Fuzzy classification of nucleotide sequences and bacterial evolution

✍ Scribed by Liaofu Luo; Fengmin Ji; Hong Li

• Publisher: Springer
• Year: 1995
• Tongue: English
• Weight: 533 KB
• Volume: 57
• Category: Article
• ISSN: 1522-9602
• DOI: 10.1016/s0092-8240(05)80755-4

✦ Synopsis

A new method for reconstructing evolutionary relationship among bacteria by use of rRNA sequence data is proposed. The method is based on the concept of fuzzy classification of probabilities p(i), p(il j ) and p(il j *) (i = A, G, C, U) of each sequence. The resulting partition tree shares common features of previous works but has some new peculiarities. 527 528 L. LUO et al.

probability p(i) (i = A, C, G, U) of base i occurring in the sequence. Some authors (Bernardi and Bernardi, 1986) noted that the G+C content (p(G)+p(C)) is an important evolutionary parameter. However, the occurrences of two nucleotides in adjacent sites of a sequence are not independent events from the point of evolution. The base correlation is another important factor to describe the molecular evolution. For example, it has been demonstrated that a good statistical correlation exists between the second informational redundancy D 2 (which is deduced from the base correlation) and evolution (Gatlin, 1972;Luo et al., 1988). Strictly speaking, the description of base correlation is more complex than base composition. It should be classified into the correlation of neighboring bases, the correlation of next-to-neighbors, etc. But we have shown that for most protein-coding sequences only the correlations of neighboring and next-to-neighboring bases are important and the long-range correlations of bases are below the fluctuation bound (correlation length <3) (Luo and Li, 1991). The conclusion is also true for rRNA sequences. In fact, from 23 16S rRNA sequences which we will analyse, only five show a long-range correlation of bases, i.e. the correlation lengths s of all 16S rRNA sequences considered are equal to 0, 1 or 2, respectively, except for S. solfataricus (s=5), M. fervidus (s=4), T. tenax (s=4) T. roseum (s=3)