An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution
An Ancestral Recombination Graph for Diploid Populations with Skewed Offspring Distribution
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DOI：
10.1534/genetics.112.144329
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发表时间：
2013-01-01
期刊：
影响因子：
3.3
通讯作者：
Eldon, Bjarki
中科院分区：
文献类型：
--
作者：
Birkner, Matthias;Blath, Jochen;Eldon, Bjarki
本文以Moran型大子代二倍体双亲本多位点群体模型为研究对象。在每一个时间步，均匀随机抽取一对二倍体个体为种群贡献后代。后代的数量相对于总体规模来说是很大的。最近，许多作者（参见Eldon和Wakeley， 2006年和2008年）都考虑了类似的“严重倾斜”的生殖机制，并由Hedgecock和Pudovkin（2011年）进行了综述。每个二倍体亲本个体为每个二倍体后代贡献一条染色体，因此祖先谱系只有在不同的个体中才能合并。这样就观察到一种时间尺度的分离现象。扩展了Mohle（1998）的结果，得到了祖先过程收敛到一个祖先重组图，该图必须同时允许多个祖先谱系合并。通常的祖先重组图是我们模型的一个特例，即当父母每次只向群体贡献一个后代时。由于二倍性和后代数量多，出现了新的效应。例如，每个基因座的边缘谱系允许同时发生多达4个群体的多重合并，即使重组率越来越高，不同的基因座仍然保持着本质上的相关性。因此，同一染色体上相隔很远的位点的家谱仍然是相关的。推导了两个基因座的聚结时间的相关性，并表明这是我们模型的聚结参数的函数。扩展Eldon和Wakeley（2008）的观察结果，除了重组率外，链接不平衡的预测还显示为我们模型的繁殖参数的函数。正如模拟结果所显示的那样，在后代数量众多的种群中，即使重组率高、样本量大，基因座之间合并时间比率的相关性也可能很高，这暗示了如何区分不同的种群模型。
A large offspring-number diploid biparental multilocus population model of Moran type is our object of study. At each time step, a pair of diploid individuals drawn uniformly at random contributes offspring to the population. The number of offspring can be large relative to the total population size. Similar "heavily skewed" reproduction mechanisms have been recently considered by various authors (cf. e.g., Eldon and Wakeley 2006, 2008) and reviewed by Hedgecock and Pudovkin (2011). Each diploid parental individual contributes exactly one chromosome to each diploid offspring, and hence ancestral lineages can coalesce only when in distinct individuals. A separation-of-timescales phenomenon is thus observed. A result of Mohle (1998) is extended to obtain convergence of the ancestral process to an ancestral recombination graph necessarily admitting simultaneous multiple mergers of ancestral lineages. The usual ancestral recombination graph is obtained as a special case of our model when the parents contribute only one offspring to the population each time. Due to diploidy and large offspring numbers, novel effects appear. For example, the marginal genealogy at each locus admits simultaneous multiple mergers in up to four groups, and different loci remain substantially correlated even as the recombination rate grows large. Thus, genealogies for loci far apart on the same chromosome remain correlated. Correlation in coalescence times for two loci is derived and shown to be a function of the coalescence parameters of our model. Extending the observations by Eldon and Wakeley (2008), predictions of linkage disequilibrium are shown to be functions of the reproduction parameters of our model, in addition to the recombination rate. Correlations in ratios of coalescence times between loci can be high, even when the recombination rate is high and sample size is large, in large offspring-number populations, as suggested by simulations, hinting at how to distinguish between different population models.