Quantifying adaptive evolution in the Drosophila immune system.
Quantifying adaptive evolution in the Drosophila immune system.
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DOI：
10.1371/journal.pgen.1000698
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发表时间：
2009-10
期刊：
影响因子：
4.5
通讯作者：
Jiggins FM
中科院分区：
文献类型：
--
作者：
Obbard DJ;Welch JJ;Kim KW;Jiggins FM
据估计，果蝇中的大部分氨基酸替换已被自然选择固定，并且由于生物体面临着它们必须适应的不断变化的病原体和寄生虫阵列，我们已经研究了寄生虫介导的选择作为可能原因的作用。为了量化这种影响，并确定哪些基因和途径最有可能参与宿主-寄生虫的军备竞赛，我们对两种果蝇的136个免疫基因和287个位置匹配的非免疫基因的群体样本进行了重新测序。利用这些数据，以及McDonald-Kreitman方法的新扩展，我们估计自然选择以几乎是其他基因两倍的速度固定免疫基因中有利的氨基酸变化。我们发现免疫基因的适应性进化速率也比其他基因更多变，一小部分免疫基因在强烈的选择下进化。这些基因可能代表宿主-寄生虫共同进化的热点，它们往往具有相似的功能或属于相同的通路，例如抗病毒RNAi通路和IMD信号通路。这些模式似乎是两个物种免疫系统进化的一般特征，因为适应性进化的速率与D。黑腹果蝇D. simulans lineages.总之，我们的数据提供了免疫系统基因相对于基因组其余部分的适应性进化速率升高的定量估计，并且它们表明对寄生虫的适应是推动分子进化的重要力量。所有生物体都受到一系列不断变化的病原体和寄生虫的攻击，人们普遍认为，随之而来的宿主-寄生虫“军备竞赛”必须推动免疫系统基因的广泛适应性进化。在这里，我们利用新的测序技术和分析方法来量化免疫基因相对于基因组其余部分的适应量。我们采集了两种果蝇（D.黑腹果蝇D. simulans），并对来自这些样本的136个免疫基因和287个非免疫基因进行了测序。基于两个物种之间的序列差异，以及每个物种内的遗传多样性，我们估计自然选择驱动免疫相关蛋白质的变化是没有免疫功能的蛋白质的两倍。有趣的是，与基因组中的其他基因相比，免疫基因之间的适应速度也更多变，一小部分免疫基因在强烈的自然选择下进化。我们认为，这些基因可能代表宿主-寄生虫基因组内的共同进化的热点。
It is estimated that a large proportion of amino acid substitutions in Drosophila have been fixed by natural selection, and as organisms are faced with an ever-changing array of pathogens and parasites to which they must adapt, we have investigated the role of parasite-mediated selection as a likely cause. To quantify the effect, and to identify which genes and pathways are most likely to be involved in the host–parasite arms race, we have re-sequenced population samples of 136 immunity and 287 position-matched non-immunity genes in two species of Drosophila. Using these data, and a new extension of the McDonald-Kreitman approach, we estimate that natural selection fixes advantageous amino acid changes in immunity genes at nearly double the rate of other genes. We find the rate of adaptive evolution in immunity genes is also more variable than other genes, with a small subset of immune genes evolving under intense selection. These genes, which are likely to represent hotspots of host–parasite coevolution, tend to share similar functions or belong to the same pathways, such as the antiviral RNAi pathway and the IMD signalling pathway. These patterns appear to be general features of immune system evolution in both species, as rates of adaptive evolution are correlated between the D. melanogaster and D. simulans lineages. In summary, our data provide quantitative estimates of the elevated rate of adaptive evolution in immune system genes relative to the rest of the genome, and they suggest that adaptation to parasites is an important force driving molecular evolution. All organisms are attacked by an ever-changing array of pathogens and parasites, and it is widely supposed that the ensuing host–parasite “arms race” must drive extensive adaptive evolution in genes of the immune system. Here we have taken advantage of new sequencing technologies and analytical approaches to quantify the amount of adaptation that is occurring in immunity genes relative to the rest of the genome. We sampled two species of fruit fly (D. melanogaster and D. simulans) from eight different populations around the world, and sequenced 136 immunity and 287 non-immunity genes from these samples. Based on the differences in the sequences between the two species, and the genetic diversity within each species, we have estimated that natural selection drives twice as much change in immune-related proteins as in proteins with no immune function. Interestingly, the rate of adaptation is also more variable among immunity genes than among other genes in the genome, with a small subset of immunity genes evolving under intense natural selection. We suggest that these genes may represent hotspots of host–parasite coevolution within the genome.
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