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BIS2C. Biodiversity and the Tree of Life. 2014. L4. Inferring Phylogenetic Trees

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Jonathan Eisen
Jonathan Eisen

BIS2C. Biodiversity and the Tree of Life. At UC Davis Spring 2014. Lecture 4. Inferring Phylogenetic Trees Slides for Lectures by Jonathan Eisen

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Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4 ! Lecture 4: ! Inferring Phylogenetic Trees ! ! ! BIS 002C Biodiversity & the Tree of Life Spring 2014 ! Prof. Jonathan Eisen 1
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Where we are going and where we have been • Previous Lecture: !Characters, Traits and States • Current Lecture: !Inferring Trees • Next Lecture: !The Tree of Life 2
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Key Concept Inferring the phylogenetic history of taxa from analysis of their character traits and states. 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 4
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 5
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.5 Constructing a Phylogenetic Tree 6
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • Species change over time (i.e., divergence happens) • Comparison and analysis of the patterns of similarity and differences among species should allow us to infer (some) information on the history of those species 7 Phylogenetic Inference
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Table 22.1: Matrix of Traits and States Across 8 Taxa 8
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.5 Constructing a Phylogenetic Tree 9
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 10
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 11 polytomy Key Concept: Polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Polytomy 12 Polytomies - some nodes have three or more descendant branches - usually reflect uncertainty about phylogenetic relationships. polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 13
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 14 How many different rooted trees are there for four taxa? A. 3 B. 5 C. 8 D. 15 polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H OCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H OCG H OGC
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 16 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC WHICH OF THESE POSSIBLE TREES IS THE BEST MODEL? Clicker Answer: Rooted Trees for Four Taxa
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 17 Phylogenetic Inference polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 18 Key Concept: Unrooted Tree
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 19 polytomy Step 1 - Identify Outgroup Phylogenetic Inference outgroup?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Outgroup: one or more taxa that are not members of the ingroup. a b c d e h g f Ingroup m n Outgroups 20 Key Concepts: Ingroups and Outgroups Ingroup: the group of taxa under study
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 21 outgroup? Phylogenetic Inference polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 22 Phylogenetic Inference outgroup polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 23 Phylogenetic Inference outgroup? polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 24 Phylogenetic Inference outgroup polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 25 Step 2 - Root with Outgroup Phylogenetic Inference outgroup polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 26 Step 2 - Root with Outgroup Phylogenetic Inference outgroup polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 27 Step 2: Consider Possible Trees for Ingroup Phylogenetic Inference polytomy
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 28 Possible Tree #1 Phylogenetic Inference
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 29 Possible Tree #2 Phylogenetic Inference
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 30 Possible Tree #3 Phylogenetic Inference
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 15 possible trees 31 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Narrowed down to three 32 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Narrowed down to three 33 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC WHICH OF THESE POSSIBLE TREES IS THE BEST MODEL?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 34
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Principle of parsimony The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). 35
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). ! Applied to character state reconstruction: ! To choose among two (or more) character state reconstruction theories for a given tree, select the one requiring the fewest changes or ‘steps’. 36 Parsimony Character State Reconstruction
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 +++ 37 Pattern 1 Pattern 2 Pattern 3 Which pattern is the most plausible? Parsimony Character State Reconstruction
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Which pattern is the most plausible? +++ Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps 38 Parsimony Character State Reconstruction
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 +++ 39 Which pattern is the most plausible? Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps Parsimony Character State Reconstruction
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Parsimony Phylogenetic Tree Inference The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). ! Applied to phylogenetic inference: ! To choose among two (or more) phylogenetic trees, select the one requiring the fewest total number of steps for all characters 40
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Revised Steps for Parsimony Phylogenetic Inference 41 1. Root the tree with outgroup 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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 A data matrix shows the character states in the taxa under consideration morphology DNA sequences Characters 1 2 3 4 5 6 7 8 9 10… Taxa Orang 1 0 1 0 0 0 A C C T… Chimp 0 1 1 0 0 1 G C C T… Gorilla 0 1 0 1 1 2 G T C T… Human 0 1 0 1 1 2 G T T T… A Data Matrix 42
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T Data matrix: Nine characters of DNA data
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T H C GO C G HO C G HO Tree 1 Tree 2 Tree 3 Data matrix: Nine characters of DNA data
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T Which Tree Requires Fewest Total # of Steps? H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 H C GO C G HO C G HO Tree 1 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T
!48 • How do we decide which pattern is the most plausible? +++ Pattern1: 7 Steps Character state reconstruction Pattern2: 2 Steps Pattern3: 6 Steps
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T T TT T T TT T T TT Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 T T TT T T TT T T TT Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A A
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0!1 ! Tree 2!! 1!0!2! Tree 3!! 1!0!2 H C GO C G HO A G AG Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!! Tree 2!! 1!0!2!0!! Tree 3!! 1!0!2!0! H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1! Tree 2!! 1!0!2!0!1! Tree 3!! 1!0!2!0!1 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1! Tree 2!! 1!0!2!0!1!2! Tree 3!! 1!0!2!0!1!2 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2! Tree 2!! 1!0!2!0!1!2!1! Tree 3!! 1!0!2!0!1!2!2 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0! Tree 2!! 1!0!2!0!1!2!1!0! Tree 3!! 1!0!2!0!1!2!2!0 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!! ! Tree 2!! 1!0!2!0!1!2!1!0!1! Tree 3!! 1!0!2!0!1!2!2!0!1 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 69
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: 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 70
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 T T TT T T TT T T TT Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • No variation = not informative 72 Key Concept: Parsimony Informativeness
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • All taxa the same except one = non informative 74 Key Concept: Parsimony Informativeness
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!4!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!5! Tree 3!! 1!0!2!0!1!2!2!0!1!6 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!4!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!5! Tree 3!! 1!0!2!0!1!2!2!0!1!6 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 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 78 Traits seen across taxa: Example 1: AACC Example 2: AAAGG Example 3: AACGGG Example 4: GGGCCC Key Concept: Parsimony Informativeness
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker 79
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 How Many of These Characters are Parsimony Informative 80 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! T!A!G!A!C!T!A!C!C! Gorilla! C!A!G!A!C!T!C!C!C! Human! ! T!T!A!G!C!T!A!C!T! A. 1 B. 3 C. 5 D. 7
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 How Many of These Characters are Parsimony Informative 81 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! T!A!G!A!C!T!A!C!C! Gorilla! C!A!G!A!C!T!C!C!C! Human! ! T!T!A!G!C!T!A!C!T! A. 1 B. 3 C. 5 D. 7
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Revised Steps for Parsimony Phylogenetic Inference 82 1. Root the tree with outgroup 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.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Revised Steps for Parsimony Phylogenetic Inference 83 1. Ignore parsimony uninformative characters 2. Root the tree with outgroup 3. Draw possible trees. 4. For each character count the minimum number of steps required on each tree. 5. Sum over all characters to get the “score” (number of steps) for each tree. 6. The most parsimonious tree(s) is/are the one(s) with lowest score.
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 84
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 pyrimidines purines A G T C Transitions and transversions 85
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 transitions pyrimidines purines A G T C Transitions and transversions 86 transitions
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 transitions transversions pyrimidines purines A G T C Transitions and transversions 87 transitions
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! 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 vice- versa (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. Transitions and transversions 88
! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 1! 0!1! 5! ! Tree1! ! 1 0 1 0! 1!1!2!0!1! 4! Tree3! ! 1 0 2 0! 1!2!2!0!1! 6 89
! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 1! 0!1! 5! ! Tree1! ! 1 0 1 0! 1!1!2!0!1! 4! Tree3! ! 1 0 2 0! 1!2!2!0!1! 6 90 Transitions vs. transversions
! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 2! 0!1! 6! ! Tree1! ! 1 0 1 0! 1!1!4!0!1! 6! Tree3! ! 1 0 2 0! 1!2!4!0!1! 8 91 What if transversions counted 2x transitions?
! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 3! 0!1! 7! ! Tree1! ! 1 0 1 0! 1!1!6!0!1! 8! Tree3! ! 1 0 2 0! 1!2!6!0!1! 10 92 What if transversions counted 3x transitions?
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 93
94 Informative characters ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! 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
95 Two characters support Tree 2 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! 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
96 One character supports Tree 1 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! 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
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Ket Concept: 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 103
Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Kinds of Phylogenetic Trees 104 A B C D A B C D A B C D Units of character divergence Units of time Cladogram Phylogram Chronogram Different kinds of trees Only the relative branching order is depicted. No meaning to branch lengths. Branch length is proportional to the amount of character change Branch length is proportional to time
!105 Hidden assumptions in analysis so far • Hidden assumptions in analysis
!106 Assumption I • Hidden assumptions in analysis ! All types of characters treated equally
!107 Character examples # Character Character States 1 Wings present, absent 2 Eye color red, white, brown 3 Leg length short, long 4 # antennal segments 11, 12 5 Nucleotide site (DNA) adenine, thymine, guanine, cytosine
!108 Hidden assumptions in analysis so far • Hidden assumptions in analysis ! All types of characters treated equally ! All types of changes treated equally
!109 Assumption III • Hidden assumptions in analysis ! All types of characters treated equally ! All types of changes treated equally ! Changes on all branches treated equally
!110 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?

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BIS2C. Biodiversity and the Tree of Life. 2014. L4. Inferring Phylogenetic Trees

  • 1. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4 ! Lecture 4: ! Inferring Phylogenetic Trees ! ! ! BIS 002C Biodiversity & the Tree of Life Spring 2014 ! Prof. Jonathan Eisen 1
  • 2. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Where we are going and where we have been • Previous Lecture: !Characters, Traits and States • Current Lecture: !Inferring Trees • Next Lecture: !The Tree of Life 2
  • 3. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Key Concept Inferring the phylogenetic history of taxa from analysis of their character traits and states. 3
  • 4. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 4
  • 5. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 5
  • 6. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.5 Constructing a Phylogenetic Tree 6
  • 7. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • Species change over time (i.e., divergence happens) • Comparison and analysis of the patterns of similarity and differences among species should allow us to infer (some) information on the history of those species 7 Phylogenetic Inference
  • 8. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Table 22.1: Matrix of Traits and States Across 8 Taxa 8
  • 9. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Figure 22.5 Constructing a Phylogenetic Tree 9
  • 10. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 10
  • 11. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 11 polytomy Key Concept: Polytomy
  • 12. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: Polytomy 12 Polytomies - some nodes have three or more descendant branches - usually reflect uncertainty about phylogenetic relationships. polytomy
  • 13. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 13
  • 14. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Question 14 How many different rooted trees are there for four taxa? A. 3 B. 5 C. 8 D. 15 polytomy
  • 15. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15
  • 16. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H OCG
  • 17. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H OCG H OGC
  • 18. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC
  • 19. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG
  • 20. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC
  • 21. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO
  • 22. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO
  • 23. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG
  • 24. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker Answer: Rooted Trees for Four Taxa 15 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC
  • 25. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 16 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC WHICH OF THESE POSSIBLE TREES IS THE BEST MODEL? Clicker Answer: Rooted Trees for Four Taxa
  • 26. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 17 Phylogenetic Inference polytomy
  • 27. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 18 Key Concept: Unrooted Tree
  • 28. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 19 polytomy Step 1 - Identify Outgroup Phylogenetic Inference outgroup?
  • 29. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Outgroup: one or more taxa that are not members of the ingroup. a b c d e h g f Ingroup m n Outgroups 20 Key Concepts: Ingroups and Outgroups Ingroup: the group of taxa under study
  • 30. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 21 outgroup? Phylogenetic Inference polytomy
  • 31. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 22 Phylogenetic Inference outgroup polytomy
  • 32. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 23 Phylogenetic Inference outgroup? polytomy
  • 33. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 24 Phylogenetic Inference outgroup polytomy
  • 34. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 25 Step 2 - Root with Outgroup Phylogenetic Inference outgroup polytomy
  • 35. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 26 Step 2 - Root with Outgroup Phylogenetic Inference outgroup polytomy
  • 36. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 27 Step 2: Consider Possible Trees for Ingroup Phylogenetic Inference polytomy
  • 37. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 28 Possible Tree #1 Phylogenetic Inference
  • 38. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 29 Possible Tree #2 Phylogenetic Inference
  • 39. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 30 Possible Tree #3 Phylogenetic Inference
  • 40. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 15 possible trees 31 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC
  • 41. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Narrowed down to three 32 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC
  • 42. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Narrowed down to three 33 H GCO H OCG H OGC H OCG H OGC H CGO G OCH G OHC G HCO C OGH C HGO C HOG O CGH O CHG O HGC WHICH OF THESE POSSIBLE TREES IS THE BEST MODEL?
  • 43. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 34
  • 44. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Principle of parsimony The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). 35
  • 45. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). ! Applied to character state reconstruction: ! To choose among two (or more) character state reconstruction theories for a given tree, select the one requiring the fewest changes or ‘steps’. 36 Parsimony Character State Reconstruction
  • 46. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 +++ 37 Pattern 1 Pattern 2 Pattern 3 Which pattern is the most plausible? Parsimony Character State Reconstruction
  • 47. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Which pattern is the most plausible? +++ Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps 38 Parsimony Character State Reconstruction
  • 48. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 +++ 39 Which pattern is the most plausible? Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps Parsimony Character State Reconstruction
  • 49. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Parsimony Phylogenetic Tree Inference The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal). ! Applied to phylogenetic inference: ! To choose among two (or more) phylogenetic trees, select the one requiring the fewest total number of steps for all characters 40
  • 50. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Revised Steps for Parsimony Phylogenetic Inference 41 1. Root the tree with outgroup 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.
  • 51. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 A data matrix shows the character states in the taxa under consideration morphology DNA sequences Characters 1 2 3 4 5 6 7 8 9 10… Taxa Orang 1 0 1 0 0 0 A C C T… Chimp 0 1 1 0 0 1 G C C T… Gorilla 0 1 0 1 1 2 G T C T… Human 0 1 0 1 1 2 G T T T… A Data Matrix 42
  • 52. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T Data matrix: Nine characters of DNA data
  • 53. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T H C GO C G HO C G HO Tree 1 Tree 2 Tree 3 Data matrix: Nine characters of DNA data
  • 54. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T Which Tree Requires Fewest Total # of Steps? H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 55. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 H C GO C G HO C G HO Tree 1 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T Tree 2 Tree 3
  • 56. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T
  • 57. !48 • How do we decide which pattern is the most plausible? +++ Pattern1: 7 Steps Character state reconstruction Pattern2: 2 Steps Pattern3: 6 Steps
  • 58. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
  • 59. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
  • 60. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
  • 61. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3C C C C C C C C C
  • 62. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 63. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T T TT T T TT T T TT Tree 1 Tree 2 Tree 3
  • 64. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 T T TT T T TT T T TT Tree 1 Tree 2 Tree 3
  • 65. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 66. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3
  • 67. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3
  • 68. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3G
  • 69. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G G
  • 70. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
  • 71. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
  • 72. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
  • 73. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G
  • 74. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G
  • 75. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G G
  • 76. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G G
  • 77. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G G G
  • 78. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G
  • 79. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G
  • 80. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A
  • 81. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
  • 82. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
  • 83. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
  • 84. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
  • 85. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G
  • 86. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G
  • 87. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G G
  • 88. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G G
  • 89. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G G G
  • 90. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A
  • 91. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G
  • 92. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A
  • 93. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A A
  • 94. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A A
  • 95. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 A A GG A G AG A G AG Tree 1 Tree 2 Tree 3 G A G G A A G A A
  • 96. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0!1 ! Tree 2!! 1!0!2! Tree 3!! 1!0!2 H C GO C G HO A G AG Tree 1 Tree 2 Tree 3
  • 97. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!! Tree 2!! 1!0!2!0!! Tree 3!! 1!0!2!0! H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 98. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1! Tree 2!! 1!0!2!0!1! Tree 3!! 1!0!2!0!1 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
  • 99. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1! Tree 2!! 1!0!2!0!1!2! Tree 3!! 1!0!2!0!1!2 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
  • 100. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2! Tree 2!! 1!0!2!0!1!2!1! Tree 3!! 1!0!2!0!1!2!2 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
  • 101. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0! Tree 2!! 1!0!2!0!1!2!1!0! Tree 3!! 1!0!2!0!1!2!2!0 H C GO C G HO C G GO Tree 1 Tree 2 Tree 3
  • 102. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!! ! Tree 2!! 1!0!2!0!1!2!1!0!1! Tree 3!! 1!0!2!0!1!2!2!0!1 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 103. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 104. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 105. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 69
  • 106. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Key Concept: 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 70
  • 107. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 ! Tree 2!! 1!0! Tree 3!! 1!0 T T TT T T TT T T TT Tree 1 Tree 2 Tree 3
  • 108. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • No variation = not informative 72 Key Concept: Parsimony Informativeness
  • 109. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1 ! Tree 2!! 1! Tree 3!! 1 T C CC C C TC C C TC Tree 1 Tree 2 Tree 3
  • 110. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 • All taxa the same except one = non informative 74 Key Concept: Parsimony Informativeness
  • 111. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 112. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 113. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 114. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 115. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 116. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 117. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!7!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!8! Tree 3!! 1!0!2!0!1!2!2!0!1!9 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 118. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!4!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!5! Tree 3!! 1!0!2!0!1!2!2!0!1!6 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 119. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! Tree 1!! 1!0 1! 0!1!1!2!0!1!4!! ! Tree 2!! 1!0!2!0!1!2!1!0!1!5! Tree 3!! 1!0!2!0!1!2!2!0!1!6 H C GO C G HO C G HO Tree 1 Tree 2 Tree 3
  • 120. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 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 78 Traits seen across taxa: Example 1: AACC Example 2: AAAGG Example 3: AACGGG Example 4: GGGCCC Key Concept: Parsimony Informativeness
  • 121. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Clicker 79
  • 122. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 How Many of These Characters are Parsimony Informative 80 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! T!A!G!A!C!T!A!C!C! Gorilla! C!A!G!A!C!T!C!C!C! Human! ! T!T!A!G!C!T!A!C!T! A. 1 B. 3 C. 5 D. 7
  • 123. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 How Many of These Characters are Parsimony Informative 81 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! T!A!G!A!C!T!A!C!C! Gorilla! C!A!G!A!C!T!C!C!C! Human! ! T!T!A!G!C!T!A!C!T! A. 1 B. 3 C. 5 D. 7
  • 124. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Revised Steps for Parsimony Phylogenetic Inference 82 1. Root the tree with outgroup 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.
  • 125. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Revised Steps for Parsimony Phylogenetic Inference 83 1. Ignore parsimony uninformative characters 2. Root the tree with outgroup 3. Draw possible trees. 4. For each character count the minimum number of steps required on each tree. 5. Sum over all characters to get the “score” (number of steps) for each tree. 6. The most parsimonious tree(s) is/are the one(s) with lowest score.
  • 126. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 84
  • 127. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 pyrimidines purines A G T C Transitions and transversions 85
  • 128. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 transitions pyrimidines purines A G T C Transitions and transversions 86 transitions
  • 129. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 transitions transversions pyrimidines purines A G T C Transitions and transversions 87 transitions
  • 130. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 ! 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 vice- versa (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. Transitions and transversions 88
  • 131. ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 1! 0!1! 5! ! Tree1! ! 1 0 1 0! 1!1!2!0!1! 4! Tree3! ! 1 0 2 0! 1!2!2!0!1! 6 89
  • 132. ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 1! 0!1! 5! ! Tree1! ! 1 0 1 0! 1!1!2!0!1! 4! Tree3! ! 1 0 2 0! 1!2!2!0!1! 6 90 Transitions vs. transversions
  • 133. ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 2! 0!1! 6! ! Tree1! ! 1 0 1 0! 1!1!4!0!1! 6! Tree3! ! 1 0 2 0! 1!2!4!0!1! 8 91 What if transversions counted 2x transitions?
  • 134. ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! T!T!A!G!C!T!A!C!T! ! Score! ! ! ! ! ! ! ! ! ! ! Total ! Tree2! ! 1 0 2 0! 1!2 3! 0!1! 7! ! Tree1! ! 1 0 1 0! 1!1!6!0!1! 8! Tree3! ! 1 0 2 0! 1!2!6!0!1! 10 92 What if transversions counted 3x transitions?
  • 135. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Lecture 4: Phylogenetic Inference • General issues • Case study • Parsimony inference for case study • Parsimony informativeness • Are all changes equal? • Character conflict 93
  • 136. 94 Informative characters ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! 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
  • 137. 95 Two characters support Tree 2 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! 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
  • 138. 96 One character supports Tree 1 ! ! ! Characters! ! ! 1!2!3!4!5!6!7!8!9! Taxa! Orang! ! C!T!G!G!A!C!C!C!T! Chimp! ! C!T!A!G!C!T!C!C!C! Gorilla! C!T!G!G!C!C!A!C!T! Human! ! 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
  • 139. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Ket Concept: 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 103
  • 140. Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 Kinds of Phylogenetic Trees 104 A B C D A B C D A B C D Units of character divergence Units of time Cladogram Phylogram Chronogram Different kinds of trees Only the relative branching order is depicted. No meaning to branch lengths. Branch length is proportional to the amount of character change Branch length is proportional to time
  • 141. !105 Hidden assumptions in analysis so far • Hidden assumptions in analysis
  • 142. !106 Assumption I • Hidden assumptions in analysis ! All types of characters treated equally
  • 143. !107 Character examples # Character Character States 1 Wings present, absent 2 Eye color red, white, brown 3 Leg length short, long 4 # antennal segments 11, 12 5 Nucleotide site (DNA) adenine, thymine, guanine, cytosine
  • 144. !108 Hidden assumptions in analysis so far • Hidden assumptions in analysis ! All types of characters treated equally ! All types of changes treated equally
  • 145. !109 Assumption III • Hidden assumptions in analysis ! All types of characters treated equally ! All types of changes treated equally ! Changes on all branches treated equally
  • 146. !110 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?