Phylogenetic Concepts

1. Phylogenetic Concepts

2. Phylogenetic Relationships • Phylogenetic relationships exist between lineages (e.g. species, genes) • These include ancestor-descendent relationships based on common ancestry • Phylogenetic relationships between species or lineages are (expected to be) tree-like • Given that all lineages are related, closeness of phylogenetic relationships is a relative concept.

3. Two lineages are more closely related to each other than to some other lineage if they share a more recent common ancestor - this is the cladistic concept of relationships • Phylogenetic hypotheses are hypotheses of common ancestry Corn Bamboo Durian Hypothetical ancestral lineage (Corn, Bamboo) Durian

4. Characters and Character States • Organisms comprise sets of features • When organisms/taxa differ with respect to a feature (e.g. its presence or absence or different nucleotide bases at specific sites in a sequence) the different conditions are called character states • The collection of character states with respect to a feature constitute a character

5. Character evolution • Heritable changes (in morphology, gene sequences, etc.) produce different character states • Similarities and differences in character states provide the basis for inferring phylogeny (i.e. provide evidence of relationships) • The utility of this evidence depends on how often the evolutionary changes that produce the different character states occur independently

6. Homoplasy - Independent evolution • Homoplasy is similarity that is not homologous (not due to common ancestry) • It is the result of independent evolution (convergence, parallelism, reversal) • Homoplasy can provide misleading evidence of phylogenetic relationships (if mistakenly interpreted as homology)

7. Homoplasy in molecular data • homoplasy can be common in molecular sequence data • There are a limited number of alternative character states ( e.g. Only A, G, C and T in DNA) • Rates of evolution are sometimes high

8. Character Polarisation • Characters are polarised according to evolutionary direction. • Apomorphy – advanced/derived state • Plesiomorphy – primitive/ancestral state • “derived” means ancestor is lacking it.

9. Character Polarisation • Criteria suggesting primitiveness of a character: • a) Presence in fossils • b) Commonness in a array of taxa • c) Early appearance in ontogeny • d) Presence in an outgroup

10. Character Polarisation • Apomorphy can be divided into synapomorphy and autapomorphy. • Autapomorphy (aut = alone) is unique derived character state. • Synapomorphy (syn = shared) is shared derived character state. ?

11. Apomorphic/Synapomorphic/Plesiomorphic A B C D E F G H I J 11 19 20 1 5 17 7 2 21 25 19 18 12 8 6 16 15 22 23 11 1 3 9 13 14 24 10 Apomorphic characters? Synapomorphic characters? Plesiomorphic characters? Homoplacious characters? 4 6 K

12. Monophyly (monophyletic group): A group recognized by synapomorphies A group that includes a most recent common ancestor plus all of its descendants Paraphyly (Paraphyletic group): A group recognized by symplesiomorphies A group that includes a most recent common ancestor plus only some of its descendants Polyphlyly (Polyphyletic group): A group based on convergent/homoplastic characters A group that does not include the most recent ancestor of all its members

13. C D A B Monophyletic (Synapomorphy) C D A B Paraphyletic (Symplesiomorphy) C D A B Polyphyletic (Homoplasy)

14. Orthologues and Paralogues paralogous b* C* A* orthologous orthologous c C* B A* a b* A mixture of orthologues and paralogues Duplication to give 2 copies = paralogues on the same genome

15. Gene trees and species trees A a Species tree Gene tree B b D c We often assume that gene trees give us species trees