Chapter 13 : Phylogenetic and Genomic Analysis

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This chapter briefly discusses the different steps in constructing evolutionary trees, including collecting data sets of homologous sequences, generating a multiple-sequence alignment, inferring tree topology, and assessing confidence in the tree. Multiple-sequence alignments are the essential prerequisite for most phylogenetic analyses. There are currently four primary methods for constructing phylogenies from protein and nucleic acid sequence alignments: the distance-based neighbor-joining (NJ) method and the character-based methods, including maximum parsimony (MP), maximum likelihood (ML), and Bayesian inference. The major advantage of bootstrap technique is that it can be applied to basically all tree construction methods, although one has to keep in mind that applying the bootstrap method multiplies the computer time needed by the number of bootstrap samples requested. Until recently, phylogenetic analyses have been routinely based on homologous sequences of a single phylogenetic marker, i.e., the 16S rRNA gene among bacteria. Given the vast number of genome sequences now available, it is possible to compute trees from whole genomes.

Citation: Gevers D, Coenye T. 2007. Phylogenetic and Genomic Analysis, p 157-168. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch13

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16s rRNA Sequencing
Bacterial Chromosomal DNA
Multilocus Sequence Typing
Horizontal Gene Transfer
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Comparison of phylogenetic trees based on 16S rRNA gene (right; scale bar indicates 1% sequence dissimilarity) and (left; scale bar indicates 5% sequence dissimilarity) sequences of a selection of species. Sequences were extracted from GenBank and were aligned by using BioNumerics 4.0 (Applied Maths, Sint-Martens-Latem, Belgium), and trees were constructed based on the NJ algorithm as implemented in BioNumerics 4.0.

Citation: Gevers D, Coenye T. 2007. Phylogenetic and Genomic Analysis, p 157-168. In Hurst C, Crawford R, Garland J, Lipson D, Mills A, Stetzenbach L (ed), Manual of Environmental Microbiology, Third Edition. ASM Press, Washington, DC. doi: 10.1128/9781555815882.ch13
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