循环瓶颈下的连锁不平衡
Linkage disequilibrium under recurrent bottlenecks
摘要：
理解选择性中性遗传变异的模式是必不可少的，以便模拟由不同形式的选择引起的中性偏差。最好理解的是单个基因座的中性遗传变异，但通过研究多个基因座的遗传变异可以获得更多的见解。相应的变异模式反映了连锁不平衡，并提供了潜在的多位点基因谱系的信息。对于人口普查规模恒定的群体，以及简单的人口统计历史，如指数人口增长和单一瓶颈，两个位点系谱的统计特性已经被深入研究。相比之下，重组和持续人口波动的综合影响却鲜为人知。针对这个问题，我们研究了两个位点的赖特-费舍尔模型的人口经常性瓶颈。我们得出的协方差的时间最近的共同祖先在两个位点的合并近似。我们发现，第一，一个有效种群大小近似描述了数字观察到的连锁不平衡提供重组发生的速度或速度比人口规模的变化慢得多。第二，当重组经常发生在瓶颈之间，但很少发生在瓶颈内部时，我们观察到长距离连锁不平衡。第三，我们证明了在后一种情况下，一种常用的连锁不平衡度量，sigma_d^2（与r^2密切相关），未能捕获长程连锁不平衡，因为每个反映长程连锁不平衡的组成项相互抵消。第四，我们分析了一个限制性的情况下，远程连锁不平衡，可以描述在一个Xi聚结过程中允许同时多个合并的祖先线。
英文摘要：
Understanding patterns of selectively neutral genetic variation is essential in order to model deviations from neutrality, caused for example by different forms of selection. Best understood is neutral genetic variation at a single locus, but additional insights can be gained by investigating genetic variation at multiple loci. The corresponding patterns of variation reflect linkage disequilibrium and provide information about the underlying multi-locus gene genealogies. The statistical properties of two-locus genealogies have been intensively studied for populations of constant census size, as well as for simple demographic histories such as exponential population growth, and single bottlenecks. By contrast, the combined effect of recombination and sustained demographic fluctuations is poorly understood. Addressing this issue, we study a two-locus Wright-Fisher model of a population subject to recurrent bottlenecks. We derive coalescent approximations for the covariance of the times to the most recent common ancestor at two loci. We find, first, that an effective population-size approximation describes the numerically observed linkage disequilibrium provided that recombination occurs either much faster or much more slowly than the population size changes. Second, when recombination occurs frequently between bottlenecks but rarely within bottlenecks, we observe long-range linkage disequilibrium. Third, we show that in the latter case, a commonly used measure of linkage disequilibrium, sigma_d^2 (closely related to r^2), fails to capture long-range linkage disequilibrium because constituent terms, each reflecting long-range linkage disequilibrium, cancel. Fourth, we analyse a limiting case in which long-range linkage disequilibrium can be described in terms of a Xi-coalescent process allowing for simultaneous multiple mergers of ancestral lines.
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