Xia Xuhua, Xie Zheng, Kjer Karl M
Department of Biology, University of Ottawa, 150 Louis, P.O. Box 450, Station A, Ottawa, Ontario K1N 6N5, Canada.
Syst Biol. 2003 Jun;52(3):283-95. doi: 10.1080/10635150390196948.
Previous phylogenetic analyses of tetrapod 18S ribosomal RNA (rRNA) sequences support the grouping of birds with mammals, whereas other molecular data, and morphological and paleontological data favor the grouping of birds with crocodiles. The 18S rRNA gene has consequently been considered odd, serving as "definitive evidence of different genes providing significantly different estimates of phylogeny in higher organisms" (p. 156; Huelsenbeck et al., 1996, Trends Ecol. Evol. 11:152-158). Our research indicates that the previous discrepancy of phylogenetic results between the 18S rRNA gene and other genes is caused mainly by (1) the misalignment of the sequences, (2) the inappropriate use of the frequency parameters, and (3) poor sequence quality. When the sequences are aligned with the aide of the secondary structure of the 18S rRNA molecule and when the frequency parameters are estimated either from all sites or from the variable domains where substitutions have occurred, the 18S rRNA sequences no longer support the grouping of the avian species with the mammalian species.
以往对四足动物18S核糖体RNA（rRNA）序列的系统发育分析支持鸟类与哺乳动物归为一组，而其他分子数据以及形态学和古生物学数据则支持鸟类与鳄鱼归为一组。因此，18S rRNA基因被认为很奇特，被视作“不同基因在高等生物中提供显著不同的系统发育估计的决定性证据”（第156页；Huelsenbeck等人，1996年，《生态与进化趋势》11:152 - 158）。我们的研究表明，先前18S rRNA基因与其他基因之间系统发育结果的差异主要是由以下原因造成的：（1）序列比对错误，（2）频率参数使用不当，以及（3）序列质量差。当序列借助18S rRNA分子的二级结构进行比对，并且频率参数是从所有位点或发生替换的可变结构域估计时，18S rRNA序列不再支持鸟类物种与哺乳动物物种归为一组。
