Tourasse N J, Gouy M
Human Genetics Center, University of Texas, 6901 Bertner Avenue, Houston, Texas 77225, USA.
Mol Phylogenet Evol. 1999 Oct;13(1):159-68. doi: 10.1006/mpev.1999.0675.
Phylogenetic analyses of gene and protein sequences have led to two major competing views of the universal phylogeny, the evolutionary tree relating the three kinds of living organisms, Bacteria, Archaea, and Eukarya. In the first scheme, called "the archaebacterial tree, " organisms of the same type are clustered together. In the second scenario, called "the eocyte tree," the archaeal phylum of Crenarchaeota is more closely related to eukaryotes than are other Archaea. A major property of the evolution of functional ribosomal and protein-encoding genes is that the rate of nucleotide and amino acid substitution varies across sequence sites. Here, using distance-based and maximum-likelihood methods, we show that universal phylogenies of ribosomal RNAs and RNA polymerases built by ignoring this variation are biased toward the archaebacterial tree because of attraction between long branches. In contrast, taking among-site rate variability into account gives support for the eocyte tree.
对基因和蛋白质序列的系统发育分析引发了关于通用系统发育的两种主要竞争观点，即涉及细菌、古菌和真核生物这三种生物的进化树。在第一种方案中，称为“古细菌树”，同类型的生物聚集在一起。在第二种情况中，称为“曙细胞树”，泉古菌门的古菌与真核生物的关系比其他古菌更为密切。功能性核糖体和蛋白质编码基因进化的一个主要特性是，核苷酸和氨基酸替换的速率在序列位点间有所不同。在此，我们使用基于距离和最大似然法表明，忽略这种变异构建的核糖体RNA和RNA聚合酶的通用系统发育因长分支间的吸引而偏向古细菌树。相比之下，考虑位点间速率变异性则支持曙细胞树。
