Protein evolution, phylogenetic tree

Molecular phylogeny is a discipline that studies species differences between DNA or protein sequences. Its basic tenet is that during evolution, the sequences have drifted apart by mutation and selection as well as by random drift and fixation of variants in certain positions. The earlier two species separated the more differences became fixed. Phylogenetic trees are constructed on the basis of mutual differences of protein and/or DNA sequence. Comparison of intraspecies variation with between-species variation may in the future yield information on the neutralist/selectionist alternative. McDonald and Kreitman (1991) devised an interesting test against neutrality that compared the ratio of silent/replacement mutation of a given locus within a species with the same ratio between two related species. Under the neutral theory this should be equal (corrected for sample size), but in fact it is not (see Li, 1997, and Hudson, 1993, for a discussion). 

The availability of complete sequences for a-actinin, spectrin, and dystrophin has allowed the ancestry and evolution of the proteins to be traced. Multiple sequence alignments and phylogenetic trees have been... 

The resemblance among cytochrome c molecules extends to the level of amino acid sequence. Because of the molecule s relatively small size and ubiquity, the amino acid sequences of cytochrome c from more than 80 widely ranging eukaryotic species were determined by direct protein sequencing by Emil Smith, Emanuel Margoliash, and others. Comparison of these sequences revealed that 26 of 104 residues have been invariant for more than one and a half billion years of evolution. A phylogenetic tree, constructed from the amino acid sequences of cytochrome c, reveals the evolutionary relationships between many animal species (Figure 18.24). 

Fig. 2 A phylogenetic tree of the animals, in which the evolution of odorant receptor (OR) genes were explored. In nematodes, Ciona and vertebrates, OR genes belong to the family of seven-transmembrane G-coupled-protein receptors (GPCR). An ancestor of insects possessing a unique OR gene family appeared after branching from the arthropod ancestor. Thus, the origin of insect OR genes is likely to have arisen independently of the GPCR family...

DayhofF (68), Hood and Talmage (7), and Smith et al. (8) have shown that it is possible to construct phylogenetic trees from V region sequences and that these closely resemble phylogenetic trees for sets of proteins (hemoglobins, etc.) that are related through evolution. 

The sequences of some proteins from different species have been determined and this has permitted researchers to construct phylogenetic trees that retrace the history of a protein in the different species from the early stages of evolution to the present day. 

Doolittle WF (1998) You are what you eat a gene transfer ratchet could account for bacterial genes in eukaryotic nuclear genomes. Trends Genet 14 307-311 Doolittle WF (1999) Phylogenetic classification and the universal tree. Science 284 2124-2129 Douzery EJ, Snell EA, Bapteste E, Delsuc F, Philippe H (2004) The timing of eukaryotic evolution does a relaxed molecular clock reconcile proteins and fossils Proc Natl Acad Sci USA 101 15386-15391... 

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