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Chapter 87 : The Problem of Complexity

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The Problem of Complexity, Page 1 of 2

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Abstract:

The current trend in publishing new species is to utilize culture and phenotypic characteristics, serology, cellular fatty acids and isoprenoid quinone profiles, DNA relatedness, and a molecular phylogenetic analysis targeting usually more than one gene. To investigate the greater use of sequence-based phylogenetic analyses in lieu of serology, fatty acid and isoprenoid quinone profiles, and even perhaps DNA relatedness, 56 strains representing 33 potentially novel species were phylogenetically assessed with 6 gene targets. First, following a phylo-genetic analysis based on sequence from the mip gene, 49 strains representing 30 potentially novel species were selected because their genetic distance from recognized species was greater than that between recognized species. Second, DNA studies on two strains indicated that they were novel, even though their mip sequence-derived genetic distance was closer to a recognized species than that between recognized species. Last, the remaining five strains were selected because they were genetically related to either of these latter two strains, based on their macrophage infectivity potentiator () sequence-derived genetic distance. The six gene targets used in this analysis, 16S rRNA gene, the gene , the RNA polymerase β-subunit (), the RNase P RNA gene (), and the DNA gyrase A subunit (), together with the zinc metallo-protease (, also known as ) gene. In the interim, the use of a combined approach using the sequenced- based phylogeny to identify “nearest neighbor” species will greatly simplify the use of total DNA relatedness studies.

Citation: M. Ratcliff R. 2006. The Problem of Complexity, p 359-366. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch87
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Figures

Image of FIGURE 1
FIGURE 1

Examples of serological cross-reactivity using a quantitative microagglutination checkerboard titration method (V. Drasar, personal communication).

Citation: M. Ratcliff R. 2006. The Problem of Complexity, p 359-366. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch87
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Image of FIGURE 2
FIGURE 2

Graphical representation of strain relatedness for each of the six gene targets. The presence of a rectangle indicates that a sequence (or sequences if there are more than one strain in the clade) was ascertained for that gene target. A partial rectangle indicates that a sequence could not be ascertained for one or more of the strains within a multistrain clade. A grey infill indicates that the genetic distance for that gene target and strain/cluster from a recognized species is greater than that between recognized species, whereas no infill indicates that the genetic distance from a recognized species is less than that between recognized species. For those clades containing more than one strain, a solid infill indicates sequence identity between strains, while a dot pattern indicates sequence variability within the clade. A black border to the rectangle indicates approximate congruence of the location of the clade with the most common topology of the phylogenetic tree.

Citation: M. Ratcliff R. 2006. The Problem of Complexity, p 359-366. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch87
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References

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Tables

Generic image for table
TABLE 1

Sequence statistics for the six gene targets

Citation: M. Ratcliff R. 2006. The Problem of Complexity, p 359-366. In Cianciotto N, Kwaik Y, Edelstein P, Fields B, Geary D, Harrison T, Joseph C, Ratcliff R, Stout J, Swanson M (ed), . ASM Press, Washington, DC. doi: 10.1128/9781555815660.ch87

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