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

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

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

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

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

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 *

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

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 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

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)

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

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

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

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

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

Alternative Representations Question

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

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

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

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

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

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).

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

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 100 84 63 91

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 *

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

Now it is your turn… Open your tutorial manual and begin Tree-thinking quiz 1 (appendix 1) The manual is available to download from: http://www.ebi.ac.uk/training/course/scuola-di-bioinformatica- 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!