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Microbial Taxonomy
and Classification
Terminology
• Taxonomy: Science of classification. Taxa are groups of organisms.
• Phylogeny/Phylogenetic Tree: Evolutionary history or relatedness of organisms.
Clade/Lineage: a sub-tree
• Systematics/Phylogenetic Classification: Classification of living matters should
be according to their phylogeny
• Homology: Common ancestry. Homology is NOT Similarity. This is because the
same trait can evolve independently (non-homologously) in separate evolutionary
lineages ("Evolutionary Convergence"; e.g., independent origin of wings in birds,
reptiles, and mammals). Conversely, closely related (or the same) species can
evolve different traits ("Evolutionary Divergence"; e.g., bacterial surface proteins,
breeds of dogs). Both convergence and divergence are evidence of natural
selection and species adaptation.
• Biological Species Concept (BSC): Members of the same species can interbreed
and produce fertile offspring. Speciation creates permanent gaps between taxa,
because no gene flow is possible after reproductive barrier is created. BSC does
NOT apply to bacteria because bacteria reproduce asexually. Thus, bacterial
species are mostly working definitions, not biological species.
Taxonomic hierarchy
• Three Domains: Eukarya are eukaryotes (their cells contain a nucleus). Archaea
(living in extreme environments) and Bacteria are prokaryotes (their cells have
no nucleus). The three-domain classification is based on a "tree of life" (the
evolutionary tree of all existing cellular organisms), reconstructed according to
the similarities of ribosomal RNA sequences (i.e., species with similar rRNA
sequences are grouped together).
• Five Kingdoms:
• Classification of bacteria