1. Tutorial 5
Phylogenetic Trees

2. Agenda How to construct a tree using Neighbor Joining algorithm
Phylogeny.fr tool
Cool story of the day:
Horizontal gene transfer

3. Neighbor Joining vs. UPGMA
Assumption: Divergence of sequences is assumed to occur at a constant rate
Distance to root is equal
Constructs an unrooted guide tree from a distance matrix
We do not assume constant rate of evolution

4. Unrooted guide tree 4

5. Neighbor Joining Algorithm
2 matrices
Calculate all pairwise distances.
Find 2 nodes i and j, such that the relative distance between i and j is minimal.
Remove the rows and columns of i and j
Add a new row and column k (the parent of i and j), and compute the distance from k to any other remaining node.
Continue until two nodes remain – connect them with an edge.

6. Step 1. Calculate all pairwise distances
A, B, C, D and E are tree nodes. Each character represents a sequence.
How can we measure distance between sequences? E D C B A 41 39 22 43 20 18 10

7. Step 1. Calculate all pairwise distances
Distance between sequences
Euclidean Distance: Given a multiple sequence alignment, calculate the square root of the sum of the score at every position between two sequences.
The score increases as the dissimilarity between residues increases.

8. Step 1. Calculate all pairwise distances
The distance between each pair of sequences is based on multiple sequence alignment
Multiple sequence alignment
a: A T G G C
b: A A G C C
c: C A G C C
d: G G G C G
e: A T G C C
𝒂 𝟏 𝒂 𝟐 𝒂 𝟑 𝒂 𝟒 𝒂 𝟓
A T G G C
A A G C C
𝒃 𝟏 𝒃 𝟐 𝒃 𝟑 𝒃 𝟒 𝒃 𝟓

9. Step 2. Two nodes with minimal relative distance
If we assume constant evolution rate we may construct a wrong tree.
Closest leaves aren’t necessarily neighbors:
i and j are neighbors, but (dij = 13) > (djk = 12)

10. Step 2. Two nodes with minimal relative distance
Find a pair of leaves that are close to each other, but far from other leaves.
This is called “relative distance”.
Negative values
As the average distance from the common ancestor to the rest of the nodes increases, Mij has a lower value.
Select pair that produce lowest value
Reevaluate M with every iteration

11. Step 2. Two nodes with minimal relative distance
Relative distance between i and j
Distance between i and j (from the distance table)
Distance between i and all other nodes
Number of leaves (=sequences) left in the tree

12. Step 2. Two nodes with minimal relative distance
Distances matrix: E D C B A 41 39 22 43 20 18 10 A B C D E

13. Step 2. Two nodes with minimal relative distance
Distances matrix: E D C B A 41 39 22 43 20 18 10
𝑟 𝐴 =47
𝑟 𝐵 =49
𝑟 𝐶 =39.3
𝑟 𝐷 =36
𝑟 𝐸 =38

14. Step 2. Two nodes with minimal relative distance
The relative distance table: E D C B A
-44
-47.3
-74 -
-57.3
-64
A,B is the pair with the minimal Mi,j distance.
The Mij Table is used only to choose the closest pairs (lowest
value) and not for calculating the distances

15. Steps 3+4. Remove i, j and add k to the matrix
The distance from k to any other leaf m can be computed as:
Dkm = (Dim + Djm – Dij)/2
Compress i and j into k, iterate algorithm for rest of tree

16. Steps 3+4. Remove i, j and add k to the matrix
Now we’ll calculate the distance from X to all other nodes: E D C k 31 29 20 18 10 A B C D E K

17. Steps 5. Continue till 2 nodes remain
The final tree: B A 12 10 20 5 6 4 9 K
What is missing? E Y Z C D

18. Phylogeny.fr

19. One click mode

20. One click mode

21. One click mode
Multiple sequence alignment (MSA) is a basic step in phylogenetic tree construction and is the base for the distance matrix

22. “A la carte” mode

23. “On-click” default settings

24. Horizontal gene transfer
Cool Story of the day
Horizontal gene transfer

25. Is horizontal gene transfer possible?

26. Viruses

27. Horizontal gene transfer in Bacteria
Horizontal gene transfer is the primary reason for bacterial antibiotic resistance and plays an important role in the evolution of bacteria.
Horizontal gene transfer is very abundant in bacteria, it is hard to talk about a bacteria’s genome, but more of the genome of a “society of bacteria”.

28. Sea slug
The sea slug Elysia chlorotica incorporates chloroplasts from the algae that it eats into its body. Photosynthesis continues for up to 12 months using genes within the chloroplast, which are directed by algal nuclear genes that were transferred to the nuclei of the slug.

29. Until the full speciation…
Bioinformatics/ David W.Mount p. 244