. McDonald, Martin Kreitman, Adaptive protein evolution at the Adh locus in Drosophila Nature. ,vol. 351, pp. 652- 654 ,(1991) , 10.1038/351652A0
Yong Fuga Li, James C. Costello, Alisha K. Holloway, Matthew W. Hahn, “REVERSE ECOLOGY” AND THE POWER OF POPULATION GENOMICS Evolution. ,vol. 62, pp. 2984- 2994 ,(2008) , 10.1111/J.1558-5646.2008.00486.X
Brian Charlesworth, The effect of background selection against deleterious mutations on weakly selected, linked variants. Genetics Research. ,vol. 63, pp. 213- 227 ,(1994) , 10.1017/S0016672300032365
Carolina Bartolomé, Xulio Maside, Soojin Yi, Anna L. Grant, Brian Charlesworth, Patterns of selection on synonymous and nonsynonymous variants in Drosophila miranda. Genetics. ,vol. 169, pp. 1495- 1507 ,(2005) , 10.1534/GENETICS.104.033068
A test for adaptive change in DNA sequences controlling transcription. Proceedings of The Royal Society B: Biological Sciences. ,vol. 261, pp. 203- 207 ,(1995) , 10.1098/RSPB.1995.0137
Jane Charlesworth, Adam Eyre-Walker, The rate of adaptive evolution in enteric bacteria Molecular Biology and Evolution. ,vol. 23, pp. 1348- 1356 ,(2006) , 10.1093/MOLBEV/MSK025
D. M. Rand, L. M. Kann, Excess amino acid polymorphism in mitochondrial DNA: contrasts among genes from Drosophila, mice, and humans. Molecular Biology and Evolution. ,vol. 13, pp. 735- 748 ,(1996) , 10.1093/OXFORDJOURNALS.MOLBEV.A025634
Robert E. Tarone, On summary estimators of relative risk. Journal of Chronic Diseases. ,vol. 34, pp. 463- 468 ,(1981) , 10.1016/0021-9681(81)90006-0