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Introduction to Phylogenies Dr Laura Emery

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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? 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

6 Phylogenies explain genealogical relationships Family tree

7 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) * *

8 1. Topology The topology describes the branching structure of the tree, which indicate patterns of relatedness. ABCABCBAC These trees display the same topology ABCCBACAB 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? ABCFD E AEDFB C BACFD E CABFE D EDFCA B

11 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)

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

13 Branch Length Question Which of these statements are true? 1.For both gene trees, the Fish is the most genetically different of the four species compared 2.For both gene trees, more substitutions have occurred since the divergence of Dog and Snake than they have since Cat and Snake 3.Gene B has accumulated more substitutions than Gene A on the Snake lineage 4.Gene B has accumulated more substitutions than Gene A on the Fish lineage 0.5 Fish Snake Dog Cat Gene A Fish Snake Dog Cat Gene B

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

15 Not all trees include branch length data CladogramPhylogram

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 EAB

17 Alternative Representations Question

18 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) CDEAB Figures Andrew Rambaut

19 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 CDEAB past present Figures Andrew Rambaut

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

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! * Figure Aiden Budd

22 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

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? 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 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? ABCDEFABCDEF

27 Review 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) * *

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: 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!


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