“Evolutionary speculation constitutes a kind of metascience, which has the same intellectual fascination for some biologists that metaphysical speculation possessed for some mediaeval scholastics. It can be considered a relatively harmless habit, like eating peanuts, unless it assumes the form of an obsession; then it becomes a vice” (Stanier, 1970)

Linnaean classification Defining characteristics –Binomial (Genus species) –Hierarchical KingdomAnimalia PhylumChordata ClassMammalia OrderPrimates FamilyHominidae Genus Homo Speciessapiens

Tree of Life: primary divisions Haeckel’s three categories Five kingdoms

Tree of Life: primary divisions Haeckel’s three categories Five kingdoms Procaryote/eucaryote

Tree of Life: three “domains” Based on 16S rRNA (Woese, 1987):

Tree of Life: three “domains” Based on 16S rRNA (Pace, 1997): environmental sequence endosymbiosis

Tree basics: meaning

Tree basics: nodes

Tree basics: rotation

Tree basics: shape

Tree basics: lengths, unrooted cladograms vs. phylograms

Tree basics: character change

Key phylogenetic terms Clade, sister taxa Cladogenesis vs. anagenesis Homology Monophyletic vs. polyphyletic vs. paraphyletic

Key phylogenetic terms Clade, sister taxa Cladogenesis vs. anagenesis Homology Monophyletic vs. polyphyletic vs. paraphyletic

Key phylogenetic terms Clade, sister taxa Cladogenesis vs. anagenesis Homology Monophyletic vs. polyphyletic vs. paraphyletic

Overall similarity vs. number of derived characters –Shared ancestral traits & homoplasies (or convergent evolution) Lysozyme amino acid changes in unrelated ruminants Phenetics vs. cladistics

Overall similarity vs. number of derived characters –Shared ancestral traits & homoplasies (or convergent evolution)

Phenetics vs. cladistics Overall similarity vs. number of derived characters –Shared ancestral traits & homoplasies (or convergent evolution) –Why does this difference matter?

Maximum Parsimony Parsimony – shortest tree (fewest homoplasies) –Assume: ancestral state is that most common outside clade

Microbial systematics Phenotypic traits for microbes GC% T m for genomic hybridizations Formerly Pseudomonas (partial list): –Ralstonia, Burkholderia, Hydrogenophaga, Sphingomonas, Methylobacterium, Cellvibrio, Xanthomonas, Acidovorax, Hydrogenophillus, Brevundimonas, Pandoraea

Molecular phylogenetics Zuckerkandl & Pauling Molecules as documents of evolutionary history. J Theor Biol. 8: Neutral theory (Motoo Kimura, 1968) –Many differences neutral (synonomous) –Neutral differences rise in frequency due to drift –Rate of fixation proportional to mutation rate Molecular clock?

16S rRNA as phylogenetic marker How pick good molecule? –Clocklike –Phylogenetic range –Size/accuracy –Changes “neutral” (p.255) Variants that fix are functionally equivalent