. The Biological bulletin. Biology; Zoology; Biology; Marine Biology. ZJO 500 750 Number of inferred substitutions 1000 Figure 1. Saturation analysis of the lie tRNA synthetases. The method of Philippe el til. (14) was applied to the set of sequences used in Figure 2. The number of substitutions between two species is estimated as the sum of the lengths of the branches linking these two species in the most parsimonious tree. Each point in the diagram corresponds to a couple of species, for which the abscissa is the number of inferred substitutions, and the ordinate is the number of observed di
. The Biological bulletin. Biology; Zoology; Biology; Marine Biology. ZJO 500 750 Number of inferred substitutions 1000 Figure 1. Saturation analysis of the lie tRNA synthetases. The method of Philippe el til. (14) was applied to the set of sequences used in Figure 2. The number of substitutions between two species is estimated as the sum of the lengths of the branches linking these two species in the most parsimonious tree. Each point in the diagram corresponds to a couple of species, for which the abscissa is the number of inferred substitutions, and the ordinate is the number of observed differences. Near the origin, the curve is linear, indicating that the He tRNA synthetases are not mutationally saturated at small evolutionary distances (within methanogens. gram-positive. Fungi), but they are highly saturated at large evolutionary distances (between the three domains but also within each domain). For a couple of species, one can observe only 250 differences, but during the course of evolution, at least 1000 substitutions have occurred. gous proteins have been previously used to root the tree of life, and previous analysis confirmed the bacterial rooting (9). After the addition of new sequences, the Archaea and Bacteria were both revealed as polyphyletic, raising doubts about any rooting result. The high level of saturation de- tected in Figure 1 could explain some, if not all. of these surprising results. In the case of the elongation factor tree, we have shown that the positions that support the bacterial rooting in clas- sical phylogenies are the most variable ones, , the least reliable (10). We conclude from our analyses that the clas- sical methods of molecular phylogeny cannot solve the problem of rooting the tree of life. We favor the cladistic analysis (sensu Hennig) of slowly evolving positions (SEP), or indels. as the basis from which to infer phylogenies (II). However, the application of this method to the current data set clearly indicates that s
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Keywords: ., bookauthorlilliefrankrat, booksubjectbiology, booksubjectzoology
