Grundy W N, Naylor G J
Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California 95065, USA.
J Exp Zool. 1999 Aug 15;285(2):128-39.
Molecular sequences provide a rich source of data for inferring the phylogenetic relationships among species. However, recent work indicates that even an accurate multiple alignment of a large sequence set may yield an incorrect phylogeny and that the quality of the phylogenetic tree improves when the input consists only of the highly conserved, motif regions of the alignment. This work introduces two methods of producing multiple alignments that include only the conserved regions of the initial alignment. The first method retains conserved motifs, whereas the second retains individual conserved sites in the initial alignment. Using parsimony analysis on a mitochondrial data set containing 19 species among which the phylogenetic relationships are widely accepted, both conserved alignment methods produce better phylogenetic trees than the complete alignment. Unlike any of the 19 inference methods used before to analyze this data, both methods produce trees that are completely consistent with the known phylogeny. The motif-based method employs far fewer alignment sites for comparable error rates. For a larger data set containing mitochondrial sequences from 39 species, the site-based method produces a phylogenetic tree that is largely consistent with known phylogenetic relationships and suggests several novel placements. J. Exp. Zool. ( Mol. Dev. Evol.) 285:128-139, 1999.
分子序列为推断物种间的系统发育关系提供了丰富的数据来源。然而，最近的研究表明，即使对一个大的序列集进行准确的多重比对，也可能产生错误的系统发育树，并且当输入仅由比对中高度保守的基序区域组成时，系统发育树的质量会提高。这项工作介绍了两种产生多重比对的方法，这些比对仅包括初始比对的保守区域。第一种方法保留保守基序，而第二种方法保留初始比对中的单个保守位点。在一个包含19个物种的线粒体数据集上进行简约分析，其中物种间的系统发育关系已被广泛接受，两种保守比对方法都比完整比对产生了更好的系统发育树。与之前用于分析此数据的19种推断方法中的任何一种不同，这两种方法产生的树与已知的系统发育完全一致。基于基序的方法在可比的错误率下使用的比对位点要少得多。对于一个包含39个物种线粒体序列的更大数据集，基于位点的方法产生的系统发育树在很大程度上与已知的系统发育关系一致，并提出了几个新的定位。《实验动物学杂志》（分子与发育进化）285:128 - 139，1999年。
