Molecular Phylogeny of Microorganisms
Aharon Oren, R. Thane Papke
Horizon Scientific Press, 2010 - Science - 220 pages
A proper understanding of the diversity, systematics, and nomenclature of microbes is increasingly important in many branches of biological science. The molecular approach to phylogenetic analysis - pioneered by Carl Woese in the 1970s and leading to the three-domain model (Archaea, Bacteria, Eucarya) - has revolutionized our thinking about evolution in the microbial world. The technological innovation of modern molecular biology and the rapid advancement in computational science have led to a flood of nucleic acid sequence information, bioinformatic tools, and phylogenetic inference methods. Phylogenetic analysis has long played a central role in microbiology and the emerging fields of comparative genomics and phylogenomics require substantial knowledge and understanding of phylogenetic analysis and computational methods. In this book, leading scientists from around the world explore current concepts in molecular phylogeny and their application with respect to microorganisms. The authors describe the different approaches applied today to elucidate the molecular phylogeny of prokaryotes (and eukaryotic protists) and review current phylogenetic methods, techniques, and software tools. Topics covered include: a historical overview, computational tools, multilocus sequence analysis, 16S rRNA phylogenetic trees, rooting of the universal tree of life, applications of conserved indels, lateral gene transfer, endosymbiosis, and the evolution of plastids.
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Methods and Programs for Calculation of Phylogenetic
Multilocus Sequence Analysis and Bacterial Species Phylogeny Estimation
Is rRNA Still a Useful Marker?
The Phyla of Prokaryotes Cultured and Uncultured
Rooting the Tree of Life
Applications of Conserved Indels for Understanding Microbial Phylogeny
The Influence of Lateral Gene
Acad Actinobacteria algae algal algorithms amino acid anaerobic Aquificae Archaea ATPase bacteria bacterial phyla Bacteroidetes Bapteste Bergey’s Manual Biol biological branch Cavalier-Smith cell Chlamydiae Chloroflexi chlorophyll chromalveolate clades classification common ancestor conserved indels CSIs cyanobacteria datasets diversity domain Doolittle endosymbiosis eukaryotes Evol evolution evolutionary history Firmicutes function Garrity gene duplications gene trees genetic genome genus Gogarten groups higher taxa homologues horizontal gene transfer inference insert Koonin lateral gene transfer LHCs lineages Ludwig Manual of Systematic markers membrane methods microbial Microbiol molecular monophyletic MRCA multiple sequence alignment Natl nucleotide organismal organisms paralogues photosynthetic phyla phyloge phylogenetic analysis phylogenetic trees phylogeny phylum plastid Proc prokaryotes proteins Proteobacteria relationships represent ribosomal RNA polymerase root rRNA gene Schleifer sequence data species tree Stackebrandt structure subunit Syst Systematic Bacteriology taxonomic thermophilic Thermotogae tion topology tree reconstruction tRNA universal tree Vinuesa Woese Zhaxybayeva