Fay JC, Wu CI. Sequence divergence, functional constraint, and selection in protein evolution. Annu Rev Genomics Hum Genet 4: 213-235

Department of Genome Sciences, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA.
Annual Review of Genomics and Human Genetics (Impact Factor: 8.96). 02/2003; 4:213-35. DOI: 10.1146/annurev.genom.4.020303.162528
Source: PubMed


The genome sequences of multiple species has enabled functional inferences from comparative genomics. A primary objective is to infer biological functions from the conservation of homologous DNA sequences between species. A second, more difficult, objective is to understand what functional DNA sequences have changed over time and are responsible for species' phenotypic differences. The neutral theory of molecular evolution provides a theoretical framework in which both objectives can be explicitly tested. Development of statistical tests within this framework has provided insight into the evolutionary forces that constrain and in some cases change DNA sequences and the resulting patterns that emerge. In this article, we review recent work on how functional constraint and changes in protein function are inferred from protein polymorphism and divergence data. We relate these studies to our understanding of the neutral theory and adaptive evolution.

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    • "Similarly, for Leu (UUR), the RSCU was 2.63 for UUA and 1.62 for UUG. The estimation of nonsynonymous (Ka) and synonymous (Ks) substitution rates is quite useful for understanding the selective constraints acting on the protein-coding sequences across closely related species (Ohta, 1995; Fay and Wu, 2003). In order to detect the influence of selection pressure in Arcidae species, the numbers of Ka, Ks and their ratios were calculated for all pairwise comparisons among the four Arcidae (Supplementary Table 2). "
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