Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
Shifts in the intensity of purifying selection: An analysis of genome-wide polymorphism data from two closely related yeast species
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DOI：
10.1101/gr.108993.110
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发表时间：
2010-11-01
期刊：
影响因子：
7
通讯作者：
Sella, Guy
中科院分区：
文献类型：
--
作者：
Elyashiv, Eyal;Bullaughey, Kevin;Sella, Guy
净化选择的强度在种群和物种之间有多大的差异？在整个基因组中，选择压力的变化有多均匀？为了解决这些问题，我们利用了最近的，全基因组多态性数据集从两个密切相关的酵母，酿酒酵母和S。paradoxus，密切关注这些物种的种群结构。我们发现，氨基酸位点上的平均净化选择强度在种群间和物种间有显著差异。正如在广泛的弱有害突变的存在下所预期的那样，纯化选择对群体内分离的单核苷酸多态性（SNP）的影响比对群体样品之间固定的SNP的影响弱得多。此外，根据近中性模型，在净化选择的强度在整个人口的变化几乎完全对应于简单的措施，其有效的大小。作为理解产生这些模式的过程的第一步，我们试图梳理出系统性的、全基因组的变化在选择效力中的相对重要性，例如那些预期来自人口统计过程的变化和基因特异性变化，这些变化可能是在选择压力发生变化后预期的。为此，我们开发了一个新的模型，种群之间的净化选择的演变，并推断其参数从全基因组数据使用的似然方法。我们发现，大多数，但不是所有的变化似乎是由系统的选择效力的变化。一个群体，清酒源菌株的S。然而，酿酒酵母也显示出广泛的基因特异性变化，可能与驯化有关。这些发现对我们理解纯化选择以及估计酵母和其他物种的分子适应率具有重要意义。[补充材料可在http://www.genome.org在线获取。]
How much does the intensity of purifying selection vary among populations and species? How uniform are the shifts in selective pressures across the genome? To address these questions, we took advantage of a recent, whole-genome polymorphism data set from two closely related species of yeast, Saccharomyces cerevisiae and S. paradoxus, paying close attention to the population structure within these species. We found that the average intensity of purifying selection on amino acid sites varies markedly among populations and between species. As expected in the presence of extensive weakly deleterious mutations, the effect of purifying selection is substantially weaker on single nucleotide polymorphisms (SNPs) segregating within populations than on SNPs fixed between population samples. Also in accordance with a Nearly Neutral model, the variation in the intensity of purifying selection across populations corresponds almost perfectly to simple measures of their effective size. As a first step toward understanding the processes generating these patterns, we sought to tease apart the relative importance of systematic, genome-wide changes in the efficacy of selection, such as those expected from demographic processes and of gene-specific changes, which may be expected after a shift in selective pressures. For that purpose, we developed a new model for the evolution of purifying selection between populations and inferred its parameters from the genome-wide data using a likelihood approach. We found that most, but not all changes seem to be explained by systematic shifts in the efficacy of selection. One population, the sake-derived strains of S. cerevisiae, however, also shows extensive gene-specific changes, plausibly associated with domestication. These findings have important implications for our understanding of purifying selection as well as for estimates of the rate of molecular adaptation in yeast and in other species.[Supplemental material is available online at http://www.genome.org.]