bis2c. biodiversity and the tree of life. 2014. l4. inferring phylogenetic trees

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

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

Lecture 4: Key Concept

Inferring the phylogenetic history of taxa from analysis of their character traits and states.

Lecture 4: Phylogenetic Inference

• General issues

• Case study

• Parsimony inference for case study

• Parsimony informativeness

• Are all changes equal?

• Character conflict

• General issues

• Case study

Figure 22.5 Constructing a Phylogenetic Tree

• 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

Phylogenetic Inference

Table 22.1: Matrix of Traits and States Across 8 Taxa

Figure 22.5 Constructing a Phylogenetic Tree

• General issues

• Case study

Slides by Jonathan Eisen for BIS2C at UC Davis Spring 2014 11

polytomy

Key Concept: Polytomy

Polytomies - some nodes have three or more descendant branches - usually reflect uncertainty about phylogenetic relationships. polytomy

Clicker Question

How many different rooted trees are there for four taxa?

A. 3 B. 5 C. 8 D. 15

polytomy

Clicker Answer: Rooted Trees for Four Taxa

WHICH OF THESE POSSIBLE TREES IS THE BEST MODEL?

polytomy

Key Concept: Unrooted Tree

polytomy

Step 1 - Identify Outgroup

outgroup?

Outgroup: one or more taxa that are not members of the ingroup.

a b c d e h g f

Ingroup

Outgroups

Key Concepts: Ingroups and Outgroups

Ingroup: the group of taxa under study

outgroup?

polytomy

outgroup

polytomy

outgroup?

polytomy

outgroup

polytomy

Step 2 - Root with Outgroup

outgroup

polytomy

Step 2 - Root with Outgroup

outgroup

polytomy

Step 2: Consider Possible Trees for Ingroup

polytomy

Possible Tree #1

Possible Tree #2

Possible Tree #3

15 possible trees

Narrowed down to three

WHICH OF THESE

POSSIBLE TREES IS THE BEST MODEL?

• General issues

• Case study

Principle of parsimony

The Principle of Parsimony: the simplest of two (or more) competing theories is to be preferred (assuming all else is equal).

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’.

Parsimony Character State Reconstruction

Pattern 1 Pattern 2 Pattern 3

Which pattern is the most plausible?

+++Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps

Pattern1: 7 Steps Pattern2: 2 Steps Pattern3: 6 Steps

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

Revised Steps for Parsimony Phylogenetic Inference

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.

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

! ! ! 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

H C GO C G HO C G HO

Tree 1 Tree 2 Tree 3

Data matrix: Nine characters of DNA data

Which Tree Requires Fewest Total # of Steps?

Tree 1

Tree 2 Tree 3

T C CC C C TC C C TC

• How do we decide which pattern is the most plausible?

+++Pattern1: 7 Steps

Character state reconstruction

Pattern2: 2 Steps Pattern3: 6 Steps

! ! ! 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

Tree 1 Tree 2 Tree 3C

T T TT T T TT T T TT

! ! ! 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

! ! ! 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

! ! ! 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!

! ! ! 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

! ! ! 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

! ! ! 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

! ! ! 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

! ! ! 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

! ! ! 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

• General issues

• Case study

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

• No variation = not informative

• All taxa the same except one = non 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

Traits seen across taxa: Example 1: AACC Example 2: AAAGG Example 3: AACGGG Example 4: GGGCCC

Clicker

How Many of These Characters are Parsimony Informative

! ! ! 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

How Many of These Characters are Parsimony Informative

! ! ! 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

1. Ignore parsimony uninformative characters

• General issues

• Case study

pyrimidines

purines

Transitions and transversions

transitions

pyrimidines

purines

transitions

transversions

pyrimidines

purines

transitions

!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.

! ! ! 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

Transitions vs. transversions

What if transversions counted 2x transitions?

What if transversions counted 3x transitions?

• General issues

• Case study

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

Two characters support Tree 2

One character supports Tree 1

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

Kinds of Phylogenetic Trees

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

Hidden assumptions in analysis so far

• Hidden assumptions in analysis

Assumption I

• Hidden assumptions in analysis ! All types of characters treated equally

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

Hidden assumptions in analysis so far

• Hidden assumptions in analysis ! All types of characters treated equally ! All types of changes treated equally

Assumption III

• Hidden assumptions in analysis ! All types of characters treated equally ! All types of changes treated equally ! Changes on all branches treated equally

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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