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Some basics: Homology = refers to a structure, behavior, or other character of two taxa that is derived from the same or equivalent feature of a common ancestor. • Homology applies to nucleotide sequences: gtcccat gtctcat A substitution has occurred at position 4. Sequence alignment: • Rapid sequence divergence or divergence over many generations can leave little in common between two sequences and make alignment difficult or impossible. • Indels ~ may be impossible to distinguish between an insertion in one sequence and a deletion in another sequence. example: mtDNA 12S rRNA in six genera of “stifftail” ducks CCACCT-GT---TTCAAAA-CTCAGGCCTT TCACCTAGC---TCCAAA--C-TAGGCCTT CTGCCT-AC---TTCCC---C-CAGGCCTT TCGCCT-AC---T-CAA---C-CAGGCTTT TCGCCT-ACATTTTCCC---C-CAGGCTTT • Many alignment methods exist; all use algorithms that seek to maximize the number of possible matching nucleotides or amino acids and minimize the number of indels. Maximum Parsimony Occam’s Razor Entia non sunt multiplicanda praeter necessitatem. William of Occam (1300-1349) The best tree is the one which requires the least number of substitutions Most parsimonious taxon 1 taxon 2 outgroup taxon 1 outgroup Less parsimonious taxon 2 Assumptions: independence • Assumes that change at one site has no effect on other sites • Good example is in RNA stem-loop structures • Substitution may result in mismatched bases and decreased stem stability • Compensatory change may occur to restore WatsonCrick base pairing A G A C C C CU U GGGG A A G C A U G C C C C U U C A GGG C A A G U A G C C CGU U GGG C A A G C A U Types of substitution A G C T • Substitutions that exchange a purine for another purine or a pyrimidine for another pyrimidine are called transitions • Substitutions that exchange a purine for a pyrimidine or vice-versa are called transversions Differing rates of DNA evolution • Functional constraints (particular features of coding regions, particular features in 5' or 3’ untranslated regions) • Variation among different gene regions with different functions (different parts of a protein may evolve at different rates). • Within proteins, variations are observed between – surface and interior amino acids in proteins (order of magnitude difference in rates in haemoglobins) – charged and non-charged amino acids – protein domains with different functions – regions which are strongly constrained to preserve particular functions and regions which are not – different types of proteins -- those with constrained interaction surfaces and those without Assumptions: variation in substitution rate across sites 4 3.5 Substitution / site / 109 years 3 2.5 2 1.5 1 0.5 0 • All sites are not equally likely to undergo a substitution Paleocene Jurassic Triassic Permian Carboniferous Devonian Silurian 140 100 200 300 400 500 600 700 Huronian Carp/Lamprey i V ertebrates/ Insects Reptiles/Fish h Algonkian 40 g Cambrian Birds/Reptiles f Mammals/ Reptiles Mammals abcde Ordovician Cretaceous 200 180 160 120 100 Corrected amino acid changes per 100 residues Rates of macromolecular evolution Pliocene Miocene Oligocene Eocene 220 j 10 6 5 800 7 8 9 Evolution of the globins 80 6 0 1 4 3 20 2 Separation of ancestors of plants and animals 0 900 1000 1100 1200 1300 1400 Millions of years since divergence After Dickerson (1971) Homology • Orthologs – Divergence (sequence change) follows speciation – Similarity can be used to construct phylogeny – Multiple orthologs can be present • Paralogs – Divergence follows duplication • Xenologs – Horizontal interspecies transfer of genes • Homoplasy (similarity not due to common ancestry) – Parallelism – Convergence – Reversal Orthologs and paralogs Homology vs. Homoplasy X X Homology: similar traits inherited from a common ancestor X X Homoplasy: similar traits are not directly caused by common ancestry (convergent evolution). Unique and unreversed characters - Hair • Because hair evolved only once and is unreversed it is homologous and provides unambiguous evidence for the clade Mammalia Human Lizard HAIR Frog change or step Dog absent present Homoplasy - independent evolution - Tails • Loss of tails evolved independently in humans and frogs - there are two steps on the true tree Lizard Human TAIL Frog Dog absent prese nt Homoplasy - misleading evidence of phylogeny • If misinterpreted as homology, the absence of tails would be evidence for a wrong tree grouping humans with frogs and lizards with dogs Human Lizard TAIL Frog Dog absent present Homology: limb structure Homoplasy: wings Homoplasy in molecular data • Incongruence and therefore homoplasy can be common in molecular sequence data • One reason is that characters have a limited number of alternative character states ( e.g. A, G, C and T) • In addition, these states are chemically identical so that homology and homoplasy are equally similar and cannot be distinguished through detailed study of structure or development Types of substitution A C A A T C C A T C G A C G A C A A A Single 1 change, 1 difference Multiple 2 changes, 1 difference Coincidental 2 changes, 1 difference C C A C A C T C T A T C A T A A A C C A A A A Parallel 2 changes, no difference Convergent 3 changes, no difference Back 2 changes, no difference Homoplasy - reversal • Reversals are evolutionary changes back to an ancestral condition • As with any homoplasy, reversals can provide misleading evidence of relationships True tree Wrong tree 1 2 3 4 5 6 7 8 9 10 1 2 7 8 3 4 5 6 9 10