Phylogenetics

PhylogeneticsReconstructing the Tree of Life

Tree of Life Web Project

http://www.tolweb.org/tree/

Fig. 26-21

Fungi

EUKARYA

Trypanosomes

Green algaeLand plants

Red algae

ForamsCiliates

Dinoflagellates

Diatoms

Animals

AmoebasCellular slime molds

Leishmania

Euglena

Green nonsulfur bacteriaThermophiles

Halophiles

Methanobacterium

Sulfolobus

ARCHAEA

COMMONANCESTOR

OF ALLLIFE

BACTERIA

(Plastids, includingchloroplasts)

Greensulfur bacteria

(Mitochondrion)

Cyanobacteria

ChlamydiaSpirochetes

Outline

1. What is a phylogeny?

2. How do you construct a phylogeny?The Molecular ClockStatistical Methods

Are Genetic Distancesand fossil recordroughly congruent?

Think about relationships among the major lineages of life and when they appeared in the fossil record

Fossil Record vs Molecular Clock

• Molecular clock and fossil record are not always congruent– Fossil record is incomplete, and soft bodied species are

usually not preserved– Mutation rates can vary among species (depending on

generation time, replication error, mismatch repair)

• But they provide complementary information– Fossil record contains extinct species, while molecular

data is based on extant taxa– Major events in fossil record could be used to calibrate

the molecular clock

Evolutionary History of HIV

Evolutionary AnalysisFreeman& Herron, 2004Time

HIV evolved multiple times from SIV (Simian Immunodeficiency Syndrome)

Charles Darwin (1809 -1882)

On the Origin of Species (1859)

– Living species are related by common ancestry

– Change through time occurs at the population not the organism level

– The main cause of adaptive evolution is natural selection

Darwin envisaged evolution as a tree

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth………The green and budding twigs may represent existing species; and those produced during former years may represent the long succession of extinct species…..….the great Tree of Life….covers the earth with ever-branching and beautiful ramifications

Charles Darwin, On the Origin of Species; pages 131-132

Reconstructing the Tree of Life

The only figure in The Origin of Species

Lamarck proposed a ladder of life

What did people believe before Darwin?

Past Future

Jean-Baptiste Lamarck

• French Naturalist (1744-1829)• “Professor of Worms and Insects”

in Paris

• The first scientific theory of evolution (inheritance of acquired traits)

Lamarck’s View of Evolution

• Continuum between physical and biological world (followed Aristotle)

• Scala Naturae (“Ladder of Life” or “Great Chain of Being”)

Being

Realm of Being

Realm of Becoming

Non-Being

God

Angels

Demons

ManAnimals

Plants

Minerals

What is wrong with a ladder?

• Evolution is not linear but branching

• Living organisms are not ancestors of one another

• The ladder implies progress

What is right with the tree?• Evolution is a branching process• If a mutation occurs, one species

is not turning into another, but there is a split, and both lineages continue to evolve

• So, evolution is not progressive - all living taxa are equally “successful”

• Phylogenies (Trees) reflect the hierarchical structuring of relationships

The only figure in The Origin of Species

The Tree of Life is a Fractalhttp://tolweb.org/tree/phylogeny.html

Genealogical structures • Phylogeny

– A depiction of the ancestry relations between species (it includes speciation events)

– Tree-like (divergent)

• Pedigree– A depiction of the ancestry relations within

populations– Net-like (reticulating)

Four butterflies connected to their parents

offspring

parents

Popu

latio

nIn

divi

dual

s

past

futu

re

Popu

latio

nLi

neag

e/

Spec

ies

Phyl

ogen

y

What happened here?

Lineage-branchingSpeciation

What happened here?

Extinction

A B C

The True History

A B C

A simplified representation

Representation of phylogenies?

Some terms used to describe a phylogenetic tree

Taxon (taxa)Tip

Internal branchInternode

Node (Speciation event)

Root

Outline

1. What is a phylogeny?

2. How do you construct a phylogeny?The Molecular ClockStatistical Methods

• A phylogenetic tree represents a hypothesis about evolutionary relationships

• Each branch point represents the divergence of two taxa (e.g. species)

• Sister taxa are groups that share an immediate common ancestor

What is a Phylogeny?

Molecular Clock

• Mutations• On average, mutations

occur at a given rate

Example:Mitochondria: 1 mutation every ~2.2%/million years.

Faster if

• Mutation rate is faster:

– Shorter generation time(greater number of meiosis or

mitosis events in a given time)

– Replication Error (e.g. Sloppy DNA or RNA polymerase, inefficient mismatch repair)

Molecular Clock

Phylogenetic Trees with Proportional Branch Lengths

• In some trees, the length of a branch can reflect the number of genetic changes that have taken place in a particular DNA sequence in that lineage

• So longer branches = greater evolutionary distance

Phylogenetic Informative Characters (mutations)

• Neutral mutations: –Mutations that are not subjected to selection

–Better for constructing phylogenies because selection could make unrelated taxa appear more similar or related taxa more different

–Examples: Noncoding regions of DNA, 3rd codon position in proteins, introns, microsatellites (“junk DNA”)

Codon Bias

In the case of amino acids

Mutations in Position 1, 2 lead to change

Mutations in Position 3 don’t matter

Species

Canislupus

Pantherapardus

Taxideataxus

Lutra lutra

Canislatrans

Order Family Genus

Carnivora

FelidaeM

ustelidaeC

anidae

Canis

LutraTaxidea

Panthera

Sistertaxa

ANCESTRALLINEAGE

Taxon A

Polytomy (unresolved branching point)

Common ancestor oftaxa A–F

Branch point(node)

Taxon B

Taxon C

Taxon D

Taxon E

Taxon F

A A A

BBB

C C C

DDD

E E E

FFF

G G G

Group IIIGroup II

Group I

(a) Monophyletic group (clade) (b) Paraphyletic group (c) Polyphyletic group

A monophyletic clade consists of an ancestral taxa and all its descendants

Examples of Paraphyletic Groups

A

B

C

D

E

F

G

Group I

(a) Monophyletic group (clade)

(in the lecture on species concepts we discussed that the “smallest” monophyletic group is a “phylogenetic species”)

Synapomorphies

• Synapomorphies are shared derived homologous traits

• They can be DNA nucleotides or other heritable traits

• They are used to group taxa that are more closely related to one another

synapomorphies

Sometimes similar looking traits are not homologous, and are not synapomorphies, but are the result of convergent evolution

How do we construct Phylogenies?

Phylogenetic Methods

• Parsimony: Minimize # steps

• Distance Matrix: minimize pairwise genetic distances

• Maximum Likelihood: Probability of the data given the tree

• Bayesian: Probability of the tree given the data

Parsimony Uses DiscreteCharacters (like mutations, or some heritable trait)

Select the tree with the minimum number of character-state transitions summed across all characters

Fig. 26-15-1

Species I

Three phylogenetic hypotheses:

Species II Species III

I

II

III

I

III

IIIII

III

Parsimony: Example 1

Fig. 26-15-2

Species I

Site

Species II

Species III

I

II

III

I

III

IIIII

III

Ancestralsequence

1/C1/C

1/C

1/C

1/C

4321

C

C C

C

T

T

T

T

T

T A

AA

A G

G

Fig. 26-15-3

Species I

Site

Species II

Species III

I

II

III

I

III

IIIII

III

Ancestralsequence

1/C1/C

1/C

1/C

1/C

4321

C

C C

C

T

T

T

T

T

T A

AA

A G

G

I I

I

II

II

II

III

III

III3/A

3/A

3/A3/A

3/A

2/T2/T

2/T 2/T

2/T4/C

4/C

4/C

4/C

4/C

Fig. 26-15-4

Species I

Site

Species II

Species III

I

II

III

I

III

IIIII

III

Ancestralsequence

1/C1/C

1/C

1/C

1/C

4321

C

C C

C

T

T

T

T

T

T A

AA

A G

G

I I

I

II

II

II

III

III

III3/A

3/A

3/A3/A

3/A

2/T2/T

2/T 2/T

2/T4/C

4/C

4/C

4/C

4/C

I I

I

II

II

II

III

III

III

7 events7 events6 events

Three possible trees

Tree 1

C B

AO

Tree 2

A B

CO

B C

AO

C B AO A B CO

B A CO

Tree 3

Parsimony: Example 2

C B AO

Map the characters (mutations) onto tree 1

12

ABC

O1 2 3 4 5

GGG

T G G A A

CCC

GAA

AAC

AAT

Map the characters (mutations) onto tree 1

ABC

O1 2 3 4 5

GGG

T G G A A

CCC

GAA

AAC

AAT

Total # number of steps = 6

C B AO

12

3

3

45

Actually, there is more than one way to map character 3

ABC

O

3

G

GAA

Either way the character contributes 2 steps to the overall tree length

C B AO

3

3

C B AO

3

3

Map the characters onto tree 2

# steps = 5

ABC

O

1 2 3 4 5

GGG

T G G A A

CCC

GAA

AAC

AAT

A B CO

12

45

3

Tree 3

Length = 6 steps

ABC

O

1 2 3 4 5

GGG

T G G A A

CCC

GAA

AAC

AAT

B A CO

12

453

3

Most parsimonious tree

Which tree had the shortest branch lengths (most parsimonious)?

Tree 1: length = 6

C B

AO

Tree 2: length = 5

B C

AO

C B AO A B CO

B A CO

Tree 3: length = 6

Example from Freeman & Herron, Fig. 4.8

Where do the Whales belong?

Freeman & Herron, Fig. 4.9: Using maximum parsimony, looks like the whales cluster with the hippos (and cows)

Parsimony• Simplest and fastest method of phylogenetic

reconstruction

• Can give misleading results if rates of evolution (rates that mutations occur) differ in different lineages

• Tends to become less accurate as genetic distances get greater

• Could be mislead by reversals, homoplasy: Because with only 4 nucleotides, after a while, same mutations occur repeatedly at a given site (called “saturation”)

Distance Matrix

Continuous orDiscrete Characters

Distance Matrix

• Calculate pairwise distances between taxa• Choose the tree that minimizes overall

distances between taxa

proportion sequence distance at 2 genes(hypothetical data)

mouse cat dog dolphin seal

Mouse 1Cat 0.05 1Dog 0.03 0.02 1Dolphin 0.08 0.15 0.03 1Seal 0.09 0.23 0.01 0.02 1

Freeman & Herron, Fig. 4.10: Using genetic distances, looks like the whales again cluster with the hippos (and cows)

Distance Matrix

• Generally more accurate than parsimony

• Like parsimony, it tends to be computationally fast

Z: Probability of the data

Maximum Likelihood (R.A. Fisher)• Probability of the data given the tree• This is a “Frequentist” method: one true answer (one

true tree)

• Draw from the data (probability distribution of DNA sequence data) to find the true tree

• Choose the tree (x, y axis) that maximizes the probability of the observed data (z axis)

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution. 17(6):368-76.

x,y: Tree space

Z: Probability of the data

Maximum Likelihood (R.A. Fisher)• Probability of the data given the tree• The aim of maximum likelihood estimation is to find

the parameter value(s) that makes the observed data most likely.

• For example: finding a mean. If you want to have a number that describes the data, like human height, you could find the mean

Felsenstein, J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. Journal of Molecular Evolution. 17(6):368-76.

x,y: Tree space

• Often yields more accurate tree than parsimony or distance

• Relies on an accurate assumption of which mutations are more probable (A->G more often than A->T or C? i.e. accurate model of molecular

evolution) • Computationally intensive

Maximum Likelihood(R.A. Fisher)

Bayesian InferenceReverend Thomas Bayes (1702-1760)

• Probability of a tree given the data• Uses prior information on the tree• Does not assume that there is one correct tree• Will modify estimate based on additional information

• Uses Bayes’ Theorem

P(A/B) = P(B/A)P(A) P(B)


• Probability of a tree given the data:

• Will modify estimate based on additional information: so as you get more data, you update your hypothesis for the tree

• Uses prior information on the tree: this is where you start

• The sequential use of the Bayes' formula (recursive): when more data become available after calculating a posterior distribution, the posterior becomes the next prior

• Does not assume that there is one correct tree


• Uses Bayes’ Theorem

P(A/B) = P(B/A)P(A) P(B)

P(A) = prior probabilityP(A/B) = posterior probability—this is the treeP(B/A) = the probability B of observing given A, is also known as the likelihood. It indicates the compatibility of the evidence with the given hypothesis.

Bayesian Inference

• Like Likelihood, often yields more accurate tree than parsimony or distance

• Computationally more intensive than parsimony or distance matrix, but less intensive than likelihood

• Needs a prior probability for the tree and model

• Sufficient Amount of Data: – With enough data most statistical methods

usually yield the same tree– Insufficient data would yield a tree that lacks

resolution (lacks statistical power)

• Gene trees vs species trees– Evolutionary history of individual genes are

not necessarily the same– Should try to get data from many genes, or

the whole genome

Potential problems of Phylogenetic Reconstruction

Challenges of Phylogenetic Reconstructions

• Different parts of the genome might have different evolutionary histories (different gene genealogies, horizontal gene transfers, allopolyploidy, etc)

• So, there might not be one true tree for a group of taxa, and relationships might be difficult to resolve because they are inherently complex

• Current trend is to use whole genome data to reconstruct phylogenies

• Gain a comprehensive picture of the evolutionary relationships among taxa for the whole genome

Neutral data are better for capturing genetic distances (the molecular clock) than genes that might be under selection

• Why?

• Typically, evolutionary biologists will use a variety of methods to reconstruct a phylogeny. • Maximum likelihood and Bayesian methods are

considered more robust.

• Tree is only as good as the data. Having many homoplastic characters (due to convergent evolution, reversals, etc.) will make the reconstruction less robust• Standard to use Bootstrapping to assess the validity of the

tree

• Understanding statistics is fundamental to understanding evolution• Much of statistics was in fact developed in order to model

evolutionary processes (such as ANOVA, analysis of variance)

Phylogenetic Reconstructions

1. Sometimes the Molecular Clock (based on genetic data) conflicts with the Geological Record. Why would this happen?

(A) Sometimes there are gaps in the geological record, because fossils do not form everywhere, and mutation rate might vary between different species

(B) Radiometric dating relies on chance events in the preservation of isotopes, making the timing events in the geological time scale less accurate than the molecular clock

(C) Mutation rates slow down as you go back in time, making estimation of timing of events less accurate as you go back in time

(D) The molecular clock is calculated from radioisotopes, while the geological record is obtained from fossil data. The two can conflict when fossils end up displaced from their original sedimentary layer

2. You are a medical researcher working on HIV. A novel strain has appeared in Madison, Wisconsin. To determine which drugs would be most effective in treating this new strain (because different strains are resistant to different drugs), you need to determine its recent evolutionary history. You decide to reconstruct the evolutionary history of HIV by using a phylogenetic approach. Thus, you collect samples from patients in various geographic locations and sequence a fragment of RNA. Using parsimony, which is the correct phylogeny for HIV-1 based on the data below?

HIV-1, Uganda, Africa ACAUGHIV-1, San Francisco, USA UGAUGHIV-1, Madison, USA UAAGGHIV-1, New York, USA UAAAGHIV-1, Paris ACAUCHIV-2 Africa (ancestral outgroup): ACCUG

3. Which of the following is most TRUE regarding phylogenetic reconstructions?

(A) Phylogenetic reconstruction based on any gene would yield the same tree

(B) Parsimony is the most accurate method for reconstructing phylogenies

(C) Some DNA sequence data is better for phylogenetic reconstruction than others, such as those that tend to be less subjected to selection (3rd codon, introns)

(D) Maximum likelihood relies on maximizing distances among taxa

4. Which of the following types of data would be most optimal for constructing a phylogeny?(a) Non-coding and regulatory sequences(b) Non-coding and non functional

sequences(c) Paralogous genes(d) Genes that have undergone purifying

selection(e) Intron sequences within rapidly

evolving genes

5. Which of the following reasons is FALSE on why the type of data chosen in the question above would be optimal for constructing a phylogeny?(a) Because selection might make taxa seem more

closely related due to convergent evolution(b) Because selection might make taxa seem more

distantly related due to disruptive evolution(c) Because selection might make taxa seem more

closely related due to purifying selection (d) Because non-coding regulatory sequences are

likely to be neutral(e) Because coding sequences are likely to be under

selection

Answers

• 1A• 2C• 3C• 4B• 5D

Phylogenetics

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