1. Introduction to Phylogenies
Dr Laura Emery

2. 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

3. Outline Applications of phylogenetics What is a phylogeny or tree?
Aspects of a tree
Phylogenetic Interpretation

4. What can I do with phylogenetics?
Deduce relationships among species or genes
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

5. What is a phylogenetic tree?
Darwin 1837
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).
In the past people can instructed phylogenies based upon morphological data, but today we tend to focus on using DNA sequence data (since that is what is inherited)
Introduce the concept of relatedness

6. Phylogenies explain genealogical relationships
In the same way that family trees do
Concept of relatedness
Family tree

7. Aspects of a tree Topology (branching order)
Branch lengths (indication of genetic change)
Nodes
Tips (sampled sequences known as taxa)
Internal nodes (hypothetical ancestors)
Root (oldest point on the tree)
Confidence (bootstraps/probabilities) *
Take the time to explain these, as people are more likely to remember it if they hear it twice.
Explain the time component *

8. 1. Topology
The topology describes the branching structure of the tree, which indicate patterns of relatedness. A B C B A C A B C
These trees display the same topology
Explain how a always clusters with b above, but the clustering patterns are different below. String analogy.
Introduce concept of relatedness A B C C A B C B A
These trees display different topologies

9. Topology Question Are these topologies the same? Answer = yes

10. Topology Question II
Which of these trees has a different topology from the others? A B C F D E A E D F B C B A C F D E C A B F E D E D F C A B
Insert diagram of five trees

11. 2. Branch lengths indicate genetic change
0.8
1.2
0.5
0.6
0.5
0.5
Longer branches indicate greater change
Change is typically represented in units of number of substitutions per site (but check the legend)

12. A scale bar can represent branch lengths
0.8
1.2
0.5
0.6
0.5
0.5
0.5
These are alternative representations of the same phylogeny

13. Branch Length Question
Which of these statements are true?
For both gene trees, the Fish is the most genetically different of the four species compared
For both gene trees, more substitutions have occurred since the divergence of Dog and Snake than they have since Cat and Snake
Gene B has accumulated more substitutions than Gene A on the Snake lineage
Gene B has accumulated more substitutions than Gene A on the Fish lineage
Fish
Snake
Dog
Cat
Gene A
0.5
Fish
Snake
Dog
Cat
Gene B

14. Alternative representations of phylogenies
Newick format
All of these representations depict the same topology
Branch lengths are indicated in blue
Red lengths are meaningless

15. Not all trees include branch length data
Cladogram Phylogram
Cladograms may be used when phylogenies based upon morphological data, and no branch lengths are available. They may also be used in publications where branch lengths are not relevant to the question of interest

16. 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 E A B
One explanation is that De is short because it has evolved slowly and reflects the present-day sampled sequence
An alternative explanation is that De is short because it is an ancient sample, and so has not had many years to accumulate substitutions
When you interpret phylogenies, then you need to make assumptions

17. Alternative Representations Question

18. 3. Nodes Nodes occur at the ends of branches
There are three types of nodes:
Tips (sampled sequences known as taxa)
Internal nodes (hypothetical ancestors)
Root (oldest point on the tree)
Explain that the taxa are the sequences ABC and D in this case
Explain what is meant by hypothetical ancestor, for example indicate the hypothesised common ancestor of sequences a and B
indicate the position of the root (in green) , More about that on the next slide
Figures Andrew Rambaut

19. The root is the oldest point on the tree
present C D E A B
past
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
Figures Andrew Rambaut

20. Trees can be drawn in an unrooted form
Rooted Unrooted These are alternative representations of the same topology C D E A B A B C D E
Pin analogy

21. 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!
*Biologically unusual (aside from ancient DNA, or known ancestors)
Most methods of phylogenetic reconstruction produce an unrooted tree
So getting the route in the right place is very important
otherwise you don't know the direction of evolution, and so your interpretation will be incorrect
Figure Aiden Budd

22. How to root a tree Midpoint rooting Outgroup rooting
Midpoint rooted
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
Unrooted
Outgroup rooted
A monophyletic group is a group of taxa that share a more recent common ancestor with each other than to any other taxa.
Recommended

23. 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).

24. 4. Confidence How good is a tree? There are three main approaches:
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
0.93
0.81
0.99 85 63
100
We will look at the straps in more detail
probabilistic

25. 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

26. 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
100 84 63 91

27. Review Topology (branching order)
Branch lengths (indication of genetic change)
Nodes
Tips (sampled sequences known as taxa)
Internal nodes (hypothetical ancestors)
Root (oldest point on the tree)
Confidence (bootstraps/probabilities) *
Potentially add a section on phylogenetic interpretation, get across the idea you have to make assumptions
Relatedness
gain and loss of character states *

28. 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

29. Now it is your turn…
Open your tutorial manual and begin Tree-thinking quiz 1 (appendix 1)
The manual is available to download from:
2013
When you are finished you can mark your own (the answers are at the end of the quiz).
Remember to ask for help at any stage!