Post on 23-Feb-2016
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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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Nayera Medhat
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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Nayera Medhat
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