Evolutionary distance

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.)...

A further opportunity for the use of stress-responsive promoters and enhancers is as probes to isolate other stress-responsive genes, the activity of which is not manifest by protein synthesis. As regards the manipulation of stress tolerance as a breeding tool, it is likely that the stress-responsive promoters and enhancers will have a role to play in controlling the expression of adaptive genes when these are transplanted over great evolutionary distances. 

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). 

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. 

Fig. 4. Adjacent genes with conserved relative transcription orientation versus evolutionary distance. The plot shows the fraction of conserved gene pairs with the same relative direction of transcription between two species. Shown are pairs with a single direction of transcription, pairs with a divergent direction of transcription, and pairs with a convergent direction of transcription. The X axis represents the small subunit rRNA distance between the species (Fig. 3). The number of conserved adjacent pairs declines nonlinearly with phylogenetic distance and was therefore depicted on a logarithmic scale. Note that the vast majority of conserved adjacent pairs with a conserved relative transcription orientation are transcribed in the same direction. Divergently transcribed pairs are better conserved than convergently transcribed ones, hinting at the conservation of divergent promotors.

The mutation rate fx of the nucleotide (or amino acid) at a sequence site is related to the popular notion of a molecular clock (Zuckerkandl and Pauling, 1965), because it determines after which time the clock ticks and anew mutation arises because of a copying error during meiosis. Whether this clock ticks uniformly is a topic of prolonged debate (summarized in Li, 1997). The question is usually treated by comparing sequence difference at (supposedly) neutral sites with evolutionary distance between species. 

The score/penalty assigned to a match/mismatch is dependent on the likelihood that this match/mismatch occurred by chance alone. If an event occurs randomly with a high frequency the score will be small, while very rare events will receive very large scores. For example, a conservative amino-acid substitution will receive a very small penalty, while the introduction of a stop codon will be penalized heavily. A variety of scoring schemes have been generated based on factors such as the bio-physical character, evolutionary distance, and the subcellular localization of the sequences being compared. 

Jenkins, J.A., Breiteneder, H., and Mills, E.N.C. 2007. Evolutionary distance from human homologs reflects allergenicity of animal food proteins. J Allergy Clin Immunol 120 1399-1405. 

K4. Kimura, M., Estimation of evolutionary distances between homologous nucleotide sequences. Proc. Natl. Acad. Sci. (USA) 78(1), 454-458 (1981). 

Sellers, P. H. (1974). On the theory and computation of evolutionary distances. SIAM J Appl Math 26,787-93. 

PAM Point Accepted Mutation. The PAM matrix is a frequency table representing substitution rates for closely related proteins at the particular evolutionary distance represented by multiple sequence alignments. 

With the divergence of two species from a common ancestor, mutations in the structural genes encoding similar proteins result in amino acid differences between the proteins produced by the now separate species. The degree of immunological similarity between any two such proteins is directly related to the evolutionary distance between the two species. Different proteins evolve at different rates. The structural basis for this difference in rate is that, for slowly evolving proteins, changes in amino acid sequence... 

Proteins such as cytochrome c are not good target antigens for the determination of species of origin because the structures of these proteins in evolutionarily distant species are very similar. Serum albumin, on the other hand, is a rapidly changing protein (Table I) that is amenable to complete immunochemical analysis with both polyclonal and monoclonal antibodies (14-16). Albumins from thousands of pairs of vertebrate species have been compared immunochemically, and the results have been used to measure evolutionary distances (22). 

---