Nei M
Institute of Molecular Evolutionary Genetics, Pennsylvania State University, University Park 16802, USA.
Annu Rev Genet. 1996;30:371-403. doi: 10.1146/annurev.genet.30.1.371.
Recent developments of statistical methods in molecular phylogenetics are reviewed. It is shown that the mathematical foundations of these methods are not well established, but computer simulations and empirical data indicate that currently used methods such as neighbor joining, minimum evolution, likelihood, and parsimony methods produce reasonably good phylogenetic trees when a sufficiently large number of nucleotides or amino acids are used. However, when the rate of evolution varies extensively from branch to branch, many methods may fail to recover the true topology. Solid statistical tests for examining the accuracy of trees obtained by neighbor joining, minimum evolution, and least-squares method are available, but the methods for likelihood and parsimony trees are yet to be refined. Parsimony, likelihood, and distance methods can all be used for inferring amino acid sequences of the proteins of ancestral organisms that have become extinct.
本文综述了分子系统发育学中统计方法的最新进展。结果表明，这些方法的数学基础尚未完全确立，但计算机模拟和实证数据表明，当使用足够数量的核苷酸或氨基酸时，目前使用的方法，如邻接法、最小进化法、似然法和简约法，能够产生相当不错的系统发育树。然而，当进化速率在不同分支间差异很大时，许多方法可能无法恢复真实的拓扑结构。有可靠的统计检验可用于检验通过邻接法、最小进化法和最小二乘法得到的树的准确性，但似然树和简约树的方法仍有待完善。简约法、似然法和距离法都可用于推断已灭绝的原始生物蛋白质的氨基酸序列。
