phylogenetic tree

PHYLOGENETIC

TREE

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

What is Phylogenetic Tree?•A branching diagram•Showing the inferred evolutionary relationships among various biological species •Based upon similarities and differences in their physical or genetic characteristics• Each node with descendants represents the inferred most recent common ancestor of the descendants

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.

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?

How Phylogenetic Tree Works?

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

Types of Phylogenetic TreeRooted 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”.

Unrooted Tree: •Make an illustration about the leaves or branches, • but not make assumption regarding a common ancestor.

The Bifurcating Tree

• A tree that bifurcates has a maximum of 2 descendants arising from each of the interior nodes.

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

Construction of Phylogenetic Tree

Construction of Phylogenetic Tree:Find the tree which best describes the relationships between species.

There are two main types:1. Character based methods2. Distance based methods

Character based methods:Use the aligned characters, such as DNA or protein sequences, directly during tree inference

Example:1. Parsimony2. Maximum likelihood

       Taxa           CharactersSpecies A ATGGCTATTCTTATAGTACGSpecies B ATCGCTAGTCTTATATTACASpecies C TTCACTAGACCTGTGGTCCASpecies D TTGACCAGACCTGTGGTCCGSpecies E TTGACCAGTTCTCTAGTTCG

Distance based methods:Transform the sequence data into pairwise distances and then use the matrix during tree building

Example:1. UPGMA2. 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 ----

Construction of Phylogenetic Tree:

UPGMA:

q Abbreviation of “Unweighted Pair Group Methodwith Arithmetic Mean”

q Originally developed for numeric taxonomy in1958 by Sokal and Michener

q Simplest algorithm for tree construction, so it's fast!

Example of UPGMA

A B C D E

A 0

B 20 0

C 60 50 0

D 100 90 40 0

E 90 80 50 30 0

Example of UPGMA

A B C D E

A 0

B 20 0

C 60 50 0

D 100 90 40 0

E 90 80 50 30 0

New averageDistance between C and AB is: C to AB = (60 + 50) / 2 = 55Distance between D and AB is: D to AB = (100 + 90) / 2 = 95Distance between E and AB is: E to AB = (90 + 80) / 2 = 8513

Example of UPGMA

AB C D E

AB 0

C 55 0

D 95 40 0

E 85 50 30 0

Example of UPGMA

AB C D E

AB 0

C 55 0

D 95 40 0

E 85 50 30 0

New averageDistance between AB and DE is: AB to DE = (95 + 85) / 2 = 90Distance between C and DE is: C to DE = (40 + 50) / 2 = 45

Example of UPGMA

AB C DE

AB 0

C 55 0

DE 90 45 0

Example of UPGMA

AB C DE

AB 0

C 55 0

DE 90 45 0

New AverageDistance between CDE and AB is: CDE to AB = (90 + 55) / 2 = 72.5

Example of UPGMA

AB CDE

AB 0

CDE 72.5 0

There are only two clusters. so this completes thecalculation!

Limitations Of Phylogenetic tree

- Limitations

1. Inaccurate evolutionary history

2. The data used is little noisy3. Problem facing in single type

of character basing4. Homoplasy would be unlikely

from natural selection5. Length of branch doesn’t mean

the timing passed

- Branches of a tree

- Fields of study1. Cladistics2. Comparative phylogenetics3. Computational phylogenetics4. Evolutionary taxonomy5. Evolutionary biology6. Phylogenetics

Applications:• Find out the evolutionary history .

• Can measure phylogenetic diversity using phylogenetic trees .

• Search for natural products .

• Infectious bacteria and viruses to trace their evolutionary histories.

Applications:• Find 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.

• To tell us when taxa originated and where.

This is what Bio- InformaticsDeals With!

Thanks!