Saakian David B, Hu Chin-Kun
Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan and A. I. Alikhanyan National Science Laboratory (Yerevan Physics Institute) Foundation, 2 Alikhanian Brothers Street, Yerevan 375036, Armenia and Physics Division of National Center for Theoretical Sciences Taipei Branch, National Taiwan University, Taipei, Taiwan.
Institute of Physics, Academia Sinica, Nankang, Taipei 11529, Taiwan.
Phys Rev E Stat Nonlin Soft Matter Phys. 2013 Nov;88(5):052717. doi: 10.1103/PhysRevE.88.052717. Epub 2013 Nov 25.
We investigate evolution models with recombination and neutrality. We consider the Crow-Kimura (parallel) mutation-selection model with the neutral fitness landscape, in which there is a central peak with high fitness A, and some of 1-point mutants have the same high fitness A, while the fitness of other sequences is 0. We find that the effect of recombination and neutrality depends on the concrete version of both neutrality and recombination. We consider three versions of neutrality: (a) all the nearest neighbor sequences of the peak sequence have the same high fitness A; (b) all the l-point mutations in a piece of genome of length l≥1 are neutral; (c) the neutral sequences are randomly distributed among the nearest neighbors of the peak sequences. We also consider three versions of recombination: (I) the simple horizontal gene transfer (HGT) of one nucleotide; (II) the exchange of a piece of genome of length l, HGT-l; (III) two-point crossover recombination (2CR). For the case of (a), the 2CR gives a rather strong contribution to the mean fitness, much stronger than that of HGT for a large genome length L. For the random distribution of neutral sequences there is a critical degree of neutrality ν(c), and for μ<μ(c) and (μ(c)-μ) is not large, the 2CR suppresses the mean fitness while HGT increases it; for ν much larger than ν(c), the 2CR and HGT-l increase the mean fitness larger than that of the HGT. We also consider the recombination in the case of smooth fitness landscapes. The recombination gives some advantage in the evolutionary dynamics, where recombination distinguishes clearly the mean-field-like evolutionary factors from the fluctuation-like ones. By contrast, mutations affect the mean-field-like and fluctuation-like factors similarly. Consequently, recombination can accelerate the non-mean-field (fluctuation) type dynamics without considerably affecting the mean-field-like factors.
我们研究了具有重组和中性的进化模型。我们考虑了具有中性适应度景观的Crow-Kimura（并行）突变选择模型，其中存在一个具有高适应度A的中心峰值，一些单点突变体具有相同的高适应度A，而其他序列的适应度为0。我们发现重组和中性的影响取决于中性和重组的具体形式。我们考虑了三种中性形式：（a）峰值序列的所有最近邻序列具有相同的高适应度A；（b）长度l≥1的一段基因组中的所有l点突变都是中性的；（c）中性序列随机分布在峰值序列的最近邻之间。我们还考虑了三种重组形式：（I）一个核苷酸的简单水平基因转移（HGT）；（II）长度为l的一段基因组的交换，即HGT-l；（III）两点交叉重组（2CR）。对于（a）的情况，对于较大的基因组长度L，2CR对平均适应度有相当大的贡献，比HGT的贡献要强得多。对于中性序列的随机分布，存在一个临界中性度ν(c)，对于μ<μ(c)且(μ(c)-μ)不大时，2CR会抑制平均适应度，而HGT会增加平均适应度；对于ν远大于ν(c)，2CR和HGT-l增加平均适应度的幅度大于HGT。我们还考虑了平滑适应度景观情况下的重组。重组在进化动力学中具有一些优势，其中重组能清晰地区分类似平均场的进化因素和类似波动的因素。相比之下，突变对类似平均场和类似波动的因素影响类似。因此，重组可以加速非平均场（波动）类型的动力学，而不会对类似平均场的因素产生太大影响。
