Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions

  title={Application of the Character Compatibility Approach to Generalized Molecular Sequence Data: Branching Order of the Proteobacterial Subdivisions},
  author={Radhey S. Gupta and Peter H. A. Sneath},
  journal={Journal of Molecular Evolution},
The character compatibility approach, which removes all homoplasic characters and involves finding the largest clique of compatible characters in a dataset, in principle, provides a powerful means for obtaining correct topology in difficult to resolve cases. However, the usefulness of this approach to generalized molecular sequence data for phylogeny determination has not been studied in the past. We have used this approach to determine the topology of 23 proteobacterial species (6 each of… 

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The unrooted parsimony analyses showed that Cerato- phyllum was immediately related to eudicots, this larger lineage was Immediately related to magnoliids, and monocots were closely related to Chloranthaceae, and all these relationships received 76%-96% bootstrap support.

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The size distribution of complete 16S-rRNA sequences from the SILVA-database and nucleotide shifts that might interfere with the secondary structure of the molecules were evaluated and it can be concluded that the V3 region is possibly more likely to mutate than are other regions.

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An algorithm that rapidly computes phylogenies according to a compatibility criterion, based on solutions to the maximum clique problem, that rapidly solves fairly large problems of this type and provides robustness against misleading characters than can pollute large-scale sequencing data.

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The Xanthomonadales-specific CSIs reported here provide novel molecular markers for the identification of these important plant and human pathogens and also as potential targets for development of drugs/agents that specifically target these bacteria.

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A close and specific relationship of V. spinosum to the Chlamydiales species, seen both in phylogenetic trees and by means of uniquely shared inserts in protein sequences, strongly indicates that these two groups of species shared a common ancestor exclusive of all other known bacteria.

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Large numbers of molecular markers consisting of conserved signature indels in protein sequences and whole proteins that are specific for either all Actinobacteria or their different clades at various taxonomic levels enable the development of a stable and reliable phylogenetic framework for this phylum.

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Multiple CSIs and CSPs have been identified for successive nested clades providing reliable information regarding their hierarchical relationships and these inferences are not affected by HGTs, which strongly support Darwin's views on evolution and classification.

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  • E. GriffithsRadhey S. Gupta
  • Biology, Environmental Science
    International microbiology : the official journal of the Spanish Society for Microbiology
  • 2004
The results provide strong and consistent evidence that the Aquificales diverged after the branching of Firmicutes, Actinob bacteria, Thermotoga, Deinococcus-Thermus, green nonsulfur bacteria, Cyanobacteria, Spirochetes, Chlamydiae, and CFBG group, but before the emergence of the Proteobacteria.

Gene arrangements and phylogeny in the class Proteobacteria.

It is shown that differences in gene arrangements among genomes could allow us to determine whether a gene transposition event has occurred before or after species divergence from parsimonious considerations.

A phylogenomic approach to bacterial phylogeny: evidence of a core of genes sharing a common history.

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The RecA protein as a model molecule for molecular systematic studies of bacteria: Comparison of trees of RecAs and 16S rRNAs from the same species

  • J. Eisen
  • Biology
    Journal of Molecular Evolution
  • 2004
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  • R. Gupta
  • Biology
    FEMS microbiology reviews
  • 2000
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A new approach, based on shared conserved inserts and deletions (indels or signature sequences) found in various proteins, that provides a reliable and internally consistent means for understanding various critical and long outstanding issues in bacterial phylogeny.

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The evolutionary homology of the chloranthoid tooth is significant in that this character is preserved in the megafossil record of angiosperms and has been used to adduce relationships of ancient angiosperm lineages.