Genotype network intersections promote evolutionary innovation
Genotype network intersections promote evolutionary innovation
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DOI：
10.1371/journal.pbio.3000300
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发表时间：
2019-05-01
期刊：
影响因子：
9.8
通讯作者：
Hayden, Eric J.
中科院分区：
文献类型：
--
作者：
Bendixsen, Devin P.;Collet, James;Hayden, Eric J.
进化创新是在进化过程中出现并增加生物多样性的新特性。创新的遗传机制仍然知之甚少。创新的系统观要求分析基因型网络--产生相同表型的巨大遗传变异网络。创新可以发生在两个不同基因型网络的交叉点。然而，基因型网络的实验表征受到了大量需要进行功能分析的遗传变异的阻碍。在这里，我们使用高通量测序来研究两个催化RNA分子（核酶）的基因型网络交叉点的适应度景观。我们确定了许多相邻RNA序列催化两种不同化学反应的能力，并将这些数据用作基因型适应度图的代理，其中两种功能非常接近。我们发现了广泛的功能重叠，许多基因型可以催化这两种功能。我们通过进化模拟证明，这些众多的交叉点促进了新功能的发现。然而，新函数的适应率取决于基因型网络中起始位置周围的局部粗糙度。因此，一个方向的适应比另一个方向更快。我们发现，中性进化时期通过允许种群在其基因型网络中扩散来增加对新功能的适应率。我们的研究揭示了基因型网络相交的适应度景观的性质以及进化创新的后果。我们的研究结果表明，自然系统中的历史性创新可能是由重叠的基因型网络促进的。
Evolutionary innovations are qualitatively novel traits that emerge through evolution and increase biodiversity. The genetic mechanisms of innovation remain poorly understood. A systems view of innovation requires the analysis of genotype networks-the vast networks of genetic variants that produce the same phenotype. Innovations can occur at the intersection of two different genotype networks. However, the experimental characterization of genotype networks has been hindered by the vast number of genetic variants that need to be functionally analyzed. Here, we use high-throughput sequencing to study the fitness landscape at the intersection of the genotype networks of two catalytic RNA molecules (ribozymes). We determined the ability of numerous neighboring RNA sequences to catalyze two different chemical reactions, and we use these data as a proxy for a genotype to fitness map where two functions come in close proximity. We find extensive functional overlap, and numerous genotypes can catalyze both functions. We demonstrate through evolutionary simulations that these numerous points of intersection facilitate the discovery of a new function. However, the rate of adaptation of the new function depends upon the local ruggedness around the starting location in the genotype network. As a consequence, one direction of adaptation is more rapid than the other. We find that periods of neutral evolution increase rates of adaptation to the new function by allowing populations to spread out in their genotype network. Our study reveals the properties of a fitness landscape where genotype networks intersect and the consequences for evolutionary innovations. Our results suggest that historic innovations in natural systems may have been facilitated by overlapping genotype networks.