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扩张种群中的基因冲浪

Gene surfing in expanding populations.

作者信息

Hallatschek Oskar, Nelson David R

机构信息

Lyman Laboratory of Physics, Harvard University, 17 Oxford Street, Cambridge, MA 02138, USA.

出版信息

Theor Popul Biol. 2008 Feb;73(1):158-70. doi: 10.1016/j.tpb.2007.08.008. Epub 2007 Sep 19.

Abstract

Large scale genomic surveys are partly motivated by the idea that the neutral genetic variation of a population may be used to reconstruct its migration history. However, our ability to trace back the colonization pathways of a species from their genetic footprints is limited by our understanding of the genetic consequences of a range expansion. Here, we study, by means of simulations and analytical methods, the neutral dynamics of gene frequencies in an asexual population undergoing a continual range expansion in one dimension. During such a colonization period, lineages can fix at the wave front by means of a "surfing" mechanism [Edmonds, C.A., Lillie, A.S., Cavalli-Sforza, L.L., 2004. Mutations arising in the wave front of an expanding population. Proc. Natl. Acad. Sci. 101, 975-979]. We quantify this phenomenon in terms of (i) the spatial distribution of lineages that reach fixation and, closely related, (ii) the continual loss of genetic diversity (heterozygosity) at the wave front, characterizing the approach to fixation. Our stochastic simulations show that an effective population size can be assigned to the wave that controls the (observable) gradient in heterozygosity left behind the colonization process. This effective population size is markedly higher in the presence of cooperation between individuals ("pushed waves") than when individuals proliferate independently ("pulled waves"), and increases only sub-linearly with deme size. To explain these and other findings, we develop a versatile analytical approach, based on the physics of reaction-diffusion systems, that yields simple predictions for any deterministic population dynamics. Our analytical theory compares well with the simulation results for pushed waves, but is less accurate in the case of pulled waves when stochastic fluctuations in the tip of the wave are important.

摘要

大规模基因组调查的部分动机在于,人们认为一个种群的中性遗传变异可用于重建其迁徙历史。然而,我们从物种的遗传足迹追溯其殖民化路径的能力,受到我们对范围扩张的遗传后果理解的限制。在此,我们通过模拟和分析方法,研究一维空间中持续范围扩张的无性种群中基因频率的中性动态。在这样一个殖民化时期,谱系可以通过一种“冲浪”机制在波前固定下来[埃德蒙兹,C.A.,利利,A.S.,卡瓦利 - 斯福尔扎,L.L.,2004年。扩张种群波前产生的突变。《美国国家科学院院刊》101,975 - 979]。我们从以下两个方面对这一现象进行量化:(i)达到固定的谱系的空间分布,以及密切相关的(ii)波前遗传多样性(杂合性)的持续丧失,这表征了固定的过程。我们的随机模拟表明,可以为控制殖民化过程后留下的(可观测的)杂合性梯度的波分配一个有效种群大小。在个体间存在合作(“推波”)时,这个有效种群大小明显高于个体独立增殖(“拉波”)时,并且仅随群落大小呈亚线性增加。为了解释这些及其他发现,我们基于反应 - 扩散系统物理学开发了一种通用的分析方法,该方法能对任何确定性种群动态给出简单预测。我们的分析理论与推波的模拟结果比较吻合,但在波尖的随机波动很重要的拉波情况下,准确性稍差。

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