Inbreeding effective population size and parentage analysis without parents
Inbreeding effective population size and parentage analysis without parents
复制标题
无父母近亲繁殖有效种群规模和亲子关系分析
DOI：
10.1111/j.1755-0998.2010.02942.x
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发表时间：
2011
影响因子：
7.7
通讯作者：
R. Waples
中科院分区：
文献类型：
--
作者：
R. Waples;R. Waples
遗传亲子分析的一个重要用途是能够直接计算每个亲本产生的后代数量 (ki)，从而计算有效种群规模 Ne。但是如果父母基因型不可用怎么办？理论上，如果有足够的标记，应该可以完全基于后代样本重建亲本基因型，如果是的话，则基于亲本 ki 值的向量。然而，这只能提供有关实际为样本贡献后代的父母的信息。忽略“无效”父母（那些没有产生后代的父母）会如何影响 Ne 的估计？令人惊讶的答案是，无效父母根本没有任何影响。我们证明： (i) 近交 Ne 的标准公式可以重写，使其仅是样本大小 和 的函数；不必知道父母的总数 (N)。同样的关系对于方差 Ne 不成立。 (ii) 即使只有子代的一个子集可用，这个新颖的公式也可以提供 Ne 的无偏估计，前提是准确确定亲本贡献，在这种情况下，与 Ne 的其他单样本估计器相比，精度也很高。 (iii) 没有必要实际重建亲代基因型；根据成对关系矩阵（可以通过某些当前软件程序估计），可以构造 ki 值向量并估计 Ne。基于无父母亲子关系分析（PwoP）的新方法可能可用作当代 Ne 的单样本估计器，前提是（i）可以准确确定关系，或者（ii）可以直接估计。
An important use of genetic parentage analysis is the ability to directly calculate the number of offspring produced by each parent (ki) and hence effective population size, Ne. But what if parental genotypes are not available? In theory, given enough markers, it should be possible to reconstruct parental genotypes based entirely on a sample of progeny, and if so the vector of parental ki values. However, this would provide information only about parents that actually contributed offspring to the sample. How would ignoring the ‘null’ parents (those that produced no offspring) affect an estimate of Ne? The surprising answer is that null parents have no effect at all. We show that: (i) The standard formula for inbreeding Ne can be rewritten so that it is a function only of sample size and ; it is not necessary to know the total number of parents (N). This same relationship does not hold for variance Ne. (ii) This novel formula provides an unbiased estimate of Ne even if only a subset of progeny is available, provided the parental contributions are accurately determined, in which case precision is also high compared to other single‐sample estimators of Ne. (iii) It is not necessary to actually reconstruct parental genotypes; from a matrix of pairwise relationships (as can be estimated by some current software programs), it is possible to construct the vector of ki values and estimate Ne. The new method based on parentage analysis without parents (PwoP) can potentially be useful as a single‐sample estimator of contemporary Ne, provided that either (i) relationships can be accurately determined, or (ii) can be estimated directly.