Adaptive evolution of nontransitive fitness in yeast.
Adaptive evolution of nontransitive fitness in yeast.
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DOI：
10.7554/elife.62238
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发表时间：
2020-12-29
期刊：
影响因子：
7.7
通讯作者：
Lang GI
中科院分区：
文献类型：
--
作者：
Buskirk SW;Rokes AB;Lang GI
一种常见的误解是，进化是一种线性的“进步进行曲”，即沿着一条传承线的每一个有机体都比它之前的所有有机体更适合进化。拒绝这种误解意味着进化是不可传递的：一系列适应性事件有时会产生比遥远的祖先更不适合的有机体。在这里，我们在1000代酵母进化实验中确定了一个非传递性的进化序列。我们表明，不可传递性是由于酵母核基因组的适应和细胞内病毒的逐步恶化而产生的，这提供了比宿主细胞内的病毒竞争对手更好的优势。扩展我们的分析，我们发现我们的大约140个种群中有近一半经历了多级选择，修复了核基因组和病毒基因组中的适应性突变。我们的结果为在1000代宿主/病毒进化实验中由于多水平选择而导致的非传递性的适应性进化提供了一个机械案例研究。生物学上普遍认为，地球上的所有生命都是从一个单一的祖先经过数十亿年的进化而来的。然而，关于这一过程仍有许多不完全了解的地方。进化通常被认为是以线性方式进行的，每一代新一代都比上一代更好地适应了环境。但也有人提出，进化也是不可传递的：这意味着，即使每一代人都比上一代人“更健康”，但这一系列适应性变化偶尔会导致生物体的健康状况不如他们远古的祖先。进化的实验室实验是测试进化理论的好方法，因为它们允许研究人员创造在自然种群中不可能观察到的场景，比如一个有机体与其灭绝的祖先竞争。Buskirk等人。用酵母建立这样的实验，以确定是否可以在生物体的直系后代中观察到非传递性效应。在实验开始时，酵母细胞是一种在酵母中常见的非传染性“杀手”病毒的宿主。含有病毒的细胞会产生一种毒素，这种毒素会摧毁其他没有病毒的酵母。酵母种群被给予营养丰富的肉汤来生长，并受到一个简单的进化压力：快速生长，这限制了可用的资源量。随着酵母的进化，他们获得了有益的基因突变，使他们能够超越邻居，并将这些特征传递给他们的后代。其中一些突变不是发生在酵母基因组中，而是发生在杀手病毒的基因组中，这阻止了感染病毒的酵母产生杀手毒素。随着时间的推移，其他突变导致受感染的酵母不再对毒素免疫。因此，当Buskirk等人。让这些酵母与他们遥远的祖先对抗，新一代被老一代产生的毒素摧毁。这些发现为沿下降路线的非传递性提供了第一个实验证据。这些结果对我们理解进化是如何工作的有着广泛的影响，这让人们对进化总是直接朝着新的、改进的特征前进的想法产生了怀疑。
A common misconception is that evolution is a linear ‘march of progress’, where each organism along a line of descent is more fit than all those that came before it. Rejecting this misconception implies that evolution is nontransitive: a series of adaptive events will, on occasion, produce organisms that are less fit compared to a distant ancestor. Here we identify a nontransitive evolutionary sequence in a 1000-generation yeast evolution experiment. We show that nontransitivity arises due to adaptation in the yeast nuclear genome combined with the stepwise deterioration of an intracellular virus, which provides an advantage over viral competitors within host cells. Extending our analysis, we find that nearly half of our ~140 populations experience multilevel selection, fixing adaptive mutations in both the nuclear and viral genomes. Our results provide a mechanistic case-study for the adaptive evolution of nontransitivity due to multilevel selection in a 1000-generation host/virus evolution experiment. It is widely accepted in biology that all life on Earth gradually evolved over billions of years from a single ancestor. Yet, there is still much about this process that is not fully understood. Evolution is often thought of as progressing in a linear fashion, with each new generation being better adapted to its environment than the last. But it has been proposed that evolution is also nontransitive: this means even if each generation is ‘fitter’ than its immediate predecessor, these series of adaptive changes will occasionally result in organisms that are less fit than their distant ancestors. Laboratory experiments of evolution are a good way to test evolutionary theories because they allow researchers to create scenarios that are impossible to observe in natural populations, such as an organism competing against its extinct ancestors. Buskirk et al. set up such an experiment using yeast to determine whether nontransitive effects can be observed in the direct descendants of an organism. At the start of the experiment, the yeast cells were host to a non-infectious ‘killer’ virus that is common among yeast. Cells containing the virus produce a toxin that destroys other yeast that lack the virus. The populations of yeast were given a nutrient-rich broth in which to grow and subjected to a simple evolutionary pressure: to grow fast, which limits the amount of resources available. As the yeast evolved, they gained beneficial genetic mutations that allowed them to outcompete their neighbors, and they passed these traits down to their descendants. Some of these mutations occurred not in the yeast genome, but in the genome of the killer virus, and this stopped the yeast infected with the virus from producing the killer toxin. Over time, other mutations resulted in the infected yeast no longer being immune to the toxin. Thus, when Buskirk et al. pitted these yeast against their distant ancestors, the new generation were destroyed by the toxins the older generation produced. These findings provide the first experimental evidence for nontransitivity along a line of descent. The results have broad implications for our understanding of how evolution works, casting doubts over the idea that evolution always involves a direct progression towards new, improved traits.