Aguileta Gabriela, Refrégier Guislaine, Yockteng Roxana, Fournier Elisabeth, Giraud Tatiana
Ecologie, Systématique et Evolution, Université Paris-Sud, Orsay cedex, France.
Infect Genet Evol. 2009 Jul;9(4):656-70. doi: 10.1016/j.meegid.2009.03.010. Epub 2009 Apr 6.
The ongoing coevolutionary struggle between hosts and pathogens, with hosts evolving to escape pathogen infection and pathogens evolving to escape host defences, can generate an 'arms race', i.e., the occurrence of recurrent selective sweeps that each favours a novel resistance or virulence allele that goes to fixation. Host-pathogen coevolution can alternatively lead to a 'trench warfare', i.e., balancing selection, maintaining certain alleles at loci involved in host-pathogen recognition over long time scales. Recently, technological and methodological progress has enabled detection of footprints of selection directly on genes, which can provide useful insights into the processes of coevolution. This knowledge can also have practical applications, for instance development of vaccines or drugs. Here we review the methods for detecting genes under positive selection using divergence data (i.e., the ratio of nonsynonymous to synonymous substitution rates, d(N)/d(S)). We also review methods for detecting selection using polymorphisms, such as methods based on F(ST) measures, frequency spectrum, linkage disequilibrium and haplotype structure. In the second part, we review examples where targets of selection have been identified in pathogens using these tests. Genes under positive selection in pathogens have mostly been sought among viruses, bacteria and protists, because of their paramount importance for human health. Another focus is on fungal pathogens owing to their agronomic importance. We finally discuss promising directions in pathogen studies, such as detecting selection in non-coding regions.
宿主与病原体之间持续的协同进化斗争，即宿主进化以逃避病原体感染，病原体进化以逃避宿主防御，可能会引发一场“军备竞赛”，也就是反复出现的选择性清除事件，每次都有利于一个新的抗性或毒力等位基因固定下来。宿主 - 病原体协同进化也可能导致“堑壕战”，即平衡选择，在长时间尺度上维持参与宿主 - 病原体识别的位点上的某些等位基因。最近，技术和方法上的进步使得能够直接在基因上检测选择印记，这可以为协同进化过程提供有用的见解。这些知识也可能有实际应用，例如疫苗或药物的开发。在这里，我们回顾了使用分歧数据（即非同义替换率与同义替换率之比，d(N)/d(S)）检测正选择基因的方法。我们还回顾了使用多态性检测选择的方法，例如基于F(ST) 度量、频率谱、连锁不平衡和单倍型结构的方法。在第二部分，我们回顾了使用这些测试在病原体中鉴定选择靶点的例子。由于对人类健康至关重要，病原体中受到正选择的基因大多在病毒、细菌和原生生物中寻找。另一个重点是真菌病原体，因为它们具有农学重要性。我们最后讨论了病原体研究中有前景的方向，例如检测非编码区域的选择。
