Experimental Evolution of the Bacteriophage Group Leviviridae

适应的遗传学将在Leviviridae中进行研究，Leviviridae是一组单链RNA噬菌体。该噬菌体将被选择在高温下生长。高温抑制野生型噬菌体的生长。然而，在高温下繁殖几代后，噬菌体适合度恢复。在这项研究中，八种不同的噬菌体物种将在高温下繁殖(通过连续转移)。与适应高温快速生长相关的遗传变化将通过对进化的噬菌体完全测序并将这些序列与每个物种的祖先序列进行比较来进行分析。将解决的具体问题包括：(1)与高温适应相关的遗传变化；(2)遗传变化的适合度效应；(3)在适应性进化过程中固定的突变的适合度效应的分布情况；(4)噬菌体物种内的进化是否可重复；(5)物种的系统发育预测与高温适应生长相关的特定变化的程度；以及(6)RNA分子的变化在多大程度上增加了重要的茎环结构在高温下的稳定性？Leviviridae的独特之处在于它们具有非常高的突变率，并且RNA分子的许多二级结构的功能已经被研究出来；因此，许多适应性变化的功能意义可以理解。此外，由于该群体的系统发育存在很好的支持，遗传变化可以放在系统发育的背景下。

The genetics of adaptation will be examined in the Leviviridae, a group of single stranded RNA phage. The phage will be selected for growth at high temperature. High temperature inhibits the growth of the wild-type phage. However, after propagating the phage at high temperature for several generations, phage fitness recovers. In this study, eight different phage species will be propagated (via serial transfer) at high temperature. The genetic changes associated with adaptation to fast growth at high temperature will be assayed by completely sequencing the evolved phage and comparing these sequences to the ancestral sequence for each species. The specific questions that will be addressed include: (1) what are the genetic changes associated with adaptation to high temperature, (2) what are the fitness effects of the genetic changes, (3) what is the distribution of fitness effects of mutations that are fixed during the course of adaptive evolution, (4) is the evolution repeatable within a phage species, (5) to what extent does the phylogeny of the species predict specific change associated with adaptation to growth at high temperature, and, (6) to what extent do changes in the RNA molecule increase the stability of important stem-loop structures at high temperature? The Leviviridae are unique in that they have a very high mutation rate and the function of much of the secondary structure of the RNA molecule has been worked out; hence, the functional significance of many adaptive changes can be understood. Moreover, because a well-supported phylogeny of the group exists, the genetic changes can be placed into a phylogenetic context.