A codon-based model of host-specific selection in parasites, with an application to the influenza A virus
A codon-based model of host-specific selection in parasites, with an application to the influenza A virus
复制标题
DOI：
10.1093/molbev/msg149
复制
发表时间：
2003-08-01
影响因子：
10.7
通讯作者：
Christiansen, FB
中科院分区：
文献类型：
--
作者：
Forsberg, R;Christiansen, FB
寄生虫有时通过获得新的宿主物种来扩大其宿主范围。在宿主改变事件之后，作用于给定寄生虫基因的选择性方案可能由于蛋白质功能的宿主特异性适应性改变或宿主特异性免疫介导的选择而改变。我们提出了一个基于密码子的模型，试图通过允许位置特异性取代过程与宿主变化事件一起改变来包括这些影响。在最大似然参数估计之后，我们采用经验贝叶斯程序来确定可能参与宿主特异性适应的候选位点。我们讨论了该模型的适用性，以确定是否有选择性的制度不同，在两组相关的生物体的更一般的问题。该模型的效用说明从禽流感病毒和人类宿主获得的A型流感病毒的核蛋白序列的数据集。
Parasites sometimes expand their host range by acquiring a new host species. After a host change event, the selective regime acting on a given parasite gene may change as a result of host-specific adaptive alterations of protein functionality or host-specific immune-mediated selection. We present a codon-based model that attempts to include these effects by allowing the position-specific substitution process to change in conjunction with a host change event. Following maximum-likelihood parameter estimation, we employ an empirical Bayesian procedure to identify candidate sites potentially involved in host-specific adaptation. We discuss the applicability of the model to the more general problem of ascertaining whether the selective regime differs in two groups of related organisms. The utility of the model is illustrated on a data set of nucleoprotein sequences from-the influenza A virus obtained from avian and human hosts.