Phylogenetic treeing

Woese, C. R., 1996. Phylogenetic trees Wliidier microbiology Current Biology 6 1060—1063. 

Studying evolutionary aspects, by the construction of phylogenetic trees from the pairwise differences between sequences for example, the classification with 70S, 30S RNAs established the separate kingdom of archaea... 

Figure 1. An unrooted phylogenetic tree of the myosins based on the amino acid sequence comparison of their head domains demonstrating the division of the myosin superfamily into nine classes. The lengths of the branches are proportional to the percent of amino acid sequence divergence and a calibration bar for 5% sequence divergence is shovk n. The different classes of myosins have been numbered using Roman numerals in rough order of their discovery and hypothetical models of the different myosin structures are shown. Question marks indicate either hypothetical or unknown structural features, and only a fraction of the known myosins are shown. (Taken, in modified form, from Cheney et al., 1993).

Figure 2. Universal phylogenetic tree determined from rRNA sequence comparisons. A matrix of evolutionary distances (99) was calculated from an alignment (260) of representative 16S RRNA sequences from each of the three urkingdoms. The length of the lines is proportional to the phylogenetic difference. (Reproduced with permission from ret 16. Copyright 19. American Society for Microbiology.)...

Fig. 1. (a) Schematic representation of the three types of anoxygenic ([1] and [2]) and oxygenic ([3]) photosynthesis found in plants and bacteria, (b) Phylogenetic tree based on 16S-rRNA sequence comparisons featuring only photo synthetic phyla. 

FIGURE 1.2 An abbreviated version of the P450 phylogenetic tree compared with an evolutionary timescale (Lewis 1996). The dashed line represents a plot of evolutionary distance (Nelson and Strobel 1987). 

Saitou, N. and M. Nei (1987). The neighbor-joining method A new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4 406 -25. 

The basis of the traditional tree of life was the vertical passing on of genetic information, i.e., from generation to generation. The discrepancies visible in the previous model of the phylogenetic tree of life can only be explained if a second process... 

An initial suggestion made by Ford Doolittle shows a jumble of interconnections between the lines of development, rather than simple branches in the phylogenetic tree. These interconnections resemble a mycelium and have almost nothing in common with the original model, except for the termini of the three kingdoms. In a review article in Science, Elizabeth Pennisi (2001) chose the colourful metaphor of a tangled bramble bush to describe the new model. 

Figure 6.2 Phylogenetic tree showing the evolutionary relationship between members of the ferritin-bacterioferritin-rubreyrthrin superfamily. Reprinted from Harrison et ah, 1998, by courtesy of Marcel Dekker, Inc.

The amino acid sequence similarities of all 36 PHA synthases were pairwise revealed, and the results of this comparison are compiled in Table 2. The data correspond well with phylogenetic tree shown in Fig. 1, and the similarities va-... 

Fig. 1. Phylogenetic tree of 36 PHA synthases. The branching order and distance score were calculated by the program TREE as described by Feng and Doolittle [63]...

Fig. 11.7. Phylogenetic tree of OCTs and OATs isoforms. (Adapted from Reference [177])...

Chlorophycean species [Proeschold et al., 2001], the HydA proteins of C. moewusii, C. reinhardtii and S. obliquus form 3 different branches which possess, one to the other, a rather similar evolutionary distance. The three different HydA branches reflect the membership to three distinct phylogenetic clades ( Moewusii -clade, Reinhardtii -clade, Scenedesmus -clade) which can be found in completely different regions of the chlorophycean phylogenetic tree. 

Figure 21.1 A simplified phylogenetic tree of the invertebrate phyla.

Fig. 3. Phylogenetic tree of iGluR subunits showing the high sequence identity.

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