An Introduction to Phylogenetics

> Sequence 1GAGGTAGTAATTAGATCCGAAA…> Sequence 2GAGGTAGTAATTAGATCTGAAA…> Sequence 3GAGGTAGTAATTAGATCTGTCA…

Anton E. Weisstein

Indiana State UniversityMarch 11-14, 2004

Outline

I. Overview

II. Building and Interpreting Phylogenies

III. Evolutionary Inference

IV. Specific Applications

What is phylogenetics?

Phylogenetics is the study of evolutionary relationships.

Relationships among species:

crocodiles

birds

lizards

snakesrodents

primates

marsupials

What is phylogenetics?Relationships among species:

crocodilesbirdslizardssnakesrodentsprimatesmarsupials

This is an example of a phylogenetic tree.

What is phylogenetics?Relationships within species:HIV subtypes

RwandaIvory Coast

UgandaU.S.U.S.

Italy

U.K.

India Rwanda

EthiopiaS. AfricaUganda

Uganda

Tanzania

Romania

BrazilCameroon

Netherlands

NetherlandsTaiwan

Russia

A

B

C

D

F G

So what is phylogeneticsgood for?

Phylogenetics has direct applications to:

• Conservation: test wood, ivory, meat products for poaching

• Agriculture: analyze specific differences between cultivars

• Forensics: DNA fingerprinting

• Medicine: determine specific biochemical function of cancer-causing genes

1990 case: Did a patient’s HIV infection result from an invasive dental procedure performed by an HIV+ dentist?

HIV Example 1:Florida dentist case

Outline

I. Overview

II. Building and Interpreting Phylogenies

III. Evolutionary Inference

IV. Specific Applications

Phylogenetic concepts:Interpreting a Phylogeny

Sequence A

Sequence BSequence C

Sequence D

Sequence E

Time

Which sequence is most closely related to B?

A, because B diverged from A more recently than from any other sequence.

Physical position in tree is not meaningful! Only tree structure matters.

Phylogenetic concepts:Rooted and Unrooted Trees

Time

A

B

C

D

Root =

A B

C D

Root

X

=?A B

C D

?

? ?

? ?

X

How Many Trees?

Unrooted trees Rooted trees

# sequences

# pairwise distances # trees

# branches /

tree # trees# branches

/tree3 3 1 3 3 4

4 6 3 5 15 6

5 10 15 7 105 8

6 15 105 9 945 10

10 45 2,027,025 17 34,459,425 18

30 435 8.69 1036 57 4.95 1038 58

N N (N - 1)2

(2N - 5)!2N - 3 (N - 3)!

2N - 3 (2N - 3)!2N - 2 (N - 2)!

2N - 2

Tree Types

Root

50 million years

sharks

seahorses

frogsowls

crocodilesarmadillosbats

Evolutionary trees measure time.

Root

sharksseahorses

frogsowls

crocodilesarmadillos

bats5% change

Phylograms measure change.

Tree Properties

Root

UltrametricityAll tips are an equal

distance from the root.X

Y

a

bc d

e

a = b + c + d + e

Root

AdditivityDistance between any two tips equals the total branch

length between them.

X

Ya

b

c de

XY = a + b + c + d + e

In simple scenarios, evolutionary trees are ultrametric and phylograms are additive.

Tree Building Exercise

UltrametricityAll tips are an equal

distance from the root. Root

X

Y

a

bc d

e

a = b + c + d + e

Using the distance matrix given, construct an ultrametric tree.

Phylogenetic Methods

Neighbor-joining• Minimizes distance between nearest neighbors

Maximum parsimony• Minimizes total evolutionary change

Maximum likelihood• Maximizes likelihood of observed data

Many different procedures exist. Three of the most popular:

Comparison of Methods

Neighbor-joining Maximum parsimony Maximum likelihood

Uses only pairwise distances

Uses only shared derived characters

Uses all data

Minimizes distance between nearest neighbors

Minimizes total distance

Maximizes tree likelihood given specific parameter values

Very fast Slow Very slow

Easily trapped in local optima

Assumptions fail when evolution is rapid

Highly dependent on assumed evolution model

Good for generating tentative tree, or choosing among multiple trees

Best option when tractable (<30 taxa, homoplasy rare)

Good for very small data sets and for testing trees built using other methods

Which procedure should we use?Neighbor-

joiningMaximumparsimony

Maximumlikelihood

All that we can!

?

• Each method has its own strengths

• Use multiple methods for cross-validation

• In some cases, none of the three gives the correct phylogeny!

Outline

I. Overview

II. Building and Interpreting Phylogenies

III. Evolutionary Inference

IV. Specific Applications

Phylogenetic concepts:Homology and Homoplasy

Homology: identical character due to shared ancestry (evolutionary signal)

Homoplasy: identical character due to evolutionary convergence or reversal (evolutionary noise)

lizards

snakes

rodentsprimates+hair

Homology Homoplasy(Convergence)

birds

snakes

rodentsbats

+flight

+flight

Homoplasy(Reversal)

worms

lizardssnakes+legs –legs

Watching the Molecular ClockMutation occurs as a random (Poisson) process. If mutations accumulate at a constant rate over time and across all branches, the phylogeny is said to obey a molecular clock.

% genetic difference

20012002

2001

2002

2000

Watching the Molecular ClockMutation occurs as a random (Poisson) process. If mutations accumulate at a constant rate over time and across all branches, the phylogeny is said to obey a molecular clock.

% genetic difference

BUT:• Natural selection favors some mutations and eliminates others• Selection varies over time and across lineages

2000

20012002

200120012002

2002

Trees are hypotheses about evolutionary history

So far, we’ve looked at understanding and formulating these hypotheses. Now, let’s turn our attention to testing them.

Tree Testing:Split Decomposition

Split decomposition is one method for testing a tree.

A

B

C

D

A

D

B

C

A

C

B

D

Under this procedure, we choose exactly four taxa (A, B, C, D) and examine the topologies of all possible unrooted trees. How many such trees are there?

Only one of these topologies is right. How can we quantitatively assess the support for each tree?

Tree Testing:Split Decomposition

The correct tree should be approximately additive; the others usually will not. For each tree, we calculate split indices that estimate the length of the internal branch:

+A

D

B

C+

A

C

B

D–

2Large split indices Long internal branch Topology strongly supported

Small split indices Short internal branch Topology weakly supported

Negative split indices Biologically impossible Topology probably wrong

=

if A

C

B

Dis the right phylogeny!

Tree Testing:Bootstrapping

Used to assess the support for individual branches

Randomly resample characters, with replacement

How often does a specific branch appear?

Repeat many times (1000 or more)

rathumanturtlefruit flyoakduckweed

100

98

73

Tree Testing:Bootstrapping

MacClade Example:

Vertebrate evolution

Outline

I. Overview

II. Building and Interpreting Phylogenies

III. Evolutionary Inference

IV. Specific Applications

HIV Example 1:Florida dentist case

• 1990 case: Did a patient’s HIV infection result from an invasive dental procedure performed by an HIV+ dentist?

• HIV evolves so fast that transmission patterns can be reconstructed from viral sequence (molecular forensics).

• Compared viral sequence from the dentist, three of his HIV+ patients, and two HIV+ local controls.

Florida dentist case

So what do the results mean?

• 2 of 3 patients closer to dentist than to local controls. Statistical significance? More powerful analyses?

• Do we have enough data to be confident in our conclusions? What additional data would help?

• If we determine that the dentist’s virus is linked to those of patients E and G, what are possible interpretations of this pattern? How could we test between them?