Flaviviruses display diverse epidemiological and ecological features. Tick-borne and mosquito-borne flaviviruses (TBFV and MBFV, respectively) are important human pathogens that alternate replication in invertebrate vectors and vertebrate hosts. The Flavivirus genus also includes insect-specific viruses (ISFVs) and viruses with unknown invertebrate hosts. It is generally accepted that viruses that alternate between taxonomically different hosts evolve slowly and that the evolution of MBFVs and TBFVs is dominated by strong constraints, with limited episodes of positive selection. We exploited the availability of flavivirus genomes to test these hypotheses and to compare their rates and patterns of evolution. We estimated the substitution rates of CFAV and CxFV (two ISFVs) and, by taking into account the time-frame of measurement, compared them with those of other flaviviruses. Results indicated that CFAV and CxFV display relatively different substitution rates. However, these data, together with estimates for single-host members of the Flaviviridae family, indicated that MBFVs do not display relatively slower evolution. Conversely, TBFVs displayed some of lowest substitution rates among flaviviruses. Analysis of selective patterns over longer evolutionary time-frames confirmed that MBFVs evolve under strong purifying selection. Interestingly, TBFVs and ISFVs did not show extremely different levels of constraint, although TBFVs alternate among hosts, whereas ISFVs do not. Additional results showed that episodic positive selection drove the evolution of MBFVs, despite their high constraint. Positive selection was also detected on two branches of the TBFVs phylogeny that define the seabird clade. Thus, positive selection was much more common during the evolution of arthropod-borne flaviviruses than previously thought. Overall, our data indicate that flavivirus evolutionary patterns are complex and most likely determined by multiple factors, not limited to the alternation between taxonomically divergent hosts. The frequency of both positive and purifying selection, especially in MBFVs, suggests that a minority of sites in the viral polyprotein experience weak constraint and can evolve to generate new viral phenotypes and possibly promote adaptation to new hosts.

中文翻译：

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分类学上不同的宿主之间的交替不是黄病毒进化的主要决定因素

黄病毒显示出不同的流行病学和生态学特征。蜱传和蚊媒黄病毒（分别为 TBFV 和 MBFV）是重要的人类病原体，它们在无脊椎动物载体和脊椎动物宿主中交替复制。黄病毒属还包括昆虫特异性病毒 (ISFV) 和未知无脊椎动物宿主的病毒。人们普遍认为，在分类学上不同的宿主之间交替的病毒进化缓慢，MBFV 和 TBFV 的进化受强约束支配，正选择的事件有限。我们利用黄病毒基因组的可用性来检验这些假设并比较它们的速率和进化模式。我们估计了 CFAV 和 CxFV（两个 ISFV）的替代率，并且通过考虑测量的时间范围，将它们与其他黄病毒进行了比较。结果表明，CFAV 和 CxFV 显示出相对不同的替代率。然而，这些数据以及对黄病毒科单宿主成员的估计表明，MBFV 的进化速度并不相对较慢。相反，TBFV 在黄病毒中显示出一些最低的替代率。对较长进化时间框架内的选择性模式的分析证实，MBFV 在强净化选择下进化。有趣的是，TBFV 和 ISFV 并没有显示出截然不同的约束级别，尽管 TBFV 在宿主之间交替，而 ISFV 则没有。其他结果表明，尽管 MBFV 的限制很高，但偶发性正选择推动了 MBFV 的进化。在定义海鸟进化枝的 TBFV 系统发育的两个分支上也检测到了阳性选择。因此，在节肢动物传播的黄病毒的进化过程中，阳性选择比以前认为的要普遍得多。总的来说，我们的数据表明黄病毒的进化模式很复杂，很可能是由多种因素决定的，不限于分类学上不同的宿主之间的交替。阳性选择和纯化选择的频率，尤其是在 MBFV 中，表明病毒多蛋白中的少数位点受到弱约束，可以进化产生新的病毒表型，并可能促进对新宿主的适应。我们的数据表明，黄病毒的进化模式很复杂，很可能是由多种因素决定的，不限于分类学上不同的宿主之间的交替。阳性选择和纯化选择的频率，尤其是在 MBFV 中，表明病毒多蛋白中的少数位点受到弱约束，可以进化产生新的病毒表型，并可能促进对新宿主的适应。我们的数据表明，黄病毒的进化模式很复杂，很可能是由多种因素决定的，不限于分类学上不同的宿主之间的交替。阳性选择和纯化选择的频率，尤其是在 MBFV 中，表明病毒多蛋白中的少数位点受到弱约束，可以进化产生新的病毒表型，并可能促进对新宿主的适应。