Phylogenetic Concepts Phylogenetic Relationships Phylogenetic relationships exist between
Phylogenetic Concepts
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.
• 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 Hypothetical ancestral lineage Bambo o Durian (Corn, Bamboo) Durian
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
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
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)
Homoplasy in molecular data • homoplasy can be common in molecular sequence data – There a limited number of alternative character states ( e. g. Only A, G, C and T in DNA) – Rates of evolution are sometimes high
Character Polarisation - Characters are polarised according to evolutionary direction. Apomorphy – advanced/derived state Plesiomorphy – primitive/ancestral state - “derived” means ancestor is lacking it.
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
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. ?
Apomorphic/Synapomorphic/Plesiomorphic A B 11 7 8 C D 2 12 19 25 E 20 F G 1 19 1 16 23 9 13 14 10 24 Apomorphic characters? Synapomorphic characters? Plesiomorphic characters? Homoplacious characters? 4 6 K I 17 21 6 22 H 11 3 15 J 5 18
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
A B C D Monophyletic (Synapomorphy) Paraphyletic (Symplesiomorphy) A B C D Polyphyletic (Homoplasy)
Orthologues and Paralogues paralogous orthologous a b* c b* C* A* orthologous C* B A* A mixture of orthologues and paralogues Duplication to give 2 copies = paralogues on the same genome
Gene trees and species trees Gene tree a A b B c D Species tree We often assume that gene trees give us species trees
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