Holland B R, Penny D, Hendy M D
Allan Wilson Centre for Molecular Ecology and Evolution, Massey University, Palmerston North, New Zealand.
Syst Biol. 2003 Apr;52(2):229-38. doi: 10.1080/10635150390192771.
We conducted a simulation study of the phylogenetic methods UPGMA, neighbor joining, maximum parsimony, and maximum likelihood for a five-taxon tree under a molecular clock. The parameter space included a small region where maximum parsimony is inconsistent, so we tested inconsistency correction for parsimony and distance correction for neighbor joining. As expected, corrected parsimony was consistent. For these data, maximum likelihood with the clock assumption outperformed each of the other methods tested. The distance-based methods performed marginally better than did maximum parsimony and maximum likelihood without the clock assumption. Data correction was generally detrimental to accuracy, especially for short sequence lengths. We identified another region of the parameter space where, although consistent for a given method, some incorrect trees were each selected with up to twice the frequency of the correct (generating) tree for sequences of bounded length. These incorrect trees are those where the outgroup has been incorrectly placed. In addition to this problem, the placement of the outgroup sequence can have a confounding effect on the ingroup tree, whereby the ingroup is correct when using the ingroup sequences alone, but with the inclusion of the outgroup the ingroup tree becomes incorrect.
我们针对分子钟条件下的五分类群树，对系统发育方法（UPGMA、邻接法、最大简约法和最大似然法）进行了模拟研究。参数空间包括一个最大简约法不一致的小区域，因此我们测试了简约法的不一致性校正和邻接法的距离校正。不出所料，校正后的简约法是一致的。对于这些数据，在有时钟假设的情况下，最大似然法的表现优于所测试的其他方法。基于距离的方法比没有时钟假设的最大简约法和最大似然法表现略好。数据校正通常对准确性不利，尤其是对于短序列长度。我们确定了参数空间的另一个区域，在该区域中，尽管对于给定方法是一致的，但对于有界长度的序列，一些错误的树被选中的频率高达正确（生成）树的两倍。这些错误的树是外类群放置错误的树。除了这个问题，外类群序列的放置对内类群树可能有混淆作用，即仅使用内类群序列时内类群是正确的，但加入外类群后内类群树就变得不正确了。
