Detecting the effects of selection at the population level in six bovine immune genes
Detecting the effects of selection at the population level in six bovine immune genes
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DOI：
10.1186/1471-2156-9-62
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发表时间：
2008-10-06
期刊：
影响因子：
2.9
通讯作者：
Bradley, Daniel G.
中科院分区：
文献类型：
--
作者：
Freeman, Abigail R.;Lynn, David J.;Bradley, Daniel G.
背景：物种或种群对新的传染病挑战的反应和生存能力是形成遗传多样性的最重要的选择性力量之一，而动物驯化之后的时期可能是新出现的疾病最重要的时期之一。全基因组的种间比较表明，包括分化簇2(CD2)、ADP-核糖基转移酶4(ART4)、酪氨酸激酶结合蛋白(TYROBP)和白介素IL2、IL5、IL13在内的基因在牛的进化过程中可能经历了正向选择。过去的适应性变化意味着较新的变异可能也受到选择性力量的影响。结果：在本文中，我们对来自欧洲、非洲和亚洲的牛队列中的这些基因进行了重新测序，以在种群水平上研究多态模式。牛的多样性格局较高，这表明与金牛群的人口历史不同。在每个细胞表面受体中都观察到了显著的编码多态性。特别是，CD2显示了两种不同的单倍型，由一系列六个衍生的非同义替换定义，这些替换显著聚集在蛋白质的胞外表面，并给出了Fay和Wu的H的显著值，有力地表明了最近的适应历史。相反，信号分子(尤其是IL13)表现出与选择效果一致的异常等位基因频谱，但编码多态性可以忽略不计。结论：我们提出了牛免疫基因最近适应历史的证据；暗示了种内和种间选择信号之间的一些对应关系。有趣的是，三个信号分子具有可以忽略的非同义变异，但显示出与三个受体相反的测试统计数据，在三个受体中，蛋白质序列多样性表明选择历史。
Background: The capacity of a species or population to respond to and survive novel infectious disease challenge is one of the most significant selective forces shaping genetic diversity and the period following animal domestication was likely one of the most important in terms of newly emerging diseases. Inter-specific genome-wide comparison has suggested that genes, including cluster of differentiation 2 (CD2), ADP-ribosyltransferase 4 (ART4), tyrosine kinase binding protein (TYROBP) and interleukins IL2, IL5, IL13, may have undergone positive selection during the evolution of the bovine lineage. Past adaptive change implies that more recent variation may have also been subject to selective forces.Results: In this paper, we re-sequence each of these genes in cattle cohorts from Europe, Africa and Asia to investigate patterns of polymorphism at the population level. Patterns of diversity are higher within Bos indicus suggesting different demographic history to that of Bos taurus. Significant coding polymorphism was observed within each of the cell-surface receptors. In particular, CD2 shows two divergent haplotypes defined by a series of six derived nonsynonymous substitutions that are significantly clustered on the extracellular surface of the protein and give significant values for Fay and Wu's H, strongly suggesting a recent adaptive history. In contrast, the signaling molecules (especially IL13) display outlying allele frequency spectra which are consistent with the effects of selection, but display negligible coding polymorphism.Conclusion: We present evidence suggestive of recent adaptive history in bovine immune genes; implying some correspondence between intra- and inter-specific signals of selection. Interestingly, three signaling molecules have negligible nonsynonymous variation but show outlying test statistics in contrast to three receptors, where it is protein sequence diversity that suggests selective history.