Bis2CFall10.Lecture5

Bis2CFall10.Lecture5 - Lecture 5: BIS 002C BIODIVERSITY AND...

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Unformatted text preview: Lecture 5: BIS 002C BIODIVERSITY AND THE TREE OF LIFE Lecture 5: Phylogenetic Inference 1 Saturday, October 2, 2010 Where we are going and where we have been • Previous lecture: 4. Character State Reconstruction and Phylogenetic Inference • Current Lecture: 5. Phylogenetic Inference • Next Lecture: 6. The Tree of Life 2 Saturday, October 2, 2010 Lecture 4 Outline • Review Parsimony Example from Lecture 4 • Parsimony informativeness • Rooting an unrooted tree • Character conflicts • Are all steps equal? • Assumptions 3 Saturday, October 2, 2010 Stay tuned Monday AM Nobel Prize in Medicine & Physiology will be announced Last year was related to microbes and co-winner was from Davis 4 Saturday, October 2, 2010 A. Prior Example 5 Saturday, October 2, 2010 Character 1: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 Tree2! ! 1 Tree3! ! 1 6 Saturday, October 2, 2010 Character 2: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 Tree2! ! 1 0 Tree3! ! 1 0 7 Saturday, October 2, 2010 Character 3: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 Tree2! ! 1 0 1 Tree3! ! 1 0 2 8 Saturday, October 2, 2010 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0 Tree2! ! 1 0 1 0 Tree3! ! 1 0 2 0 9 Saturday, October 2, 2010 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1 Tree2! ! 1 0 1 0! 1 Tree3! ! 1 0 2 0! 1 10 Saturday, October 2, 2010 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 Tree2! ! 1 0 1 0! 1! 1 Tree3! ! 1 0 2 0! 1! 2 11 Saturday, October 2, 2010 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! ! Tree2! ! 1 0 1 0! 1! 1! 2 Tree3! ! 1 0 2 0! 1! 2! 2 12 Saturday, October 2, 2010 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0 Tree3! ! 1 0 2 0! 1! 2! 2! 0 13 Saturday, October 2, 2010 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 14 Saturday, October 2, 2010 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 8! 1! 1! 2! 0! 1! 7 1! 2! 2! 0! 1! 9 15 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 8! 1! 1! 2! 0! 1! 7 1! 2! 2! 0! 1! 9 16 Wasp Beetle Tree1 Mantid Beetle Fly Wasp 8 Tree2 Mantid Fly Fly Wasp 7 Tree3 Mantid Saturday, October 2, 2010 9 Beetle 17 B. Parsimony informativeness 18 Saturday, October 2, 2010 Parsimony informativeness Not all traits are useful in determining which tree is most parsimonious Parsimony-uninformative characters do not provide any differentiation among trees in parsimony analysis 19 Saturday, October 2, 2010 Example: Character 2 ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 Tree2! ! 1 Tree3! ! 1 20 Saturday, October 2, 2010 Character 2: Minimal number of changes Wasp Beetle T T Tree1 Mantid Beetle Fly Wasp T T T T 0 Tree2 Mantid Fly Fly Wasp T T T T 0 Tree3 Mantid Saturday, October 2, 2010 0 Beetle T T 21 Example: Character 2 ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 Tree2! ! 1 0 Tree3! ! 1 0 22 Saturday, October 2, 2010 Parsimony informativeness No variation = not informative 23 Saturday, October 2, 2010 Example 2: Character 1 ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T 24 Saturday, October 2, 2010 Character 1: minimal number of changes Wasp Beetle C C Tree1 Mantid Beetle Fly Wasp C C T C 1 Tree2 Mantid Fly Fly Wasp C T T C 1 Tree3 Mantid Saturday, October 2, 2010 1 Beetle C C 25 Example 2: Character 1 ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 Tree2! ! 1 Tree3! ! 1 26 Saturday, October 2, 2010 Parsimony informativeness • Two types of non informative characters No variation All taxa the same except one 27 Saturday, October 2, 2010 Using these rules to simplify the data matrix ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 28 Saturday, October 2, 2010 • CLICKER 29 Saturday, October 2, 2010 1. Invariant characters ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 30 Saturday, October 2, 2010 1. Invariant characters ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 30 Saturday, October 2, 2010 1. Invariant characters ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 30 Saturday, October 2, 2010 1. Invariant characters ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 30 Saturday, October 2, 2010 Block these out ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 31 Saturday, October 2, 2010 2. One taxon different ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 32 Saturday, October 2, 2010 2. One taxon different ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 32 Saturday, October 2, 2010 2. One taxon different ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 32 Saturday, October 2, 2010 2. One taxon different ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 32 Saturday, October 2, 2010 Block out these too ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 33 Saturday, October 2, 2010 Parsimony-informative Simple rule for determining which characters in a data matrix are parsimony-informative? Must be at least two states, each present in at least two taxa 34 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Must be at least two states, each present in at least two taxa ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 35 Saturday, October 2, 2010 Basic procedure for finding/searching for the most parsimonious tree: 1.Draw possible trees. 2.For each character count the minimum number of steps required on each tree. 3.Sum over all characters to get the “score” (number of steps) for each tree. 4.The most parsimonious tree(s) is/are the one(s) with lowest score. 36 Saturday, October 2, 2010 Revised procedure for finding/searching for the most parsimonious tree: 1.Ignore parsimony uninformative characters 2.Draw possible trees. 3.For each character count the minimum number of steps required on each tree. 4.Sum over all characters to get the “score” (number of steps) for each tree. 5.The most parsimonious tree(s) is/are the one(s) with lowest score. 37 Saturday, October 2, 2010 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 38 Character 4: Count changes on each tree ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 8! 1! 1! 2! 0! 1! 7 1! 2! 2! 0! 1! 9 39 Reassessment, ignoring non informative characters ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 40 C. Choosing a root for an unrooted tree 41 Saturday, October 2, 2010 Tree2 Beetle Wasp Mantid Fly • Rooting an unrooted tree 1. Identify an outgroup 2. Place root on tree such that outgroup is separated from all members of the ingroup 3. Redraw tree in rooted form 42 Saturday, October 2, 2010 Tree2 Beetle Wasp Mantid Fly • Which, if any, would be a good candidate for an outgroup relative to the others? 43 Saturday, October 2, 2010 Tree2 Beetle Wasp Mantid M W Fly B F polytomy 44 Saturday, October 2, 2010 • CLICKER 45 Saturday, October 2, 2010 Outgroup? A: Beetle B: Mantid C: Wasp D: Fly Beetle Tree2 Wasp Mantid M W Fly B F polytomy 46 Saturday, October 2, 2010 Outgroup? A: Beetle B: Mantid C: Wasp D: Fly Beetle Tree2 Wasp Mantid M W Fly B F polytomy 47 Saturday, October 2, 2010 What does this mantid rooted tree look like? Tree2 Beetle Wasp Mantid Fly 48 Saturday, October 2, 2010 • CLICKER 49 Saturday, October 2, 2010 What does this mantid rooted tree look like? Tree2 Beetle Wasp Mantid Fly A M F W B M B W B F M F C B W 50 Saturday, October 2, 2010 What does this mantid rooted tree look like? Tree2 Beetle Wasp Mantid Fly A M F W B M B W B F M F C B W 51 Saturday, October 2, 2010 52 Saturday, October 2, 2010 How to root this tree using mantid as an outgroup? Tree2 Beetle Wasp Mantid Fly 53 Saturday, October 2, 2010 Draw root node on branch connecting outgroup to others Tree2 Beetle Wasp Mantid Fly 54 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle Wasp 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle Wasp 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle Wasp 55 Saturday, October 2, 2010 Unwind tree to make it into a vertical tree Tree2 Beetle Wasp Mantid Fly Mantid Beetle Wasp Fly 55 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Mantid Fly A M F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Mantid Fly A M F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Mantid Fly A M F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Mantid Fly A M F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Beetle Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Beetle Tree2 Wasp Fly A F W B M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Wasp Fly A F W M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Wasp Fly A F W M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Wasp Fly A F W M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Wasp Fly A F W M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Wasp Fly A F W M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Wasp Fly A F W M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 Fly A F M B W B F M F C B W 56 Saturday, October 2, 2010 How does tree2 map to A? Tree2 A M B W B F M F C B W 56 Saturday, October 2, 2010 Wasp Beetle M W B F Tree1 8 Mantid Beetle Fly Wasp M B W F Tree2 Mantid Fly Fly Wasp M F B W 7 Tree3 Mantid Saturday, October 2, 2010 9 Beetle 57 D. Conflict Among Characters 58 Saturday, October 2, 2010 Wasp Beetle Tree1 Mantid Beetle Fly Wasp 8 Tree2 Mantid Fly Fly Wasp 7 Tree3 Mantid Saturday, October 2, 2010 9 Beetle 59 Informative characters ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 60 Saturday, October 2, 2010 Two characters support Tree 2 ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 61 Saturday, October 2, 2010 One character supports Tree 1 ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 62 Saturday, October 2, 2010 Character conflict ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T Score Tree1! ! 1 0 2 0! 1! 2 1! 0! 1! ! Tree2! ! 1 0 1 0! 1! 1! 2! 0! 1 Tree3! ! 1 0 2 0! 1! 2! 2! 0! 1 63 Saturday, October 2, 2010 Character conflict leads to homoplasy 64 Saturday, October 2, 2010 Character 7 Wasp Beetle C A Tree1 Mantid Beetle Fly Wasp C A A C 1 Tree2 Mantid Fly Fly Wasp C A A C 2 Tree3 Mantid Saturday, October 2, 2010 2 Beetle C A Character 7 for Tree 2 2 Steps A C C 3 Steps A C C A C C 3 Steps A A C C A C C 2 Steps A A C A A A 66 A C Saturday, October 2, 2010 Character 7 for Tree 2 In each minimal reconstruction, no matter how you root, there will be homoplasy 2 Steps A C C 3 Steps A C C A A C C A C C 3 Steps A A C 2 Steps A C A C A A A 67 Saturday, October 2, 2010 C Rooted Tree 2 Mantid Beetle Wasp Fly Saturday, October 2, 2010 Character 7 on Rooted Tree 2 C A C A Saturday, October 2, 2010 All reconstructions will have homoplasy C A C A Saturday, October 2, 2010 All reconstructions will have homoplasy C A C C C C A Saturday, October 2, 2010 All reconstructions will have homoplasy C A C A A A A Saturday, October 2, 2010 Character conflict • Here, as in many cases, there are only small differences among trees and there is conflict among some characters • What can one do? Gather/analyze more data Use alternative methods to analyze data 73 Saturday, October 2, 2010 E. Should all types of changes count equally? 74 Saturday, October 2, 2010 Transitions and transversions A purines G pyrimidines T Saturday, October 2, 2010 C Transitions and transversions A purines transitions G pyrimidines transitions T Saturday, October 2, 2010 C Transitions and transversions A purines transitions G transversions pyrimidines transitions T Saturday, October 2, 2010 C Transitions and transversions Different kinds of nucleotide substitutions Transitions: changes from one purine to another purine (A↔G) or from one pyrimidine to another pyrimidine (C↔T) Transversions: changes from a purine to a pyrimidine or viceversa (A↔C, A↔T, G↔C, G↔T) For many molecular data sets it has been found that transitions are more likely to occur than transversions. Saturday, October 2, 2010 ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 79 Transitions vs. transversions ! ! ! ! Taxa Mantid! ! Wasp! ! Beetle! ! Fly! ! Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! Characters 1! 2! 3! 4! 5! 6! 7! 8! 9 C! T! G! G! A! C! C! C! T C! T! A! G! C! T! C! C! C C! T! G! G! C! C! A! C! T T! T! A! G! C! T! A! C! T ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 1! 0! 1! 5! 1! 1! 2! 0! 1! 4 1! 2! 2! 0! 1! 6 80 Extra Slide Added for Section B Lecture Tree 1 1 2 3 4 1 Tree 2 2 3 4 Saturday, October 2, 2010 Extra Slide Added for Section B Lecture Tree 1 1 2 3 4 1 Tree 2 2 3 4 Transition Transversion Saturday, October 2, 2010 Extra Slide Added for Section B Lecture Tree 1 1 2 3 4 1 Tree 2 2 3 4 Change in height Replace heart with kidney Saturday, October 2, 2010 What if transversions counted 2x transitions? ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 2! 0! 1! 6! 1! 1! 4! 0! 1! 6 1! 2! 4! 0! 1! 8 84 What if transversions counted 3x transitions? ! ! ! Characters ! ! 1! 2! 3! 4! 5! 6! 7! 8! 9 Taxa Mantid! C! T! G! G! A! C! C! C! T ! Wasp! ! C! T! A! G! C! T! C! C! C Beetle! C! T! G! G! C! C! A! C! T ! Fly! ! T! T! A! G! C! T! A! C! T Score! ! Tree1! ! Tree2! ! Tree3! ! Saturday, October 2, 2010 ! 1 1 1 ! 0 0 0 ! 2 1 2 ! 0! 0! 0! ! ! ! ! ! Total 1! 2 3! 0! 1! 7! 1! 1! 6! 0! 1! 8 1! 2! 6! 0! 1! 10 85 F. Assumptions 86 Saturday, October 2, 2010 Hidden assumptions in analysis so far • Hidden assumptions in analysis 87 Saturday, October 2, 2010 Assumption I • Hidden assumptions in analysis All types of characters treated equally 88 Saturday, October 2, 2010 Character examples # 1 2 3 4 5 Character Wings Eye color Leg length # antennal segments Nucleotide site (DNA) Character States present, absent red, white, brown short, long 11, 12 adenine, thymine, guanine, cytosine 89 Saturday, October 2, 2010 Hidden assumptions in analysis so far • Hidden assumptions in analysis All types of characters treated equally All types of changes treated equally 90 Saturday, October 2, 2010 Assumption III • Hidden assumptions in analysis All types of characters treated equally All types of changes treated equally Changes on all branches treated equally 91 Saturday, October 2, 2010 Assumption III • Why might some branches be different from others? • Rates of evolution are not uniform across taxa. Some lineages (e.g., HIV) evolve much more rapidly than others (e.g., humans) • Perhaps changes in lineages that evolve rapidly should count “less” since they are more common? 92 Saturday, October 2, 2010 Phylograms vs. Cladograms Cladogram No meaning to branch lengths. Phylogram Branch length is proportional to the amount of character change A B C D Rooted A B D C B C Unrooted B C A Branch lengths meaningful A No meaning to branch lengths. Saturday, October 2, 2010 D D Hidden assumptions in analysis so far • Hidden assumptions in analysis All types of characters treated equally All types of changes treated equally Changes on all branches treated equally Difference between minimum number of steps and other possibilities does not matter • All of these assumptions are oversimplifications and most phylogenetic methods used are significantly more complex 94 Saturday, October 2, 2010 Likelihood methods • Rather than searching for trees with the fewest changes, likelihood based methods assign trees probabilities • The probabilities that are calculated do not favor one reconstruction 100% over others • They are based on a probabilistic model of evolution of characters. • Longer branches have higher probabilities of changes occurring on them • Probabilities of different types of changes can be accounted for readily 95 Saturday, October 2, 2010 ...
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