Yang Z
Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA.
Syst Biol. 1998 Mar;47(1):125-33. doi: 10.1080/106351598261067.
The effect of the evolutionary rate of a gene on the accuracy of phylogeny reconstruction was examined by computer stimulation. The evolutionary rate is measured by the tree length, that is, the expected total number of nucleotide substitutions per site on the phylogeny. DNA sequence data were simulated using both fixed trees with specified branch lengths and random trees with branch lengths generated from a model of cladogenesis. The parsimony and likelihood methods were used for phylogeny reconstruction, and the proportion of correctly recovered branch partitions by each method was estimated. Phylogenetic methods including parsimony appear quite tolerant of multiple substitutions at the same site. The optimum levels of sequence divergence were even higher than upper limits previously suggested for saturation of substitutions, indicating that the problem of saturation may have been exaggerated. Instead, the lack of information at low levels of divergence should be seriously considered in evaluation of a gene's phylogenetic utility, especially when the gene sequence is short. The performance of parsimony, relative to that of likelihood, does not necessarily decrease with the increase of the evolutionary rate.
通过计算机模拟研究了基因进化速率对系统发育重建准确性的影响。进化速率通过树长来衡量，即系统发育树上每个位点预期的核苷酸替换总数。使用具有指定分支长度的固定树和从分支发生模型生成分支长度的随机树来模拟DNA序列数据。采用简约法和似然法进行系统发育重建，并估计每种方法正确恢复分支划分的比例。包括简约法在内的系统发育方法似乎对同一位点的多次替换相当宽容。最佳的序列分歧水平甚至高于先前提出的替换饱和上限，这表明饱和问题可能被夸大了。相反，在评估基因的系统发育效用时，尤其是当基因序列较短时，应认真考虑低水平分歧时信息的缺乏。相对于似然法，简约法的性能不一定会随着进化速率的增加而下降。
