Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.
Pairwise comparisons of mitochondrial DNA sequences in stable and exponentially growing populations.
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作者：
M. Slatkin;R. Hudson
我们考虑线粒体 DNA 或基因组其他非重组部分的成对序列差异在大小恒定的群体中以及在大小长期呈指数增长的群体中的分布。我们表明，在大小恒定的群体中，成对差异的样本分布通常会大大偏离预期的几何分布，因为单个基因样本中合并事件的历史对成对差异施加了显着的相关性。因此，观察到的成对差异与几何分布的拟合优度检验（假设每个成对比较是独立的）并不是对基因是从恒定大小的恐慌群体中采样的假设的有效检验。在呈指数增长的人口中，当前人口规模和增长率的乘积远大于 1，我们的分析和模拟结果表明，大多数合并事件发生得相对较早，并且发生在有限的时间范围内。因此，“基因树”将接近“星型系统发育”，并且成对差异的分布将接近泊松分布。在这种情况下，如果假设突变率 mu 和当前种群规模 N0 已知，则可以估计种群增长率 r。 r 的估计值是 ri/mu = ln(N0r) - gamma 的解，其中 i 是平均成对差，gamma 约为 0.577 是欧拉常数。
We consider the distribution of pairwise sequence differences of mitochondrial DNA or of other nonrecombining portions of the genome in a population that has been of constant size and in a population that has been growing in size exponentially for a long time. We show that, in a population of constant size, the sample distribution of pairwise differences will typically deviate substantially from the geometric distribution expected, because the history of coalescent events in a single sample of genes imposes a substantial correlation on pairwise differences. Consequently, a goodness-of-fit test of observed pairwise differences to the geometric distribution, which assumes that each pairwise comparison is independent, is not a valid test of the hypothesis that the genes were sampled from a panmictic population of constant size. In an exponentially growing population in which the product of the current population size and the growth rate is substantially larger than one, our analytical and simulation results show that most coalescent events occur relatively early and in a restricted range of times. Hence, the "gene tree" will be nearly a "star phylogeny" and the distribution of pairwise differences will be nearly a Poisson distribution. In that case, it is possible to estimate r, the population growth rate, if the mutation rate, mu, and current population size, N0, are assumed known. The estimate of r is the solution to ri/mu = ln(N0r) - gamma, where i is the average pairwise difference and gamma approximately 0.577 is Euler's constant.