Phylogenetic tree

It was made for our group presentation of Bio- Informatics course

1. P H Y L O G E N E T I C T R E E

2. Team- NoFrazzle Nazmul Ahsan 151-15- 4668 Farhan Tawsif Chowdhury 151-15-4705 Md. Mahbubur Rahman 151-15-4761 Md. Sanzidul Islam 151-15-5223 Sadia Sultana Sharmin 151-15-5191

3. What is Phylogenetic Tree? A branching diagram S howing the inferred evolutionary relationships among various biological species  B ased upon similarities and differences in their physical or genetic characteristics E ach node with descendants represents the inferred most recent common ancestor of the descendants

4. History  Early representations of "branching" phylogenetic trees include a "paleontological chart" showing the geological relationships among plants and animals in the book  Elementary Geology , by Edward Hitchcock in 1840 .   Charles Darwin in 1859 also produced one of the first illustrations and crucially popularized the notion of an evolutionary "tree" in his seminal book  The Origin of Species .

5. Why might we care? The Purposes! Understanding human origins Understanding biogeography, e.g. what’s the relative importance of dispersal versus vicariance ? Learning about the tempo of evolution, e.g. was the Cambrian explosion really an explosion? Did mammals and birds wait until dinosaurs went extinct to inherit the earth or were they already started before the asteroid hit? Understanding the origin of particular traits Understanding the processes of molecular evolution Origin of disease, e.g. where did humans get AIDs from?

6. How Phylogenetic Tree Works?

7. What does this tree looks like? What do the lines represent?

8. Types of P hylogenetic Tree R ooted Tree: Make inferences about the most common ancestor of the leaves or branches of the tree. Most commonly the root is referred to as an “outgroup”. U nrooted Tree: Make an illustration about the leaves or branches, but not make assumption regarding a common ancestor.

9. The B ifurcating T ree A tree that bifurcates has a maximum of 2 descendants arising from each of the interior nodes.

10. The Multi-furcating T ree A tree that multi-furcates has multiple descendants arising from each of the interior nodes.

11. Construction of Phylogenetic Tree

12. Construction of Phylogenetic Tree: Find the tree which best describes the relationships between species. There are two main types: Character based methods Distance based methods

13. Character based methods: Use the aligned characters, such as DNA or protein sequences, directly during tree inference Example: Parsimony Maximum likelihood Taxa Characters Species A A T GG C T A TT C TT A T A G T A C G Species B A T C G C T A G T C TT A T A TT A C A Species C TT C A C T A G A CC T G T GG T CC A Species D TT G A CC A G A CC T G T GG T CC G Species E TT G A CC A G TT C T C T A G TT C G

14. Distance based methods: Transform the sequence data into pairwise distances and then use the matrix during tree building Example: UPGMA Neighbor-joining A B C D E Species A ---- 0.20 0.50 0.45 0.40 Species B 0.23 ---- 0.40 0.55 0.50 Species C 0.87 0.59 ---- 0.15 0.40 Species D 0.73 1.12 0.17 ---- 0.25 Species E 0.59 0.89 0.61 0.31 ----

15. Construction of Phylogenetic Tree:

16. UPGMA: q Abbreviation of “Unweighted Pair Group Method with Arithmetic Mean ” q Originally developed for numeric taxonomy in 1958 by Sokal and Michener q Simplest algorithm for tree construction, so it's fast!

17. Example of UPGMA A B C D E A B 20 C 60 50 D 100 90 40 E 90 80 50 30

18. Example of UPGMA A B C D E A B 20 C 60 50 D 100 90 40 E 90 80 50 30 New average Distance between C and AB is: C to AB = (60 + 50) / 2 = 55 Distance between D and AB is: D to AB = (100 + 90) / 2 = 95 Distance between E and AB is: E to AB = (90 + 80) / 2 = 85 13

19. Example of UPGMA AB C D E AB C 55 D 95 40 E 85 50 30

20. Example of UPGMA AB C D E AB C 55 D 95 40 E 85 50 30 New average Distance between AB and DE is: AB to DE = (95 + 85) / 2 = 90 Distance between C and DE is: C to DE = (40 + 50) / 2 = 45

21. Example of UPGMA AB C DE AB C 55 DE 90 45

22. Example of UPGMA AB C DE AB C 55 DE 90 45 New Average Distance between CDE and AB is: CDE to AB = (90 + 55) / 2 = 72.5

23. Example of UPGMA AB CDE AB CDE 72.5 There are only two clusters. so this completes the calculation!

24. Limitations Of Phylogenetic tree

25. - Limitations Inaccurate evolutionary history The data used is little noisy Problem facing in single type of character basing Homoplasy would be unlikely from natural selection Length of branch doesn’t mean the timing passed

26. - Branches of a tree

27. - Fields of study Cladistics Comparative phylogenetics Computational phylogenetics Evolutionary taxonomy Evolutionary biology Phylogenetics

28. Applications: Find out the evolutionary history . C an measure phylogenetic diversity using phylogenetic trees . S earch for natural products . I nfectious bacteria and viruses to trace their evolutionary histories.

29. Applications: F ind out what trends they've undergone in their history . To guide our search for new species. Find out how our species spread geographically in their evolution. T o tell us when taxa originated and where.

30. This is what Bio- Informatics Deals With! Thanks!