Department of Biological Sciences, University of Tulsa, Tulsa, OK 74104, USA.
Department of Biochemistry & Molecular Biology, Oklahoma State University, Stillwater, OK 74078-3035, USA.
Viruses. 2019 May 5;11(5):418. doi: 10.3390/v11050418.
Diverse studies of viral evolution have led to the recognition that the evolutionary rates of viral taxa observed are dependent on the time scale being investigated-with short-term studies giving fast substitution rates, and orders of magnitude lower rates for deep calibrations. Although each of these factors may contribute to this time dependent rate phenomenon, a more fundamental cause should be considered. We sought to test computationally whether the basic phenomena of virus evolution (mutation, replication, and selection) can explain the relationships between the evolutionary and phylogenetic distances. We tested, by computational inference, the hypothesis that the phylogenetic distances between the pairs of sequences are functions of the evolutionary path lengths between them. A Basic simulation revealed that the relationship between simulated genetic and mutational distances is non-linear, and can be consistent with different rates of nucleotide substitution at different depths of branches in phylogenetic trees.
病毒进化的多种研究表明，所观察到的病毒分类群的进化率取决于所研究的时间尺度——短期研究给出快速的替代率，而深度校准的速率则要低几个数量级。尽管这些因素中的每一个都可能促成这种与时间相关的速率现象，但应该考虑更根本的原因。我们试图通过计算来检验病毒进化的基本现象（突变、复制和选择）是否可以解释进化和系统发育距离之间的关系。我们通过计算推断测试了这样一个假设，即序列对之间的系统发育距离是它们之间进化路径长度的函数。一项基础模拟表明，模拟遗传和突变距离之间的关系是非线性的，并且可以与系统发育树中不同分支深度的核苷酸替代率不同相一致。
