基于Ks分布的被子植物演化的时间尺度研究

Timescale of angiosperm evolution based on Ks distribution

关键词:  同义突变率(Ks)分布, 被子植物, 时间矫正, 系统发育树, 进化速率

Key words:  Ks distribution, angiosperms, time correction, phylogenetic tree, evolutionary rate

摘要:

物种演化时间估算是生命演化研究的重要部分。近年来,许多研究发现由于不同基因和不同物种的进化速率差异显著,因此需要新的方法对进化事件发生时间进行重新估计。为了对被子植物演化时间的重新估计,该研究基于共享多倍化事件或共享分歧事件应该有共同同义突变率(Ks)峰值的理念,建立了基于基因组数据的进化速率矫正模型。结果表明:(1)对获取Ks分布三种常见方式进行比较分析,明确了通过提取共线性区块上Ks值的中位数的方式最优。(2)模拟了Ks值随时间累积系数(v)变化过程下的Ks分布,当假设v服从正态分布时,Ks分布出现了长尾现象。(3)将矫正方法应用到被子植物中,发现不同谱系的被子植物具有同步的辐射进化和适应性进化现象。并且,被子植物的进化速率虽然差异显著,但不同分支间的进化速率仍具有部分一致性,如木兰类植物进化速率最慢,真双子叶植物次之,单子叶植物进化速率最快。最终得到了相对可靠的物种同义突变率演化时间轴,为植物研究提供了系统发育和演化的支撑。

Abstract:

Estimating the time scale of species evolution is an important part of life evolution study. It is found that there are significant differences in the evolution rates of different genes and species in recent years, which challenges the molecular clock hypothesis to a great extent. Therefore, new methods are needed to re-estimate the evolutionary event time. The whole genome sequence of angiosperms makes it possible to estimate the evolutionary time from the whole genome perspective. In order to re-estimate the evolution time of angiosperms, an evolution rate correction model based on genomic data is established according to the idea that shared polyploidy events or shared divergence events should have the same Ks peak. The results were as follows:(1)Three common ways to obtain Ks distribution were compared and analyzed, which showed that the best way was to extract the median of Ks values on collinear blocks.(2)The change process of Ks distribution was simulated with time accumulation coefficient(v)of Ks values. When v was assumed to obey the normal distribution, the Ks distribution had a long tail phenomenon.(3)The correction process was described in detail, which was conducive to the understanding and wide spread of this method. From the application of correction method in angiosperms, it was found that the Ks peak before correction was not linear with time, while the Ks peak after correction was directly proportional to time, indicating that it is very necessary to estimate the time of species evolution events after correcting the Ks peak. It was also found that although the evolution rate of angiosperms was significantly different, the evolution rate between different branches was still partially consistent. For example, Magnoliids had the slowest evolutionary rate, followed by Eudicots and Monocots. When the environment changed greatly, most species of different lineages of angiosperms had synchronous radial evolution and adaptive evolution. Finally, a relatively reliable angiosperm evolution time axis was establish, which helps to understand the evolution process and model, especially to understand the phylogenetic relationship and the causes of diversity and provides phylogenetic and evolutionary support for plant research.