PHYLOGENETIC TREE

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Nayera Medhat

OVERVIEW Phylogenetic Tree

Phylogeny Applications

Types of phylogenetic tree

Terminology

Data used to build a tree

Building phylogenetic trees

Software for building trees

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PHYLOGENETIC TREE Phylogenetic trees illustrate the evolutionary

relationships among groups of organisms, or among a family of related nucleic acid or protein sequences

• E.g., how might have this family been derived during evolutionDescent with modification:

Evolutionary tree of elephant family, based on fossil evidence)

The evolutionary history of a species or a group of species over geologic time

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PHYLOGENY APPLICATIONS Tree of life: Analyzing changes that have

occurred in evolution of different organisms

Phylogenetic relationships among genes can help predict which ones might have similar functions

Follow changes occurring in rapidly changing species (e.g., HIV virus)

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TYPES OF PHYLOGENETIC TREE

rooted trees: a single node is designated as a common ancestor, and a unique path leads from it through evolutionary time to any other node

Unrooted trees : only specify the relationship between nodes and say nothing about the direction in which evolution occured

A B CD

• A

B

C

D

• •

Rooted, binarytree

Unrooted, binarytree

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TERMINOLOGYORFP MG01127.1

NCU01640.1

ORFP YDL020C

Scastellii

Skluyeri

orf6.4920.prot

AN0709.2

H.

Root(ancestral species)

Leaves(modern observations)

Nodes(common ancestor)

Branch lengths (“distance”) ~ time

Edges

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ORFP MG01127.1

NCU01640.1

ORFP YDL020C

Scastellii

Skluyeri

orf6.4920.prot

AN0709.2

H.

Root(ancestral species)

Branch lengths (“distance”) ~ time

12345

678

( ( ( (3,4) , (5,6)) , 7) ,(1,2) ,8)This tree can also be denoted in text format

Nayera Medhat

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Nayera Medhat

WHAT DATA IS USED TOBUILD TREES?

Traditionally: morphological features (e.g.,number of legs, beak shape, etc.)

Today: Mostly molecular data (e.g., DNA and protein sequences)

Data Can be classified into two categories: Numerical data: Distance between objectse.g., distance(man, mouse)=500,distance(man, chimp)=100Usually derived from sequence data Discrete characters:Each character has finite

number of statese.g., number of legs = 1, 2, 4DNA = {A, C, T, G}

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Building phylogenetic trees Distance based methodsa. Calculate evolutionary distances between sequencesb. Build a tree based on those distances

a. Calculate evolutionary distances between sequences & make a matrix

AGCTGGTGCA

AGTTGCAACA

So the evolutionary distance between the two sequences=4

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DISTANCE BASED METHODS •Input: given an n x n matrix M where Mij>=0 and Mij is

the distance between objects i and j •Goal: Build an edge-weighted tree where each leaf

corresponds to on object of M and so that distances measured on the tree between leaves i and j correspond to Mij

E D C B A

0 A0 12 B

0 12 12 C0 6 12 14 D

0 3 7 13 15 E

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DISTANCE BASED METHODS

b. Build a tree based on the distances of the sequences

Find the tree with the shortest overall branch lengths

E D C B A

0 A

0 12 B

0 12 14 C

0 6 12 14 D

0 3 7 13 15 E

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SOFTWARE

Most commonly used packages contain softwarefor all three methods: may want to use more than 1

to have confidence in built tree

(http://bioinformatics.psb.ugent.be/hypergeny/home.php)

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REFERENCES1) Maddison WP, Maddison DR. (1989). Interactive analysis of phylogeny and

character evolution using the computer program MacClade. Folia Primatol (Basel), 53(1-4):190-202.

2) Felsenstein, J. (1996). Inferring phylogenies from protein sequences by

parsimony, distance, and likelihood methods. Methods Enzymol., 266:418-27.

3) http://www.nature.com/scitable/topicpage/Reading-a-Phylogenetic-Tree-The-Meaning-of-41956

4) O'Hara, R. J. Population thinking and tree thinking in systematics. Zoologica Scripta 26, 323–329 (1997)

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QUESTIONS AND FEEDBACK