ESTIMATING EFFECTIVE POPULATION-SIZE FROM SAMPLES OF SEQUENCES - INEFFICIENCY OF PAIRWISE AND SEGREGATING SITES AS COMPARED TO PHYLOGENETIC ESTIMATES
ESTIMATING EFFECTIVE POPULATION-SIZE FROM SAMPLES OF SEQUENCES - INEFFICIENCY OF PAIRWISE AND SEGREGATING SITES AS COMPARED TO PHYLOGENETIC ESTIMATES
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DOI：
10.1017/s0016672300030354
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发表时间：
1992-04-01
影响因子：
1.5
通讯作者：
FELSENSTEIN, J
中科院分区：
文献类型：
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作者：
FELSENSTEIN, J
已知在已知突变率的中性突变下，假设其中没有重组的核苷酸序列的样品允许估计分离群体的有效大小。本文研究的情况下，非常长的序列，每对序列允许一个精确的估计，这两个基因拷贝的分歧时间。所有拷贝对的平均发散时间估计为有效群体数的两倍，并且估计值也可以从分离位点的数目导出。人们也可以估计这些复制品的系谱。本文展示了如何最大似然估计的有效人口数可以来自这样的系谱树。成对和分离的网站估计被证明是效率远远低于这种最大似然估计，这是通过计算机模拟验证。结果表明，有很多收获，明确考虑到这些家谱树结构。
It is known that under neutral mutation at a known mutation rate a sample of nucleotide sequences, within which there is assumed to be no recombination, allows estimation of the effective size of an isolated population. This paper investigates the case of very long sequences, where each pair of sequences allows a precise estimate of the divergence time of those two gene copies. The average divergence time of all pairs of copies estimates twice the effective population number and an estimate can also be derived from the number of segregating sites. One can alternatively estimate the genealogy of the copies. This paper shows how a maximum likelihood estimate of the effective population number can be derived from such a genealogical tree. The pairwise and the segregating sites estimates are shown to be much less efficient than this maximum likelihood estimate, and this is verified by computer simulation. The result implies that there is much to gain by explicitly taking the tree structure of these genealogies into account.