Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.
Estimating effective population size from linkage disequilibrium between unlinked loci: theory and application to fruit fly outbreak populations.
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DOI：
10.1371/journal.pone.0069078
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Gilchrist AS
中科院分区：
文献类型：
--
作者：
Sved JA;Cameron EC;Gilchrist AS
有大量的文献使用连锁不平衡（LD）估计有效种群大小使用非连锁位点。估计对抽样过程非常敏感，目前还没有理论来处理可能的偏差。我们推导了具有多等位基因（微卫星）位点随机交配的理想种群的分析公式。“Burrows复合索引”以一种新颖的方式引入了“复合单倍型表”。我们表明，在二倍体大小的样本中，复合单倍型表的平均值受到因子的偏倚，而不是传统单倍型表的通常因子。但是，使用这些公式分析人口数据得出的估计值低得不切实际。我们提供理论和模拟来证明这种对低估计的偏差是由于零等位基因造成的，并引入随机排列校正来补偿偏差。我们还考虑了引入基因座内不平衡因素的影响，并发现该因素会导致估计偏差。然而，这种偏差可以使用相同的随机排列校正来克服，从而产生比原始变异更低的变异，并且对零等位基因也不敏感。所得到的公式被用于对40个昆士兰果蝇样本的估计，这些样本来自有着广泛不同期望的种群。该物种中大多数微卫星位点的连锁关系是已知的。我们发现，与使用所有基因座相比，使用已知非连锁基因座的估计值几乎没有差异，这对于连锁关系未知的保护研究非常重要。
There is a substantial literature on the use of linkage disequilibrium (LD) to estimate effective population size using unlinked loci. The estimates are extremely sensitive to the sampling process, and there is currently no theory to cope with the possible biases. We derive formulae for the analysis of idealised populations mating at random with multi-allelic (microsatellite) loci. The ‘Burrows composite index’ is introduced in a novel way with a ‘composite haplotype table’. We show that in a sample of diploid size , the mean value of or from the composite haplotype table is biased by a factor of , rather than the usual factor for a conventional haplotype table. But analysis of population data using these formulae leads to estimates that are unrealistically low. We provide theory and simulation to show that this bias towards low estimates is due to null alleles, and introduce a randomised permutation correction to compensate for the bias. We also consider the effect of introducing a within-locus disequilibrium factor to , and find that this factor leads to a bias in the estimate. However this bias can be overcome using the same randomised permutation correction, to yield an altered with lower variance than the original , and one that is also insensitive to null alleles. The resulting formulae are used to provide estimates on 40 samples of the Queensland fruit fly, Bactrocera tryoni, from populations with widely divergent expectations. Linkage relationships are known for most of the microsatellite loci in this species. We find that there is little difference in the estimated values from using known unlinked loci as compared to using all loci, which is important for conservation studies where linkage relationships are unknown.
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