R Nielsen, Cornell University, Ithaca, New York, USA
H Akashi, Pennsylvania State University, Pennsylvania, USA
Published online: December 2007
DOI: 10.1002/9780470015902.a0006114.pub2
The role of selection on silent-site evolution in humans is controversial. Mounting evidence suggests that selection for optimal base composition, codon usage or both may be common.
Keywords: silent substitutions; silent sites; selection; codon usage bias; weak selection; codon bias; population genetics
| References | |
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| Sharp PM, Averof M, Lloyd AT, Matassi G and Peden JF (1995) DNA sequence evolution: the sounds of silence. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 349: 241–247. | |
| Smith NG and Eyre-Walker A (2001) Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans. Molecular Biology and Evolution 18: 982–986. | |
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| Further Reading | |
| Akashi H (1999) Within- and between-species DNA sequence variation and the ‘footprint’ of natural selection. Gene 238: 39–51. | |
| Andersson SG and Kurland CG (1990) Codon preferences in free-living microorganisms. Microbiological Reviews 54: 198–210. | |
| Bernardi G (1995) The human genome: organization and evolutionary history. Annual Review of Genetics 29: 445–476. | |
| Bustamante CD, Nielsen R and Hartl DL (2002) A maximum likelihood method for analyzing pseudogene evolution: implications for silent site evolution in humans and rodents. Molecular Biology and Evolution 19: 110–117. | |
| Gorlov IP, Kimmel M and Amos CI (2006) Strength of the purifying selection against different categories of the point mutations in the coding regions of the human genome. Human Molecular Genetics 15: 1143–1150. | |
| Iida K and Akashi H (2000) A test of translational selection at ‘silent’ sites in the human genome: base composition comparisons in alternatively spliced genes. Gene 261: 93–105. | |
| Ikemura T (1985) Codon usage and tRNA content in unicellular and multicellular organisms. Molecular Biology and Evolution 2: 13–34. | |
| Karlin S and Burge C (1995) Dinucleotide relative abundance extremes: a genomic signature. Trends in Genetics 11: 283–290. | |
| Orban TI and Olah E (2001) Purifying selection on silent sites – a constraint from splicing regulation? Trends in Genetics 17: 252–253. | |
| Parmley JL, Chamary JV and Hurst LD (2006) Evidence for purifying selection against synonymous mutations in mammalian exonic splicing enhancers. Molecular Biology and Evolution 23: 301–309. | |
| Sharp PM, Averof M, Lloyd AT, Matassi G and Peden JF (1995) DNA sequence evolution: the sounds of silence. Philosophical Transactions of the Royal Society of London, Series B, Biological Sciences 349: 241–247. | |
| Smith NG and Eyre-Walker A (2001) Synonymous codon bias is not caused by mutation bias in G+C-rich genes in humans. Molecular Biology and Evolution 18: 982–986. | |
| Subramanian S and Kumar S (2006) Higher intensity of purifying selection on >90% of the human genes revealed by the intrinsic replacement mutation rates. Molecular Biology and Evolution 23: 2283–2287. | |
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