Sved John A, McRae Allan F, Visscher Peter M
School of Biological Sciences, University of Sydney, Sydney, Australia.
Am J Hum Genet. 2008 Dec;83(6):737-43. doi: 10.1016/j.ajhg.2008.10.019. Epub 2008 Nov 13.
Observed linkage disequilibrium (LD) between genetic markers in different populations descended independently from a common ancestral population can be used to estimate their absolute time of divergence, because the correlation of LD between populations will be reduced each generation by an amount that, approximately, depends only on the recombination rate between markers. Although drift leads to divergence in allele frequencies, it has less effect on divergence in LD values. We derived the relationship between LD and time of divergence and verified it with coalescent simulations. We then used HapMap Phase II data to estimate time of divergence between human populations. Summed over large numbers of pairs of loci, we find a positive correlation of LD between African and non-African populations at levels of up to approximately 0.3 cM. We estimate that the observed correlation of LD is consistent with an effective separation time of approximately 1,000 generations or approximately 25,000 years before present. The most likely explanation for such relatively low separation times is the existence of substantial levels of migration between populations after the initial separation. Theory and results from coalescent simulations confirm that low levels of migration can lead to a downward bias in the estimate of separation time.
在不同群体中，遗传标记之间观察到的连锁不平衡（LD）独立地源于一个共同的祖先群体，这可用于估计它们的绝对分化时间，因为群体间LD的相关性每一代都会以大约仅取决于标记之间重组率的量减少。尽管漂变会导致等位基因频率的分化，但它对LD值分化的影响较小。我们推导了LD与分化时间之间的关系，并通过合并模拟进行了验证。然后我们使用HapMap二期数据来估计人类群体之间的分化时间。对大量的基因座对进行汇总后，我们发现在非洲和非非洲群体之间，LD在高达约0.3 cM的水平上呈正相关。我们估计观察到的LD相关性与大约1000代或大约距今25000年前的有效分离时间一致。这种相对较短的分离时间最可能的解释是初始分离后群体之间存在大量的迁移。合并模拟的理论和结果证实，低水平的迁移会导致分离时间估计的向下偏差。
