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  1. Reconstructing the History of Lineages Chapter 11 Tereza Jezkova School of Life Sciences, University of Nevada, Las Vegas March 2011

  2. PHYLOGENETICS study of evolutionary relatedness among organisms (through molecular data and morphological data)

  3. Cladograms Sister taxa taxon O E D C B A Common Ancestor

  4. THE basic logic of phylogenetics: • a natural taxon is a monophyletic group • (all descendant taxa and their common ancestor) monophyletic monophyletic O E D C B A Common Ancestor Common Ancestor Fig. 11.4A

  5. THE basic logic of phylogenetic systematics: • a natural taxon is a monophyletic group • (all descendant taxa and their common ancestor) O E D C B A Fig. 11.4A

  6. Other kinds of groups are not natural: • paraphyletic groups (some, but not all descendant taxa and their common ancestor) O E D C B A Fig. 11.4B

  7. Example of a paraphyletic group: • Reptiles are paraphyletic if birds are removed

  8. Other kinds of groups are not natural: • polyphyletic groups(descendant taxa trace back through two or more ancestors before reaching a common ancestor) O E D C B A Fig. 11.4C

  9. Example of a polyphyletic group: warm-blooded animals (Mammals+Birds)

  10. Characters (morphological, ecological, behavioral, molecular): • traits that vary across taxa and clades character state change primitive character state derived character state

  11. homologous characters (homology): • characters whose traits are shared between two or more taxa or clades because of inheritance from a common ancestor

  12. homologous characters (homology): • characters whose traits are shared between two or more taxa or clades because of inheritance from a common ancestor pouch KOALA pouch POSSUM pouch

  13. homoplasious characters (homoplasy): • characters whose traits are shared between two or more taxa but evolved independently

  14. homoplasious characters (homoplasy): • characters whose traits are shared between two or more taxa but evolved independently NOT USEFUL FINS FINS FINS FINS

  15. character state evolution character state change primitive character state derived character state

  16. characters: dinosaurs birds crocodiles feathers Feathers are derived character state for birds Primitive character state is not to have feathers

  17. characters: dinosaurs lizards crocodiles snakes leglessness Leglessness is a derived character state for snakes Primitive character state is to have legs

  18. primitive vs. derived characters: • unique derived (one clade) • shared derived (two or more clades)

  19. primitive vs. derived characters: • shared primitive shared-primitive for this clade

  20. primitive vs. derived characters: shared-derived for this clade shared-primitive for this clade

  21. primitive vs. derived characters: • shared primitive characters are not useful in diagnosing a monophyletic group

  22. primitive vs. derived characters: • Unique derived characters are not useful in diagnosing a monophyletic group

  23. primitive vs. derived characters: • Only shared derived characters can be used to diagnose a monophyletic group.

  24. primitive vs. derived characters: • Onlyshared derived characters can be used to diagnose a monophyletic group. Correct Incorrect

  25. Outgroupsused to polarize primitive derived direction of character state changes in the ingroup outgroup O E D C B A Fig. 11.5

  26. Reconstructing trees • Choose the taxa • ex: Vertebrates

  27. Reconstructing trees 2. Determine the characters

  28. Reconstructing trees 3. Determine polarity of characters

  29. Reconstructing trees 4. Group taxa by shared derived characters

  30. Reconstructing trees 5. Repeat with all characters work out conflicts (none in this example)

  31. Reconstructing trees 6. Complete the tree

  32. Reconstructing trees 6. Use parsimony principle to choose the best tree one change better (shorter tree) than two

  33. EXCERCISE Outgroup Species A Species B Species C Species D Species E

  34. Data Matrix

  35. Data Matrix ABCE ABCE CE ABCDE C C D AB ABDE B

  36. Molecular phylogenetics

  37. EXCERCISE #Elephas_maximus_(Asian_elephant) AG-G--CT--TGA-AG--GA-AT-TC--T-TGAG-A-A-CAACAAAGCA--A-TCATTTGA-T-TTA---A-GT--AT-AGATGC-T-CAGTATA-AGA-AA-A-A-CA-AA-G-AGAGAC-ATTC-CATCC-C-A--A---TTCCT-T-TGA-ATGT--GTTTTATG-AG-TT-TAT-CAGTCAG-A-ACA--T—CA-T-AT--C-CTT--C-AACA--AGC-AT-TTTGA---GAAA-GGC-A-GAGACAA-T-G-CAT--TAGATT--TTCTT-A-C---CAAA-TCCTATG-A-T

  38. EXCERCISE