Genetic Variability Under the Seedbank Coalescent
Genetic Variability Under the Seedbank Coalescent
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DOI：
10.1534/genetics.115.176818
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发表时间：
2015-07-01
期刊：
影响因子：
3.3
通讯作者：
Wilke-Berenguer, Maite
中科院分区：
文献类型：
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作者：
Blath, Jochen;Casanova, Adrian Gonzalez;Wilke-Berenguer, Maite
我们借助一种名为种子库合并的新合并结构，分析了在存在大型种子库的情况下种群的遗传变异性模式。如果种子库的大小和个体休眠时间与活跃种群的大种群的大小和休眠时间相同，这种祖先过程自然地表现为维持种子库的大种群谱系的比例限制。突变在活跃的谱系上表现为泊松过程，在休眠的谱系上也可能以减速的速度出现。“休眠”谱系的存在导致了对最近共同祖先和非经典遗传多样性模式的质的改变。为了说明这一点，我们提供了一个带有种子库组件和突变的Wright-Fisher模型，该模型受到最近微生物休眠模型的启发，其系谱可以通过种子库合并来描述。基于我们的合并模型，我们推导出对最近的共同祖先的时间的期望和方差、分离位置的数量、成对差异和单一个体的递归。在有无种子库的情况下，比较了常用距离统计量的分布估计值(通过模拟获得)。此外，还通过仿真研究了种子库对期望场地频谱的影响。我们的结果表明，大种子库的存在显著改变了一些距离统计数据的分布，以及位置-频谱。因此，人们应该能够从遗传数据中检测到自然种群中存在大型种子库。
We analyze patterns of genetic variability of populations in the presence of a large seedbank with the help of a new coalescent structure called the seedbank coalescent. This ancestral process appears naturally as a scaling limit of the genealogy of large populations that sustain seedbanks, if the seedbank size and individual dormancy times are of the same order as those of the active population. Mutations appear as Poisson processes on the active lineages and potentially at reduced rate also on the dormant lineages. The presence of "dormant" lineages leads to qualitatively altered times to the most recent common ancestor and nonclassical patterns of genetic diversity. To illustrate this we provide a Wright-Fisher model with a seedbank component and mutation, motivated from recent models of microbial dormancy, whose genealogy can be described by the seedbank coalescent. Based on our coalescent model, we derive recursions for the expectation and variance of the time to most recent common ancestor, number of segregating sites, pairwise differences, and singletons. Estimates (obtained by simulations) of the distributions of commonly employed distance statistics, in the presence and absence of a seedbank, are compared. The effect of a seedbank on the expected site-frequency spectrum is also investigated using simulations. Our results indicate that the presence of a large seedbank considerably alters the distribution of some distance statistics, as well as the site-frequency spectrum. Thus, one should be able to detect from genetic data the presence of a large seedbank in natural populations.