Shapiro Joshua A, Huang Wei, Zhang Chenhui, Hubisz Melissa J, Lu Jian, Turissini David A, Fang Shu, Wang Hurng-Yi, Hudson Richard R, Nielsen Rasmus, Chen Zhu, Wu Chung-I
Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637, USA.
Proc Natl Acad Sci U S A. 2007 Feb 13;104(7):2271-6. doi: 10.1073/pnas.0610385104. Epub 2007 Feb 6.
Determining the extent of adaptive evolution at the genomic level is central to our understanding of molecular evolution. A suitable observation for this purpose would consist of polymorphic data on a large and unbiased collection of genes from two closely related species, each having a large and stable population. In this study, we sequenced 419 genes from 24 lines of Drosophila melanogaster and its close relatives. Together with data from Drosophila simulans, these data reveal the following. (i) Approximately 10% of the loci in regions of normal recombination are much less polymorphic at silent sites than expected, hinting at the action of selective sweeps. (ii) The level of polymorphism is negatively correlated with the rate of nonsynonymous divergence across loci. Thus, even under strict neutrality, the ratio of amino acid to silent nucleotide changes (A:S) between Drosophila species is expected to be 25-40% higher than the A:S ratio for polymorphism when data are pooled across the genome. (iii) The observed A/S ratio between species among the 419 loci is 28.9% higher than the (adjusted) neutral expectation. We estimate that nearly 30% of the amino acid substitutions between D. melanogaster and its close relatives were adaptive. (iv) This signature of adaptive evolution is observable only in regions of normal recombination. Hence, the low level of polymorphism observed in regions of reduced recombination may not be driven primarily by positive selection. Finally, we discuss the theories and data pertaining to the interpretation of adaptive evolution in genomic studies.
在基因组水平上确定适应性进化的程度是我们理解分子进化的核心。为此目的进行的合适观察应包括来自两个密切相关物种的大量且无偏倚的基因集合的多态性数据，每个物种都有一个大且稳定的种群。在本研究中，我们对24个黑腹果蝇品系及其近亲的419个基因进行了测序。结合拟果蝇的数据，这些数据揭示了以下几点。（i）正常重组区域中约10%的位点在沉默位点处的多态性远低于预期，这暗示了选择性清除的作用。（ii）多态性水平与各基因座非同义分化率呈负相关。因此，即使在严格的中性条件下，当跨基因组汇总数据时，果蝇物种之间氨基酸与沉默核苷酸变化的比率（A:S）预计比多态性的A:S比率高25 - 40%。（iii）在419个基因座中观察到的物种间A/S比率比（调整后的）中性预期高28.9%。我们估计黑腹果蝇与其近亲之间近30%的氨基酸替换是适应性的。（iv）这种适应性进化的特征仅在正常重组区域中可观察到。因此，在重组减少区域观察到的低多态性水平可能并非主要由正选择驱动。最后，我们讨论了与基因组研究中适应性进化解释相关的理论和数据。
