Phylogenetic distance

The local context of a gene in the genome and its conservation is an invaluable tool for the prediction of orthology and function. Not only does the conservation of local context decrease with phylogenetic distance, but also the amount of information in the local context varies... 

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.

In the fatty acid derivatives (Chart 8.3.FA/PO), the identity of prostaglandins from gorgonians and alcyonaceans in the sea, and mammals on land, has stimulated much experimentation (Varvas 1994) and computer calculations (Hess 1999). Although it is expected that biosynthetic routes in the sea differ from land because of the large phylogenetic distances of the organisms and the different functions of the metabolites at issue (Pietra 1995), details about the biosynthetic pathways are still to come (Varvas 1994). 

Fig. 4. Phylogenetic tree of Basidiomycota based on the primary structure of the 18S rRNA gene. Alignment, distance matrix and calculation of phylogenetic distances were made by means of different programs as described in the legend of figure 1. Hmnan pathogenic genera are indicated by arrows. T = Teleomorphic species A = anamorphic species Y = yeasts or yeast stages.

Jarosch M, Bresinsky A Speciation and phylogenetic distances within Paxillus s. str. (Basidiomycetes, Boletales). Plant Biol 1999 1 701-706. 

Fig. 1. Phylogenetic tree of the archaea indicating the phylogenetic relationship between various methanogenic genera, Archaeoglobus and Pyrococcus. The branching orders are based upon rRNA sequence comparisons according to Woese et al.[5,20] and Burggraf et al. [23]. The line lengths do not correspond to the phylogenetic distances.

Fig. 1. Phylogenetic (distance) tree for the 16S rRNAs of the halobacteria, reproduced from Lodwick et al. [3], The bar represents 0.01 substitutions per site.

Evidence for a horizontal sialidase gene transfer between bacteria has been obtained by comparison of the similarities of bacterial sialidases so far sequenced [246,660,768,799]. It was found that some of the sialidases are related in accordance with the phylogenetic distances of their producers, e.g. Micromonospora viridifaciens and Actinomyces viscosus... 

The most widely used models of amino acid substitution include distance-based methods, which are based on matrixes such as PAM and BLOSUM. Again, such matrices are described fiuther in other chapters in this book. Briefly, Dayhoff s PAM 001 matrix (Dayhoff, 1979) is an empirical model that scales probabilities of change from one amino acid to another in terms of an expected 1% change between two amino acid sequences. This matrix is used to make a transition probability matrix that allows prediction of the probability of changing from one amino acid to another and also predicts equilibriiun amino acid composition. Phylogenetic distances are calculated with the assumption that the probabilities in the matrix are correct. The... 

One prerequisite for the molecular assessment of microbial diversity in natural environments is the availability of an extensive molecular database of cultured organisms which serve as a reference for the comparison of sequences from both isolates and uncultured strains. The comparison of sequences fi om environmental rDNA clone sequences to each other and to cultured strains will not only allow determination of the phylogenetic distance between the gene sequences but they will also facilitate the recognition of putative target sites for oligonucleotides, suitable for the specific detection of the respective strains directly in their natural habitat. The 16S rDNA database is already so extensive that about 90% of all described species can be placed rather accurately within the radiation of the main lines of descent. Examples for large 16S rDNA databases are the Ribosomal Database Project [9] and ARB [10]. 

Table 1. Examples of the phylogenetic distance of 16S rDNA clones to their nearest 16S rDNA sequence which are clone sequences (in percent similarity). Analysis is based on 1000 nucleotides.

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