Significance of population size on the fixation of nonsynonymous mutations in genes under varying levels of selection pressure

Genetics

Volumn 193, Issue 3, 2013, Pages 995-1002

  Subramanian, Sankar ^a  

^a GRIFFITH UNIVERSITY   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BOS TAURUS; GENE EXPRESSION; GENE MUTATION; HUMAN; MOUSE; NONHUMAN; POPULATION SIZE; PRIORITY JOURNAL; RAT; RHESUS MONKEY; SWINE; TISSUE SPECIFICITY;

ALLELES; AMINO ACID SUBSTITUTION; ANIMALS; EVOLUTION, MOLECULAR; GENE EXPRESSION; GENE FREQUENCY; HUMANS; MACACA MULATTA; MICE; MUTATION; ORGAN SPECIFICITY; POPULATION; RATS; SELECTION, GENETIC; SWINE;

PRIMATES; RODENTIA;

EID: 84876441770     PISSN: 00166731     EISSN: 19432631     Source Type: Journal    
DOI: 10.1534/genetics.112.147900     Document Type: Article

References (32)

1. Altschul, S. F., T. L. Madden, A. A. Schaffer, J. Zhang, Z. Zhang et al., 1997 Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25: 3389-3402.
2. Chamary, J. V., J. L. Parmley, and L. D. Hurst, 2006 Hearing silence: non-neutral evolution at synonymous sites in mammals. Nat. Rev. Genet. 7: 98-108.
3. Charlesworth, B., 2009 Fundamental concepts in genetics: effective population size and patterns of molecular evolution and variation. Nat. Rev. Genet. 10: 195-205.
4. Duret, L., and D. Mouchiroud, 2000 Determinants of substitution rates in mammalian genes: expression pattern affects selection intensity but not mutation rate. Mol. Biol. Evol. 17: 68-74.
5. Duret, L., D. Mouchiroud, and M. Gouy, 1994 HOVERGEN: a database of homologous vertebrate genes. Nucleic Acids Res. 22: 2360-2365.
6. Eyre-Walker, A., P. D. Keightley, N. G. Smith, and D. Gaffney, 2002 Quantifying the slightly deleterious mutation model of molecular evolution. Mol. Biol. Evol. 19: 2142-2149.
7. Hanada, K., S. H. Shiu, and W. H. Li, 2007 The nonsynonymous/ synonymous substitution rate ratio vs. the radical/conservative replacement rate ratio in the evolution of mammalian genes. Mol. Biol. Evol. 24: 2235-2241.
8. Johnson, K. P., and J. Seger, 2001 Elevated rates of nonsynonymous substitution in island birds. Mol. Biol. Evol. 18: 874-881.
9. Keightley, P. D., and A. Eyre-Walker, 2000 Deleterious mutations and the evolution of sex. Science 290: 331-333.
10. Kimura, M., 1983 The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge, UK.
11. Kryazhimskiy, S., and J. B. Plotkin, 2008 The population genetics of dN/dS. PLoS Genet. 4: e1000304.
12. Larkin, M. A., G. Blackshields, N. P. Brown, R. Chenna, P. A. McGettigan et al., 2007 Clustal W and Clustal X version 2.0. Bioinformatics 23: 2947-2948.
13. Li, W. H., 1997 Molecular Evolution. Sinauer, Sunderland, MA.
14. Liao, B. Y., N. M. Scott, and J. Zhang, 2006 Impacts of gene essentiality, expression pattern, and gene compactness on the evolutionary rate of mammalian proteins. Mol. Biol. Evol. 23: 2072-2080.
15. Mikkelsen, T. S., L. W. Hillier, E. E. Eichler, M. C. Zody, D. B. Jaffe et al., 2005 Initial sequence of the chimpanzee genome and comparison with the human genome. Nature 437: 69-87.
16. Moran, N. A., 1996 Accelerated evolution and Muller's rachet in endosymbiotic bacteria. Proc. Natl. Acad. Sci. USA 93: 2873-2878.
17. Nielsen, R., and Z. Yang, 2003 Estimating the distribution of selection coefficients from phylogenetic data with applications to mitochondrial and viral DNA. Mol. Biol. Evol. 20: 1231-1239.
18. Ohta, T., 1972 Evolutionary rate of Cistrons and DNA divergence. J. Mol. Evol. 1: 150-157.
19. Ohta, T., 1992 The nearly neutral theory of molecular evolution. Annu. Rev. Ecol. Syst. 23: 263-286.
20. Ohta, T., 1993 An examination of the generation-time effect on molecular evolution. Proc. Natl. Acad. Sci. USA 90: 10676-10680.
21. Ohta, T., and M. Kimura, 1971 On the constancy of the evolutionary rate of Cistrons. J. Mol. Evol. 1: 18-25.
22. Piganeau, G., and A. Eyre-Walker, 2009 Evidence for variation in the effective population size of animal mitochondrial DNA. PLoS ONE 4: e4396.
23. Popadin, K., L. V. Polishchuk, L. Mamirova, D. Knorre, and K. Gunbin, 2007 Accumulation of slightly deleterious mutations in mitochondrial protein-coding genes of large vs. small mammals. Proc. Natl. Acad. Sci. USA 104: 13390-13395.
24. Su, A. I., T. Wiltshire, S. Batalov, H. Lapp, K. A. Ching et al., 2004 A gene atlas of the mouse and human protein-encoding transcriptomes. Proc. Natl. Acad. Sci. USA 101: 6062-6067.
25. Subramanian, S., 2011 Fixation of deleterious mutations at critical positions in human proteins. Mol. Biol. Evol. 28: 2687-2693.
26. Williamson, S. H., R. Hernandez, A. Fledel-Alon, L. Zhu, R. Nielsen et al., 2005 Simultaneous inference of selection and population growth from patterns of variation in the human genome. Proc. Natl. Acad. Sci. USA 102: 7882-7887.
27. Woolfit, M., and L. Bromham, 2003 Increased rates of sequence evolution in endosymbiotic bacteria and fungi with small effective population sizes. Mol. Biol. Evol. 20: 1545-1555.
28. Woolfit, M., and L. Bromham, 2005 Population size and molecular evolution on islands. Proc. Biol. Sci. 272: 2277-2282.
29. Yanai, I., H. Benjamin, M. Shmoish, V. Chalifa-Caspi, M. Shklar et al., 2005 Genome-wide midrange transcription profiles reveal expression level relationships in human tissue specification. Bioinformatics 21: 650-659.
30. Yang, Z., 2007 PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 24: 1586-1591.
31. Zhang, J., 2000 Rates of conservative and radical nonsynonymous nucleotide substitutions in mammalian nuclear genes. J. Mol. Evol. 50: 56-68.
32. Zhang, L., and W. H. Li, 2004 Mammalian housekeeping genes evolve more slowly than tissue-specific genes. Mol. Biol. Evol. 21: 236-239.