Phylogenetic trees rooting

Certain residues with a variable degree of conservation can be investigated for their usefulness as evolutionary markers that can provide insight into the history of each enzyme family or clan and allow comparative analysis with other families or clans. Krem and Di Cera [75] identified several such markers with proven evolutionary usefulness. In addition to the use of these markers for rooting the phylogenetic trees, attempts were made to classify serine proteases into functional groups based on these markers or their coding sequences. 

FIGURE 2 Rooted universal phylogenetic tree highlighting major components of the microbial loop. CFB indicates the Cytophaga-Flavobacter-Bacteriodes lineage. (Adapted from Woese, 1994). 

A search for remnants of an RNA world in extant extremophiles that are deeply rooted in the phylogenetic tree of life ... 

A search for remnants of an RNA world in extant extremophiles that are deeply rooted in the phylogenetic tree of life. They could include RNA genes that, unlike the common retrotransposons found in eukaryotes that are just selfish genes, may have some function in the cell. The search should also include viruses from hyperther-mophilic archaeans that have already been shown, in the study at Yellowstone, to be unlike anything that has been seen before and that have characteristics of all three domains of life. 

Figure 2 Phylogenetic tree of vertebrate TAS2 R genes. The arrow points to where the tree is rooted with vertebrate VI Rs. Image is adapted from...

Studies on the pathways of central metabolism of the archaebacteria take on special significance when it is realised that, from the universal phylogenetic tree in rooted form, Woese et al. [66] have proposed that the domain of the archaebacteria be known as archaea to denote their apparently primitive nature, especially with respect to the eukaryotes. Furthermore, within the archaea, thermophily is regarded as the ancestral phenotype. 

Fig. 2. Universal phylogenetic tree in rooted form, showing the three domains, based upon the corresponding tree in ref. [49] and more recent results concerning eukaryote phylogeny (M.L. Sogin, personal communication). The position of the root was determined by the Dayhoff strategy , described...

Even with more than three species the overall tree can often be well-approximated by a star phylogeny. In these cases, the phylogenetic tree consists of one ancestor and many leaves, each labeled by their proximity to the root, and the proximities can be set to approximately match the proximities between all pairs of species. 

Fig. 2. A sample phylogenetic tree for mammals (numbers are only approximate). Because proximities are multiplicative, the proximity of chimp to LCA (the last common ancestor, or the root of the tree), for example, is 0.85 x 0.6 =...

The methods described above produce imrooted trees (i.e., trees having no evolutionary polarity). To evaluate evolutionary hypotheses, it is often necessary to locate the root of the tree. Rooting phylogenetic trees is not a trivial problem (Nixon and Carpenter, 1993). 

---