Mutation bias interacts with composition bias to influence adaptive evolution.
Mutation bias interacts with composition bias to influence adaptive evolution.
复制标题
DOI：
10.1371/journal.pcbi.1008296
复制
发表时间：
2020-09
影响因子：
4.3
通讯作者：
Payne JL
中科院分区：
文献类型：
--
作者：
Cano AV;Payne JL
突变是一个有偏的随机过程，某些类型的突变比其他类型的突变发生得更频繁。以前的工作已经使用合成基因型-表型景观来研究这种突变偏好如何影响适应性进化。在这里，我们考虑746经验基因型-表型景观，其中每一个描述的结合亲和力的靶DNA序列的转录因子，研究的适应性进化的结合亲和力增加的突变偏差的影响。通过使用经验基因型-表型景观，我们只需要对景观地形和每个景观包含的DNA序列做一些假设。后者尤其重要，因为景观所包含的序列集决定了突变的类型，这些突变可以沿着突变路径到达适应性峰值。也就是说，景观可以表现出一种成分偏差，即在整个景观或沿着特定的突变路径上，相对于零期望值，特定类型的突变在统计上富集，这与突变过程中的任何偏差无关。我们的研究结果揭示了在不同的群体遗传条件下，组成偏差与突变过程中的偏差相互作用的方式，以及这种相互作用如何影响适应性进化的基本特性，如其可预测性，以及遗传多样性和突变鲁棒性的进化。突变通常被描述为一个随机过程，因为它具有不可预测的性质。然而，这种随机性并不意味着均匀分布的结果，因为某些DNA序列的变化比其他人发生得更频繁。突变偏差可以是适应性进化中的一个导向因素，影响种群向更高适应性基因型的突变轨迹。因为这些轨迹通常只是所有可能的突变轨迹的一个小子集，它们可以表现出组成偏差-一种特定类型的DNA序列变化的富集，如转换或颠换突变。在这里，我们使用真核生物转录调控的经验数据来研究突变偏好和组成偏好如何相互作用，以影响适应性进化。
Mutation is a biased stochastic process, with some types of mutations occurring more frequently than others. Previous work has used synthetic genotype-phenotype landscapes to study how such mutation bias affects adaptive evolution. Here, we consider 746 empirical genotype-phenotype landscapes, each of which describes the binding affinity of target DNA sequences to a transcription factor, to study the influence of mutation bias on adaptive evolution of increased binding affinity. By using empirical genotype-phenotype landscapes, we need to make only few assumptions about landscape topography and about the DNA sequences that each landscape contains. The latter is particularly important because the set of sequences that a landscape contains determines the types of mutations that can occur along a mutational path to an adaptive peak. That is, landscapes can exhibit a composition bias—a statistical enrichment of a particular type of mutation relative to a null expectation, throughout an entire landscape or along particular mutational paths—that is independent of any bias in the mutation process. Our results reveal the way in which composition bias interacts with biases in the mutation process under different population genetic conditions, and how such interaction impacts fundamental properties of adaptive evolution, such as its predictability, as well as the evolution of genetic diversity and mutational robustness. Mutation is often depicted as a random process due its unpredictable nature. However, such randomness does not imply uniformly distributed outcomes, because some DNA sequence changes happen more frequently than others. Mutation bias can be an orienting factor in adaptive evolution, influencing the mutational trajectories populations follow toward higher-fitness genotypes. Because these trajectories are typically just a small subset of all possible mutational trajectories, they can exhibit composition bias—an enrichment of a particular kind of DNA sequence change, such as transition or transversion mutations. Here, we use empirical data from eukaryotic transcriptional regulation to study how mutation bias and composition bias interact to influence adaptive evolution.
登录
查看更多内容
影响因子：
4.5
作者：
Hershberg R;Petrov DA
通讯作者：
Petrov DA
DOI：
10.1126/science.1162327
发表时间：
2009-06-26
期刊：
Science (New York, N.Y.)
影响因子：
--
作者：
Badis G;Berger MF;Philippakis AA;Talukder S;Gehrke AR;Jaeger SA;Chan ET;Metzler G;Vedenko A;Chen X;Kuznetsov H;Wang CF;Coburn D;Newburger DE;Morris Q;Hughes TR;Bulyk ML
通讯作者：
Bulyk ML
影响因子：
3.9
作者：
GOJOBORI, T;LI, WH;GRAUR, D
通讯作者：
GRAUR, D
影响因子：
46.9
作者：
Berger, Michael F.;Philippakis, Anthony A.;Bulyk, Martha L.
通讯作者：
Bulyk, Martha L.
影响因子：
7.7
作者：
Diss G;Lehner B
通讯作者：
Lehner B