Site-specific evolutionary rate shifts are defined as protein sites, where the rate of substitution has changed dramatically across the phylogeny. With respect to a given clade, sites may either undergo a rate acceleration or a rate deceleration, reflecting a site that was conserved and became variable, or vice-versa, respectively. Sites displaying such a dramatic evolutionary change may point to a loss or gain of function at the protein site, reflecting adaptation, or they may indicate epistatic interactions among sites. Here, we analyzed full genomes of HIV and SIV-1 and identified 271 rate-shifting sites along the HIV-1/SIV phylogeny. The majority of rate shifts occurred at long branches, often corresponding to cross-species transmission branches. We noted that in most proteins, the number of rate accelerations and decelerations was equal, and we suggest that this reflects epistatic interactions among sites. However, several accessory proteins were enriched for either accelerations or decelerations, and we suggest that this may be a signature of adaptation to new hosts. Interestingly, the non-pandemic HIV-1 group O clade exhibited a substantially higher number of rate-shift events than the pandemic group M clade. We propose that this may be a reflection of the height of the species barrier between gorillas and humans versus chimpanzees and humans. Our results provide a genome-wide view of the constraints operating on proteins of HIV-1 and SIV.

中文翻译：

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HIV-1和SIV的特定于站点的进化速率变化

特定于位点的进化速率转移定义为蛋白质位点，其中取代的速率在整个系统发育过程中发生了巨大变化。对于给定的进化枝，站点可能经历速率加速或速率减速，分别反映了一个保守且可变的站点，反之亦然。表现出如此剧烈的进化变化的位点可能表明蛋白质位点的功能丧失或获得，反映了适应性，或者它们可能指示位点之间的上位相互作用。在这里，我们分析了HIV和SIV-1的完整基因组，并沿着HIV-1 / SIV系统发育鉴定了271个速率转移位点。大多数速率变化发生在长分支上，通常对应于跨物种传播分支。我们注意到，在大多数蛋白质中，加速率和减速率的数量相等，并且我们建议这反映了站点之间的上位交互。然而，一些辅助蛋白被富集用于加速或减速，我们建议这可能是适应新宿主的标志。有趣的是，非大流行HIV-1组O进化枝比大流行组M进化枝具有更高的速率变化事件。我们认为，这可能反映了大猩猩和人类与黑猩猩和人类之间物种隔离的高度。我们的结果提供了对HIV-1和SIV蛋白质的限制作用的全基因组视图。非大流行HIV-1组O进化枝比大流行组M进化枝具有更高的速率转移事件。我们认为，这可能反映了大猩猩和人类与黑猩猩和人类之间物种隔离的高度。我们的结果提供了对HIV-1和SIV蛋白质的限制作用的全基因组视图。非大流行HIV-1组O进化枝比大流行组M进化枝具有更高的速率转移事件。我们认为，这可能反映了大猩猩和人类与黑猩猩和人类之间物种隔离的高度。我们的结果提供了对HIV-1和SIV蛋白质的限制作用的全基因组视图。