Population genetics and molecular evolution of DNA sequences in transposable elements. II. Accumulation of variation and evolution of a new subfamily
Population genetics and molecular evolution of DNA sequences in transposable elements. II. Accumulation of variation and evolution of a new subfamily
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转座元件中 DNA 序列的群体遗传学和分子进化。
DOI：
10.1093/molbev/msz220
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发表时间：
2019
期刊：
影响因子：
--
通讯作者：
Kijima and H. Innan
中科院分区：
文献类型：
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作者：
Iwasaki;W. M.;Kijima and H. Innan
为了了解转座元件(TES)的DNA序列是如何进化的，人们进行了广泛的模拟。我们首先使用了我们之前的模型，其中TES的拷贝数主要由针对异位重组的选择来控制。研究发现，随着模拟运行的进行，系统发育的形状发生了很大的变化，从单系树变成了具有两个簇的二态树。我们的结果表明，从单晶相到二晶相的相变通常是缓慢的，并伴随着两种类型之间的变化积累而形成的内部分支的生长。然后，当一个种群灭绝时，这个阶段立即改变回单态阶段。在这种情况下，单态和二态相反复出现，很难长期保持两种或两种以上不同类型的TES。那么，一个新的亚家族如何进化呢？为了解决这个问题，我们开发了一个新的模型，在这个模型中，异位重组在某些条件下被限制在两种类型之间，例如它们之间的突变积累。在这种模式下，由于选择分别作用于每种类型的副本数，因此两种类型可以长期保持。正如预期的那样，我们的模拟表明，一种新类型的出现并相当稳定地存在，它将被识别为一个新的亚家族，随后将进一步积累突变。研究表明，异位重组在基因组中的调控方式是一个新亚家族进化的重要因素。
In order to understand how DNA sequences of transposable elements (TEs) evolve, extensive simulations were carried out. We first used our previous model, in which the copy number of TEs is mainly controlled by selection against ectopic recombination. It was found that along a simulation run, the shape of phylogeny changes quite much, from monophyletic trees to dimorphic trees with two clusters. Our results demonstrated that the change of the phase is usually slow from a monomorphic phase to a dimorphic phase, accompanied with a growth of an internal branch by accumulation of variation between two types. Then, the phase immediately changes back to a monomorphic phase when one group gets extinct. Under this condition, monomorphic and dimorphic phases arise repeatedly, and it is very difficult to maintain two or more different types of TEs for a long time. Then, how a new subfamily can evolve? To solve this, we developed a new model, in which ectopic recombination is restricted between two types under some condition, for example, accumulation of mutations between them. Under this model, because selection works on the copy number of each types separately, two types can be maintained for a long time. As expected, our simulations demonstrated that a new type arises and persists quite stably, and that it will be recognized as a new subfamily followed by further accumulation of mutations. It is indicated that how ectopic recombination is regulated in a genome is an important factor for the evolution of a new subfamily.