for immunologists 2013

Introduction to Phylogenies

Dr Laura Emery

Laura.Emery@ebi.ac.uk

www.ebi.ac.uk/training

Objectives

After this tutorial you should be able to…

• Use essential phylogenetic terminology effectively

• Discuss aspects of phylogenies and their implications for phylogenetic interpretation

• Apply phylogenetic principles to interpret simple trees

This course will not:

• Provide you with an overview of phylogenetic methods

• Enable you to use tools to construct your own phylogenies

• Enable you to evaluate whether a sensible phylogenetic model or method was selected to construct a phylogeny

Outline

• Introduction

• Aspects of a tree1. Topology

2. Branch lengths

3. Nodes

4. Confidence

• Simple phylogenetic interpretation

• Including homology, gene duplication, co-evolution

What can I do with phylogenetics?

• Deduce relationships among species or genes or cells

• Deduce the origin of pathogens

• Identify biological processes that affect how your sequence has evolved e.g. identify genes or residues undergoing positive selection

• Explore the evolution of traits through history

• Estimate the timing of major historical events

• Explore the impact of geography on species diversification

What is a phylogenetic tree?

A tree is an explanation of how sequences evolved, their genealogical relationships and thus how they came to be the way they are today (or at the time of sampling).

Darwin 1837

Phylogenies explain genealogical relationships

• Family tree

Aspects of a tree

1. Topology (branching order)

2. Branch lengths (indication of genetic

change)

3. Nodes

i. Tips (sampled sequences known as taxa)

ii. Internal nodes (hypothetical ancestors)

iii. Root (oldest point on the tree)

4. Confidence (bootstraps/probabilities)

1. Topology

The topology describes the branching structure of the tree, which indicate patterns of relatedness.

A B C ABCB A CThese trees display the

same topology

A B C CBAC A BThese trees

display different topologies

Topology Question

Are these topologies the same?

Answer = yes

Topology Question II

Which of these trees has a different topology from the others?

A B CF DE A E DF BC B A CF DE

C A BF ED E D FC AB

2. Branch lengths indicate genetic change

• Longer branches indicate greater change

• Change is typically represented in units of number of substitutions per site (but check the legend)

1.20.6

0.8

0.5

0.5

0.5

A scale bar can represent branch lengths

0.5

These are alternative representations of the same phylogeny

1.20.6

0.8

0.5

0.5

0.5

Alternative representations of phylogenies

All of these representations depict the same topologyBranch lengths are indicated in blue

Red lengths are meaningless

Not all trees include branch length data

Cladogram Phylogram

Distance and substitution rate are confounded• Branch lengths indicate the genetic change that

has occurred

• We often don’t know if long branch lengths reflect:

• A rapid evolutionary rate

• An ancient divergence time

• A combination of both

• Genetic change = Evolutionary rate x Divergence time (substitutions/site) (substitutions/site/year) (years)

C

D

EA B

3. Nodes

• Nodes occur at the ends of branches

• There are three types of nodes:

i. Tips (sampled sequences known as taxa)

ii. Internal nodes (hypothetical ancestors)

iii. Root (oldest point on the tree)

C D EA B

Figures Andrew Rambaut

The root is the oldest point on the tree

• The root indicates the direction of evolution

• It is also the (hypothesised) most recent common ancestor (MRCA) of all of the samples in the tree

C D EA B

past

present

Figures Andrew Rambaut

Trees can be drawn in an unrooted form

Rooted Unrooted

These are alternative representations of the same topology

C D EA BA

B

C

D

E

There are multiple rooted tree topologies for any given unrooted tree

• Most tree-building methods produce unrooted trees

• Identifying the correct root is often critical for interpretation!

*

Figure Aiden Budd

How to root a tree

• Midpoint rooting

• Assume constant evolutionary rate

• Often not the case!

• Outgroup rooting

• The outgroup is one or more taxa that are known to have diverged prior to the group being studied

• The node where the outgroup lineage joins the other taxa is the root

Midpoint rooted

Outgroup rooted

Unrooted

Recommended

Root Question

This tree shows a cladogram i.e. the branch lengths do not indicate genetic change.

Indicate any root positions where bird and crocodile are not sister taxa (each other's closest relatives).

Alternative Representations Question

4. Confidence

How good is a tree?A tree is a collection of hypotheses so we assess our confidence in each of its parts or branches independently

There are three main approaches:

• Bootstraps

• Bayesian methods

• Approximate likelihood ratio test (aLRT) methods

85

63

100

probabilistic

0.93

0.81

0.99

What is a monophyletic group?

A monophyletic group (also described as a clade) is a group of taxa that share a more recent common ancestor with each other than to any other taxa.

monophyletic group

Confidence Question

Which of the bootstrap values indicates our confidence in the grouping of A, B, C, and D together as a monophyletic group? Do you think we can be confident in this grouping?

A

B

C

D

E

F

84

63

91

100

Note: high bootstrap values do not always mean that we have confidence in a branch. False confidence can be generated under some phylogenetic methods

for immunologists 2013

Part two: Phylogenetic interpretation

Dr Laura Emery

Laura.Emery@ebi.ac.uk

www.ebi.ac.uk/training

Phylogenetic interpretation skill set

1. Tree-thinking skills

• relatedness, confidence, homology

2. Knowledge of phylogenetic methods and their limitations

3. Knowledge of biological processes affecting sequence evolution

• gene duplication, recombination, horizontal gene transfer, population genetic processes, and many more!

4. Knowledge of the data you wish to interpret

Simple phylogenetic interpretation question• Which is true?

• A) Mouse is more closely related to fish than frog is to fish

• B) Lizard is more closely related to fish than mouse is to fish

• C) Human and frog are equally related to fish

Homology is similarity due to shared ancestryExample: limbs and wings

• Limbs are homologous they share a common ancestor

• Wings are not homologous they are an analogous as they have evolved similarity independently

Gene duplication

Gene duplication and subsequent divergence can result in novel gene functions (it can also result in pseudogenes)

• Genes that are homologous due to gene duplication are paralogous

• Genes that are homologous due to speciation are orthologous

• Can you spot any MHC class II gene duplication events?

Harstad et al BMC Genomics 2008

Teleost MHC class II phylogeny

Park et al 2012. Scientific Reports

• Immunology genes have a high dN/dS ratio indicative of positive selection

• Rapid evolutionary rate

• Difficult to align

• Violate assumptions of many phylogenetic models

Immunology related genes have atypical patterns of molecular evolution

Positive selection can lead to ladder-like phylogenies

Example: influenza haemagglutination phylogeny and immunological mapping

Smith et al 2004. Science

Phylogenetics can inform us of host-pathogen interactions and co-evolution

• "Mirror" phylogenies are indicative of host-parasite vertical inheritance

Jiggins web page: http://www.gen.cam.ac.uk/research/jiggins/research.html

What does this phylogeny tell us about Human Cytomegalovirus (HCMV)?

Nicholson et al 2009. Virol J

Human

Chimp

Rhesus

Simian

Baboon

Rat

Murine

T-cell receptors and immunoglobulin chains are homologous

Richards et al 2000

An extremely brief introduction to methods, analyses, & pitfalls

There is only one true tree

• The true tree refers to what actually happened in the evolutionary past

• All methods attempt to reconstruct the true phylogeny

• Even the best method may not give you the true tree

Phylogenetic Methods: The general approach• We want to find the tree that best explains our

aligned sequences

• We need to be able to define “best explains”

• we need a model of sequence evolution

• we need a criterion (or set of criteria) to use to choose between alternative trees

• then evaluate all possible trees

(NB: if N=20, then 2 x 1020 possible unrooted trees!)

• or take a short cut

Paul Sharp

The problem of multiple substitutions

• More likely to have occurred between distantly related species

• > We need an explicit model of evolution to account for these

A

A

A T

G*

*

*

*

hidden mutation

s

Methodological approaches

1. Distance matrix methods (pre-computed distances)

• UPGMA assumes perfect molecular clock Sokal & Michener (1958)

• Minimum evolution (e.g. Neighbor-joining, NJ) Saitou & Nei (1987)

2. Maximum parsimony Fitch (1971)

• Minimises number of mutational steps

3. Maximum likelihood, ML• Evaluates statistical likelihood of alternative trees,

based on an explicit model of substitution

4. Bayesian methods• Like ML but can incorporate prior knowledge

Phylogenetic analyses are not straightforwardData assessment

- known biology- additional data

(e.g. geography)

Decide upon and impleme

ntmethod

Phylogenetic

Result(s)

Formulate hypothes

es

Answered your

question?

Investigate unexpected and

unresolved aspects further

- consider including more

dataFinal phylogeny

and analysis

Can you

validate this?

YesNo

No

Yes

Further Reading

• Molecular Evolution: A Phylogenetic Approach (1998) Roderic D M Page & Edward C Holmes, Blackwell Science, Oxford.

• The Phylogenetic Handbook (2003), Marco Salemi and Anne-Mieke Vandamme Eds, Cambridge University Press, Cambridge.

• Inferring Phylogenies (2003) Joseph Felsenstein, Sinauer.

• Molecular Evolution (1997) Wen-Hsiung Li , Sinauer

Phylogenetics at the EBI

• Clustal phylogeny currently available

• RAxML coming soon…

• www.EBI.ac.uk/tools/phylogeny

AcknowledgementsPeople

• Andrew Rambaut (University of Edinburgh) …and the EBI training team

• Paul Sharp (University of Edinburgh)

• Nick Goldman (EMBL-EBI)

• Benjamin Redelings (Duke University)

• Brian Moore (University of California, Davis)

• Olivier Gascuel (University of Montpelier)

• Aiden Budd (EMBL-Heidelberg)

Funding EMBL member states and…

Thank you!

www.ebi.ac.uk

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