Topology of viral evolution
Topology of viral evolution
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DOI：
10.1073/pnas.1313480110
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发表时间：
2013-11-12
影响因子：
11.1
通讯作者：
Rabadan, Raul
中科院分区：
文献类型：
--
作者：
Chan, Joseph Minhow;Carlsson, Gunnar;Rabadan, Raul
树结构是目前公认的代表生物体、物种或其他类群之间进化关系的范例。然而，水平或网状基因组交换在自然界中普遍存在，并且混淆了系统发育树的特征。借鉴代数拓扑，我们提出了一个独特的进化框架，全面捕获克隆和网状进化。我们表明，克隆进化可以概括为一棵树，而网状进化则表现出维度大于零的非平凡拓扑。我们的方法有效地表征了 RNA 病毒的克隆进化、重配和重组。除了检测网状进化之外，我们还简洁地概括了涉及两种以上亲本毒株的复杂遗传交换的历史，例如 H7N9 禽流感的三重重配和循环 HIV-1 重组体的形成。此外，我们还发现了反复出现的大规模网状进化模式，包括禽流感重配过程中频繁出现的 PB2-PB1-PA-NP 共分离。最后，我们限制了网状事件的发生率（即禽流感每年发生 20 次重组）。我们的方法提供了一种进化视角，不仅捕获了排除系统发育的网状事件，而且还表明了系统发育推断可能准确的进化尺度。
The tree structure is currently the accepted paradigm to represent evolutionary relationships between organisms, species or other taxa. However, horizontal, or reticulate, genomic exchanges are pervasive in nature and confound characterization of phylogenetic trees. Drawing from algebraic topology, we present a unique evolutionary framework that comprehensively captures both clonal and reticulate evolution. We show that whereas clonal evolution can be summarized as a tree, reticulate evolution exhibits nontrivial topology of dimension greater than zero. Our method effectively characterizes clonal evolution, reassortment, and recombination in RNA viruses. Beyond detecting reticulate evolution, we succinctly recapitulate the history of complex genetic exchanges involving more than two parental strains, such as the triple reassortment of H7N9 avian influenza and the formation of circulating HIV-1 recombinants. In addition, we identify recurrent, large-scale patterns of reticulate evolution, including frequent PB2-PB1-PA-NP cosegregation during avian influenza reassortment. Finally, we bound the rate of reticulate events (i.e., 20 reassortments per year in avian influenza). Our method provides an evolutionary perspective that not only captures reticulate events precluding phylogeny, but also indicates the evolutionary scales where phylogenetic inference could be accurate.