Some basics :

1. 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: • g t c c c a t • g t c t c a t A substitution has occurred at position 4.

2. 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.

3. 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

4. taxon 1 taxon 1 taxon 2 taxon 2 outgroup outgroup Most parsimonious Less parsimonious

5. A A G G C C C C C C G C U U U U C C A A G G G G G G G C A A A A G G U U A G C C C C U U C A G G G A A C G U 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 Watson-Crick base pairing

6. A C G T Types of substitution • 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

7. 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

8. Substitution / site / 109 years Introns Pseudogenes 5’ flanking region 3’ flanking region Non-degenerate sites 3’ untranslated region 5’ untranslated region Twofold degenerate sites Fourfold degenerate sites Assumptions: variation in substitution rate across sites • All sites are not equally likely to undergo a substitution

9. ertebrates/ Carp/Lamprey 220 Birds/Reptiles Reptiles/Fish Mammals Mammals/ Insects Reptiles V 200 g j a b c d e f h i 10 180 9 8 7 160 6 Evolution of 5 Fibrinopeptides 140 the globins 1.1 MY 120 Hemoglobin Corrected amino acid changes per 100 residues 5.8 MY 100 80 60 1 Cytochrome c 40 4 20.0 MY Separation of ancestors 3 of plants and animals 20 2 0 Carboniferous Algonkian Ordovician Cambrian Cretaceous Devonian Huronian Permian Jurassic riassic Silurian T 100 200 300 400 500 600 700 800 900 1000 1 100 1200 1300 1400 Millions of years since divergence Eocene Miocene Pliocene Oligocene After Dickerson (1971) Paleocene Rates of macromolecular evolution

11. 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

12. Orthologs and paralogs

13. Homologyvs.Homoplasy X X X X Homology: similar traits inherited from a common ancestor Homoplasy: similar traits are not directly caused by common ancestry (convergent evolution).

14. 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 absent present Dog Frog change or step

15. Homoplasy - independent evolution- Tails • Loss of tails evolved independently in humans and frogs - there are two steps on the true tree Human Lizard TAIL absent present Dog Frog

16. 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 Lizard Human TAIL absent present Dog Frog

17. Homology: limb structure

18. Homoplasy: wings

20. 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

21. A C A T G C C T A C A G A C A C A A A Multiple 2 changes, 1 difference Coincidental 2 changes, 1 difference Single 1 change, 1 difference C C T T A A C A C T A C A C A T A C A C A A A Convergent 3 changes, no difference Parallel 2 changes, no difference Back 2 changes, no difference Types of substitution

22. 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 9 7 8 3 4 6 1 3 4 6 7 8 9 10 1 2 5 10 2 5